# HG changeset patch
# User jackcurragh
# Date 1649081243 0
# Node ID ba39548ca2732c9fefa7e1b31a6c461544518e62
# Parent  dfb484045b7e780f1a4d86b60780344375e40ec9
Uploaded

diff -r dfb484045b7e -r ba39548ca273 bedGraphToBigWig/bedGraphToBigWig
Binary file bedGraphToBigWig/bedGraphToBigWig has changed
diff -r dfb484045b7e -r ba39548ca273 bedGraphToBigWig/bedGraphToBigWig.xml
--- a/bedGraphToBigWig/bedGraphToBigWig.xml	Mon Apr 04 14:06:57 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-<tool id="bedGraphToBigWig" name="Convert a bed file to a BigWig" version="1.0">
-    <description>Converting your ribosome profile bed file to a bigwig which is used for track creation on GWIPS-Viz</description>
-    <command><![CDATA[
-        $__tool_directory__/bedGraphToBigWig ${input1} ${input2} ${output1}
-    ]]></command>
-    <inputs>
-        <param name="input1" type="data" format="bed" label="Bed File" />
-        <param name="input2" type="data" format="tabular" label="Chromosome Sizes" />
-    </inputs>
-    <outputs>
-       <data name="output1" format="bigwig"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input1" value="test.bed" ftype="bed" />
-            <param name="input2" value="test.chrom.sizes" ftype="tabular" />
-            <output name="output1" file="test.bw" ftype="bigwig" lines_diff="4" />
-        </test>
-    </tests>
-    <help>
-
-    </help>
-    <citations/>
-</tool>
diff -r dfb484045b7e -r ba39548ca273 bedGraphToBigWig/run_bedgraph_to_bigwig.sh
--- a/bedGraphToBigWig/run_bedgraph_to_bigwig.sh	Mon Apr 04 14:06:57 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-#!usr/bin/env bash 
-
diff -r dfb484045b7e -r ba39548ca273 bedGraphToBigWig/test-data/test.bed
--- a/bedGraphToBigWig/test-data/test.bed	Mon Apr 04 14:06:57 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-YBL056W	1038	1039	1
-YBR017C	2669	2670	1
-YBR262C	398	399	1
-YCR077C	1248	1249	1
-YDR050C	24	25	1
-YDR056C	334	335	1
-YDR091C	155	156	1
-YDR406W	462	463	1
-YER091C	511	512	1
-YER091C	1534	1535	1
-YFR021W	1427	1428	1
-YGR068C	1976	1977	1
-YGR097W	343	344	1
-YGR141W	1282	1283	1
-YGR192C	378	379	1
-YGR214W	332	333	1
-YHR010W	345	346	1
-YHR115C	569	570	1
-YHR126C	691	692	1
-YHR174W	557	558	1
-YIL020C	306	307	1
-YIL048W	2353	2354	1
-YIR003W	1589	1590	1
-YJL001W	305	306	1
-YJL042W	1079	1080	1
-YJL060W	593	594	1
-YJL081C	716	717	1
-YJL145W	1096	1097	1
-YJL200C	1815	1816	1
-YJR137C	344	345	1
-YJR139C	475	476	1
-YKL035W	1536	1537	1
-YKL060C	584	585	1
-YKL103C	984	985	1
-YKR039W	724	725	1
-YLR027C	1014	1015	1
-YLR058C	809	810	1
-YLR154C_G	298	299	1
-YLR154C_G	393	394	1
-YLR154C_G	397	398	2
-YLR154C_G	399	400	1
-YLR154C_G	430	431	1
-YLR154W_A	511	512	1
-YLR154W_C	673	674	1
-YLR154W_C	720	721	1
-YLR154W_E	294	295	1
-YLR154W_E	296	297	4
-YLR154W_E	297	298	2
-YLR154W_E	298	299	27
-YLR154W_E	299	300	7
-YLR154W_F	616	617	1
-YLR154W_F	682	683	1
-YLR162W	545	546	1
-YLR162W	665	666	1
-YLR162W	667	668	1
-YLR162W	822	823	1
-YLR166C	1600	1601	1
-YLR190W	977	978	1
-YLR249W	498	499	1
-YMR122W_A	345	346	1
-YMR251W_A	318	319	1
-YOL039W	605	606	1
-YOL040C	552	553	1
-YOL073C	431	432	1
-YOL105C	2035	2036	1
-YOR027W	1922	1923	1
-YOR096W	398	399	1
-YOR271C	76	77	1
-YOR348C	430	431	1
-YOR348C	743	744	1
-YOR375C	1034	1035	1
-YPL004C	432	433	1
-YPR035W	552	553	1
-YPR035W	1072	1073	1
-YPR074C	2041	2042	1
-YPR094W	376	377	1
-YPR116W	1373	1374	1
-YPR163C	869	870	1
-YPR174C	872	873	1
diff -r dfb484045b7e -r ba39548ca273 bedGraphToBigWig/test-data/test.bw
Binary file bedGraphToBigWig/test-data/test.bw has changed
diff -r dfb484045b7e -r ba39548ca273 bedGraphToBigWig/test-data/test.chrom.sizes
--- a/bedGraphToBigWig/test-data/test.chrom.sizes	Mon Apr 04 14:06:57 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6691 +0,0 @@
-YAL012W	1785
-YAL069W	915
-YAL068W_A	855
-YAL068C	963
-YAL067W_A	828
-YAL067C	2382
-YAL066W	909
-YAL065C	987
-YAL064W_B	981
-YAL064C_A	981
-YAL064W	885
-YAL063C_A	891
-YAL063C	4569
-YAL062W	1974
-YAL061W	1854
-YAL060W	1749
-YAL059C_A	1023
-YAL059W	1239
-YAL058W	2109
-YAL056C_A	951
-YAL056W	3243
-YAL055W	1143
-YAL054C	2742
-YAL053W	2952
-YAL051W	3744
-YAL049C	1341
-YAL048C	2589
-YAL047W_A	930
-YAL047C	2469
-YAL046C	957
-YAL045C	909
-YAL044W_A	933
-YAL044C	1113
-YAL043C	2958
-YAL042C_A	978
-YAL042W	1848
-YAL041W	3165
-YAL040C	2343
-YAL039C	1410
-YAL038W	2103
-YAL037C_B	1575
-YAL037C_A	693
-YAL037W	1404
-YAL036C	1710
-YAL035W	3609
-YAL034C_B	954
-YAL034W_A	1470
-YAL034C	1842
-YAL033W	1122
-YAL032C	1740
-YAL031W_A	909
-YAL031C	2883
-YAL030W	954
-YAL029C	5016
-YAL028W	2187
-YAL027W	1386
-YAL026C_A	1038
-YAL026C	4668
-YAL025C	1521
-YAL024C	4908
-YAL023C	2880
-YAL022C	2154
-YAL021C	3114
-YAL020C	1602
-YAL019W_A	1170
-YAL019W	3996
-YAL018C	1578
-YAL017W	4671
-YAL016C_B	786
-YAL016C_A	915
-YAL016W	2508
-YAL015C	1800
-YAL014C	1368
-YAL013W	1818
-YAL011W	2478
-YAL010C	2082
-YAL009W	1380
-YAL008W	1197
-YAL007C	1248
-YAL005C	2529
-YAL004W	1248
-YAL003W	1221
-YAL002W	4425
-YAL001C	4083
-YAR002W	2220
-YAR002C_A	1260
-YAR003W	1881
-YAR007C	2466
-YAR008W	1428
-YAR009C	4191
-YAR010C	1923
-YAR014C	2730
-YAR015W	1521
-YAR018C	1908
-YAR019C	3525
-YAR019W_A	933
-YAR020C	768
-YAR023C	1140
-YAR027W	1308
-YAR028W	1305
-YAR029W	825
-YAR030C	942
-YAR031W	1497
-YAR033W	1305
-YAR035W	2664
-YAR035C_A	681
-YAR042W	4167
-YAR047C	921
-YAR050W	5214
-YAR053W	897
-YAR060C	936
-YAR064W	900
-YAR066W	1212
-YAR068W	1086
-YAR069C	894
-YAR070C	900
-YAR071W	2004
-YAR073W	1812
-YAR075W	1074
-Q0010	987
-Q0017	762
-Q0032	891
-Q0045	2205
-Q0070	2493
-Q0065	2271
-Q0060	1848
-Q0055	3165
-Q0050	3105
-Q0075	1665
-Q0080	747
-Q0085	1380
-Q0092	741
-Q0105	1758
-Q0120	2517
-Q0115	2154
-Q0110	1872
-Q0130	831
-Q0140	1797
-Q0142	777
-Q0143	753
-Q0144	930
-Q0160	1308
-Q0182	1005
-Q0250	1356
-Q0255	2019
-Q0275	1410
-Q0297	526
-YER054C	2247
-YER114C	3723
-YER169W	2991
-YEL077C	4397
-YEL077W_A	1083
-YEL076C_A	1251
-YEL076C	1251
-YEL075W_A	1212
-YEL075C	969
-YEL074W	939
-YEL073C	924
-YEL072W	1296
-YEL071W	2091
-YEL070W	2109
-YEL069C	2295
-YEL068C	933
-YEL067C	1188
-YEL066W	1140
-YEL065W	2487
-YEL064C	2043
-YEL063C	2373
-YEL062W	2448
-YEL061C	3603
-YEL060C	2508
-YEL059C_A	825
-YEL059W	909
-YEL058W	2274
-YEL057C	1302
-YEL056W	1806
-YEL055C	3669
-YEL054C	1098
-YEL053W_A	948
-YEL053C	2802
-YEL052W	2130
-YEL051W	1371
-YEL050W_A	792
-YEL050C	1782
-YEL049W	963
-YEL048C	1059
-YEL047C	2013
-YEL046C	1764
-YEL045C	1026
-YEL044W	1101
-YEL043W	3471
-YEL042W	2157
-YEL041W	2088
-YEL040W	2004
-YEL039C	942
-YEL038W	1284
-YEL037C	1797
-YEL036C	2103
-YEL035C	1101
-YEL034C_A	1203
-YEL034W	1074
-YEL033W	1020
-YEL032W	3516
-YEL032C_A	762
-YEL031W	4248
-YEL030C_A	915
-YEL030W	2535
-YEL029C	1539
-YEL028W	1062
-YEL027W	1083
-YEL026W	981
-YEL025C	4167
-YEL024W	1248
-YEL023C	2649
-YEL022W	4980
-YEL021W	1404
-YEL020C_B	798
-YEL020W_A	864
-YEL020C	2283
-YEL019C	1404
-YEL018C_A	1134
-YEL018W	1440
-YEL017C_A	732
-YEL017W	1614
-YEL016C	2082
-YEL015W	2256
-YEL014C	906
-YEL013W	2337
-YEL012W	1257
-YEL011W	2715
-YEL010W	951
-YEL009C_A	1008
-YEL009C	1446
-YEL008W	981
-YEL008C_A	693
-YEL007W	2601
-YEL006W	1608
-YEL005C	1449
-YEL004W	1629
-YEL003W	936
-YEL002C	1893
-YEL001C	1278
-YER001W	2889
-YER002W	1296
-YER003C	1890
-YER004W	1296
-YER005W	2493
-YER006W	2163
-YER006C_A	918
-YER007W	2157
-YER007C_A	1146
-YER008C	4611
-YER009W	978
-YER010C	1305
-YER011W	1365
-YER012W	1197
-YER013W	4038
-YER014W	2220
-YER014C_A	1062
-YER015W	2835
-YER016W	1635
-YER017C	2886
-YER018C	1266
-YER019W	2034
-YER019C_A	867
-YER020W	1950
-YER021W	2172
-YER022W	2664
-YER023W	1461
-YER023C_A	813
-YER024W	3372
-YER025W	2184
-YER026C	1431
-YER027C	1854
-YER028C	1785
-YER029C	1191
-YER030W	1062
-YER031C	1272
-YER032W	3231
-YER033C	3831
-YER034W	1158
-YER035W	1038
-YER036C	2433
-YER037W	1566
-YER038C	1995
-YER038W_A	981
-YER039C	1350
-YER039C_A	819
-YER040W	2793
-YER041W	2880
-YER042W	1155
-YER043C	1950
-YER044C	1047
-YER044C_A	1827
-YER045C	2070
-YER046W	1032
-YER046W_A	930
-YER047C	3294
-YER048C	1776
-YER048W_A	885
-YER049W	2535
-YER050C	1017
-YER051W	2079
-YER052C	2184
-YER053C	1503
-YER053C_A	714
-YER055C	1494
-YER056C	2202
-YER056C_A	966
-YER057C	990
-YER058W	924
-YER059W	1863
-YER060W	2187
-YER060W_A	2193
-YER061C	1929
-YER062C	1353
-YER063W	1257
-YER064C	2118
-YER065C	2274
-YER066W	1158
-YER066C_A	1101
-YER067W	1086
-YER067C_A	924
-YER068W	2364
-YER068C_A	1032
-YER069W	3192
-YER070W	3267
-YER071C	981
-YER072W	990
-YER073W	2163
-YER074W	1008
-YER074W_A	858
-YER075C	3387
-YER076C	1509
-YER076W_A	948
-YER077C	2667
-YER078C	2136
-YER078W_A	765
-YER079W	1233
-YER079C_A	939
-YER080W	2484
-YER081W	2010
-YER082C	2265
-YER083C	1458
-YER084W	987
-YER084W_A	1113
-YER085C	1122
-YER086W	2331
-YER087W	2331
-YER087C_A	1152
-YER087C_B	849
-YER088C	2613
-YER088C_A	924
-YER088W_B	747
-YER089C	1995
-YER090W	2124
-YER090C_A	690
-YER091C	2904
-YER091C_A	822
-YER092W	978
-YER093C	4893
-YER093C_A	1014
-YER094C	1218
-YER095W	1803
-YER096W	2139
-YER097W	930
-YER098W	2865
-YER099C	1557
-YER100W	1353
-YER101C	1893
-YER102W	1203
-YER103W	2529
-YER104W	1227
-YER105C	4776
-YER106W	1509
-YER107C	1698
-YER107W_A	921
-YER109C	3000
-YER110C	3942
-YER111C	3882
-YER112W	1164
-YER113C	2721
-YER115C	1176
-YER116C	1425
-YER117W	1014
-YER118C	1704
-YER119C	1947
-YER119C_A	972
-YER120W	1335
-YER121W	945
-YER122C	2082
-YER123W	2175
-YER124C	2322
-YER125W	3030
-YER126C	1386
-YER127W	1674
-YER128W	1212
-YER129W	4029
-YER130C	1932
-YER131W	960
-YER132C	5862
-YER133W	1539
-YER133W_A	942
-YER134C	1137
-YER135C	993
-YER136W	1956
-YER137C	1047
-YER137W_A	906
-YER138C	5868
-YER137C_A	1923
-YER138W_A	705
-YER139C	1281
-YER140W	2271
-YER141W	2061
-YER142C	1491
-YER143W	1887
-YER144C	3018
-YER145C	1815
-YER145C_A	1038
-YER146W	882
-YER147C	2475
-YER147C_A	1011
-YER148W	1323
-YER148W_A	1179
-YER149C	1863
-YER150W	1047
-YER151C	3339
-YER152C	1932
-YER152W_A	1167
-YER153C	1365
-YER154W	1809
-YER155C	7104
-YER156C	1617
-YER157W	3006
-YER158C	2322
-YER158W_A	816
-YER159C	1029
-YER160C	5868
-YER159C_A	1923
-YER161C	1602
-YER162C	2865
-YER163C	1299
-YER164W	5007
-YER165W	2334
-YER165C_A	957
-YER166W	5316
-YER167W	3156
-YER168C	2241
-YER170W	1278
-YER171W	2937
-YER172C	7092
-YER172C_A	981
-YER173W	2580
-YER174C	1335
-YER175C	1500
-YER175W_A	765
-YER176W	3966
-YER177W	1404
-YER178W	1863
-YER179W	1605
-YER180C	1404
-YER180C_A	858
-YER181C	924
-YER182W	1335
-YER183C	1236
-YER184C	2985
-YER185W	1512
-YER186C	1521
-YER187W	1026
-YER188W	1320
-YER188C_A	900
-YER189W	969
-YER190W	5646
-YER190C_A	1176
-YER190C_B	1083
-YJL091C	2073
-YJL026W	1800
-YJL026C_A	822
-YJR125C	1827
-YJL225C	5877
-YJL225W_A	1083
-YJL223C	963
-YJL222W_B	738
-YJL222W_A	828
-YJL222W	5250
-YJL221C	2370
-YJL220W	1053
-YJL219W	2304
-YJL218W	1191
-YJL217W	1197
-YJL216C	2346
-YJL215C	960
-YJL214W	2310
-YJL213W	1596
-YJL212C	3000
-YJL211C	1044
-YJL210W	1416
-YJL209W	2565
-YJL208C	1590
-YJL207C	6645
-YJL206C	2877
-YJL205C	762
-YJL204C	3123
-YJL203W	1443
-YJL202C	948
-YJL201W	2400
-YJL200C	2970
-YJL199C	927
-YJL198W	3246
-YJL197W	4365
-YJL197C_A	882
-YJL196C	1533
-YJL195C	1302
-YJL194W	2142
-YJL193W	1809
-YJL192C	1305
-YJL191W	1017
-YJL190C	993
-YJL189W	756
-YJL188C	909
-YJL187C	3060
-YJL186W	2361
-YJL185C	1482
-YJL184W	972
-YJL183W	1869
-YJL182C	918
-YJL181W	2436
-YJL180C	1578
-YJL179W	930
-YJL178C	1416
-YJL177W	1155
-YJL176C	3078
-YJL175W	1113
-YJL174W	1431
-YJL173C	969
-YJL172W	2331
-YJL171C	1791
-YJL170C	1230
-YJL169W	969
-YJL168C	2802
-YJL167W	1659
-YJL166W	885
-YJL165C	3168
-YJL164C	1794
-YJL163C	2268
-YJL162C	2352
-YJL161W	1143
-YJL160C	1464
-YJL159W	1842
-YJL158C	1284
-YJL157C	3093
-YJL156W_A	822
-YJL156C	2700
-YJL155C	1959
-YJL154C	3435
-YJL153C	2202
-YJL152W	960
-YJL151C	1002
-YJL150W	903
-YJL149W	2592
-YJL148W	1302
-YJL147C	1749
-YJL146W	2010
-YJL145W	1485
-YJL144W	915
-YJL143W	1077
-YJL142C	993
-YJL141C	3024
-YJL140W	1266
-YJL139C	1887
-YJL138C	1788
-YJL137C	1743
-YJL136W_A	684
-YJL136C	864
-YJL135W	918
-YJL134W	1830
-YJL133C_A	825
-YJL133W	1545
-YJL132W	2853
-YJL131C	1671
-YJL130C	7245
-YJL129C	4308
-YJL128C	2607
-YJL127W_A	717
-YJL127C_B	759
-YJL127C	2523
-YJL126W	1524
-YJL125C	1752
-YJL124C	1119
-YJL123C	2037
-YJL122W	1128
-YJL121C	1317
-YJL120W	924
-YJL119C	924
-YJL118W	1260
-YJL117W	1536
-YJL116C	1614
-YJL115W	1440
-YJL114W	1281
-YJL113W	5247
-YJL112W	2745
-YJL111W	2253
-YJL110C	2256
-YJL109C	5910
-YJL108C	1752
-YJL107C	1764
-YJL106W	2538
-YJL105W	2283
-YJL104W	1050
-YJL103C	2457
-YJL102W	3060
-YJL101C	2637
-YJL100W	2424
-YJL099W	2841
-YJL098W	3777
-YJL097W	1254
-YJL096W	1086
-YJL095W	5037
-YJL094C	3222
-YJL093C	2676
-YJL092W	4125
-YJL090C	2895
-YJL089W	3090
-YJL088W	1617
-YJL087C	3084
-YJL086C	969
-YJL085W	2472
-YJL084C	3741
-YJL083W	2415
-YJL082W	2796
-YJL081C	2070
-YJL080C	4269
-YJL079C	1500
-YJL078C	3246
-YJL077W_B	699
-YJL077C	996
-YJL077W_A	687
-YJL076W	4170
-YJL075C	1017
-YJL074C	4293
-YJL073W	2538
-YJL072C	1242
-YJL071W	2325
-YJL070C	3267
-YJL069C	2385
-YJL068C	1500
-YJL067W	951
-YJL066C	1359
-YJL065C	1104
-YJL064W	996
-YJL063C	1317
-YJL062W_A	858
-YJL062W	3093
-YJL061W	2742
-YJL060W	1935
-YJL059W	1827
-YJL058C	2232
-YJL057C	2604
-YJL056C	3243
-YJL055W	1338
-YJL054W	2037
-YJL053W	1740
-YJL052C_A	720
-YJL052W	1599
-YJL051W	3069
-YJL050W	3822
-YJL049W	1953
-YJL048C	1791
-YJL047C_A	735
-YJL047C	3129
-YJL046W	1830
-YJL045W	2505
-YJL044C	1977
-YJL043W	1374
-YJL042W	4797
-YJL041W	3072
-YJL039C	5652
-YJL038C	1260
-YJL037W	1275
-YJL036W	1872
-YJL035C	1353
-YJL034W	2649
-YJL033W	2913
-YJL032W	915
-YJL031C	1584
-YJL030W	1191
-YJL029C	3069
-YJL028W	936
-YJL027C	1017
-YJL025W	2145
-YJL024C	1185
-YJL023C	1644
-YJL022W	909
-YJL020C	4074
-YJL020W_A	858
-YJL019W	2649
-YJL016W	2286
-YJL015C	885
-YJL014W	2205
-YJL013C	2148
-YJL012C	2766
-YJL011C	1086
-YJL010C	2601
-YJL009W	927
-YJL008C	2307
-YJL007C	915
-YJL006C	1572
-YJL005W	6681
-YJL004C	1212
-YJL003W	957
-YJL002C	2031
-YJL001W	1248
-YJR001W	2409
-YJR002W	2382
-YJR003C	2160
-YJR004C	2553
-YJR005W	2703
-YJR005C_A	882
-YJR006W	2064
-YJR007W	1515
-YJR008W	1617
-YJR009C	1599
-YJR010W	2136
-YJR010C_A	885
-YJR011C	1386
-YJR012C	1224
-YJR013W	1812
-YJR014W	1197
-YJR015W	2133
-YJR016C	2358
-YJR017C	1113
-YJR018W	963
-YJR019C	1650
-YJR020W	933
-YJR021C	1545
-YJR022W	930
-YJR023C	1002
-YJR024C	1335
-YJR025C	1134
-YJR027W	5868
-YJR026W	1923
-YJR029W	5868
-YJR028W	1923
-YJR030C	2838
-YJR031C	4827
-YJR032W	1782
-YJR033C	4674
-YJR034W	927
-YJR035W	3858
-YJR036C	3279
-YJR037W	984
-YJR038C	963
-YJR039W	3966
-YJR040W	2940
-YJR041C	4125
-YJR042W	2835
-YJR043C	1653
-YJR044C	1023
-YJR045C	2565
-YJR046W	2415
-YJR047C	1074
-YJR048W	930
-YJR049C	2193
-YJR050W	1308
-YJR051W	2106
-YJR052W	2298
-YJR053W	2325
-YJR054W	2094
-YJR055W	1095
-YJR056C	1311
-YJR057W	1251
-YJR058C	1044
-YJR059W	3057
-YJR060W	1656
-YJR061W	3408
-YJR062C	1974
-YJR063W	978
-YJR064W	2289
-YJR065C	1950
-YJR066W	8013
-YJR067C	1026
-YJR068W	1662
-YJR069C	1194
-YJR070C	1578
-YJR071W	969
-YJR072C	1758
-YJR073C	1221
-YJR074W	1257
-YJR075W	1791
-YJR076C	1848
-YJR077C	1536
-YJR078W	1962
-YJR079W	930
-YJR080C	1785
-YJR082C	942
-YJR083C	1530
-YJR084W	1872
-YJR085C	918
-YJR086W	933
-YJR087W	951
-YJR088C	1479
-YJR089W	3465
-YJR090C	4056
-YJR091C	3876
-YJR092W	4944
-YJR093C	1584
-YJR094C	1683
-YJR094W_A	879
-YJR095W	1569
-YJR096W	1449
-YJR097W	1119
-YJR098C	2571
-YJR099W	1311
-YJR100C	1584
-YJR101W	1401
-YJR102C	1209
-YJR103W	2337
-YJR104C	1065
-YJR105W	1623
-YJR106W	2778
-YJR107W	1587
-YJR108W	972
-YJR109C	3957
-YJR110W	2667
-YJR111C	1452
-YJR112W	1206
-YJR112W_A	930
-YJR113C	1344
-YJR114W	993
-YJR115W	1110
-YJR116W	1440
-YJR117W	1962
-YJR118C	1212
-YJR119C	2787
-YJR120W	951
-YJR121W	2136
-YJR122W	2094
-YJR123W	1278
-YJR124C	1947
-YJR126C	3036
-YJR127C	4743
-YJR128W	960
-YJR129C	1620
-YJR130C	2520
-YJR131W	2250
-YJR132W	3747
-YJR133W	1230
-YJR134C	2724
-YJR135C	1320
-YJR135W_A	864
-YJR136C	1866
-YJR137C	4929
-YJR138W	5355
-YJR139C	1680
-YJR140C	5547
-YJR140W_A	750
-YJR141W	1644
-YJR142W	1629
-YJR143C	2889
-YJR144W	1410
-YJR145C	1386
-YJR146W	954
-YJR147W	1677
-YJR148W	1731
-YJR149W	1815
-YJR150C	1497
-YJR151C	4086
-YJR151W_A	651
-YJR152W	2232
-YJR153W	1686
-YJR154W	1641
-YJR155W	1467
-YJR156C	1623
-YJR157W	963
-YJR158W	2304
-YJR159W	1674
-YJR160C	2409
-YJR161C	1752
-YJR162C	951
-YBL047C	4746
-YBR012W_B	5871
-YBR078W	1890
-YBR140C	9879
-YBL113C	2958
-YBL113W_A	1083
-YBL112C	918
-YBL111C	2604
-YBL109W	936
-YBL108C_A	729
-YBL108W	906
-YBL107W_A	705
-YBL107C	1191
-YBL106C	3633
-YBL105C	4056
-YBL104C	3717
-YBL103C	2061
-YBL102W	1248
-YBL101C	3954
-YBL100W_C	720
-YBL100W_B	5913
-YBL100W_A	1917
-YBL100C	915
-YBL099W	2238
-YBL098W	1983
-YBL097W	2865
-YBL096C	909
-YBL095W	1413
-YBL094C	933
-YBL093C	1263
-YBL092W	993
-YBL091C_A	1128
-YBL091C	1866
-YBL090W	1134
-YBL089W	1980
-YBL088C	8964
-YBL087C	1014
-YBL086C	2001
-YBL085W	3543
-YBL084C	2877
-YBL083C	1026
-YBL082C	1977
-YBL081W	1707
-YBL080C	2226
-YBL079W	5109
-YBL078C	954
-YBL077W	1032
-YBL076C	3819
-YBL075C	2550
-YBL074C	1668
-YBL073W	912
-YBL072C	1203
-YBL071C_B	699
-YBL071W_A	849
-YBL071C	909
-YBL070C	921
-YBL069W	1890
-YBL068W_A	837
-YBL068W	1581
-YBL067C	2844
-YBL066C	4047
-YBL065W	945
-YBL064C	1386
-YBL063W	3936
-YBL062W	981
-YBL061C	2691
-YBL060W	2664
-YBL059C_A	930
-YBL059W	1182
-YBL058W	1872
-YBL057C	1227
-YBL056W	2007
-YBL055C	1857
-YBL054W	2178
-YBL053W	975
-YBL052C	3096
-YBL051C	2607
-YBL050W	1479
-YBL049W	1017
-YBL048W	912
-YBL046W	1926
-YBL045C	1974
-YBL044W	969
-YBL043W	1374
-YBL042C	2520
-YBL041W	1326
-YBL040C	1260
-YBL039W_B	780
-YBL039C	2340
-YBL039C_A	684
-YBL038W	1299
-YBL037W	3678
-YBL036C	1374
-YBL035C	2718
-YBL034C	5142
-YBL033C	1638
-YBL032W	1746
-YBL031W	1617
-YBL030C	1557
-YBL029C_A	885
-YBL029W	1731
-YBL028C	921
-YBL027W	1170
-YBL026W	888
-YBL025W	1038
-YBL024W	2655
-YBL023C	3207
-YBL022C	4002
-YBL021C	1035
-YBL020W	2325
-YBL019W	2163
-YBL018C	1002
-YBL017C	5340
-YBL016W	1662
-YBL015W	2181
-YBL014C	3285
-YBL013W	1806
-YBL012C	1002
-YBL011W	2880
-YBL010C	1443
-YBL009W	2631
-YBL008W_A	840
-YBL008W	3123
-YBL007C	4335
-YBL006C	1143
-YBL006W_A	750
-YBL005W	3531
-YBL005W_B	5868
-YBL005W_A	1923
-YBL004W	8082
-YBL003C	999
-YBL002W	996
-YBL001C	915
-YBR001C	2943
-YBR002C	1461
-YBR003W	2022
-YBR004C	1902
-YBR005W	1242
-YBR006W	2094
-YBR007C	2811
-YBR008C	2247
-YBR009C	912
-YBR010W	1011
-YBR011C	1464
-YBR012C	1020
-YBR012W_A	1923
-YBR013C	990
-YBR014C	1212
-YBR015C	2394
-YBR016W	987
-YBR017C	3357
-YBR018C	1701
-YBR019C	2700
-YBR020W	2187
-YBR021W	2502
-YBR022W	1134
-YBR023C	4098
-YBR024W	1506
-YBR025C	1785
-YBR026C	1743
-YBR027C	933
-YBR028C	2178
-YBR029C	1974
-YBR030W	2259
-YBR031W	1689
-YBR032W	903
-YBR033W	3360
-YBR034C	1647
-YBR035C	1287
-YBR036C	1833
-YBR037C	1488
-YBR038W	3492
-YBR039W	1536
-YBR040W	1497
-YBR041W	2610
-YBR042C	1794
-YBR043C	2670
-YBR044C	2319
-YBR045C	2520
-YBR046C	1605
-YBR047W	1128
-YBR048W	1071
-YBR049C	3033
-YBR050C	1617
-YBR051W	951
-YBR052C	1233
-YBR053C	1677
-YBR054W	1635
-YBR055C	3300
-YBR056W	2106
-YBR056W_A	801
-YBR056C_B	759
-YBR057C	1701
-YBR058C	2946
-YBR058C_A	843
-YBR059C	3927
-YBR060C	2463
-YBR061C	1533
-YBR062C	1143
-YBR063C	1815
-YBR064W	1029
-YBR065C	1695
-YBR066C	1263
-YBR067C	1233
-YBR068C	2430
-YBR069C	2460
-YBR070C	1314
-YBR071W	1236
-YBR072W	1245
-YBR072C_A	762
-YBR073W	3477
-YBR074W	3531
-YBR076W	1665
-YBR076C_A	867
-YBR077C	1089
-YBR079C	3495
-YBR080C	2877
-YBR081C	4599
-YBR082C	1047
-YBR083W	2061
-YBR084W	3528
-YBR084C_A	1170
-YBR085W	1524
-YBR085C_A	858
-YBR086C	3441
-YBR087W	1665
-YBR088C	1377
-YBR089W	1200
-YBR089C_A	900
-YBR090C	969
-YBR091C	930
-YBR092C	2004
-YBR093C	2004
-YBR094W	2862
-YBR095C	1893
-YBR096W	1293
-YBR097W	4965
-YBR098W	2676
-YBR099C	984
-YBR101C	1473
-YBR102C	2862
-YBR103W	2208
-YBR103C_A	744
-YBR104W	1590
-YBR105C	1689
-YBR106W	1167
-YBR107C	1338
-YBR108W	3444
-YBR109C	1044
-YBR109W_A	825
-YBR110W	1950
-YBR111C	1296
-YBR111W_A	891
-YBR112C	3501
-YBR113W	1083
-YBR114W	2973
-YBR115C	4779
-YBR116C	1128
-YBR117C	2646
-YBR118W	1977
-YBR119W	1497
-YBR120C	1089
-YBR121C	2604
-YBR121C_A	759
-YBR122C	1134
-YBR123C	2550
-YBR124W	960
-YBR125C	1782
-YBR126C	2088
-YBR126W_A	807
-YBR126W_B	744
-YBR127C	2154
-YBR128C	1635
-YBR129C	1587
-YBR130C	1878
-YBR131W	2715
-YBR131C_A	690
-YBR132C	2391
-YBR133C	3084
-YBR134W	1002
-YBR135W	1053
-YBR136W	7707
-YBR137W	1140
-YBR138C	2175
-YBR139W	2127
-YBR141C	1614
-YBR141W_A	696
-YBR142W	2922
-YBR143C	1914
-YBR144C	915
-YBR145W	1656
-YBR146W	1437
-YBR147W	1491
-YBR148W	2430
-YBR149W	1635
-YBR150C	3885
-YBR151W	1551
-YBR152W	1476
-YBR153W	1335
-YBR154C	1248
-YBR155W	1758
-YBR156C	2697
-YBR157C	1368
-YBR158W	2250
-YBR159W	1644
-YBR160W	1497
-YBR161W	1731
-YBR162C	1968
-YBR162W_A	798
-YBR163W	2358
-YBR164C	1152
-YBR165W	1434
-YBR166C	1959
-YBR167C	1023
-YBR168W	1842
-YBR169C	2682
-YBR170C	2343
-YBR171W	1221
-YBR172C	2823
-YBR173C	1047
-YBR174C	915
-YBR175W	1548
-YBR176W	1539
-YBR177C	1956
-YBR178W	975
-YBR179C	3168
-YBR180W	2319
-YBR181C	1311
-YBR182C	1959
-YBR182C_A	795
-YBR183W	1551
-YBR184W	2172
-YBR185C	1437
-YBR186W	2295
-YBR187W	1443
-YBR188C	1023
-YBR189W	1188
-YBR190W	912
-YBR191W	1083
-YBR191W_A	675
-YBR192W	1734
-YBR193C	1272
-YBR194W	972
-YBR195C	1869
-YBR196C	2265
-YBR196C_A	750
-YBR196C_B	705
-YBR197C	1254
-YBR198C	2997
-YBR199W	1995
-YBR200W	2256
-YBR200W_A	765
-YBR201W	1236
-YBR201C_A	804
-YBR202W	3138
-YBR203W	3375
-YBR204C	1728
-YBR205W	1815
-YBR206W	924
-YBR207W	1998
-YBR208C	6108
-YBR209W	918
-YBR210W	1029
-YBR211C	1575
-YBR212W	2619
-YBR213W	1425
-YBR214W	2184
-YBR215W	2478
-YBR216C	2625
-YBR217W	1161
-YBR218C	4143
-YBR219C	984
-YBR220C	2283
-YBR221C	1701
-YBR221W_A	705
-YBR222C	2232
-YBR223C	2235
-YBR223W_A	720
-YBR224W	1116
-YBR225W	3303
-YBR226C	1011
-YBR227C	2163
-YBR228W	1515
-YBR229C	3465
-YBR230C	1005
-YBR230W_A	801
-YBR231C	1512
-YBR232C	960
-YBR233W	1842
-YBR233W_A	885
-YBR234C	1755
-YBR235W	3963
-YBR236C	1911
-YBR237W	3150
-YBR238C	2796
-YBR239C	2190
-YBR240C	1953
-YBR241C	2067
-YBR242W	1317
-YBR243C	1947
-YBR244W	1089
-YBR245C	3990
-YBR246W	1764
-YBR247C	2052
-YBR248C	2259
-YBR249C	1713
-YBR250W	2172
-YBR251W	1524
-YBR252W	1044
-YBR253W	966
-YBR254C	1128
-YBR255W	2685
-YBR255C_A	963
-YBR256C	1317
-YBR257W	1440
-YBR258C	1029
-YBR259W	2667
-YBR260C	2601
-YBR261C	1299
-YBR262C	921
-YBR263W	2073
-YBR264C	1200
-YBR265W	1563
-YBR267W	1782
-YBR266C	1053
-YBR268W	918
-YBR269C	1017
-YBR270C	2238
-YBR271W	1860
-YBR272C	2043
-YBR273C	1911
-YBR274W	2184
-YBR275C	6351
-YBR276C	3024
-YBR277C	1002
-YBR278W	1206
-YBR279W	1938
-YBR280C	2514
-YBR281C	3237
-YBR282W	1041
-YBR283C	2073
-YBR284W	2994
-YBR285W	1035
-YBR286W	2214
-YBR287W	1884
-YBR288C	2052
-YBR289W	3318
-YBR290W	1566
-YBR291C	1500
-YBR292C	972
-YBR293W	2025
-YBR294W	3180
-YBR295W	4251
-YBR296C	2325
-YBR296C_A	720
-YBR297W	2007
-YBR298C	2445
-YBR298C_A	822
-YBR299W	2355
-YBR300C	1098
-YBR301W	963
-YBR302C	1740
-YDR293C	4353
-YDL183C	1563
-YDL112W	4911
-YDL033C	1854
-YDR036C	2103
-YDR100W	1032
-YDR166C	3516
-YDR351W	3195
-YDR420W	6009
-YDR496C	2571
-YDL248W	1752
-YDL247W_A	675
-YDL247W	2430
-YDL246C	1674
-YDL245C	2304
-YDL244W	1623
-YDL243C	1590
-YDL242W	954
-YDL241W	972
-YDL240C_A	738
-YDL240W	3654
-YDL239C	2973
-YDL238C	2070
-YDL237W	1773
-YDL236W	1539
-YDL235C	1104
-YDL234C	2841
-YDL233W	1977
-YDL232W	711
-YDL231C	3978
-YDL230W	1608
-YDL229W	2442
-YDL228C	1242
-YDL227C	2361
-YDL226C	1659
-YDL225W	2256
-YDL224C	2550
-YDL223C	3741
-YDL222C	1530
-YDL221W	1152
-YDL220C	3375
-YDL219W	1053
-YDL218W	1554
-YDL217C	1224
-YDL216C	1923
-YDL215C	3879
-YDL214C	2700
-YDL213C	1278
-YDL212W	1233
-YDL211C	1719
-YDL210W	2316
-YDL209C	1620
-YDL208W	1071
-YDL207W	2217
-YDL206W	2889
-YDL205C	1584
-YDL204W	1782
-YDL203C	2472
-YDL202W	1350
-YDL201W	1461
-YDL200C	1167
-YDL199C	2664
-YDL198C	1503
-YDL197C	2178
-YDL196W	930
-YDL195W	4422
-YDL194W	3255
-YDL193W	1728
-YDL192W	1146
-YDL191W	963
-YDL190C	3486
-YDL189W	1974
-YDL188C	1734
-YDL187C	930
-YDL186W	1434
-YDL185C_A	828
-YDL185W	3816
-YDL184C	678
-YDL182W	1887
-YDL181W	858
-YDL180W	2244
-YDL179W	1515
-YDL178W	2193
-YDL177C	1113
-YDL176W	2727
-YDL175C	1635
-YDL174C	2364
-YDL173W	1488
-YDL172C	1080
-YDL171C	7038
-YDL170W	2187
-YDL169C	1272
-YDL168W	1761
-YDL167C	2760
-YDL166C	1194
-YDL165W	1176
-YDL164C	2868
-YDL163W	903
-YDL162C	957
-YDL161W	1965
-YDL160C_A	843
-YDL160C	2121
-YDL159W_A	732
-YDL159W	2148
-YDL159C_B	777
-YDL158C	909
-YDL157C	957
-YDL156W	2169
-YDL155W	1884
-YDL154W	3306
-YDL153C	2433
-YDL152W	966
-YDL151C	1182
-YDL150W	1869
-YDL149W	3594
-YDL148C	3033
-YDL147W	1938
-YDL146W	2076
-YDL145C	4206
-YDL144C	1671
-YDL143W	2187
-YDL142C	1452
-YDL141W	2673
-YDL140C	5802
-YDL139C	1272
-YDL138W	2892
-YDL137W	1146
-YDL136W	963
-YDL135C	1209
-YDL134C	1710
-YDL133C_A	678
-YDL133W	1914
-YDL132W	3048
-YDL131W	1923
-YDL130W_A	861
-YDL130W	921
-YDL129W	1476
-YDL128W	1836
-YDL127W	1527
-YDL126C	3108
-YDL125C	1077
-YDL124W	1539
-YDL123W	1023
-YDL122W	3030
-YDL121C	1050
-YDL120W	1125
-YDL119C	1524
-YDL118W	981
-YDL117W	3258
-YDL116W	2781
-YDL115C	1662
-YDL114W_A	714
-YDL114W	1527
-YDL113C	2523
-YDL111C	1398
-YDL110C	1053
-YDL109C	2544
-YDL108W	1521
-YDL107W	1656
-YDL106C	2280
-YDL105W	1809
-YDL104C	1824
-YDL103C	2034
-YDL102W	3894
-YDL101C	2142
-YDL100C	1665
-YDL099W	1626
-YDL098C	1185
-YDL097C	1905
-YDL096C	927
-YDL095W	3054
-YDL094C	1110
-YDL093W	2832
-YDL092W	1041
-YDL091C	1968
-YDL090C	1896
-YDL089W	2055
-YDL088C	2187
-YDL087C	1386
-YDL086W	1422
-YDL086C_A	1035
-YDL085C_A	807
-YDL085W	2238
-YDL084W	1941
-YDL083C	1032
-YDL082W	1200
-YDL081C	921
-YDL080C	2430
-YDL079C	2106
-YDL078C	1632
-YDL077C	3750
-YDL076C	1485
-YDL075W	942
-YDL074C	2703
-YDL073W	3555
-YDL072C	1212
-YDL071C	975
-YDL070W	2517
-YDL069C	1290
-YDL068W	930
-YDL067C	780
-YDL066W	1887
-YDL065C	1629
-YDL064W	1074
-YDL063C	2463
-YDL062W	1026
-YDL061C	771
-YDL060W	2967
-YDL059C	1317
-YDL058W	5973
-YDL057W	1587
-YDL056W	3102
-YDL055C	1686
-YDL054C	2061
-YDL053C	1158
-YDL052C	1512
-YDL051W	1428
-YDL050C	972
-YDL049C	1407
-YDL048C	2073
-YDL047W	1536
-YDL046W	1122
-YDL045W_A	888
-YDL045C	1521
-YDL044C	1923
-YDL043C	1401
-YDL042C	2289
-YDL041W	954
-YDL040C	3165
-YDL039C	2697
-YDL037C	1587
-YDL036C	1989
-YDL035C	3486
-YDL034W	945
-YDL032W	912
-YDL031W	3588
-YDL030W	2193
-YDL029W	1776
-YDL028C	2895
-YDL027C	1863
-YDL026W	912
-YDL025C	2463
-YDL025W_A	705
-YDL024C	2007
-YDL022C_A	849
-YDL023C	921
-YDL022W	1776
-YDL021W	1536
-YDL020C	2196
-YDL019C	4452
-YDL018C	1278
-YDL017W	2124
-YDL016C	903
-YDL015C	1533
-YDL014W	1584
-YDL013W	2460
-YDL012C	924
-YDL011C	924
-YDL010W	1296
-YDL009C	924
-YDL008W	1098
-YDL007C_A	858
-YDL007W	1914
-YDL006W	1446
-YDL005C	1896
-YDL004W	1083
-YDL003W	2301
-YDL002C	1212
-YDL001W	1893
-YDR001C	2856
-YDR002W	1206
-YDR003W	1233
-YDR003W_A	723
-YDR004W	1983
-YDR005C	1788
-YDR006C	3306
-YDR007W	1275
-YDR008C	951
-YDR009W	2163
-YDR010C	933
-YDR011W	5106
-YDR012W	1689
-YDR013W	1227
-YDR014W	2544
-YDR014W_A	1089
-YDR015C	840
-YDR016C	885
-YDR017C	3753
-YDR018C	1791
-YDR019C	1803
-YDR020C	1299
-YDR021W	1800
-YDR022C	1191
-YDR023W	1989
-YDR024W	1086
-YDR025W	1071
-YDR026C	2313
-YDR027C	3270
-YDR028C	3645
-YDR029W	915
-YDR030C	2121
-YDR031W	966
-YDR032C	1197
-YDR033W	1563
-YDR034C	2973
-YDR034C_D	5913
-YDR034C_C	1917
-YDR034C_A	777
-YDR034W_B	756
-YDR035W	1713
-YDR037W	2376
-YDR038C	3876
-YDR039C	3876
-YDR040C	3876
-YDR041W	1212
-YDR042C	1203
-YDR043C	1296
-YDR044W	1587
-YDR045C	933
-YDR046C	2415
-YDR047W	1689
-YDR048C	915
-YDR049W	2499
-YDR050C	1347
-YDR051C	1605
-YDR052C	2715
-YDR053W	996
-YDR054C	1488
-YDR055W	1935
-YDR056C	1218
-YDR057W	2229
-YDR058C	1581
-YDR059C	1047
-YDR060W	3678
-YDR061W	2220
-YDR062W	2286
-YDR063W	1050
-YDR064W	1056
-YDR065W	1698
-YDR066C	1191
-YDR067C	1275
-YDR068W	1533
-YDR069C	3381
-YDR070C	882
-YDR071C	1176
-YDR072C	2184
-YDR073W	1110
-YDR074W	3291
-YDR075W	1527
-YDR076W	1821
-YDR077W	1617
-YDR078C	1272
-YDR079W	936
-YDR079C_A	819
-YDR080W	3579
-YDR081C	3378
-YDR082W	2085
-YDR083W	1779
-YDR084C	1200
-YDR085C	2463
-YDR086C	843
-YDR087C	1437
-YDR088C	1749
-YDR089W	3210
-YDR090C	1533
-YDR091C	2427
-YDR092W	1062
-YDR093W	5439
-YDR094W	936
-YDR095C	1011
-YDR096W	3285
-YDR097C	4329
-YDR098C	1458
-YDR098C_B	5868
-YDR098C_A	1923
-YDR099W	1422
-YDR101C	2382
-YDR102C	933
-YDR103W	3354
-YDR104C	4338
-YDR105C	2022
-YDR106W	1455
-YDR107C	2619
-YDR108W	2697
-YDR109C	2748
-YDR110W	2301
-YDR111C	2124
-YDR112W	909
-YDR113C	1722
-YDR114C	903
-YDR115W	918
-YDR116C	1458
-YDR117C	2298
-YDR118W	2559
-YDR118W_A	717
-YDR119W	2907
-YDR119W_A	801
-YDR120C	2313
-YDR121W	1191
-YDR122W	3795
-YDR123C	1515
-YDR124W	1575
-YDR125C	1962
-YDR126W	1611
-YDR127W	5367
-YDR128W	4047
-YDR129C	2529
-YDR130C	1476
-YDR131C	2271
-YDR132C	2088
-YDR133C	936
-YDR135C	5148
-YDR136C	1173
-YDR137W	2592
-YDR138W	2859
-YDR139C	834
-YDR140W	1266
-YDR141C	5697
-YDR142C	1728
-YDR143C	2433
-YDR144C	2391
-YDR145W	2220
-YDR146C	2730
-YDR147W	2205
-YDR148C	1992
-YDR149C	1308
-YDR150W	8847
-YDR151C	1578
-YDR152W	1398
-YDR153C	1836
-YDR154C	951
-YDR155C	1089
-YDR156W	1014
-YDR157W	1002
-YDR158W	1698
-YDR159W	4506
-YDR160W	3159
-YDR161W	1764
-YDR162C	1311
-YDR163W	1128
-YDR164C	2775
-YDR165W	1935
-YDR167W	1221
-YDR168W	2121
-YDR169C	2142
-YDR169C_A	750
-YDR170C	6630
-YDR170W_A	1923
-YDR171W	1728
-YDR172W	2658
-YDR173C	1668
-YDR174W	1341
-YDR175C	1560
-YDR176W	2709
-YDR177W	1248
-YDR178W	1146
-YDR179C	1089
-YDR179W_A	1992
-YDR180W	5082
-YDR181C	2046
-YDR182W	2076
-YDR182W_A	804
-YDR183W	1293
-YDR183C_A	858
-YDR184C	1485
-YDR185C	1140
-YDR186C	3234
-YDR187C	1119
-YDR188W	2241
-YDR189W	2601
-YDR190C	1992
-YDR191W	1713
-YDR192C	1893
-YDR193W	999
-YDR194C	2595
-YDR194W_A	753
-YDR195W	2202
-YDR196C	1326
-YDR197W	1770
-YDR198C	2040
-YDR199W	966
-YDR200C	2415
-YDR201W	1098
-YDR202C	1656
-YDR203W	918
-YDR204W	1608
-YDR205W	2775
-YDR206W	3255
-YDR207C	3111
-YDR208W	2940
-YDR209C	1014
-YDR210W	828
-YDR210W_B	5913
-YDR210W_A	1917
-YDR210C_D	5868
-YDR210C_C	1923
-YDR211W	2739
-YDR212W	2280
-YDR213W	3342
-YDR214W	1653
-YDR215C	1014
-YDR216W	4572
-YDR217C	4530
-YDR218C	1872
-YDR219C	1998
-YDR220C	894
-YDR221W	2709
-YDR222W	1848
-YDR223W	2004
-YDR224C	996
-YDR225W	999
-YDR226W	1269
-YDR227W	4677
-YDR228C	2481
-YDR229W	1962
-YDR230W	948
-YDR231C	1218
-YDR232W	2247
-YDR233C	1488
-YDR234W	2682
-YDR235W	2235
-YDR236C	1257
-YDR237W	1479
-YDR238C	3522
-YDR239C	2964
-YDR240C	2079
-YDR241W	888
-YDR242W	2250
-YDR243C	2367
-YDR244W	2439
-YDR245W	1782
-YDR246W	1260
-YDR246W_A	801
-YDR247W	1986
-YDR248C	1182
-YDR249C	1722
-YDR250C	876
-YDR251W	3093
-YDR252W	1050
-YDR253C	1176
-YDR254W	1977
-YDR255C	1866
-YDR256C	2148
-YDR257C	2085
-YDR258C	3036
-YDR259C	1752
-YDR260C	1113
-YDR261C	2289
-YDR261W_B	5913
-YDR261W_A	1917
-YDR261C_D	5415
-YDR261C_C	1923
-YDR262W	1419
-YDR263C	1893
-YDR264C	2895
-YDR265W	1614
-YDR266C	2520
-YDR267C	1593
-YDR268W	1740
-YDR269C	924
-YDR270W	3615
-YDR271C	972
-YDR272W	1425
-YDR273W	1698
-YDR274C	972
-YDR275W	1308
-YDR276C	768
-YDR277C	1902
-YDR278C	918
-YDR279W	1653
-YDR280W	1518
-YDR281C	915
-YDR282C	1845
-YDR283C	5580
-YDR284C	1470
-YDR285W	3228
-YDR286C	945
-YDR287W	1479
-YDR288W	1512
-YDR289C	1830
-YDR290W	930
-YDR291W	3834
-YDR292C	2466
-YDR294C	2370
-YDR295C	2625
-YDR296W	1281
-YDR297W	1650
-YDR298C	1239
-YDR299W	2205
-YDR300C	1887
-YDR301W	4674
-YDR302W	1260
-YDR303C	3258
-YDR304C	1278
-YDR305C	1254
-YDR306C	2037
-YDR307W	2589
-YDR308C	1023
-YDR309C	1752
-YDR310C	3789
-YDR311W	2529
-YDR312W	1962
-YDR313C	1461
-YDR314C	2679
-YDR315C	1446
-YDR316W	2016
-YDR316W_B	5868
-YDR316W_A	1923
-YDR317W	1845
-YDR318W	1707
-YDR319C	1425
-YDR320C	2607
-YDR320C_A	819
-YDR320W_B	738
-YDR321W	1746
-YDR322W	1704
-YDR322C_A	891
-YDR323C	2148
-YDR324C	2931
-YDR325W	3708
-YDR326C	4917
-YDR327W	927
-YDR328C	1185
-YDR329C	1926
-YDR330W	2103
-YDR331W	1836
-YDR332W	2670
-YDR333C	2772
-YDR334W	5145
-YDR335W	4275
-YDR336W	1545
-YDR337W	1461
-YDR338C	2688
-YDR339C	1170
-YDR340W	903
-YDR341C	2424
-YDR342C	2313
-YDR343C	2313
-YDR344C	1044
-YDR345C	2304
-YDR346C	2046
-YDR347W	1566
-YDR348C	2100
-YDR349C	2391
-YDR350C	2655
-YDR352W	1554
-YDR353W	1560
-YDR354W	1743
-YDR354C_A	744
-YDR355C	903
-YDR356W	3435
-YDR357C	969
-YDR358W	2274
-YDR359C	3549
-YDR360W	1035
-YDR361C	1452
-YDR362C	2619
-YDR363W	1971
-YDR363W_A	870
-YDR364C	1968
-YDR365C	2487
-YDR365W_B	5868
-YDR365W_A	1923
-YDR366C	999
-YDR367W	1266
-YDR368W	1539
-YDR369C	3165
-YDR370C	1929
-YDR371W	2136
-YDR371C_A	705
-YDR372C	1638
-YDR373W	1173
-YDR374C	1521
-YDR374W_A	870
-YDR375C	1971
-YDR376W	2082
-YDR377W	906
-YDR378C	861
-YDR379W	3630
-YDR379C_A	840
-YDR380W	2508
-YDR381W	1281
-YDR381C_A	945
-YDR382W	933
-YDR383C	1317
-YDR384C	1428
-YDR385W	3129
-YDR386W	2499
-YDR387C	2268
-YDR388W	2049
-YDR389W	2565
-YDR390C	2511
-YDR391C	1299
-YDR392W	1614
-YDR393W	1971
-YDR394W	1887
-YDR395W	3435
-YDR396W	1101
-YDR397C	1041
-YDR398W	2532
-YDR399W	1266
-YDR400W	1623
-YDR401W	1164
-YDR402C	2070
-YDR403W	2211
-YDR404C	1116
-YDR405W	1392
-YDR406W	5190
-YDR406W_A	846
-YDR407C	4470
-YDR408C	1245
-YDR409W	3315
-YDR410C	1320
-YDR411C	1626
-YDR412W	1308
-YDR413C	1176
-YDR414C	1689
-YDR415C	1725
-YDR416W	3180
-YDR417C	972
-YDR418W	1098
-YDR419W	2499
-YDR421W	3453
-YDR422C	3048
-YDR423C	1830
-YDR424C	879
-YDR425W	2478
-YDR426C	978
-YDR427W	1782
-YDR428C	1386
-YDR429C	1425
-YDR430C	3570
-YDR431W	912
-YDR432W	1845
-YDR433W	1041
-YDR434W	2205
-YDR435C	1587
-YDR436W	2733
-YDR437W	1023
-YDR438W	1713
-YDR439W	1644
-YDR440W	2349
-YDR441C	1146
-YDR442W	993
-YDR443C	4863
-YDR444W	2664
-YDR445C	1008
-YDR446W	1509
-YDR447C	1011
-YDR448W	1905
-YDR449C	1923
-YDR450W	1041
-YDR451C	1662
-YDR452W	2625
-YDR453C	1191
-YDR454C	1164
-YDR455C	909
-YDR456W	2502
-YDR457W	10407
-YDR458C	2592
-YDR459C	1725
-YDR460W	1566
-YDR461W	711
-YDR461C_A	843
-YDR462W	1044
-YDR463W	2160
-YDR464W	4908
-YDR464C_A	789
-YDR465C	1839
-YDR466W	3297
-YDR467C	927
-YDR468C	1275
-YDR469W	1128
-YDR470C	2109
-YDR471W	1011
-YDR472W	1452
-YDR473C	2010
-YDR475C	3231
-YDR476C	1275
-YDR477W	2502
-YDR478W	1197
-YDR479C	2265
-YDR480W	1572
-YDR481C	2301
-YDR482C	1008
-YDR483W	1929
-YDR484W	2526
-YDR485C	2988
-YDR486C	1290
-YDR487C	1227
-YDR488C	2202
-YDR489W	1485
-YDR490C	2901
-YDR491C	1092
-YDR492W	1551
-YDR493W	972
-YDR494W	1686
-YDR495C	3636
-YDR497C	2355
-YDR498C	1752
-YDR499W	2844
-YDR500C	867
-YDR501W	2166
-YDR502C	1755
-YDR503C	1425
-YDR504C	984
-YDR505C	3126
-YDR506C	2427
-YDR507C	4029
-YDR508C	2592
-YDR509W	948
-YDR510W	906
-YDR510C_A	717
-YDR511W	1002
-YDR512C	1164
-YDR513W	1032
-YDR514C	2052
-YDR515W	1944
-YDR516C	2103
-YDR517W	1719
-YDR518W	2154
-YDR519W	1008
-YDR520C	2919
-YDR521W	936
-YDR522C	2109
-YDR523C	2073
-YDR524C	2049
-YDR524W_C	690
-YDR524C_B	801
-YDR524C_A	720
-YDR525W	930
-YDR525W_A	840
-YDR526C	1071
-YDR527W	1920
-YDR528W	1872
-YDR529C	984
-YDR530C	1578
-YDR531W	1704
-YDR532C	1758
-YDR533C	1314
-YDR534C	2187
-YDR535C	1101
-YDR536W	2310
-YDR537C	1206
-YDR538W	1329
-YDR539W	2112
-YDR540C	1140
-YDR541C	1635
-YDR542W	963
-YDR543C	900
-YDR544C	1029
-YDR545W	5913
-YDR545C_A	1080
-YIL122W	1656
-YIL048W	4056
-YIR019C	4704
-YIL177C	5877
-YIL177W_A	1083
-YIL176C	963
-YIL173W	5250
-YIL172C	2370
-YIL171W_A	1053
-YIL169C	3588
-YIL166C	2229
-YIL165C	960
-YIL164C	1200
-YIL163C	954
-YIL162W	2199
-YIL161W	1308
-YIL160C	1854
-YIL159W	4728
-YIL158W	1215
-YIL157C	1194
-YIL156W_A	1002
-YIL156W_B	822
-YIL156W	3816
-YIL155C	2550
-YIL154C	1641
-YIL153W	1782
-YIL152W	1308
-YIL151C	3957
-YIL150C	2316
-YIL149C	5640
-YIL148W	987
-YIL147C	4263
-YIL146C	2190
-YIL145C	1530
-YIL144W	2676
-YIL143C	3132
-YIL142C_A	933
-YIL142W	2184
-YIL141W	990
-YIL140W	3072
-YIL139C	1338
-YIL138C	1086
-YIL137C	3441
-YIL136W	1782
-YIL135C	1911
-YIL134C_A	804
-YIL134W	1536
-YIL133C	1200
-YIL132C	1242
-YIL131C	2055
-YIL130W	3495
-YIL129C	7731
-YIL128W	3699
-YIL127C	1221
-YIL126W	4680
-YIL125W	3645
-YIL124W	1494
-YIL123W	2031
-YIL121W	2229
-YIL120W	2292
-YIL119C	1824
-YIL118W	1296
-YIL117C	1557
-YIL116W	1758
-YIL115W_A	972
-YIL115C	4983
-YIL114C	1446
-YIL113W	1230
-YIL112W	3852
-YIL111W	1056
-YIL110W	1734
-YIL109C	3381
-YIL108W	2691
-YIL107C	3084
-YIL106W	1545
-YIL105C	2661
-YIL105W_A	741
-YIL104C	2124
-YIL103W	1878
-YIL102C_A	828
-YIL102C	906
-YIL101C	2544
-YIL100C_A	939
-YIL100W	954
-YIL099W	2250
-YIL098C	1068
-YIL097W	2151
-YIL096C	1611
-YIL095W	3033
-YIL094C	1716
-YIL093C	1395
-YIL092W	2502
-YIL091C	2766
-YIL090W	2076
-YIL089W	1218
-YIL088C	2073
-YIL087C	1074
-YIL086C	909
-YIL085C	2154
-YIL084C	1584
-YIL083C	1698
-YIL082W_A	5097
-YIL082W	1473
-YIL079C	1683
-YIL078W	2805
-YIL077C	1563
-YIL076W	1491
-YIL075C	3438
-YIL074C	2010
-YIL073C	3528
-YIL072W	2418
-YIL071W_A	1077
-YIL071C	1935
-YIL070C	1401
-YIL069C	1008
-YIL068W_A	984
-YIL068C	3018
-YIL067C	2637
-YIL066W_A	1044
-YIL066C	3210
-YIL065C	1068
-YIL064W	1374
-YIL063C	1584
-YIL062C	1065
-YIL061C	1503
-YIL060W	1035
-YIL059C	966
-YIL058W	885
-YIL057C	1095
-YIL056W	2523
-YIL055C	2484
-YIL054W	918
-YIL053W	1353
-YIL052C	966
-YIL051C	1038
-YIL050W	1458
-YIL049W	1362
-YIL047C_A	969
-YIL047C	3309
-YIL046W_A	765
-YIL046W	2523
-YIL045W	2217
-YIL044C	1497
-YIL043C	1455
-YIL042C	1785
-YIL041W	1581
-YIL040W	1017
-YIL039W	2022
-YIL038C	3111
-YIL037C	2571
-YIL036W	2364
-YIL035C	1719
-YIL034C	1464
-YIL033C	1851
-YIL032C	957
-YIL031W	3705
-YIL030W_A	939
-YIL030C	4560
-YIL029W_A	972
-YIL029C	1029
-YIL028W	999
-YIL027C	1026
-YIL026C	4053
-YIL025C	975
-YIL024C	1170
-YIL023C	1641
-YIL022W	1896
-YIL021W	1557
-YIL021C_A	870
-YIL020C_A	939
-YIL020C	1386
-YIL019W	1641
-YIL018W	1365
-YIL017C	3366
-YIL016W	1080
-YIL015W	2364
-YIL014C_A	915
-YIL014W	2493
-YIL013C	4836
-YIL012W	942
-YIL011W	1410
-YIL010W	1248
-YIL009C_A	1146
-YIL009W	2685
-YIL008W	900
-YIL007C	1263
-YIL006W	1722
-YIL005W	2706
-YIL004C	1029
-YIL003W	1482
-YIL002W_A	810
-YIL002C	3441
-YIL001W	2142
-YIR001C	1353
-YIR002C	3582
-YIR003W	2640
-YIR004W	1899
-YIR005W	1047
-YIR006C	5043
-YIR007W	2895
-YIR008C	1830
-YIR009W	936
-YIR010W	2331
-YIR011C	1560
-YIR012W	1896
-YIR013C	966
-YIR014W	1329
-YIR015W	1035
-YIR016W	1398
-YIR017C	1164
-YIR017W_A	1200
-YIR018W	1338
-YIR018C_A	738
-YIR020C	903
-YIR020W_A	843
-YIR020C_B	1335
-YIR021W	1692
-YIR021W_A	813
-YIR022W	1104
-YIR023W	3513
-YIR023C_A	924
-YIR024C	1251
-YIR025W	1707
-YIR026C	1695
-YIR027C	1983
-YIR028W	2508
-YIR029W	1632
-YIR030C	1335
-YIR030W_A	984
-YIR031C	2265
-YIR032C	1188
-YIR033W	3942
-YIR034C	1722
-YIR035C	1365
-YIR036C	1392
-YIR036W_A	1002
-YIR037W	1092
-YIR038C	1305
-YIR039C	2214
-YIR040C	933
-YIR041W	975
-YIR042C	1311
-YFL068W	835
-YFL067W	1128
-YFL066C	1779
-YFL065C	909
-YFL064C	1125
-YFL063W	1056
-YFL062W	1740
-YFL061W	1278
-YFL060C	1269
-YFL059W	1497
-YFL058W	1623
-YFL057C	1059
-YFL056C	1239
-YFL055W	2277
-YFL054C	2541
-YFL053W	2376
-YFL052W	1998
-YFL051C	1083
-YFL050C	3177
-YFL049W	2472
-YFL048C	1938
-YFL047W	2745
-YFL046W	1224
-YFL045C	1365
-YFL044C	1506
-YFL042C	2625
-YFL041W_A	792
-YFL041W	2469
-YFL040W	2223
-YFL039C	1728
-YFL038C	1221
-YFL037W	1974
-YFL036W	4656
-YFL034C_B	1464
-YFL034C_A	969
-YFL034W	3822
-YFL033C	5913
-YFL032W	921
-YFL031W	1317
-YFL031C_A	702
-YFL030W	1758
-YFL029C	1707
-YFL028C	1470
-YFL027C	2094
-YFL026W	1896
-YFL025C	3690
-YFL024C	3099
-YFL023W	2991
-YFL022C	2112
-YFL021C_A	1455
-YFL021W	2133
-YFL020C	969
-YFL019C	954
-YFL018C	2100
-YFL017W_A	834
-YFL017C	1080
-YFL016C	2136
-YFL015W_A	918
-YFL015C	1095
-YFL014W	930
-YFL013W_A	1404
-YFL013C	2679
-YFL012W_A	975
-YFL012W	1047
-YFL011W	2241
-YFL010W_A	885
-YFL010C	1236
-YFL009W	2940
-YFL008W	4278
-YFL007W	7032
-YFL005W	1248
-YFL004W	3087
-YFL003C	3237
-YFL002W_A	5913
-YFL002W_B	1917
-YFL002C	2421
-YFL001W	1929
-YFR001W	1215
-YFR002W	3120
-YFR003C	1068
-YFR004W	1521
-YFR005C	1947
-YFR006W	2208
-YFR007W	1662
-YFR008W	1266
-YFR009W	2859
-YFR009W_A	858
-YFR010W	2100
-YFR010W_A	789
-YFR011C	1113
-YFR012W	1209
-YFR012W_A	687
-YFR013W	2964
-YFR014C	1941
-YFR015C	2727
-YFR016C	4302
-YFR017C	1188
-YFR018C	1692
-YFR019W	7437
-YFR020W	1299
-YFR021W	2103
-YFR022W	2802
-YFR023W	2436
-YFR024C_A	1980
-YFR025C	1608
-YFR026C	1110
-YFR027W	1446
-YFR028C	2256
-YFR029W	2637
-YFR030W	3708
-YFR031C	4113
-YFR031C_A	1365
-YFR032C	1470
-YFR032C_A	780
-YFR032C_B	864
-YFR033C	1044
-YFR034C	1539
-YFR034W_A	888
-YFR035C	945
-YFR036W	975
-YFR036W_A	1251
-YFR037C	2274
-YFR038W	3162
-YFR039C	2133
-YFR040W	3609
-YFR041C	1488
-YFR042W	1203
-YFR043C	1314
-YFR044C	2046
-YFR045W	1530
-YFR046C	1686
-YFR047C	1488
-YFR048W	2589
-YFR049W	972
-YFR050C	1401
-YFR051C	2241
-YFR052W	1425
-YFR052C_A	906
-YFR053C	2058
-YFR054C	1179
-YFR056C	969
-YFR055W	1623
-YFR057W	1056
-YKL023C_A	828
-YKR046C	1452
-YKR103W	4257
-YKL225W	948
-YKL224C	972
-YKL223W	933
-YKL222C	2718
-YKL221W	2022
-YKL220C	2736
-YKL219W	1824
-YKL218C	1581
-YKL217W	2451
-YKL216W	1545
-YKL215C	4461
-YKL214C	1212
-YKL213C	2748
-YKL212W	2472
-YKL211C	2055
-YKL210W	3675
-YKL209C	4473
-YKL208W	1416
-YKL207W	1362
-YKL206C	1404
-YKL205W	3903
-YKL204W	2499
-YKL203C	8025
-YKL202W	1182
-YKL201C	4137
-YKL198C	2589
-YKL197C	3732
-YKL196C	1203
-YKL195W	1812
-YKL194C	1989
-YKL193C	1617
-YKL192C	978
-YKL191W	2205
-YKL190W	1128
-YKL189W	1800
-YKL188C	3162
-YKL187C	2853
-YKL186C	1155
-YKL185W	2367
-YKL184W	2001
-YKL183C_A	813
-YKL183W	1521
-YKL182W	6756
-YKL181W	1884
-YKL180W	1155
-YKL179C	2640
-YKL178C	2013
-YKL177W	939
-YKL176C	3087
-YKL175W	2112
-YKL174C	2457
-YKL173W	3627
-YKL172W	1884
-YKL171W	3387
-YKL170W	1017
-YKL169C	984
-YKL168C	2775
-YKL167C	1014
-YKL166C	1797
-YKL165C_A	834
-YKL165C	3360
-YKL164C	1626
-YKL163W	1578
-YKL162C_A	753
-YKL162C	1809
-YKL161C	1902
-YKL160W	1038
-YKL159C	1236
-YKL157W	3459
-YKL156W	849
-YKL156C_A	717
-YKL155C	2487
-YKL154W	1335
-YKL153W	1110
-YKL152C	1344
-YKL151C	1614
-YKL150W	1509
-YKL149C	1818
-YKL148C	2523
-YKL147C	1218
-YKL146W	2679
-YKL145W	2004
-YKL145W_A	693
-YKL144C	1239
-YKL143W	1992
-YKL142W	1260
-YKL141W	1197
-YKL140W	2247
-YKL139W	2187
-YKL138C_A	810
-YKL138C	996
-YKL137W	936
-YKL136W	999
-YKL135C	2781
-YKL134C	2919
-YKL133C	1992
-YKL132C	1893
-YKL131W	1122
-YKL130C	1341
-YKL129C	4419
-YKL128C	1488
-YKL127W	2313
-YKL126W	2643
-YKL125W	2484
-YKL124W	2340
-YKL123W	981
-YKL122C	1104
-YKL121W	3159
-YKL120W	1575
-YKL119C	1248
-YKL118W	912
-YKL117W	1251
-YKL116C	2157
-YKL115C	993
-YKL114C	1704
-YKL113C	1749
-YKL112W	2796
-YKL111C	936
-YKL110C	1542
-YKL109W	2265
-YKL108W	1962
-YKL107W	1530
-YKL106C_A	720
-YKL106W	1956
-YKL105C	3999
-YKL104C	2754
-YKL103C	2145
-YKL102C	906
-YKL101W	5157
-YKL100C	2364
-YKL100W_A	690
-YKL099C	1353
-YKL098W	1674
-YKL097C	1011
-YKL096C_B	750
-YKL096W_A	879
-YKL096W	1320
-YKL095W	1437
-YKL094W	1542
-YKL093W	1620
-YKL092C	3915
-YKL091C	1533
-YKL090W	1932
-YKL089W	2250
-YKL088W	2316
-YKL087C	1275
-YKL086W	984
-YKL085W	1605
-YKL084W	951
-YKL083W	1215
-YKL082C	1905
-YKL081W	1839
-YKL080W	1779
-YKL079W	2571
-YKL078W	2808
-YKL077W	1779
-YKL076C	984
-YKL075C	1953
-YKL074C	2184
-YKL073W	3246
-YKL072W	2901
-YKL071W	1371
-YKL070W	1110
-YKL069W	1143
-YKL068W_A	837
-YKL068W	3480
-YKL067W	1062
-YKL066W	1044
-YKL065W_A	822
-YKL065C	1221
-YKL064W	3510
-YKL063C	1104
-YKL062W	2493
-YKL061W	942
-YKL060C	1680
-YKL059C	1926
-YKL058W	969
-YKL057C	3714
-YKL056C	1104
-YKL055C	1437
-YKL054C	2817
-YKL053C_A	861
-YKL053W	975
-YKL052C	1479
-YKL051W	1662
-YKL050C	3369
-YKL049C	1290
-YKL048C	2523
-YKL047W	2151
-YKL046C	1950
-YKL045W	2187
-YKL044W	921
-YKL043W	1701
-YKL042W	1692
-YKL041W	1275
-YKL040C	1371
-YKL039W	2172
-YKL038W	4113
-YKL037W	957
-YKL036C	993
-YKL035W	2100
-YKL034W	2877
-YKL033W_A	1311
-YKL033W	3717
-YKL032C	2394
-YKL031W	1014
-YKL030W	1206
-YKL029C	2610
-YKL028W	2049
-YKL027W	1944
-YKL026C	1104
-YKL025C	2640
-YKL024C	1215
-YKL023W	1434
-YKL022C	3123
-YKL021C	2007
-YKL020C	3849
-YKL019W	1551
-YKL018C_A	900
-YKL018W	1590
-YKL017C	2652
-YKL016C	1125
-YKL015W	3540
-YKL014C	5895
-YKL013C	1116
-YKL012W	2352
-YKL011C	1662
-YKL010C	5052
-YKL009W	1311
-YKL008C	1857
-YKL007W	1407
-YKL006C_A	894
-YKL006W	1017
-YKL005C	2385
-YKL004W	1806
-YKL003C	996
-YKL002W	1299
-YKL001C	1209
-YKR001C	2715
-YKR002W	2307
-YKR003W	1947
-YKR004C	1734
-YKR005C	2178
-YKR006C	1395
-YKR007W	1155
-YKR008W	2478
-YKR009C	3303
-YKR010C	2916
-YKR011C	1662
-YKR012C	978
-YKR013W	1590
-YKR014C	1305
-YKR015C	2307
-YKR016W	2223
-YKR017C	2256
-YKR018C	2778
-YKR019C	2448
-YKR020W	1095
-YKR021W	3348
-YKR022C	1569
-YKR023W	2193
-YKR024C	2829
-YKR025W	1449
-YKR026C	1518
-YKR027W	2898
-YKR028W	3702
-YKR029C	2856
-YKR030W	1422
-YKR031C	5652
-YKR032W	915
-YKR033C	1026
-YKR034W	1410
-YKR035C	1242
-YKR035W_A	1215
-YKR036C	2532
-YKR037C	1488
-YKR038C	1761
-YKR039W	2409
-YKR040C	1104
-YKR041W	1353
-YKR042W	1698
-YKR043C	1416
-YKR044W	1932
-YKR045C	1152
-YKR047W	906
-YKR048C	1854
-YKR049C	1002
-YKR050W	3270
-YKR051W	1857
-YKR052C	1515
-YKR053C	1815
-YKR054C	12879
-YKR055W	1476
-YKR056W	2520
-YKR057W	864
-YKR058W	2451
-YKR059W	1788
-YKR060W	1425
-YKR061W	1878
-YKR062W	1587
-YKR063C	2109
-YKR064W	3192
-YKR065C	1194
-YKR066C	1686
-YKR067W	2832
-YKR068C	1182
-YKR069W	2382
-YKR070W	1659
-YKR071C	1647
-YKR072C	2289
-YKR073C	921
-YKR074W	1068
-YKR075C	1524
-YKR075W_A	870
-YKR076W	1713
-YKR077W	1692
-YKR078W	2358
-YKR079C	3117
-YKR080W	1563
-YKR081C	1635
-YKR082W	4074
-YKR083C	1002
-YKR084C	2436
-YKR085C	1188
-YKR086W	3816
-YKR087C	1638
-YKR088C	1614
-YKR089C	3333
-YKR090W	2721
-YKR091W	1341
-YKR092C	1821
-YKR093W	2406
-YKR094C	987
-YKR095W	6228
-YKR095W_A	867
-YKR096W	4188
-YKR097W	2250
-YKR098C	2754
-YKR099W	3036
-YKR100C	1668
-YKR101W	2565
-YKR102W	4110
-YKR104W	1521
-YKR105C	2349
-YKR106W	2448
-YOL100W	3846
-YOL034W	3882
-YOR033C	2709
-YOR108W	2415
-YOR172W	2961
-YOR239W	2487
-YOR321W	2862
-YOL166W_A	756
-YOL166C	939
-YOL165C	1032
-YOL164W_A	783
-YOL164W	2541
-YOL163W	1110
-YOL162W	1248
-YOL161C	963
-YOL160W	942
-YOL159C_A	873
-YOL159C	1116
-YOL158C	2421
-YOL157C	2370
-YOL156W	2304
-YOL155W_A	735
-YOL155C	3504
-YOL154W	1350
-YOL152W	2463
-YOL151W	1629
-YOL150C	912
-YOL149W	1296
-YOL148C	2415
-YOL147C	1311
-YOL146W	1185
-YOL145C	3834
-YOL144W	2055
-YOL143C	1110
-YOL142W	1323
-YOL141W	2688
-YOL140W	1872
-YOL139C	1242
-YOL138C	4626
-YOL137W	2094
-YOL136C	1794
-YOL135C	1269
-YOL134C	990
-YOL133W	966
-YOL132W	2016
-YOL131W	927
-YOL130W	3180
-YOL129W	1155
-YOL128C	1728
-YOL127W	1029
-YOL126C	1734
-YOL125W	2031
-YOL124C	1902
-YOL123W	2205
-YOL122C	2328
-YOL121C	1035
-YOL120C	1161
-YOL119C	2106
-YOL118C	909
-YOL117W	2538
-YOL116W	1749
-YOL115W	2355
-YOL114C	1209
-YOL113W	2568
-YOL112W	2079
-YOL111C	1239
-YOL110W	1314
-YOL109W	942
-YOL108C	1056
-YOL107W	1629
-YOL106W	954
-YOL105C	2271
-YOL104C	1659
-YOL103W_B	5868
-YOL103W_A	1923
-YOL103W	2430
-YOL102C	1293
-YOL101C	1539
-YOL099C	1092
-YOL098C	3714
-YOL097W_A	786
-YOL097C	1899
-YOL096C	1539
-YOL095C	2721
-YOL094C	1572
-YOL093W	1482
-YOL092W	1527
-YOL091W	2430
-YOL090W	3495
-YOL089C	3693
-YOL088C	1434
-YOL087C	3951
-YOL086W_A	873
-YOL086C	1647
-YOL085W_A	813
-YOL085C	942
-YOL084W	3576
-YOL083W	1839
-YOL083C_A	741
-YOL082W	1848
-YOL081W	9840
-YOL080C	1470
-YOL079W	999
-YOL078W	4131
-YOL077W_A	807
-YOL077C	1476
-YOL076W	2991
-YOL075C	4485
-YOL073C	1569
-YOL072W	1968
-YOL071W	1089
-YOL070C	2106
-YOL069W	1956
-YOL068C	2112
-YOL067C	1134
-YOL066C	2376
-YOL065C	1755
-YOL064C	1674
-YOL063C	3474
-YOL062C	2076
-YOL061W	2091
-YOL060C	2721
-YOL059W	1923
-YOL058W	1863
-YOL057W	2736
-YOL056W	1512
-YOL055C	2256
-YOL054W	1821
-YOL053W	1788
-YOL052C_A	786
-YOL052C	1791
-YOL051W	3846
-YOL050C	921
-YOL049W	2076
-YOL048C	1629
-YOL047C	1671
-YOL046C	1275
-YOL045W	3906
-YOL044W	1752
-YOL043C	1743
-YOL042W	1692
-YOL041C	1980
-YOL040C	1029
-YOL039W	921
-YOL038C_A	696
-YOL038W	1365
-YOL037C	954
-YOL036W	2886
-YOL035C	903
-YOL033W	2211
-YOL032W	1341
-YOL031C	1866
-YOL030W	2055
-YOL029C	1206
-YOL028C	1338
-YOL027C	2322
-YOL026C	942
-YOL025W	2583
-YOL024W	1119
-YOL023W	2631
-YOL022C	1827
-YOL021C	3606
-YOL020W	2379
-YOL019W_A	753
-YOL019W	2256
-YOL018C	1794
-YOL017W	2745
-YOL016C	1944
-YOL015W	2361
-YOL014W	975
-YOL013W_B	891
-YOL013W_A	792
-YOL013C	2256
-YOL012C	1005
-YOL011W	2661
-YOL010W	1704
-YOL009C	1416
-YOL008W	1224
-YOL007C	1626
-YOL006C	2910
-YOL005C	963
-YOL004W	5211
-YOL003C	1737
-YOL002C	1554
-YOL001W	1482
-YOR001W	2802
-YOR002W	2235
-YOR003W	2037
-YOR004W	1365
-YOR005C	3435
-YOR006C	1542
-YOR007C	1641
-YOR008C	1737
-YOR008C_A	825
-YOR008W_B	702
-YOR009W	2064
-YOR010C	1356
-YOR011W	4785
-YOR011W_A	807
-YOR012W	1014
-YOR013W	1071
-YOR014W	2874
-YOR015W	960
-YOR016C	1224
-YOR017W	3003
-YOR018W	3114
-YOR019W	2793
-YOR020C	921
-YOR020W_A	873
-YOR021C	1242
-YOR022C	2748
-YOR023C	2301
-YOR024W	924
-YOR025W	1944
-YOR026W	1626
-YOR027W	2370
-YOR028C	1488
-YOR029W	936
-YOR030W	2460
-YOR031W	810
-YOR032C	1905
-YOR032W_A	801
-YOR034C	2850
-YOR034C_A	843
-YOR035C	2970
-YOR036W	1467
-YOR037W	1701
-YOR038C	3228
-YOR039W	1377
-YOR040W	1458
-YOR041C	1032
-YOR042W	1836
-YOR043W	2061
-YOR044W	1074
-YOR045W	786
-YOR046C	2049
-YOR047C	1935
-YOR048C	3621
-YOR049C	1665
-YOR050C	948
-YOR051C	1839
-YOR052C	1053
-YOR053W	942
-YOR054C	2625
-YOR055W	1035
-YOR056C	1980
-YOR057W	1788
-YOR058C	3258
-YOR059C	1953
-YOR060C	1374
-YOR061W	1620
-YOR062C	1407
-YOR063W	1764
-YOR064C	1260
-YOR065W	1530
-YOR066W	2490
-YOR067C	2334
-YOR069W	2628
-YOR068C	945
-YOR070C	2514
-YOR071C	2397
-YOR072W	915
-YOR072W_A	849
-YOR072W_B	762
-YOR073W	2373
-YOR074C	1515
-YOR073W_A	834
-YOR075W	1641
-YOR076C	2844
-YOR077W	1299
-YOR078W	1245
-YOR079C	1542
-YOR080W	2799
-YOR081C	2850
-YOR082C	942
-YOR083W	1488
-YOR084W	1764
-YOR085W	1653
-YOR086C	4161
-YOR087W	2628
-YOR089C	1233
-YOR090C	2319
-YOR091W	1638
-YOR092W	2442
-YOR093C	5547
-YOR094W	1152
-YOR095C	1377
-YOR096W	1173
-YOR097C	1128
-YOR098C	3831
-YOR099W	1782
-YOR100C	1584
-YOR101W	1530
-YOR102W	951
-YOR103C	993
-YOR104W	1449
-YOR105W	927
-YOR106W	1452
-YOR107W	1530
-YOR108C_A	810
-YOR109W	3924
-YOR110W	1908
-YOR111W	1299
-YOR112W	2886
-YOR113W	3345
-YOR114W	1485
-YOR115C	1407
-YOR116C	4983
-YOR117W	1905
-YOR118W	2304
-YOR119C	2055
-YOR120W	1539
-YOR121C	906
-YOR122C	981
-YOR123C	1995
-YOR124C	4419
-YOR125C	1302
-YOR126C	1317
-YOR127W	3624
-YOR128C	2316
-YOR129C	3282
-YOR130C	1479
-YOR131C	1257
-YOR132W	2256
-YOR133W	3129
-YOR134W	1830
-YOR135C	942
-YOR136W	1710
-YOR137C	2469
-YOR138C	2616
-YOR139C	993
-YOR140W	2901
-YOR141C	3246
-YOR142W	1590
-YOR142W_B	5868
-YOR142W_A	1923
-YOR143C	1560
-YOR144C	2976
-YOR145C	1425
-YOR146W	906
-YOR147W	2469
-YOR148C	1158
-YOR149C	2151
-YOR150W	1092
-YOR151C	4275
-YOR152C	1371
-YOR153W	5136
-YOR154W	2364
-YOR155C	1953
-YOR156C	2781
-YOR157C	1386
-YOR158W	1557
-YOR159C	885
-YOR160W	3519
-YOR161C	2220
-YOR161W_A	681
-YOR161W_B	861
-YOR161C_C	747
-YOR162C	3033
-YOR163W	1167
-YOR164C	1539
-YOR165W	2931
-YOR166C	1977
-YOR167C	804
-YOR168W	3030
-YOR169C	1065
-YOR170W	906
-YOR171C	2475
-YOR173W	1662
-YOR174W	1455
-YOR175C	2460
-YOR176W	1782
-YOR177C	1995
-YOR178C	2982
-YOR179C	1167
-YOR180C	1416
-YOR181W	2502
-YOR182C	792
-YOR183W	990
-YOR184W	1788
-YOR185C	1263
-YOR186W	1035
-YOR186C_A	810
-YOR187W	1914
-YOR188W	4014
-YOR189W	951
-YOR190W	1938
-YOR191W	5460
-YOR192C	2400
-YOR192C_C	837
-YOR192C_B	5913
-YOR192C_A	1917
-YOR193W	1731
-YOR194C	1461
-YOR195W	3066
-YOR196C	1845
-YOR197W	1899
-YOR198C	2013
-YOR199W	930
-YOR200W	999
-YOR201C	1839
-YOR202W	1263
-YOR203W	954
-YOR204W	2415
-YOR205C	2271
-YOR206W	2733
-YOR207C	4050
-YOR208W	2853
-YOR209C	1890
-YOR210W	813
-YOR211C	3246
-YOR212W	1872
-YOR213C	1347
-YOR214C	1311
-YOR215C	1158
-YOR216C	2055
-YOR217W	3186
-YOR218C	1020
-YOR219C	3396
-YOR220W	1398
-YOR221C	1683
-YOR222W	1524
-YOR223W	1479
-YOR224C	1041
-YOR225W	930
-YOR226C	1071
-YOR227W	4341
-YOR228C	1509
-YOR229W	2004
-YOR230W	1914
-YOR231W	2127
-YOR231C_A	801
-YOR232W	1287
-YOR233W	3003
-YOR234C	924
-YOR235W	915
-YOR236W	1236
-YOR237W	1905
-YOR238W	1512
-YOR241W	2247
-YOR242C	1716
-YOR243C	2631
-YOR244W	1938
-YOR245C	1857
-YOR246C	1593
-YOR247W	1233
-YOR248W	903
-YOR249C	2658
-YOR250C	1938
-YOR251C	1515
-YOR252W	1137
-YOR253W	1131
-YOR254C	2592
-YOR255W	1437
-YOR256C	3030
-YOR257W	1086
-YOR258W	1254
-YOR259C	1914
-YOR260W	2337
-YOR261C	1617
-YOR262W	1644
-YOR263C	1008
-YOR264W	1893
-YOR265W	921
-YOR266W	1872
-YOR267C	2880
-YOR268C	999
-YOR269W	2085
-YOR270C	3123
-YOR271C	1584
-YOR272W	1983
-YOR273C	2580
-YOR274W	1887
-YOR275C	2586
-YOR276W	1086
-YOR277C	909
-YOR278W	1428
-YOR279C	1533
-YOR280C	1401
-YOR281C	1461
-YOR282W	921
-YOR283W	1293
-YOR284W	1332
-YOR285W	1020
-YOR286W	1050
-YOR287C	1503
-YOR288C	1557
-YOR289W	1356
-YOR290C	5712
-YOR291W	5019
-YOR292C	1530
-YOR293W	918
-YOR293C_A	750
-YOR294W	1212
-YOR295W	1287
-YOR296W	4470
-YOR297C	1179
-YOR298W	2040
-YOR298C_A	1056
-YOR299W	2841
-YOR300W	909
-YOR301W	1908
-YOR302W	678
-YOR303W	1836
-YOR304W	3963
-YOR304C_A	831
-YOR305W	1329
-YOR306C	2166
-YOR307C	1962
-YOR308C	2364
-YOR309C	981
-YOR310C	2136
-YOR311C	1473
-YOR312C	1119
-YOR313C	1617
-YOR314W	930
-YOR314W_A	711
-YOR315W	1641
-YOR316C	1920
-YOR316C_A	810
-YOR317W	2703
-YOR318C	906
-YOR319W	1242
-YOR320C	2076
-YOR322C	3057
-YOR323C	1971
-YOR324C	2409
-YOR325W	1074
-YOR326W	5325
-YOR327C	948
-YOR328W	5295
-YOR329C	3219
-YOR329W_A	810
-YOR330C	4365
-YOR331C	1158
-YOR332W	1302
-YOR333C	1017
-YOR334W	2013
-YOR335C	3477
-YOR335W_A	681
-YOR336W	4698
-YOR337W	2880
-YOR338W	1692
-YOR339C	1071
-YOR340C	1581
-YOR341W	5595
-YOR342C	1560
-YOR343C	927
-YOR343W_B	5913
-YOR343W_A	1917
-YOR344C	1476
-YOR345C	951
-YOR346W	3558
-YOR347C	2121
-YOR348C	2484
-YOR349W	3645
-YOR350C	2592
-YOR351C	2094
-YOR352W	1632
-YOR353C	2976
-YOR354C	2679
-YOR355W	2169
-YOR356W	2496
-YOR357C	1089
-YOR358W	1329
-YOR359W	2172
-YOR360C	2181
-YOR361C	2892
-YOR362C	1467
-YOR363C	3591
-YOR364W	969
-YOR365C	2712
-YOR366W	954
-YOR367W	1203
-YOR368W	1806
-YOR369C	1032
-YOR370C	2412
-YOR371C	3294
-YOR372C	2265
-YOR373W	3156
-YOR374W	2160
-YOR375C	1965
-YOR376W	969
-YOR376W_A	756
-YOR377W	2178
-YOR378W	2148
-YOR379C	939
-YOR380W	2241
-YOR381W	2736
-YOR381W_A	768
-YOR382W	1062
-YOR383C	1215
-YOR384W	2685
-YOR385W	1473
-YOR386W	2298
-YOR387C	1221
-YOR388C	1731
-YOR389W	2475
-YOR390W	1728
-YOR391C	1314
-YOR392W	1044
-YOR393W	1914
-YOR394W	1095
-YOR394C_A	768
-YOR396W	5991
-YOR396C_A	1083
-YCR009C	1398
-YCR084C	2742
-YCL076W	1344
-YCL073C	2448
-YCL069W	1977
-YCL068C	1383
-YCL067C	1233
-YCL066W	1128
-YCL065W	969
-YCL064C	1683
-YCL063W	1872
-YCL061C	3891
-YCL059C	1551
-YCL058C	1059
-YCL058W_A	942
-YCL057C_A	894
-YCL057W	2739
-YCL056C	1035
-YCL055W	1608
-YCL054W	3126
-YCL052C	1851
-YCL051W	2352
-YCL050C	1566
-YCL049C	1539
-YCL048W_A	840
-YCL048W	1992
-YCL047C	1377
-YCL045C	2883
-YCL046W	924
-YCL044C	1854
-YCL043C	2169
-YCL041C	1095
-YCL042W	960
-YCL040W	2103
-YCL039W	2838
-YCL038C	2187
-YCL037C	1905
-YCL036W	2301
-YCL035C	933
-YCL034W	1665
-YCL033C	1107
-YCL032W	1641
-YCL031C	1494
-YCL030C	3000
-YCL029C	1923
-YCL028W	1818
-YCL027W	2139
-YCL026C_B	1182
-YCL026C_A	1182
-YCL025C	2502
-YCL023C	948
-YCL024W	3714
-YCL022C	1116
-YCL021W_A	978
-YCL019W	5913
-YCL020W	1917
-YCL018W	1695
-YCL017C	2094
-YCL016C	1743
-YCL014W	5511
-YCL012C	1005
-YCL011C	1884
-YCL010C	1380
-YCL009C	1530
-YCL008C	1758
-YCL007C	993
-YCL005W_A	822
-YCL005W	1371
-YCL004W	2166
-YCL002C	1392
-YCL001W	1167
-YCL001W_A	1062
-YCL001W_B	855
-YCR001W	915
-YCR002C	1569
-YCR003W	1152
-YCR004C	1344
-YCR005C	1983
-YCR006C	1074
-YCR007C	1320
-YCR008W	2412
-YCR010C	1452
-YCR011C	3750
-YCR012W	1851
-YCR013C	1248
-YCR014C	2349
-YCR015C	1554
-YCR016W	1473
-YCR017C	3462
-YCR018C	1266
-YCR018C_A	855
-YCR019W	1692
-YCR020C	1248
-YCR020C_A	867
-YCR020W_B	837
-YCR021C	1599
-YCR022C	945
-YCR023C	2436
-YCR024C	2079
-YCR024C_B	867
-YCR024C_A	723
-YCR025C	1011
-YCR026C	2829
-YCR027C	1230
-YCR028C	2139
-YCR028C_A	1008
-YCR030C	3213
-YCR031C	1014
-YCR032W	7104
-YCR033W	4281
-YCR034W	1644
-YCR035C	1785
-YCR036W	1602
-YCR037C	3372
-YCR038C	2529
-YCR038W_A	726
-YCR039C	1233
-YCR040W	1128
-YCR041W	933
-YCR042C	4824
-YCR043C	984
-YCR044C	1674
-YCR045C	2076
-YCR045W_A	951
-YCR046C	1110
-YCR047C	1428
-YCR047W_A	807
-YCR049C	1047
-YCR048W	2433
-YCR050C	909
-YCR051W	1269
-YCR052W	2052
-YCR053W	2145
-YCR054C	2292
-YCR057C	3372
-YCR059C	1377
-YCR060W	936
-YCR061W	2496
-YCR064C	1011
-YCR063W	1074
-YCR065W	2295
-YCR066W	2064
-YCR067C	3798
-YCR068W	2163
-YCR069W	1557
-YCR071C	1041
-YCR072C	2148
-YCR073C	4596
-YCR073W_A	1548
-YCR075C	1383
-YCR075W_A	828
-YCR076C	1353
-YCR077C	2991
-YCR079W	1929
-YCR081W	4884
-YCR081C_A	837
-YCR082W	987
-YCR083W	984
-YCR085W	954
-YCR086W	1173
-YCR087W	1116
-YCR087C_A	1062
-YCR088W	2379
-YCR089W	5430
-YCR090C	1149
-YCR091W	2763
-YCR092C	3657
-YCR093W	6927
-YCR094W	1776
-YCR095C	1689
-YCR095W_A	759
-YCR096C	960
-YCR097W	981
-YCR097W_A	867
-YCR098C	2157
-YCR099C	1068
-YCR100C	1551
-YCR101C	1149
-YCR102C	1707
-YCR102W_A	798
-YCR104W	975
-YCR105W	1686
-YCR106W	3099
-YCR107W	1692
-YCR108C	792
-YGL196W	1887
-YGL131C	4812
-YGL059W	2076
-YGR017W	1494
-YGR088W	2289
-YGR147C	1467
-YGR212W	2007
-YGL263W	1743
-YGL262W	1128
-YGL261C	963
-YGL260W	831
-YGL259W	1098
-YGL258W_A	834
-YGL258W	1221
-YGL257C	2277
-YGL256W	1749
-YGL255W	1731
-YGL254W	1500
-YGL253W	2061
-YGL252C	2367
-YGL251C	4164
-YGL250W	1326
-YGL249W	2715
-YGL248W	1710
-YGL247W	1194
-YGL246C	1764
-YGL245W	2727
-YGL244W	2277
-YGL243W	1803
-YGL242C	1146
-YGL241W	3615
-YGL240W	1353
-YGL239C	915
-YGL238W	3483
-YGL237C	1398
-YGL236C	2610
-YGL235W	1137
-YGL234W	3009
-YGL233W	3333
-YGL232W	1470
-YGL231C	1173
-YGL230C	1044
-YGL229C	3057
-YGL228W	2334
-YGL227W	3477
-YGL226C_A	861
-YGL226W	972
-YGL225W	1614
-YGL224C	1443
-YGL223C	1854
-YGL222C	1128
-YGL221C	1467
-YGL220W	963
-YGL219C	1980
-YGL218W	1251
-YGL217C	942
-YGL216W	3018
-YGL215W	1959
-YGL214W	1086
-YGL213C	1794
-YGL212W	1551
-YGL211W	1680
-YGL210W	1269
-YGL209W	1749
-YGL208W	1848
-YGL207W	3708
-YGL206C	5562
-YGL205W	2847
-YGL204C	906
-YGL203C	2790
-YGL202W	2103
-YGL201C	3654
-YGL200C	1212
-YGL199C	1071
-YGL198W	1308
-YGL197W	5064
-YGL195W	8619
-YGL194C_A	843
-YGL194C	1959
-YGL193C	912
-YGL192W	2403
-YGL191W	990
-YGL190C	2181
-YGL189C	960
-YGL188C_A	741
-YGL188C	774
-YGL187C	1068
-YGL186C	2340
-YGL185C	1740
-YGL184C	1998
-YGL183C	1260
-YGL182C	924
-YGL181W	1791
-YGL180W	3294
-YGL179C	2283
-YGL178W	3180
-YGL177W	948
-YGL176C	2265
-YGL175C	1638
-YGL174W	1401
-YGL173C	5187
-YGL172W	2019
-YGL171W	2295
-YGL170C	1842
-YGL169W	1881
-YGL168W	933
-YGL167C	3453
-YGL166W	1278
-YGL165C	1179
-YGL164C	1923
-YGL163C	3297
-YGL162W	1500
-YGL161C	1533
-YGL160W	2313
-YGL159W	1713
-YGL158W	2139
-YGL157W	1644
-YGL156W	3852
-YGL155W	1731
-YGL154C	1419
-YGL153W	1626
-YGL152C	1278
-YGL151W	3999
-YGL150C	5070
-YGL149W	906
-YGL148W	1731
-YGL147C	1176
-YGL146C	1536
-YGL145W	2706
-YGL144C	2658
-YGL143C	1842
-YGL142C	2451
-YGL141W	3333
-YGL140C	4260
-YGL139W	3009
-YGL138C	1638
-YGL137W	3270
-YGL136C	1563
-YGL135W	1254
-YGL134W	1902
-YGL133W	4395
-YGL132W	936
-YGL130W	1980
-YGL129C	1953
-YGL128C	1452
-YGL127C	984
-YGL126W	1743
-YGL125W	2403
-YGL124C	2535
-YGL123W	1365
-YGL123C_A	831
-YGL122C	2178
-YGL121C	981
-YGL120C	2904
-YGL119W	2106
-YGL118C	1038
-YGL117W	1398
-YGL116W	2433
-YGL115W	1569
-YGL114W	2778
-YGL113W	2607
-YGL112C	2151
-YGL111W	1992
-YGL110C	2475
-YGL109W	924
-YGL108C	1023
-YGL107C	2541
-YGL106W	1050
-YGL105W	1731
-YGL104C	2061
-YGL103W	1050
-YGL102C	1029
-YGL101W	1248
-YGL100W	1650
-YGL099W	2523
-YGL098W	1338
-YGL097W	2049
-YGL096W	1431
-YGL095C	2334
-YGL094C	3948
-YGL093W	3354
-YGL092W	4554
-YGL091C	1587
-YGL090W	1866
-YGL089C	963
-YGL088W	966
-YGL087C	1014
-YGL086W	2850
-YGL085W	1425
-YGL084C	2283
-YGL083W	3015
-YGL082W	1746
-YGL081W	1563
-YGL080W	993
-YGL079W	1257
-YGL078C	2172
-YGL077C	2292
-YGL076C	1335
-YGL075C	1764
-YGL074C	927
-YGL073W	3102
-YGL072C	960
-YGL071W	2673
-YGL070C	969
-YGL069C	1065
-YGL068W	1185
-YGL067W	1755
-YGL066W	2574
-YGL065C	2112
-YGL064C	2286
-YGL063W	1713
-YGL063C_A	750
-YGL062W	4137
-YGL061C	1344
-YGL060W	2526
-YGL058W	1119
-YGL057C	1464
-YGL056C	2184
-YGL055W	2133
-YGL054C	1017
-YGL053W	1314
-YGL052W	906
-YGL051W	1305
-YGL050W	1422
-YGL049C	3345
-YGL048C	1818
-YGL047W	1209
-YGL045W	2229
-YGL044C	1491
-YGL043W	1530
-YGL042C	906
-YGL041C_B	783
-YGL041W_A	1065
-YGL041C	804
-YGL040C	1629
-YGL039W	1647
-YGL038C	2043
-YGL037C	1251
-YGL036W	3330
-YGL035C	2115
-YGL034C	966
-YGL033W	1257
-YGL032C	864
-YGL031C	1068
-YGL030W	918
-YGL029W	963
-YGL028C	2229
-YGL027C	3102
-YGL026C	2724
-YGL025C	1794
-YGL024W	936
-YGL023C	2508
-YGL022W	2757
-YGL021W	2883
-YGL020C	1308
-YGL019W	1437
-YGL018C	1155
-YGL017W	2112
-YGL016W	3846
-YGL015C	993
-YGL014W	3267
-YGL014C_A	762
-YGL013C	3807
-YGL012W	2022
-YGL011C	1359
-YGL010W	1125
-YGL009C	2940
-YGL008C	3357
-YGL007C_A	687
-YGL007W	978
-YGL006W_A	711
-YGL006W	4122
-YGL005C	1440
-YGL004C	1854
-YGL003C	2301
-YGL002W	1251
-YGL001C	1650
-YGR001C	1347
-YGR002C	2031
-YGR003W	2835
-YGR004W	1989
-YGR005C	1803
-YGR006W	1356
-YGR007W	1572
-YGR008C	855
-YGR009C	2556
-YGR010W	1788
-YGR011W	927
-YGR012W	1782
-YGR013W	2463
-YGR014W	4521
-YGR015C	1587
-YGR016W	1173
-YGR018C	930
-YGR019W	2016
-YGR020C	957
-YGR021W	1473
-YGR022C	930
-YGR023W	2256
-YGR024C	1314
-YGR025W	903
-YGR026W	1437
-YGR027C	927
-YGR027W_B	5868
-YGR027W_A	1923
-YGR028W	1689
-YGR029W	1170
-YGR030C	1077
-YGR031W	1629
-YGR031C_A	1092
-YGR032W	6288
-YGR033C	1320
-YGR034W	984
-YGR035C	951
-YGR035W_A	822
-YGR036C	1320
-YGR037C	864
-YGR038W	1269
-YGR038C_B	5868
-YGR038C_A	1923
-YGR039W	912
-YGR040W	1707
-YGR041W	2244
-YGR042W	1416
-YGR043C	1602
-YGR044C	1503
-YGR045C	963
-YGR046W	1758
-YGR047C	3678
-YGR048W	1686
-YGR049W	1164
-YGR050C	957
-YGR051C	924
-YGR052W	1710
-YGR053C	1452
-YGR054W	2529
-YGR055W	2325
-YGR056W	3387
-YGR057C	1329
-YGR058W	1608
-YGR059W	2139
-YGR060W	1530
-YGR061C	4677
-YGR062C	1551
-YGR063C	909
-YGR064W	969
-YGR065C	2382
-YGR066C	1479
-YGR067C	3015
-YGR068C	2361
-YGR068W_A	696
-YGR069W	936
-YGR070W	4068
-YGR071C	3183
-YGR072W	1764
-YGR073C	972
-YGR074W	1041
-YGR075C	1329
-YGR076C	1074
-YGR077C	2370
-YGR078C	1200
-YGR079W	1713
-YGR080W	1599
-YGR081C	1233
-YGR082W	1152
-YGR083C	2556
-YGR084C	1620
-YGR085C	1125
-YGR086C	1620
-YGR087C	2292
-YGR089W	3411
-YGR090W	4314
-YGR091W	2085
-YGR092W	2319
-YGR093W	2124
-YGR094W	3915
-YGR095C	1272
-YGR096W	1545
-YGR097W	4041
-YGR098C	5493
-YGR099W	2667
-YGR100W	3453
-YGR101W	1641
-YGR102C	1152
-YGR103W	2418
-YGR104C	1524
-YGR105W	834
-YGR106C	1398
-YGR107W	1050
-YGR108W	2016
-YGR109C	1743
-YGR109W_B	5244
-YGR109W_A	1473
-YGR110W	1938
-YGR111W	1803
-YGR112W	1770
-YGR113W	1632
-YGR114C	990
-YGR115C	1380
-YGR116W	4956
-YGR117C	2031
-YGR118W	1038
-YGR119C	2226
-YGR120C	1389
-YGR121C	2079
-YGR121W_A	816
-YGR122W	1809
-YGR122C_A	729
-YGR123C	2142
-YGR124W	2319
-YGR125W	3711
-YGR126W	1293
-YGR127W	1539
-YGR128C	2742
-YGR129W	1248
-YGR130C	3051
-YGR131W	1125
-YGR132C	1464
-YGR133W	1152
-YGR134W	3969
-YGR135W	1377
-YGR136W	1326
-YGR137W	975
-YGR138C	2445
-YGR139W	939
-YGR140W	3471
-YGR141W	2004
-YGR142W	1833
-YGR143W	2916
-YGR144W	1581
-YGR145W	2724
-YGR146C	1236
-YGR146C_A	762
-YGR148C	1068
-YGR149W	1899
-YGR150C	3195
-YGR151C	936
-YGR152C	1419
-YGR153W	1254
-YGR154C	1671
-YGR155W	2124
-YGR156W	1878
-YGR157W	3210
-YGR158C	1353
-YGR159C	1845
-YGR160W	1212
-YGR161C	1392
-YGR161W_C	879
-YGR161W_B	5913
-YGR161W_A	1917
-YGR161C_D	5868
-YGR161C_C	1923
-YGR162W	3459
-YGR163W	1626
-YGR164W	936
-YGR165W	1638
-YGR166W	2283
-YGR167W	1302
-YGR168C	1731
-YGR169C	1815
-YGR169C_A	879
-YGR170W	4017
-YGR171C	2328
-YGR172C	1347
-YGR173W	1707
-YGR174C	1113
-YGR174W_A	687
-YGR175C	2091
-YGR176W	948
-YGR177C	2208
-YGR178C	2769
-YGR179C	1821
-YGR180C	1638
-YGR181W	918
-YGR182C	954
-YGR183C	801
-YGR184C	6453
-YGR185C	1785
-YGR186W	2808
-YGR187C	1785
-YGR188C	3666
-YGR189C	2124
-YGR190C	966
-YGR191W	2412
-YGR192C	1599
-YGR193C	1833
-YGR194C	2403
-YGR195W	1341
-YGR196C	3054
-YGR197C	2244
-YGR198W	3054
-YGR199W	2880
-YGR200C	2967
-YGR201C	1278
-YGR202C	1875
-YGR203W	1047
-YGR204W	3441
-YGR204C_A	714
-YGR205W	1473
-YGR206W	906
-YGR207C	1386
-YGR208W	1530
-YGR209C	915
-YGR210C	1836
-YGR211W	2061
-YGR213C	1554
-YGR214W	1359
-YGR215W	933
-YGR216C	2430
-YGR217W	6720
-YGR218W	3855
-YGR219W	942
-YGR220C	1410
-YGR221C	2469
-YGR222W	1482
-YGR223C	1947
-YGR224W	2442
-YGR225W	2382
-YGR226C	810
-YGR227W	2178
-YGR228W	945
-YGR229C	2118
-YGR230W	1014
-YGR231C	1533
-YGR232W	1287
-YGR233C	4137
-YGR234W	1800
-YGR235C	1302
-YGR236C	888
-YGR237C	2958
-YGR238C	3249
-YGR239C	1467
-YGR240C	3564
-YGR240C_A	801
-YGR241C	2307
-YGR242W	909
-YGR243W	1041
-YGR244C	1884
-YGR245C	2904
-YGR246C	2391
-YGR247W	1320
-YGR248W	1368
-YGR249W	1971
-YGR250C	2946
-YGR251W	1191
-YGR252W	1920
-YGR253C	1383
-YGR254W	1914
-YGR255C	2040
-YGR256W	2079
-YGR257C	1701
-YGR258C	3696
-YGR259C	1041
-YGR260W	2205
-YGR261C	3030
-YGR262C	1386
-YGR263C	1875
-YGR264C	2856
-YGR265W	1011
-YGR266W	2706
-YGR267C	1332
-YGR268C	1197
-YGR269W	927
-YGR270W	4740
-YGR270C_A	819
-YGR271W	6504
-YGR271C_A	1302
-YGR273C	1125
-YGR274C	3801
-YGR275W	1074
-YGR276C	2262
-YGR277C	1518
-YGR278W	2334
-YGR279C	1761
-YGR280C	1416
-YGR281W	5034
-YGR282C	1542
-YGR283C	1626
-YGR284C	1533
-YGR285C	1902
-YGR286C	1728
-YGR287C	2370
-YGR288W	2022
-YGR289C	2451
-YGR290W	1044
-YGR291C	822
-YGR292W	2355
-YGR293C	1062
-YGR294W	963
-YGR295C	1746
-YGR296W	6180
-YGR296C_A	1176
-YGR296C_B	1083
-YLR454W	8487
-YLR060W	2388
-YLR186W	1359
-YLR398C	4464
-YLL067C	4218
-YLL067W_A	1083
-YLL066W_B	771
-YLL066C	4218
-YLL066W_A	1083
-YLL065W	951
-YLL064C	963
-YLL063C	2025
-YLL062C	1575
-YLL061W	2352
-YLL060C	1302
-YLL059C	1107
-YLL058W	2328
-YLL057C	1839
-YLL056C	1497
-YLL055W	2196
-YLL054C	3132
-YLL053C	1059
-YLL052C	1050
-YLL051C	2739
-YLL050C	1032
-YLL049W	1140
-YLL048C	5586
-YLL047W	984
-YLL046C	1350
-YLL045C	1371
-YLL044W	1047
-YLL043W	2610
-YLL042C	1104
-YLL041C	1401
-YLL040C	10035
-YLL039C	1746
-YLL038C	1344
-YLL037W	981
-YLL036C	2112
-YLL035W	2499
-YLL034C	3114
-YLL033W	1293
-YLL032C	3078
-YLL031C	3654
-YLL030C	942
-YLL029W	2850
-YLL028W	2361
-YLL027W	1353
-YLL026W	3327
-YLL025W	975
-YLL024C	2520
-YLL023C	1440
-YLL022C	1758
-YLL021W	5001
-YLL020C	906
-YLL019C	2814
-YLL019W_A	693
-YLL018C_A	897
-YLL018C	2274
-YLL015W	5280
-YLL014W	927
-YLL013C	3240
-YLL012W	2322
-YLL011W	2070
-YLL010C	1884
-YLL009C	810
-YLL008W	2859
-YLL007C	2598
-YLL006W_A	777
-YLL006W	1881
-YLL005C	3207
-YLL004W	2451
-YLL003W	3441
-YLL002W	1911
-YLL001W	2874
-YLR001C	3189
-YLR002C	2592
-YLR003C	1476
-YLR004C	2172
-YLR005W	1986
-YLR006C	2739
-YLR007W	1611
-YLR008C	1107
-YLR009W	1200
-YLR010C	1083
-YLR011W	1176
-YLR012C	900
-YLR013W	1026
-YLR014C	3315
-YLR015W	2118
-YLR016C	1215
-YLR017W	1614
-YLR018C	1500
-YLR019W	1794
-YLR020C	2217
-YLR021W	1140
-YLR022C	1353
-YLR023C	2232
-YLR024C	6219
-YLR025W	1323
-YLR026C	1623
-YLR027C	1857
-YLR028C	2376
-YLR029C	1215
-YLR030W	1392
-YLR031W	1161
-YLR032W	4110
-YLR033W	2109
-YLR034C	2022
-YLR035C	2688
-YLR035C_A	4068
-YLR036C	1212
-YLR037C	975
-YLR038C	852
-YLR039C	3771
-YLR040C	1275
-YLR041W	921
-YLR042C	1086
-YLR043C	912
-YLR044C	2292
-YLR045C	3267
-YLR046C	1413
-YLR047C	2661
-YLR048W	1359
-YLR049C	1887
-YLR050C	1086
-YLR051C	1254
-YLR052W	1353
-YLR053C	927
-YLR054C	2775
-YLR055C	2409
-YLR056W	1698
-YLR057W	3150
-YLR058C	2010
-YLR059C	1410
-YLR061W	966
-YLR062C	978
-YLR063W	1698
-YLR064W	1422
-YLR065C	1146
-YLR066W	1155
-YLR067C	3498
-YLR068W	1056
-YLR069C	2886
-YLR070C	1671
-YLR071C	3849
-YLR072W	2682
-YLR073C	1203
-YLR074C	1101
-YLR075W	1266
-YLR076C	1023
-YLR077W	2352
-YLR078C	1335
-YLR079W	1455
-YLR080W	1935
-YLR081W	2325
-YLR082C	1779
-YLR083C	2604
-YLR084C	4263
-YLR085C	1917
-YLR086W	4857
-YLR087C	9477
-YLR088W	2445
-YLR089C	2379
-YLR090W	1980
-YLR091W	1482
-YLR092W	3282
-YLR093C	1362
-YLR094C	2109
-YLR095C	3039
-YLR096W	4044
-YLR097C	1635
-YLR098C	2547
-YLR099C	1785
-YLR099W_A	864
-YLR100W	1644
-YLR101C	996
-YLR102C	1398
-YLR103C	2553
-YLR104W	996
-YLR105C	1734
-YLR106C	15333
-YLR107W	1815
-YLR108C	2058
-YLR109W	1131
-YLR110C	1002
-YLR111W	933
-YLR112W	1020
-YLR113W	1908
-YLR114C	2895
-YLR115W	3180
-YLR116W	2031
-YLR117C	2664
-YLR118C	1284
-YLR119W	1242
-YLR120C	2310
-YLR120W_A	702
-YLR121C	2127
-YLR122C	978
-YLR123C	930
-YLR124W	945
-YLR125W	1011
-YLR126C	1356
-YLR127C	3162
-YLR128W	1410
-YLR129W	3432
-YLR130C	1869
-YLR131C	2913
-YLR132C	1473
-YLR133W	2349
-YLR134W	2292
-YLR135W	2847
-YLR136C	1458
-YLR137W	1704
-YLR138W	3558
-YLR139C	2532
-YLR140W	927
-YLR141W	1692
-YLR142W	2031
-YLR143W	2658
-YLR144C	2940
-YLR145W	1206
-YLR146C	1503
-YLR146W_A	789
-YLR147C	906
-YLR148W	3357
-YLR149C	2793
-YLR149C_A	687
-YLR150W	1422
-YLR151C	1623
-YLR152C	2331
-YLR153C	2652
-YLR154C	933
-YLR154W_A	786
-YLR154W_B	765
-YLR154W_C	975
-YLR154W_E	804
-YLR154W_F	741
-YLR154C_G	750
-YLR154C_H	732
-YLR155C	1689
-YLR156W	945
-YLR156C_A	732
-YLR157C	1689
-YLR157W_D	813
-YLR157C_B	5868
-YLR157C_A	1923
-YLR157W_E	765
-YLR157C_C	732
-YLR158C	1689
-YLR159W	945
-YLR159C_A	732
-YLR160C	1689
-YLR161W	945
-YLR162W	957
-YLR162W_A	789
-YLR163C	1989
-YLR163W_A	714
-YLR164W	1107
-YLR165C	1365
-YLR166C	3216
-YLR167W	1059
-YLR168C	1293
-YLR169W	954
-YLR170C	1071
-YLR171W	990
-YLR172C	1503
-YLR173W	2427
-YLR174W	1839
-YLR175W	2052
-YLR176C	3036
-YLR177W	2487
-YLR178C	1260
-YLR179C	1206
-YLR180W	1749
-YLR181C	1593
-YLR182W	3012
-YLR183C	2070
-YLR184W	948
-YLR185W	867
-YLR187W	3681
-YLR188W	2688
-YLR189C	4197
-YLR190W	2076
-YLR191W	1761
-YLR192C	1398
-YLR193C	1128
-YLR194C	1365
-YLR195C	1968
-YLR196W	2331
-YLR197W	2115
-YLR198C	960
-YLR199C	1431
-YLR200W	945
-YLR201C	1383
-YLR202C	927
-YLR203C	1911
-YLR204W	936
-YLR205C	1554
-YLR206W	2442
-YLR207W	3102
-YLR208W	1494
-YLR209C	1536
-YLR210W	1983
-YLR211C	1281
-YLR212C	2022
-YLR213C	1869
-YLR214W	2661
-YLR215C	1683
-YLR216C	1716
-YLR217W	924
-YLR218C	1053
-YLR219W	2787
-YLR220W	1569
-YLR221C	1263
-YLR222C	3054
-YLR222C_A	831
-YLR223C	3858
-YLR224W	1710
-YLR225C	1824
-YLR226W	1788
-YLR227C	2082
-YLR227W_B	5868
-YLR227W_A	1923
-YLR228C	3045
-YLR229C	1176
-YLR230W	906
-YLR231C	1962
-YLR232W	948
-YLR233C	2700
-YLR234W	2571
-YLR235C	999
-YLR236C	924
-YLR237W	2397
-YLR238W	2037
-YLR239C	1587
-YLR240W	3228
-YLR241W	2949
-YLR242C	1566
-YLR243W	1419
-YLR244C	1764
-YLR245C	1029
-YLR246W	1680
-YLR247C	5271
-YLR248W	2433
-YLR249W	3735
-YLR250W	1305
-YLR251W	1194
-YLR252W	906
-YLR253W	2310
-YLR254C	1170
-YLR255C	954
-YLR256W	5109
-YLR256W_A	1923
-YLR257W	1566
-YLR258W	2718
-YLR259C	2319
-YLR260W	2664
-YLR261C	927
-YLR262C	1248
-YLR262C_A	795
-YLR263W	3084
-YLR264W	804
-YLR264C_A	717
-YLR265C	1629
-YLR266C	2706
-YLR267W	2313
-YLR268W	1245
-YLR269C	951
-YLR270W	1653
-YLR271W	1425
-YLR272C	4131
-YLR273C	2547
-YLR274W	2928
-YLR275W	933
-YLR276C	2385
-YLR277C	2940
-YLR278C	4626
-YLR279W	990
-YLR280C	951
-YLR281C	1068
-YLR282C	942
-YLR283W	1545
-YLR284C	1443
-YLR285W	1386
-YLR285C_A	771
-YLR286C	2289
-YLR286W_A	735
-YLR287C	1668
-YLR287C_A	792
-YLR288C	2025
-YLR289W	2538
-YLR290C	1434
-YLR291C	1746
-YLR292C	1182
-YLR293C	1260
-YLR294C	930
-YLR295C	975
-YLR296W	927
-YLR297W	990
-YLR298C	1296
-YLR299W	2583
-YLR299C_A	693
-YLR300W	1947
-YLR301W	1335
-YLR302C	963
-YLR303W	1935
-YLR304C	2937
-YLR305C	6303
-YLR306W	1167
-YLR307W	1506
-YLR307C_A	864
-YLR308W	1539
-YLR309C	3336
-YLR310C	5370
-YLR311C	948
-YLR312C	1797
-YLR312W_A	1362
-YLR313C	2193
-YLR314C	2163
-YLR315W	1062
-YLR316C	1569
-YLR317W	1035
-YLR318W	3255
-YLR319C	2967
-YLR320W	4965
-YLR321C	1881
-YLR322W	915
-YLR323C	1380
-YLR324W	2172
-YLR325C	837
-YLR326W	1323
-YLR327C	861
-YLR328W	1806
-YLR329W	1395
-YLR330W	2616
-YLR331C	978
-YLR332W	1731
-YLR333C	927
-YLR334C	981
-YLR335W	2763
-YLR336C	3300
-YLR337C	3054
-YLR338W	1458
-YLR339C	1152
-YLR340W	1539
-YLR341W	2034
-YLR342W	6231
-YLR342W_A	774
-YLR343W	2268
-YLR344W	984
-YLR345W	2130
-YLR346C	906
-YLR347C	3186
-YLR347W_A	741
-YLR348C	1497
-YLR349W	1107
-YLR350W	1251
-YLR351C	1476
-YLR352W	3024
-YLR353W	2412
-YLR354C	1608
-YLR355C	1788
-YLR356W	1194
-YLR357W	3270
-YLR358C	1164
-YLR359W	2049
-YLR360W	1920
-YLR361C	2337
-YLR361C_A	897
-YLR362W	2754
-YLR363C	1257
-YLR363W_A	858
-YLR364W	930
-YLR365W	933
-YLR364C_A	723
-YLR366W	906
-YLR367W	993
-YLR368W	2397
-YLR369W	2574
-YLR370C	1137
-YLR371W	4671
-YLR372W	1638
-YLR373C	3306
-YLR374C	990
-YLR375W	1632
-YLR376C	1329
-YLR377C	1647
-YLR378C	2043
-YLR379W	975
-YLR380W	1827
-YLR381W	2802
-YLR382C	3285
-YLR383W	3945
-YLR384C	4650
-YLR385C	999
-YLR386W	3243
-YLR387C	1899
-YLR388W	771
-YLR389C	3684
-YLR390W	939
-YLR390W_A	1317
-YLR392C	2157
-YLR393W	1440
-YLR394W	2049
-YLR395C	837
-YLR396C	2676
-YLR397C	2943
-YLR399C	2661
-YLR399W_A	705
-YLR400W	1074
-YLR401C	2607
-YLR402W	792
-YLR403W	2652
-YLR404W	1458
-YLR405W	1704
-YLR406C	942
-YLR406C_A	750
-YLR407W	1287
-YLR408C	969
-YLR409C	3420
-YLR410W	4041
-YLR410W_B	5913
-YLR410W_A	1917
-YLR411W	1326
-YLR412W	1425
-YLR412C_A	807
-YLR413W	2628
-YLR414C	1392
-YLR415C	939
-YLR416C	999
-YLR417W	2301
-YLR418C	1782
-YLR419W	4908
-YLR420W	1695
-YLR421C	1071
-YLR422W	6399
-YLR423C	1854
-YLR424W	2727
-YLR425W	4524
-YLR426W	1581
-YLR427W	2613
-YLR428C	945
-YLR429W	2556
-YLR430W	7296
-YLR431C	1962
-YLR432W	2172
-YLR433C	2262
-YLR434C	984
-YLR435W	1218
-YLR436C	4425
-YLR437C	1002
-YLR437C_A	828
-YLR438W	1875
-YLR438C_A	870
-YLR439W	1560
-YLR440C	2730
-YLR441C	1368
-YLR442C	3537
-YLR443W	1947
-YLR444C	903
-YLR445W	1167
-YLR446W	1902
-YLR447C	1638
-YLR448W	1131
-YLR449W	1779
-YLR450W	3738
-YLR451W	3261
-YLR452C	2697
-YLR453C	1788
-YLR455W	1515
-YLR456W	1215
-YLR457C	1560
-YLR458W	981
-YLR459W	1785
-YLR460C	1731
-YLR461W	963
-YLR462W	1209
-YLR463C	1152
-YLR464W	1251
-YLR465C	909
-YLR466W	4749
-YLR466C_A	1083
-YLR466C_B	717
-YLR467W	5970
-YLR467C_A	1083
-YNL271C	6462
-YNL201C	3177
-YNL124W	2079
-YNR016C	7302
-YNL339C	6180
-YNL339W_B	1083
-YNL339W_A	1176
-YNL338W	759
-YNL337W	855
-YNL336W	1746
-YNL335W	1278
-YNL334C	1269
-YNL333W	1497
-YNL332W	1623
-YNL331C	1731
-YNL330C	1902
-YNL329C	3693
-YNL328C	1041
-YNL327W	3726
-YNL326C	1611
-YNL325C	3240
-YNL324W	996
-YNL323W	1845
-YNL322C	1542
-YNL321W	3327
-YNL320W	1455
-YNL319W	1041
-YNL318C	2223
-YNL317W	1998
-YNL316C	1605
-YNL315C	1557
-YNL314W	1368
-YNL313C	3315
-YNL312W	1422
-YNL311C	2892
-YNL310C	1125
-YNL309W	1863
-YNL308C	2376
-YNL307C	1728
-YNL306W	1254
-YNL305C	1494
-YNL304W	1854
-YNL303W	948
-YNL302C	1035
-YNL301C	1161
-YNL300W	909
-YNL299W	2529
-YNL298W	3129
-YNL297C	5511
-YNL296W	915
-YNL295W	2175
-YNL294C	2202
-YNL293W	2502
-YNL292W	1812
-YNL291C	2247
-YNL290W	1623
-YNL289W	1440
-YNL288W	1722
-YNL287W	3408
-YNL286W	1458
-YNL285W	972
-YNL284C_B	5868
-YNL284C_A	1923
-YNL284C	1569
-YNL283C	2112
-YNL282W	1188
-YNL281W	1062
-YNL280C	1917
-YNL279W	2586
-YNL278W	3783
-YNL277W_A	789
-YNL277W	2061
-YNL276C	996
-YNL275W	2331
-YNL274C	1653
-YNL273W	4317
-YNL272C	2880
-YNL270C	2322
-YNL269W	996
-YNL268W	2436
-YNL267W	3801
-YNL266W	1020
-YNL265C	1497
-YNL264C	1653
-YNL263C	1545
-YNL262W	7269
-YNL261W	2040
-YNL260C	1197
-YNL259C	822
-YNL258C	2865
-YNL257C	4290
-YNL256W	3075
-YNL255C	1062
-YNL254C	1806
-YNL253W	1869
-YNL252C	1446
-YNL251C	2328
-YNL250W	4539
-YNL249C	2229
-YNL248C	1848
-YNL247W	2904
-YNL246W	1395
-YNL245C	1140
-YNL244C	927
-YNL243W	3507
-YNL242W	5379
-YNL241C	2118
-YNL240C	2076
-YNL239W	1965
-YNL238W	3045
-YNL237W	1980
-YNL236W	3525
-YNL235C	1032
-YNL234W	1881
-YNL233W	3279
-YNL232W	1479
-YNL231C	1656
-YNL230C	1740
-YNL229C	1665
-YNL228W	1377
-YNL227C	2373
-YNL226W	1011
-YNL225C	2346
-YNL224C	2904
-YNL223W	2085
-YNL222W	1221
-YNL221C	3228
-YNL220W	1902
-YNL219C	2268
-YNL218W	2364
-YNL217W	1581
-YNL216W	3084
-YNL215W	1563
-YNL214W	1200
-YNL213C	1245
-YNL212W	2949
-YNL211C	861
-YNL210W	1413
-YNL209W	2442
-YNL208W	1200
-YNL207W	1878
-YNL206C	1968
-YNL205C	1023
-YNL204C	1503
-YNL203C	1212
-YNL202W	1479
-YNL200C	1341
-YNL199C	2205
-YNL198C	903
-YNL197C	2586
-YNL196C	1497
-YNL195C	1386
-YNL194C	1506
-YNL193W	2277
-YNL192W	3996
-YNL191W	1674
-YNL190W	1215
-YNL189W	2229
-YNL188W	1902
-YNL187W	1674
-YNL186W	2979
-YNL185C	1077
-YNL184C	927
-YNL183C	2973
-YNL182C	2268
-YNL181W	1824
-YNL180C	1596
-YNL179C	1038
-YNL178W	1323
-YNL177C	1530
-YNL176C	2511
-YNL175C	1812
-YNL174W	1173
-YNL173C	1701
-YNL172W	5847
-YNL171C	969
-YNL170W	996
-YNL169C	2103
-YNL168C	1380
-YNL167C	2544
-YNL166C	1947
-YNL165W	1821
-YNL164C	1656
-YNL163C	3933
-YNL162W_A	819
-YNL162W	921
-YNL161W	2871
-YNL160W	1665
-YNL159C	1470
-YNL158W	1197
-YNL157W	1107
-YNL156C	1500
-YNL155W	1425
-YNL154C	2241
-YNL153C	990
-YNL152W	1830
-YNL151C	1356
-YNL150W	1008
-YNL149C	990
-YNL148C	1365
-YNL147W	948
-YNL146C_A	795
-YNL146W	903
-YNL145W	717
-YNL144C	2823
-YNL144W_A	684
-YNL143C	993
-YNL142W	2100
-YNL141W	1644
-YNL140C	1170
-YNL139C	5394
-YNL138W_A	858
-YNL138W	2181
-YNL137C	2061
-YNL136W	1878
-YNL135C	945
-YNL134C	1731
-YNL133C	1122
-YNL132W	3771
-YNL131W	1059
-YNL130C	1782
-YNL130C_A	747
-YNL129W	1323
-YNL128W	1905
-YNL127W	3462
-YNL126W	3141
-YNL125C	2622
-YNL123W	3594
-YNL122C	948
-YNL121C	2454
-YNL120C	1086
-YNL119W	2082
-YNL118C	3513
-YNL117W	2265
-YNL116W	2169
-YNL115C	2535
-YNL114C	972
-YNL113W	1029
-YNL112W	2241
-YNL111C	963
-YNL110C	1263
-YNL109W	1146
-YNL108C	1413
-YNL107W	1281
-YNL106C	4152
-YNL105W	1029
-YNL104C	2460
-YNL103W_A	690
-YNL103W	2619
-YNL102W	5007
-YNL101W	2742
-YNL100W	1305
-YNL099C	1317
-YNL098C	1569
-YNL097C_B	723
-YNL097C	1593
-YNL097W_A	756
-YNL096C	1173
-YNL095C	2529
-YNL094W	2364
-YNL093W	1263
-YNL092W	1803
-YNL091W	4323
-YNL090W	1179
-YNL089C	1077
-YNL088W	4887
-YNL087W	4137
-YNL086W	909
-YNL085W	3093
-YNL084C	1650
-YNL083W	2085
-YNL082W	3222
-YNL081C	1032
-YNL080C	1701
-YNL079C	1200
-YNL078W	1824
-YNL077W	2187
-YNL076W	2355
-YNL075W	1473
-YNL074C	1959
-YNL073W	2331
-YNL072W	1524
-YNL071W	2049
-YNL070W	783
-YNL069C	1197
-YNL068C	3189
-YNL067W_A	747
-YNL067W_B	741
-YNL067W	1176
-YNL066W	1863
-YNL065W	2361
-YNL064C	1830
-YNL063W	1545
-YNL062C	2037
-YNL061W	2457
-YNL059C	2868
-YNL058C	1551
-YNL057W	933
-YNL056W	1194
-YNL055C	1452
-YNL054W_A	1923
-YNL054W	4098
-YNL053W	2070
-YNL052W	1062
-YNL051W	1812
-YNL050C	1413
-YNL049C	3231
-YNL048W	2247
-YNL047C	2571
-YNL046W	1119
-YNL045W	2616
-YNL044W	1131
-YNL043C	921
-YNL042W_B	858
-YNL042W	1791
-YNL041C	3120
-YNL040W	1971
-YNL039W	2385
-YNL038W	1290
-YNL037C	1683
-YNL036W	1266
-YNL035C	1770
-YNL034W	2439
-YNL033W	1455
-YNL032W	1446
-YNL031C	1011
-YNL030W	912
-YNL029C	2169
-YNL028W	918
-YNL027W	2637
-YNL026W	2055
-YNL025C	1572
-YNL024C_A	819
-YNL024C	1341
-YNL023C	3498
-YNL022C	2073
-YNL021W	2721
-YNL020C	2517
-YNL019C	1455
-YNL018C	2439
-YNL017C	939
-YNL016W	1962
-YNL015W	828
-YNL014W	3735
-YNL013C	978
-YNL012W	2496
-YNL011C	1935
-YNL010W	1326
-YNL009W	1863
-YNL008C	2631
-YNL007C	1659
-YNL006W	1512
-YNL005C	1716
-YNL004W	1965
-YNL003C	1455
-YNL002C	1569
-YNL001W	1761
-YNR001C	2040
-YNR001W_A	819
-YNR002C	1449
-YNR003C	1554
-YNR003W_A	699
-YNR004W	1041
-YNR005C	1005
-YNR006W	2469
-YNR007C	1533
-YNR008W	2586
-YNR009W	1350
-YNR010W	1050
-YNR011C	3231
-YNR012W	2106
-YNR013C	3285
-YNR014W	1239
-YNR015W	1755
-YNR017W	1269
-YNR018W	1275
-YNR019W	2529
-YNR020C	1413
-YNR021W	1815
-YNR022C	1020
-YNR023W	2301
-YNR024W	1161
-YNR025C	960
-YNR026C	2016
-YNR027W	1554
-YNR028W	1527
-YNR029C	1890
-YNR030W	2256
-YNR031C	5340
-YNR032W	1707
-YNR032C_A	822
-YNR033W	2964
-YNR034W	1566
-YNR034W_A	897
-YNR035C	1629
-YNR036C	1062
-YNR037C	876
-YNR038W	2490
-YNR039C	2418
-YNR040W	1371
-YNR041C	1719
-YNR042W	1029
-YNR043W	1791
-YNR044W	2778
-YNR045W	2070
-YNR046W	1008
-YNR047W	3282
-YNR048W	1782
-YNR049C	1233
-YNR050C	1941
-YNR051C	2148
-YNR052C	1902
-YNR053C	2061
-YNR054C	1551
-YNR055C	2361
-YNR056C	2286
-YNR057C	1314
-YNR058W	2043
-YNR059W	2343
-YNR060W	2760
-YNR061C	1260
-YNR062C	1584
-YNR063W	2424
-YNR064C	1473
-YNR065C	3951
-YNR066C	1911
-YNR067C	3954
-YNR068C	1419
-YNR069C	2070
-YNR070W	4602
-YNR071C	1629
-YNR072W	2295
-YNR073C	2109
-YNR074C	1737
-YNR075W	1725
-YNR075C_A	693
-YNR076W	963
-YNR077C	855
-YPL222W	2667
-YPL153C	3066
-YPL085W	7188
-YPL016W	4545
-YPR045C	2013
-YPR123C	1035
-YPR124W	1821
-YPR190C	2565
-YPL283C	6159
-YPL283W_B	1083
-YPL283W_A	1176
-YPL282C	1095
-YPL281C	1914
-YPL280W	1314
-YPL279C	1728
-YPL278C	903
-YPL277C	2064
-YPL274W	2364
-YPL273W	1578
-YPL272C	2154
-YPL271W	789
-YPL270W	2922
-YPL269W	2535
-YPL268W	3210
-YPL267W	1230
-YPL266W	1557
-YPL265W	2427
-YPL264C	1662
-YPL263C	2556
-YPL262W	2067
-YPL261C	909
-YPL260W	2256
-YPL259C	2028
-YPL258C	2256
-YPL257W_B	5868
-YPL257W_A	1923
-YPL257W	1182
-YPL256C	2238
-YPL255W	1758
-YPL254W	2067
-YPL253C	2544
-YPL252C	1119
-YPL251W	903
-YPL250C	1011
-YPL249C_A	903
-YPL250W_A	888
-YPL249C	3285
-YPL248C	3246
-YPL247C	2172
-YPL246C	1389
-YPL245W	1965
-YPL244C	1620
-YPL243W	2400
-YPL242C	5088
-YPL241C	1407
-YPL240C	2730
-YPL239W	1203
-YPL238C	990
-YPL237W	1458
-YPL236C	1695
-YPL235W	2016
-YPL234C	1095
-YPL233W	1251
-YPL232W	1473
-YPL231W	6264
-YPL230W	1776
-YPL229W	1221
-YPL228W	2250
-YPL227C	1605
-YPL226W	4191
-YPL225W	1041
-YPL224C	2055
-YPL223C	1107
-YPL222C_A	846
-YPL221W	2982
-YPL220W	1254
-YPL219W	2079
-YPL218W	1173
-YPL217C	4152
-YPL216W	3909
-YPL215W	1608
-YPL214C	2223
-YPL213W	1317
-YPL212C	2235
-YPL211W	1146
-YPL210C	2523
-YPL209C	1704
-YPL208W	2352
-YPL207W	3033
-YPL206C	1566
-YPL205C	945
-YPL204W	2085
-YPL203W	1743
-YPL202C	1851
-YPL201C	1986
-YPL200W	1071
-YPL199C	1323
-YPL198W	1335
-YPL197C	1014
-YPL196W	1422
-YPL195W	3399
-YPL194W	2439
-YPL193W	1746
-YPL192C	1002
-YPL191C	1683
-YPL190C	3009
-YPL189C_A	807
-YPL189W	2430
-YPL188W	1845
-YPL187W	1098
-YPL186C	1515
-YPL185W	996
-YPL184C	2439
-YPL183W_A	882
-YPL183C	3642
-YPL182C	984
-YPL181W	2121
-YPL180W	3000
-YPL179W	2250
-YPL178W	1227
-YPL177C	1521
-YPL176C	2952
-YPL175W	1959
-YPL174C	3207
-YPL173W	1494
-YPL172C	1989
-YPL171C	1803
-YPL170W	1059
-YPL169C	2400
-YPL168W	1893
-YPL167C	5115
-YPL166W	1242
-YPL165C	1722
-YPL164C	2748
-YPL163C	1383
-YPL162C	1422
-YPL161C	2502
-YPL160W	3873
-YPL159C	1362
-YPL158C	2877
-YPL157W	1548
-YPL156C	1455
-YPL155C	2721
-YPL154C	1818
-YPL152W_A	699
-YPL152W	1677
-YPL151C	1956
-YPL150W	3306
-YPL149W	1485
-YPL148C	1122
-YPL147W	3213
-YPL146C	1968
-YPL145C	1905
-YPL144W	1047
-YPL143W	924
-YPL142C	918
-YPL141C	3198
-YPL140C	2121
-YPL139C	1983
-YPL138C	1662
-YPL137C	4431
-YPL136W	969
-YPL135W	1098
-YPL135C_A	774
-YPL134C	1533
-YPL133C	1941
-YPL132W	1503
-YPL131W	1494
-YPL130W	1272
-YPL129W	1335
-YPL128C	2289
-YPL127C	1377
-YPL126W	3291
-YPL125W	3699
-YPL124W	1362
-YPL123C	1905
-YPL122C	2142
-YPL121C	1269
-YPL120W	2274
-YPL119C_A	864
-YPL119C	2454
-YPL118W	1635
-YPL117C	1467
-YPL116W	2694
-YPL115C	3987
-YPL114W	1020
-YPL113C	1791
-YPL112C	1785
-YPL111W	1602
-YPL110C	4272
-YPL109C	2574
-YPL108W	1107
-YPL107W	1347
-YPL106C	2682
-YPL105C	3150
-YPL104W	2577
-YPL103C	2007
-YPL102C	903
-YPL101W	1971
-YPL100W	2091
-YPL099C	1149
-YPL098C	942
-YPL097W	2079
-YPL096C_A	807
-YPL096W	1692
-YPL095C	1971
-YPL094C	1425
-YPL093W	2544
-YPL092W	1977
-YPL091W	2052
-YPL090C	1311
-YPL089C	2631
-YPL088W	1629
-YPL087W	1554
-YPL086C	2274
-YPL084W	3135
-YPL083C	2004
-YPL082C	6204
-YPL081W	1194
-YPL080C	927
-YPL079W	1083
-YPL078C	1335
-YPL077C	1323
-YPL076W	1443
-YPL075W	2958
-YPL074W	2865
-YPL073C	1086
-YPL072W	2100
-YPL071C	1071
-YPL070W	2439
-YPL069C	1608
-YPL068C	1482
-YPL067C	1197
-YPL066W	2040
-YPL065W	1329
-YPL064C	1506
-YPL063W	2031
-YPL062W	1005
-YPL061W	2103
-YPL060W	1842
-YPL059W	1053
-YPL058C	5136
-YPL057C	1749
-YPL056C	906
-YPL055C	1599
-YPL054W	1506
-YPL053C	1941
-YPL052W	1479
-YPL051W	1197
-YPL050C	1788
-YPL049C	1959
-YPL048W	1848
-YPL047W	900
-YPL046C	900
-YPL045W	2997
-YPL044C	1149
-YPL043W	2658
-YPL042C	2268
-YPL041C	1224
-YPL040C	3609
-YPL039W	1551
-YPL038W_A	792
-YPL038W	1134
-YPL037C	1074
-YPL036W	3444
-YPL035C	948
-YPL034W	1098
-YPL033C	1446
-YPL032C	3078
-YPL031C	1518
-YPL030W	2304
-YPL029W	2814
-YPL028W	1797
-YPL027W	1338
-YPL026C	2109
-YPL025C	1158
-YPL024W	1326
-YPL023C	2574
-YPL022W	3903
-YPL021W	1164
-YPL020C	2466
-YPL019C	3108
-YPL018W	1710
-YPL017C	2100
-YPL015C	1674
-YPL014W	1746
-YPL013C	966
-YPL012W	4287
-YPL011C	1662
-YPL010W	1170
-YPL009C	3717
-YPL008W	3186
-YPL007C	2367
-YPL006W	4113
-YPL005W	2421
-YPL004C	1626
-YPL003W	1989
-YPL002C	1302
-YPL001W	1725
-YPR001W	2061
-YPR002W	2151
-YPR002C_A	798
-YPR003C	2865
-YPR004C	1635
-YPR005C	1485
-YPR006C	2328
-YPR007C	2643
-YPR008W	2685
-YPR009W	1407
-YPR010C	4212
-YPR010C_A	819
-YPR011C	1581
-YPR012W	855
-YPR013C	1554
-YPR014C	930
-YPR015C	1344
-YPR016C	1338
-YPR016W_A	861
-YPR017C	1032
-YPR018W	2421
-YPR019W	3402
-YPR020W	948
-YPR021C	3309
-YPR022C	4002
-YPR023C	1806
-YPR024W	2844
-YPR025C	1782
-YPR026W	4236
-YPR027C	1434
-YPR028W	1143
-YPR029C	3099
-YPR030W	3966
-YPR031W	2847
-YPR032W	3702
-YPR033C	2241
-YPR034W	2034
-YPR035W	1713
-YPR036W	2037
-YPR036W_A	804
-YPR037C	1191
-YPR038W	960
-YPR039W	936
-YPR040W	1671
-YPR041W	1818
-YPR042C	3828
-YPR043W	879
-YPR044C	954
-YPR046W	1146
-YPR047W	2010
-YPR048W	2472
-YPR049C	4137
-YPR050C	1014
-YPR051W	1131
-YPR052C	882
-YPR053C	1056
-YPR054W	1767
-YPR055W	3798
-YPR056W	1617
-YPR057W	1626
-YPR058W	1524
-YPR059C	987
-YPR060C	1371
-YPR061C	1506
-YPR062W	1077
-YPR063C	1023
-YPR064W	1020
-YPR065W	1707
-YPR066W	1500
-YPR067W	1158
-YPR068C	2013
-YPR069C	1482
-YPR070W	2301
-YPR071W	1236
-YPR072W	2283
-YPR073C	1086
-YPR074C	2643
-YPR074W_A	771
-YPR075C	1683
-YPR076W	975
-YPR077C	972
-YPR078C	1719
-YPR079W	1746
-YPR080W	1977
-YPR081C	2457
-YPR082C	1032
-YPR083W	2340
-YPR084W	1971
-YPR085C	1932
-YPR086W	1638
-YPR087W	921
-YPR088C	2226
-YPR089W	3267
-YPR091C	2913
-YPR092W	906
-YPR093C	1467
-YPR094W	924
-YPR095C	4281
-YPR096C	903
-YPR097W	3822
-YPR098C	1086
-YPR099C	957
-YPR100W	1023
-YPR101W	1128
-YPR102C	1125
-YPR103W	1464
-YPR104C	3411
-YPR105C	3186
-YPR106W	1932
-YPR107C	1227
-YPR108W	1890
-YPR108W_A	813
-YPR109W	1485
-YPR110C	1608
-YPR111W	2295
-YPR112C	3264
-YPR113W	1263
-YPR114W	1548
-YPR115W	3852
-YPR116W	1434
-YPR117W	8070
-YPR118W	1836
-YPR119W	2076
-YPR120C	1908
-YPR121W	2319
-YPR122W	4227
-YPR125W	1965
-YPR126C	909
-YPR127W	1638
-YPR128C	1587
-YPR129W	1650
-YPR130C	1008
-YPR131C	1188
-YPR132W	1038
-YPR133C	1833
-YPR133W_A	753
-YPR134W	1407
-YPR135W	3384
-YPR136C	1113
-YPR137W	2322
-YPR137C_B	5868
-YPR137C_A	1923
-YPR138C	2070
-YPR139C	1503
-YPR140W	1746
-YPR141C	2790
-YPR142C	1164
-YPR143W	1353
-YPR144C	2259
-YPR145W	2319
-YPR145C_A	837
-YPR146C	930
-YPR147C	1515
-YPR148C	1908
-YPR149W	1122
-YPR150W	1122
-YPR151C	1221
-YPR152C	1998
-YPR153W	1023
-YPR154W	1248
-YPR155C	2451
-YPR156C	2469
-YPR157W	2004
-YPR158W	1359
-YPR158W_B	5871
-YPR158W_A	1923
-YPR158C_D	5868
-YPR158C_C	1923
-YPR159W	2763
-YPR159C_A	702
-YPR160W	3309
-YPR160W_A	681
-YPR160C_A	885
-YPR161C	2574
-YPR162C	2190
-YPR163C	1911
-YPR164W	4824
-YPR165W	1230
-YPR166C	948
-YPR167C	1386
-YPR168W	1074
-YPR169W	2079
-YPR170C	936
-YPR170W_B	858
-YPR169W_A	819
-YPR170W_A	786
-YPR171W	2331
-YPR172W	1203
-YPR173C	1914
-YPR174C	1266
-YPR175W	2670
-YPR176C	1578
-YPR177C	972
-YPR178W	1998
-YPR179C	2568
-YPR180W	1644
-YPR181C	2907
-YPR182W	861
-YPR183W	1404
-YPR184W	5211
-YPR185W	2817
-YPR186C	1890
-YPR187W	1068
-YPR188C	1092
-YPR189W	4899
-YPR191W	1707
-YPR192W	1518
-YPR193C	1071
-YPR194C	3234
-YPR195C	930
-YPR196W	2013
-YPR197C	1164
-YPR198W	2232
-YPR199C	1485
-YPR200C	993
-YPR201W	1815
-YPR202W	1317
-YPR203W	909
-YPR204W	3699
-YPR204C_A	1083
-YHR013C	1317
-YHR147C	1245
-YHL050C	2694
-YHL050W_A	1083
-YHL049C	1416
-YHL048C_A	735
-YHL048W	1746
-YHL047C	2463
-YHL046W_A	927
-YHL046C	963
-YHL045W	948
-YHL044W	1308
-YHL043W	1113
-YHL042W	1053
-YHL041W	1050
-YHL040C	2484
-YHL039W	2358
-YHL038C	2493
-YHL037C	1002
-YHL036W	2241
-YHL035C	5379
-YHL034W_A	1062
-YHL034C	1485
-YHL033C	1371
-YHL032C	2730
-YHL031C	1272
-YHL030W_A	1062
-YHL030W	6207
-YHL029C	2640
-YHL028W	2418
-YHL027W	2478
-YHL026C	1548
-YHL025W	1599
-YHL024W	2742
-YHL023C	4041
-YHL022C	1797
-YHL021C	1998
-YHL020C	1815
-YHL019W_A	1194
-YHL019C	2418
-YHL018W	963
-YHL017W	2199
-YHL016C	2808
-YHL015W_A	684
-YHL015W	966
-YHL014C	1818
-YHL013C	1524
-YHL012W	2082
-YHL011C	1563
-YHL010C	2358
-YHL009C	1593
-YHL009W_B	6009
-YHL009W_A	1842
-YHL008C	2484
-YHL007C	3420
-YHL006W_A	954
-YHL006C	1053
-YHL005C	993
-YHL004W	1785
-YHL003C	1836
-YHL002C_A	1089
-YHL002W	1959
-YHL001W	1017
-YHR001W	1914
-YHR001W_A	834
-YHR002W	1674
-YHR003C	1890
-YHR004C	1941
-YHR005C	2019
-YHR005C_A	882
-YHR006W	2226
-YHR007C	2193
-YHR007C_A	816
-YHR008C	1302
-YHR009C	2172
-YHR010W	1011
-YHR011W	1941
-YHR012W	1449
-YHR014W	1476
-YHR015W	2580
-YHR016C	2007
-YHR017W	1758
-YHR018C	1992
-YHR019C	2265
-YHR020W	2667
-YHR021C	849
-YHR021W_A	1056
-YHR022C	1371
-YHR022C_A	690
-YHR023W	6387
-YHR024C	2049
-YHR025W	1674
-YHR026W	1242
-YHR027C	3582
-YHR028C	3057
-YHR028W_A	921
-YHR029C	1485
-YHR030C	2055
-YHR031C	2772
-YHR032W	2346
-YHR032W_A	780
-YHR032C_A	720
-YHR033W	1872
-YHR034C	1635
-YHR035W	2493
-YHR036W	2016
-YHR037W	2328
-YHR038W	1293
-YHR039C	2535
-YHR039C_A	945
-YHR040W	1701
-YHR041C	1233
-YHR042W	2676
-YHR043C	1341
-YHR044C	1341
-YHR045W	2283
-YHR046C	1488
-YHR047C	3171
-YHR048W	2145
-YHR049W	1332
-YHR049C_A	897
-YHR050W	2250
-YHR050W_A	771
-YHR051W	1047
-YHR052W	1731
-YHR052W_A	795
-YHR053C	786
-YHR054C	1665
-YHR054W_A	795
-YHR055C	786
-YHR056C	3252
-YHR056W_A	1035
-YHR057C	1218
-YHR058C	1488
-YHR059W	993
-YHR060W	1146
-YHR061C	1545
-YHR062C	1482
-YHR063C	1740
-YHR063W_A	936
-YHR064C	2217
-YHR065C	2106
-YHR066W	1962
-YHR067W	1443
-YHR068W	1764
-YHR069C	1680
-YHR069C_A	963
-YHR070W	2100
-YHR070C_A	1011
-YHR071W	1290
-YHR071C_A	921
-YHR072W	2796
-YHR072W_A	777
-YHR073W	3591
-YHR073W_A	777
-YHR073C_B	681
-YHR074W	2745
-YHR075C	1803
-YHR076W	1632
-YHR077C	3870
-YHR078W	2259
-YHR079C	3948
-YHR079C_A	876
-YHR080C	4638
-YHR081W	1155
-YHR082C	3690
-YHR083W	1590
-YHR084W	2667
-YHR085W	1605
-YHR086W	2172
-YHR086W_A	762
-YHR087W	936
-YHR088W	1488
-YHR089C	1218
-YHR090C	1449
-YHR091C	2532
-YHR092C	2331
-YHR093W	1149
-YHR094C	2313
-YHR095W	1095
-YHR096C	2379
-YHR097C	1701
-YHR098C	3390
-YHR099W	11835
-YHR100C	1158
-YHR101C	1608
-YHR102W	3843
-YHR103W	3159
-YHR104W	1584
-YHR105W	1245
-YHR106W	1629
-YHR107C	1824
-YHR108W	2358
-YHR109W	2358
-YHR110W	1239
-YHR111W	1923
-YHR112C	1737
-YHR113W	2073
-YHR114W	2502
-YHR115C	1851
-YHR116W	1056
-YHR117W	2520
-YHR118C	1908
-YHR119W	3843
-YHR120W	3480
-YHR121W	1164
-YHR122W	1296
-YHR123W	1776
-YHR124W	2484
-YHR125W	906
-YHR126C	1080
-YHR127W	1332
-YHR128W	1251
-YHR129C	1755
-YHR130C	936
-YHR131C	3153
-YHR131W_A	846
-YHR132C	1893
-YHR132W_A	996
-YHR133C	1476
-YHR134W	1410
-YHR135C	2217
-YHR136C	1047
-YHR137W	2142
-YHR137C_A	1251
-YHR138C	945
-YHR139C	1581
-YHR139C_A	912
-YHR140W	1320
-YHR141C	921
-YHR142W	1551
-YHR143W	1578
-YHR143W_A	813
-YHR144C	1539
-YHR145C	957
-YHR146W	1998
-YHR148W	1152
-YHR149C	2805
-YHR150W	2340
-YHR151C	2181
-YHR152W	1122
-YHR153C	1197
-YHR154W	3813
-YHR155W	4287
-YHR156C	1623
-YHR157W	1149
-YHR158C	4095
-YHR159W	2115
-YHR160C	1452
-YHR161C	2514
-YHR162W	990
-YHR163W	1350
-YHR164C	5169
-YHR165C	7842
-YHR165W_A	912
-YHR166C	2481
-YHR167W	1386
-YHR168W	2157
-YHR169W	1896
-YHR170W	2157
-YHR171W	2493
-YHR172W	3072
-YHR173C	939
-YHR174W	1914
-YHR175W	1170
-YHR175W_A	750
-YHR176W	1899
-YHR177W	1962
-YHR178W	2832
-YHR179W	1803
-YHR180W	1092
-YHR180W_A	783
-YHR180C_B	705
-YHR181W	1287
-YHR182W	2958
-YHR182C_A	1074
-YHR183W	2070
-YHR184W	2316
-YHR185C	1314
-YHR186C	5274
-YHR187W	1530
-YHR188C	2433
-YHR189W	1173
-YHR190W	1935
-YHR191C	1002
-YHR192W	1437
-YHR193C	1125
-YHR193C_A	975
-YHR194W	2340
-YHR195W	1566
-YHR196W	2328
-YHR197W	2892
-YHR198C	1566
-YHR199C	1533
-YHR199C_A	822
-YHR200W	1407
-YHR201C	1794
-YHR202W	2409
-YHR203C	1386
-YHR204W	2991
-YHR205W	3075
-YHR206W	2469
-YHR207C	2181
-YHR208W	1782
-YHR209W	1476
-YHR210C	1626
-YHR211W	3828
-YHR212C	936
-YHR212W_A	804
-YHR213W	1197
-YHR213W_A	834
-YHR213W_B	900
-YHR214W	1212
-YHR214W_A	1086
-YHR214C_B	5982
-YHR214C_C	2037
-YHR214C_D	894
-YHR214C_E	900
-YHR215W	2004
-YHR216W	2172
-YHR217C	1062
-YHR218W	2412
-YHR218W_A	918
-YHR219W	2475
-YHR219C_A	1083
-YML071C	2424
-YML004C	1581
-YMR061W	2634
-YMR128W	4404
-YMR196W	3867
-YMR259C	4863
-YML133C	4725
-YML133W_B	1083
-YML133W_A	1176
-YML132W	1740
-YML131W	1698
-YML130C	2292
-YML129C	813
-YML128C	2142
-YML127W	2346
-YML126C	2076
-YML125C	1539
-YML124C	1938
-YML123C	2364
-YML122C	981
-YML121W	1533
-YML120C	2142
-YML119W	1674
-YML118W	2118
-YML117W	4005
-YML116W_A	903
-YML116W	2229
-YML115C	2208
-YML114C	2133
-YML113W	1347
-YML112W	1491
-YML111W	3363
-YML110C	1524
-YML109W	3429
-YML108W	918
-YML107C	1605
-YML106W	1281
-YML105C	1422
-YML104C	3984
-YML103C	5568
-YML102W	2007
-YML101C_A	918
-YML101C	954
-YML100W_A	774
-YML100W	3897
-YML099W_A	930
-YML099C	3243
-YML098W	1104
-YML097C	1956
-YML096W	2178
-YML095C	1233
-YML094C_A	1002
-YML094W	1092
-YML093W	3300
-YML092C	1353
-YML091C	4209
-YML090W	987
-YML089C	969
-YML088W	2607
-YML087C	1539
-YML086C	2181
-YML085C	1944
-YML084W	909
-YML083C	1857
-YML082W	2550
-YML081C_A	780
-YML081W	4356
-YML080W	1872
-YML079W	1206
-YML078W	1149
-YML077W	1080
-YML076C	3435
-YML075C	3765
-YML074C	1836
-YML073C	1131
-YML072C	5238
-YML070W	2355
-YML069W	2259
-YML068W	1995
-YML067C	1659
-YML066C	1710
-YML065W	3345
-YML064C	1338
-YML063W	1368
-YML062C	1779
-YML061C	3180
-YML060W	1731
-YML059C	5640
-YML058W_A	807
-YML058W	915
-YML057C_A	990
-YML057W	2415
-YML056C	2175
-YML055W	1137
-YML054C	2376
-YML054C_A	759
-YML053C	1239
-YML052W	1509
-YML051W	1908
-YML050W	1536
-YML049C	4686
-YML048W	1812
-YML047W_A	966
-YML047C	1659
-YML046W	2490
-YML045W	5868
-YML045W_A	1923
-YML043C	2124
-YML042W	2613
-YML041C	1443
-YML039W	5868
-YML040W	1923
-YML038C	1929
-YML037C	1623
-YML036W	1146
-YML035C	3033
-YML034C_A	999
-YML034W	3105
-YML032C	2016
-YML031C_A	936
-YML031W	2568
-YML030W	1080
-YML029W	3117
-YML028W	1191
-YML027W	1758
-YML026C	1041
-YML025C	1461
-YML024W	1011
-YML023C	2271
-YML022W	1164
-YML021C	1680
-YML020W	2595
-YML019W	1599
-YML018C	1782
-YML017W	2382
-YML016C	2679
-YML015C	1641
-YML014W	1440
-YML013W	2355
-YML012C_A	978
-YML012W	1236
-YML011C	1134
-YML010W	3792
-YML009W_B	1077
-YML009C_A	927
-YML009C	813
-YML008C	1752
-YML007C_A	711
-YML007W	2553
-YML006C	2925
-YML005W	1989
-YML003W	1473
-YML002W	2814
-YML001W	1227
-YMR001C	2718
-YMR001C_A	831
-YMR002W	1071
-YMR003W	1197
-YMR004W	2136
-YMR005W	1767
-YMR006C	2721
-YMR007W	981
-YMR008C	2595
-YMR009W	1140
-YMR010W	1818
-YMR011W	2226
-YMR012W	4434
-YMR013C	2160
-YMR013C_A	750
-YMR013W_A	681
-YMR014W	2160
-YMR015C	2217
-YMR016C	2958
-YMR017W	1794
-YMR018W	2145
-YMR019W	3450
-YMR020W	2127
-YMR021C	1854
-YMR022W	1098
-YMR023C	2181
-YMR024W	1773
-YMR025W	1488
-YMR026C	1800
-YMR027W	2013
-YMR028W	1701
-YMR029C	2172
-YMR030W	1731
-YMR031C	3132
-YMR031W_A	927
-YMR032W	2610
-YMR030W_A	891
-YMR033W	2004
-YMR034C	1905
-YMR035W	1134
-YMR036C	2265
-YMR037C	2715
-YMR038C	1350
-YMR039C	1479
-YMR040W	1083
-YMR041C	1608
-YMR042W	1134
-YMR043W	1461
-YMR044W	2028
-YMR045C	5868
-YMR046C	1923
-YMR046W_A	729
-YMR047C	3942
-YMR048W	1554
-YMR049C	3024
-YMR050C	5868
-YMR051C	1923
-YMR052W	1215
-YMR052C_A	966
-YMR053C	3153
-YMR054W	3273
-YMR055C	1521
-YMR056C	1530
-YMR057C	972
-YMR058W	2511
-YMR059W	987
-YMR060C	1584
-YMR062C	1926
-YMR063W	1320
-YMR064W	2157
-YMR065W	2115
-YMR066W	3297
-YMR067C	1851
-YMR068W	1881
-YMR069W	1458
-YMR070W	2073
-YMR071C	1104
-YMR072W	1152
-YMR073C	1206
-YMR074C	1038
-YMR075W	2655
-YMR075C_A	966
-YMR076C	4434
-YMR077C	1266
-YMR078C	2826
-YMR079W	1515
-YMR080C	3516
-YMR081C	1617
-YMR082C	957
-YMR083W	1728
-YMR084W	1389
-YMR085W	1899
-YMR086W	3483
-YMR086C_A	939
-YMR087W	1455
-YMR088C	2289
-YMR089C	3078
-YMR090W	1284
-YMR091C	1908
-YMR092C	2448
-YMR093W	2142
-YMR094W	2037
-YMR095C	1275
-YMR096W	1494
-YMR097C	1704
-YMR098C	2439
-YMR099C	1494
-YMR100W	2463
-YMR101C	1632
-YMR102C	3105
-YMR103C	963
-YMR104C	2634
-YMR105C	2310
-YMR105W_A	795
-YMR106C	2490
-YMR107W	948
-YMR108W	2664
-YMR109W	4260
-YMR110C	2199
-YMR111C	1989
-YMR112C	996
-YMR113W	1884
-YMR114C	1707
-YMR115W	2106
-YMR116C	1560
-YMR117C	1242
-YMR118C	1191
-YMR119W	2475
-YMR119W_A	975
-YMR120C	2379
-YMR121C	1215
-YMR122C	975
-YMR122W_A	855
-YMR123W	969
-YMR124W	3432
-YMR125W	3186
-YMR126C	1629
-YMR127C	1617
-YMR129W	4614
-YMR130W	1509
-YMR131C	2136
-YMR132C	1227
-YMR133W	1887
-YMR134W	1314
-YMR135C	1968
-YMR135W_A	1134
-YMR136W	2283
-YMR137C	2586
-YMR138W	1176
-YMR139W	1713
-YMR140W	2070
-YMR141C	909
-YMR142C	1200
-YMR141W_A	825
-YMR143W	1032
-YMR144W	1629
-YMR145C	2283
-YMR146C	1644
-YMR147W	1272
-YMR148W	1047
-YMR149W	1461
-YMR150C	1173
-YMR151W	1038
-YMR152W	1698
-YMR153W	2028
-YMR153C_A	936
-YMR154C	2784
-YMR155W	2244
-YMR156C	1317
-YMR157C	1368
-YMR158W	1068
-YMR158C_A	738
-YMR158W_B	921
-YMR159C	1053
-YMR160W	3051
-YMR161W	1275
-YMR162C	5571
-YMR163C	2718
-YMR164C	2877
-YMR165C	3189
-YMR166C	1707
-YMR167W	2910
-YMR168C	2427
-YMR169C	2121
-YMR170C	2121
-YMR171C	2253
-YMR172W	2760
-YMR172C_A	984
-YMR173W	1893
-YMR173W_A	1785
-YMR174C	807
-YMR175W	840
-YMR175W_A	795
-YMR176W	4836
-YMR177W	2133
-YMR178W	1425
-YMR179W	2877
-YMR180C	1563
-YMR181C	1065
-YMR182C	1236
-YMR182W_A	687
-YMR183C	1488
-YMR184W	1197
-YMR185W	3546
-YMR186W	2718
-YMR187C	1896
-YMR188C	1314
-YMR189W	3705
-YMR190C	4944
-YMR191W	1722
-YMR192W	2763
-YMR193W	1377
-YMR193C_A	987
-YMR194W	903
-YMR194C_B	822
-YMR194C_A	825
-YMR195W	984
-YMR197C	1254
-YMR198W	2385
-YMR199W	2241
-YMR200W	1371
-YMR201C	1716
-YMR202W	1269
-YMR203W	1764
-YMR204C	1863
-YMR205C	3480
-YMR206W	1542
-YMR207C	6972
-YMR208W	1932
-YMR209C	1974
-YMR210W	1950
-YMR211W	2028
-YMR212C	2949
-YMR213W	2373
-YMR214W	1734
-YMR215W	2175
-YMR216C	2829
-YMR217W	2178
-YMR218C	3909
-YMR219W	5577
-YMR220W	1956
-YMR221C	2115
-YMR222C	1272
-YMR223W	2016
-YMR224C	2679
-YMR225C	897
-YMR226C	1404
-YMR227C	2373
-YMR228W	1626
-YMR229C	5790
-YMR230W	918
-YMR230W_A	789
-YMR231W	3690
-YMR232W	2634
-YMR233W	1281
-YMR234W	1647
-YMR235C	1824
-YMR236W	1074
-YMR237W	2775
-YMR238W	1977
-YMR239C	2016
-YMR240C	1911
-YMR241W	1545
-YMR242C	1119
-YMR242W_A	690
-YMR243C	1929
-YMR244W	1668
-YMR244C_A	915
-YMR245W	1221
-YMR246W	2685
-YMR247C	5289
-YMR247W_A	744
-YMR250W	2358
-YMR251W	1701
-YMR251W_A	780
-YMR252C	1005
-YMR253C	1845
-YMR254C	909
-YMR255W	1167
-YMR256C	783
-YMR257C	3003
-YMR258C	2262
-YMR260C	1062
-YMR261C	3765
-YMR262W	1542
-YMR263W	1206
-YMR264W	1212
-YMR265C	1986
-YMR266W	3462
-YMR267W	1533
-YMR268C	1935
-YMR269W	1236
-YMR270C	1698
-YMR271C	1284
-YMR272C	1755
-YMR272W_A	714
-YMR272W_B	708
-YMR273C	3348
-YMR274C	1548
-YMR275C	3531
-YMR276W	1722
-YMR277W	2799
-YMR278W	2469
-YMR279C	2223
-YMR280C	4902
-YMR281W	1515
-YMR282C	2343
-YMR283C	2142
-YMR284W	2409
-YMR285C	2148
-YMR286W	861
-YMR287C	3510
-YMR288W	3516
-YMR289W	1725
-YMR290C	2118
-YMR290W_A	948
-YMR291W	2361
-YMR292W	1017
-YMR293C	1995
-YMR294W	1722
-YMR294W_A	960
-YMR295C	1194
-YMR296C	2277
-YMR297W	2199
-YMR298W	1053
-YMR299C	1539
-YMR300C	2133
-YMR301C	2673
-YMR302C	3153
-YMR303C	1647
-YMR304W	4293
-YMR304C_A	951
-YMR305C	1770
-YMR306W	5958
-YMR306C_A	990
-YMR307W	2280
-YMR307C_A	795
-YMR308C	3870
-YMR309C	3039
-YMR310C	1554
-YMR311C	1290
-YMR312W	1422
-YMR313C	2529
-YMR314W	1305
-YMR315W	1650
-YMR315W_A	708
-YMR316W	1611
-YMR316C_A	912
-YMR316C_B	909
-YMR317W	4023
-YMR318C	1683
-YMR319C	2259
-YMR320W	906
-YMR321C	918
-YMR322C	1314
-YMR323W	1914
-YMR324C	843
-YMR325W	975
diff -r dfb484045b7e -r ba39548ca273 bowtie_genome_wrapper/bowtie_genomic_wrapper.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie_genome_wrapper/bowtie_genomic_wrapper.py	Mon Apr 04 14:07:23 2022 +0000
@@ -0,0 +1,472 @@
+#!/usr/bin/env python
+
+"""
+Runs Bowtie on single-end or paired-end data.
+
+usage: bowtie_wrapper.py [options]
+    -t, --threads=t: The number of threads to run
+    -o, --output=o: The output file
+    --output_unmapped_reads=: File name for unmapped reads (single-end)
+    --output_unmapped_reads_l=: File name for unmapped reads (left, paired-end)
+    --output_unmapped_reads_r=: File name for unmapped reads (right, paired-end)
+    --output_suppressed_reads=: File name for suppressed reads because of max setting (single-end)
+    --output_suppressed_reads_l=: File name for suppressed reads because of max setting (left, paired-end)
+    --output_suppressed_reads_r=: File name for suppressed reads because of max setting (right, paired-end)
+    --output_mapping_stats=: File name for mapping statistics (output on stderr by bowtie)
+    -i, --input1=i: The (forward or single-end) reads file in Sanger FASTQ format
+    -I, --input2=I: The reverse reads file in Sanger FASTQ format
+    -4, --dataType=4: The type of data (SOLiD or Solexa)
+    -2, --paired=2: Whether the data is single- or paired-end
+    -g, --genomeSource=g: The type of reference provided
+    -r, --ref=r: The reference genome to use or index
+    -s, --skip=s: Skip the first n reads
+    -a, --alignLimit=a: Only align the first n reads
+    -T, --trimH=T: Trim n bases from high-quality (left) end of each read before alignment
+    -L, --trimL=L: Trim n bases from low-quality (right) end of each read before alignment
+    -m, --mismatchSeed=m: Maximum number of mismatches permitted in the seed
+    -M, --mismatchQual=M: Maximum permitted total of quality values at mismatched read positions
+    -l, --seedLen=l: Seed length
+    -n, --rounding=n: Whether or not to round to the nearest 10 and saturating at 30
+    -P, --maxMismatches=P: Maximum number of mismatches for -v alignment mode
+    -w, --tryHard=: Whether or not to try as hard as possible to find valid alignments when they exist
+    -V, --allValAligns=V: Whether or not to report all valid alignments per read or pair
+    -v, --valAlign=v: Report up to n valid alignments per read or pair
+    -G, --suppressAlign=G: Suppress all alignments for a read if more than n reportable alignments exist
+    -b, --best=b: Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions
+    -B, --maxBacktracks=B: Maximum number of backtracks permitted when aligning a read
+    -R, --strata=R: Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable
+    -j, --minInsert=j: Minimum insert size for valid paired-end alignments
+    -J, --maxInsert=J: Maximum insert size for valid paired-end alignments
+    -O, --mateOrient=O: The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand
+    -A, --maxAlignAttempt=A: Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate
+    -f, --forwardAlign=f: Whether or not to attempt to align the forward reference strand
+    -E, --reverseAlign=E: Whether or not to attempt to align the reverse-complement reference strand
+    -F, --offrate=F: Override the offrate of the index to n
+    -8, --snpphred=8: SNP penalty on Phred scale
+    -6, --snpfrac=6: Fraction of sites expected to be SNP sites
+    -7, --keepends=7: Keep extreme-end nucleotides and qualities
+    -S, --seed=S: Seed for pseudo-random number generator
+    -C, --params=C: Whether to use default or specified parameters
+    -u, --iautoB=u: Automatic or specified behavior
+    -K, --ipacked=K: Whether or not to use a packed representation for DNA strings
+    -Q, --ibmax=Q: Maximum number of suffixes allowed in a block
+    -Y, --ibmaxdivn=Y: Maximum number of suffixes allowed in a block as a fraction of the length of the reference
+    -D, --idcv=D: The period for the difference-cover sample
+    -U, --inodc=U: Whether or not to disable the use of the difference-cover sample
+    -y, --inoref=y: Whether or not to build the part of the reference index used only in paired-end alignment
+    -z, --ioffrate=z: How many rows get marked during annotation of some or all of the Burrows-Wheeler rows
+    -W, --iftab=W: The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query
+    -X, --intoa=X: Whether or not to convert Ns in the reference sequence to As
+    -N, --iendian=N: Endianness to use when serializing integers to the index file
+    -Z, --iseed=Z: Seed for the pseudorandom number generator
+    -x, --indexSettings=x: Whether or not indexing options are to be set
+    -H, --suppressHeader=H: Suppress header
+    --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'
+"""
+
+import optparse
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+
+# Allow more than Sanger encoded variants
+DEFAULT_ASCII_ENCODING = '--phred33-quals'
+GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = {'fastqsanger': '--phred33-quals', 'fastqillumina': '--phred64-quals', 'fastqsolexa': '--solexa-quals'}
+# FIXME: Integer quality scores are supported only when the '--integer-quals' argument is specified to bowtie; this is not currently able to be set in the tool/wrapper/config
+
+
+def stop_err( msg ):
+    sys.exit('%s\n' % msg)
+
+
+def __main__():
+    parser = optparse.OptionParser()
+    parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to run' )
+    parser.add_option( '-o', '--output', dest='output', help='The output file' )
+    parser.add_option( '', '--output_unmapped_reads', dest='output_unmapped_reads', help='File name for unmapped reads (single-end)' )
+    parser.add_option( '', '--output_unmapped_reads_l', dest='output_unmapped_reads_l', help='File name for unmapped reads (left, paired-end)' )
+    parser.add_option( '', '--output_unmapped_reads_r', dest='output_unmapped_reads_r', help='File name for unmapped reads (right, paired-end)' )
+    parser.add_option( '', '--output_suppressed_reads', dest='output_suppressed_reads', help='File name for suppressed reads because of max setting (single-end)' )
+    parser.add_option( '', '--output_suppressed_reads_l', dest='output_suppressed_reads_l', help='File name for suppressed reads because of max setting (left, paired-end)' )
+    parser.add_option( '', '--output_suppressed_reads_r', dest='output_suppressed_reads_r', help='File name for suppressed reads because of max setting (right, paired-end)' )
+    parser.add_option( '', '--output_mapping_stats', dest='output_mapping_stats', help='File for mapping statistics (i.e. stderr from bowtie)' )
+    parser.add_option( '-4', '--dataType', dest='dataType', help='The type of data (SOLiD or Solexa)' )
+    parser.add_option( '-i', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' )
+    parser.add_option( '-I', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
+    parser.add_option( '-2', '--paired', dest='paired', help='Whether the data is single- or paired-end' )
+    parser.add_option( '-g', '--genomeSource', dest='genomeSource', help='The type of reference provided' )
+    parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' )
+    parser.add_option( '-s', '--skip', dest='skip', help='Skip the first n reads' )
+    parser.add_option( '-a', '--alignLimit', dest='alignLimit', help='Only align the first n reads' )
+    parser.add_option( '-T', '--trimH', dest='trimH', help='Trim n bases from high-quality (left) end of each read before alignment' )
+    parser.add_option( '-L', '--trimL', dest='trimL', help='Trim n bases from low-quality (right) end of each read before alignment' )
+    parser.add_option( '-m', '--mismatchSeed', dest='mismatchSeed', help='Maximum number of mismatches permitted in the seed' )
+    parser.add_option( '-M', '--mismatchQual', dest='mismatchQual', help='Maximum permitted total of quality values at mismatched read positions' )
+    parser.add_option( '-l', '--seedLen', dest='seedLen', help='Seed length' )
+    parser.add_option( '-n', '--rounding', dest='rounding', help='Whether or not to round to the nearest 10 and saturating at 30' )
+    parser.add_option( '-P', '--maxMismatches', dest='maxMismatches', help='Maximum number of mismatches for -v alignment mode' )
+    parser.add_option( '-w', '--tryHard', dest='tryHard', help='Whether or not to try as hard as possible to find valid alignments when they exist' )
+    parser.add_option( '-V', '--allValAligns', dest='allValAligns', help='Whether or not to report all valid alignments per read or pair' )
+    parser.add_option( '-v', '--valAlign', dest='valAlign', help='Report up to n valid alignments per read or pair' )
+    parser.add_option( '-G', '--suppressAlign', dest='suppressAlign', help='Suppress all alignments for a read if more than n reportable alignments exist' )
+    parser.add_option( '-b', '--best', dest='best', help="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions" )
+    parser.add_option( '-B', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read' )
+    parser.add_option( '-R', '--strata', dest='strata', help='Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable' )
+    parser.add_option( '-j', '--minInsert', dest='minInsert', help='Minimum insert size for valid paired-end alignments' )
+    parser.add_option( '-J', '--maxInsert', dest='maxInsert', help='Maximum insert size for valid paired-end alignments' )
+    parser.add_option( '-O', '--mateOrient', dest='mateOrient', help='The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand' )
+    parser.add_option( '-A', '--maxAlignAttempt', dest='maxAlignAttempt', help='Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate' )
+    parser.add_option( '-f', '--forwardAlign', dest='forwardAlign', help='Whether or not to attempt to align the forward reference strand' )
+    parser.add_option( '-E', '--reverseAlign', dest='reverseAlign', help='Whether or not to attempt to align the reverse-complement reference strand' )
+    parser.add_option( '-F', '--offrate', dest='offrate', help='Override the offrate of the index to n' )
+    parser.add_option( '-S', '--seed', dest='seed', help='Seed for pseudo-random number generator' )
+    parser.add_option( '-8', '--snpphred', dest='snpphred', help='SNP penalty on Phred scale' )
+    parser.add_option( '-6', '--snpfrac', dest='snpfrac', help='Fraction of sites expected to be SNP sites' )
+    parser.add_option( '-7', '--keepends', dest='keepends', help='Keep extreme-end nucleotides and qualities' )
+    parser.add_option( '-C', '--params', dest='params', help='Whether to use default or specified parameters' )
+    parser.add_option( '-u', '--iautoB', dest='iautoB', help='Automatic or specified behavior' )
+    parser.add_option( '-K', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings' )
+    parser.add_option( '-Q', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block' )
+    parser.add_option( '-Y', '--ibmaxdivn', dest='ibmaxdivn', help='Maximum number of suffixes allowed in a block as a fraction of the length of the reference' )
+    parser.add_option( '-D', '--idcv', dest='idcv', help='The period for the difference-cover sample' )
+    parser.add_option( '-U', '--inodc', dest='inodc', help='Whether or not to disable the use of the difference-cover sample' )
+    parser.add_option( '-y', '--inoref', dest='inoref', help='Whether or not to build the part of the reference index used only in paired-end alignment' )
+    parser.add_option( '-z', '--ioffrate', dest='ioffrate', help='How many rows get marked during annotation of some or all of the Burrows-Wheeler rows' )
+    parser.add_option( '-W', '--iftab', dest='iftab', help='The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query' )
+    parser.add_option( '-X', '--intoa', dest='intoa', help='Whether or not to convert Ns in the reference sequence to As' )
+    parser.add_option( '-N', '--iendian', dest='iendian', help='Endianness to use when serializing integers to the index file' )
+    parser.add_option( '-Z', '--iseed', dest='iseed', help='Seed for the pseudorandom number generator' )
+    parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' )
+    parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
+    parser.add_option( '--galaxy_input_format', dest='galaxy_input_format', default="fastqsanger", help='galaxy input format' )
+    parser.add_option( '--do_not_build_index', dest='do_not_build_index', action="store_true", default=False, help='Flag to specify that provided file is already indexed, use as is' )
+    (options, args) = parser.parse_args()
+    if options.mismatchSeed and options.maxMismatches:
+        parser.error("options --mismatchSeed and --maxMismatches are mutually exclusive")
+    stdout = ''
+
+    # make temp directory for placement of indices and copy reference file there if necessary
+    tmp_index_dir = tempfile.mkdtemp()
+    # get type of data (solid or solexa)
+    if options.dataType == 'solid':
+        colorspace = '-C'
+    else:
+        colorspace = ''
+    # index if necessary
+    if options.genomeSource == 'history' and not options.do_not_build_index:
+        # set up commands
+        if options.index_settings == 'indexPreSet':
+            indexing_cmds = '%s' % colorspace
+        else:
+            try:
+                if options.iautoB and options.iautoB == 'set':
+                    iautoB = '--noauto'
+                else:
+                    iautoB = ''
+                if options.ipacked and options.ipacked == 'packed':
+                    ipacked = '--packed'
+                else:
+                    ipacked = ''
+                if options.ibmax and int( options.ibmax ) >= 1:
+                    ibmax = '--bmax %s' % options.ibmax
+                else:
+                    ibmax = ''
+                if options.ibmaxdivn and int( options.ibmaxdivn ) >= 0:
+                    ibmaxdivn = '--bmaxdivn %s' % options.ibmaxdivn
+                else:
+                    ibmaxdivn = ''
+                if options.idcv and int( options.idcv ) >= 3:
+                    idcv = '--dcv %s' % options.idcv
+                else:
+                    idcv = ''
+                if options.inodc and options.inodc == 'nodc':
+                    inodc = '--nodc'
+                else:
+                    inodc = ''
+                if options.inoref and options.inoref == 'noref':
+                    inoref = '--noref'
+                else:
+                    inoref = ''
+                if options.iftab and int( options.iftab ) >= 1:
+                    iftab = '--ftabchars %s' % options.iftab
+                else:
+                    iftab = ''
+                if options.intoa and options.intoa == 'yes':
+                    intoa = '--ntoa'
+                else:
+                    intoa = ''
+                if options.iendian and options.iendian == 'big':
+                    iendian = '--big'
+                else:
+                    iendian = '--little'
+                if options.iseed and int( options.iseed ) > 0:
+                    iseed = '--seed %s' % options.iseed
+                else:
+                    iseed = ''
+                indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s' % \
+                                ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc,
+                                  inoref, options.ioffrate, iftab, intoa, iendian,
+                                  iseed, colorspace )
+            except ValueError as e:
+                # clean up temp dir
+                if os.path.exists( tmp_index_dir ):
+                    shutil.rmtree( tmp_index_dir )
+                stop_err( "Something is wrong with the indexing parameters and the indexing and alignment could not be run. Make sure you don't have any non-numeric values where they should be numeric.\n" + str( e ) )
+        ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
+        ref_file_name = ref_file.name
+        ref_file.close()
+        os.symlink( options.ref, ref_file_name )
+        cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name )
+        try:
+            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
+            with open(tmp, 'w') as tmp_stderr:
+                returncode = subprocess.call(args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno())
+            if returncode != 0:
+                # get stderr, allowing for case where it's very large
+                stderr = ''
+                buffsize = 1048576
+                with open(tmp, 'r') as tmp_stderr:
+                    try:
+                        while True:
+                            stderr += tmp_stderr.read(buffsize)
+                            if not stderr or len(stderr) % buffsize != 0:
+                                break
+                    except OverflowError:
+                        pass
+                raise Exception(stderr)
+        except Exception as e:
+            # clean up temp dir
+            if os.path.exists( tmp_index_dir ):
+                shutil.rmtree( tmp_index_dir )
+            stop_err( 'Error indexing reference sequence\n' + str( e ) )
+        stdout += 'File indexed. '
+    else:
+        ref_file_name = options.ref
+    # set up aligning and generate aligning command options
+    # automatically set threads in both cases
+    tmp_suppressed_file_name = None
+    tmp_unmapped_file_name = None
+    if options.suppressHeader == 'true':
+        suppressHeader = '--sam-nohead'
+    else:
+        suppressHeader = ''
+    if options.maxInsert and int( options.maxInsert ) > 0:
+        maxInsert = '-X %s' % options.maxInsert
+    else:
+        maxInsert = ''
+    if options.mateOrient:
+        mateOrient = '--%s' % options.mateOrient
+    else:
+        mateOrient = ''
+    quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING )
+    if options.params == 'preSet':
+        aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \
+            ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding )
+    else:
+        try:
+            if options.skip and int( options.skip ) > 0:
+                skip = '-s %s' % options.skip
+            else:
+                skip = ''
+            if options.alignLimit and int( options.alignLimit ) >= 0:
+                alignLimit = '-u %s' % options.alignLimit
+            else:
+                alignLimit = ''
+            if options.trimH and int( options.trimH ) > 0:
+                trimH = '-5 %s' % options.trimH
+            else:
+                trimH = ''
+            if options.trimL and int( options.trimL ) > 0:
+                trimL = '-3 %s' % options.trimL
+            else:
+                trimL = ''
+            if options.maxMismatches and (options.maxMismatches == '0' or options.maxMismatches == '1' or
+                                          options.maxMismatches == '2' or options.maxMismatches == '3'):
+                maxMismatches = '-v %s' % options.maxMismatches
+            else:
+                maxMismatches = ''
+            if options.mismatchSeed and (options.mismatchSeed == '0' or options.mismatchSeed == '1' or
+                                         options.mismatchSeed == '2' or options.mismatchSeed == '3'):
+                mismatchSeed = '-n %s' % options.mismatchSeed
+            else:
+                mismatchSeed = ''
+            if options.mismatchQual and int( options.mismatchQual ) >= 1:
+                mismatchQual = '-e %s' % options.mismatchQual
+            else:
+                mismatchQual = ''
+            if options.seedLen and int( options.seedLen ) >= 5:
+                seedLen = '-l %s' % options.seedLen
+            else:
+                seedLen = ''
+            if options.rounding == 'noRound':
+                rounding = '--nomaqround'
+            else:
+                rounding = ''
+            if options.minInsert and int( options.minInsert ) > 0:
+                minInsert = '-I %s' % options.minInsert
+            else:
+                minInsert = ''
+            if options.maxAlignAttempt and int( options.maxAlignAttempt ) >= 0:
+                maxAlignAttempt = '--pairtries %s' % options.maxAlignAttempt
+            else:
+                maxAlignAttempt = ''
+            if options.forwardAlign == 'noForward':
+                forwardAlign = '--nofw'
+            else:
+                forwardAlign = ''
+            if options.reverseAlign == 'noReverse':
+                reverseAlign = '--norc'
+            else:
+                reverseAlign = ''
+            if options.maxBacktracks and int( options.maxBacktracks ) > 0 and \
+                    ( options.mismatchSeed == '2' or options.mismatchSeed == '3' ):
+                maxBacktracks = '--maxbts %s' % options.maxBacktracks
+            else:
+                maxBacktracks = ''
+            if options.tryHard == 'doTryHard':
+                tryHard = '-y'
+            else:
+                tryHard = ''
+            if options.valAlign and int( options.valAlign ) >= 0:
+                valAlign = '-k %s' % options.valAlign
+            else:
+                valAlign = ''
+            if options.allValAligns == 'doAllValAligns':
+                allValAligns = '-a'
+            else:
+                allValAligns = ''
+            if options.suppressAlign and int( options.suppressAlign ) >= 0:
+                suppressAlign = '-m %s' % options.suppressAlign
+            else:
+                suppressAlign = ''
+            if options.best == 'doBest':
+                best = '--best'
+            else:
+                best = ''
+            if options.strata == 'doStrata':
+                strata = '--strata'
+            else:
+                strata = ''
+            if options.offrate and int( options.offrate ) >= 0:
+                offrate = '-o %s' % options.offrate
+            else:
+                offrate = ''
+            if options.seed and int( options.seed ) >= 0:
+                seed = '--seed %s' % options.seed
+            else:
+                seed = ''
+            if options.paired == 'paired':
+                if options.output_unmapped_reads_l and options.output_unmapped_reads_r:
+                    tmp_unmapped_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
+                    tmp_unmapped_file_name = tmp_unmapped_file.name
+                    tmp_unmapped_file.close()
+                    output_unmapped_reads = '--un %s' % tmp_unmapped_file_name
+                else:
+                    output_unmapped_reads = ''
+                if options.output_suppressed_reads:
+                    tmp_suppressed_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
+                    tmp_suppressed_file_name = tmp_suppressed_file.name
+                    tmp_suppressed_file.close()
+                    output_suppressed_reads = '--max %s' % tmp_suppressed_file_name
+                else:
+                    output_suppressed_reads = ''
+            else:
+                if options.output_unmapped_reads:
+                    output_unmapped_reads = '--un %s' % options.output_unmapped_reads
+                else:
+                    output_unmapped_reads = ''
+                if options.output_suppressed_reads:
+                    output_suppressed_reads = '--max %s' % options.output_suppressed_reads
+                else:
+                    output_suppressed_reads = ''
+            snpfrac = ''
+            if options.snpphred and int( options.snpphred ) >= 0:
+                snpphred = '--snpphred %s' % options.snpphred
+            else:
+                snpphred = ''
+                if options.snpfrac and float( options.snpfrac ) >= 0:
+                    snpfrac = '--snpfrac %s' % options.snpfrac
+            if options.keepends and options.keepends == 'doKeepends':
+                keepends = '--col-keepends'
+            else:
+                keepends = ''
+            aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \
+                            '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \
+                            ( maxInsert, mateOrient, options.threads, suppressHeader,
+                              colorspace, skip, alignLimit, trimH, trimL, maxMismatches,
+                              mismatchSeed, mismatchQual, seedLen, rounding, minInsert,
+                              maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks,
+                              tryHard, valAlign, allValAligns, suppressAlign, best,
+                              strata, offrate, seed, snpphred, snpfrac, keepends,
+                              output_unmapped_reads, output_suppressed_reads,
+                              quality_score_encoding )
+        except ValueError as e:
+            # clean up temp dir
+            if os.path.exists( tmp_index_dir ):
+                shutil.rmtree( tmp_index_dir )
+            stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) )
+    try:
+        # have to nest try-except in try-finally to handle 2.4
+        try:
+            # prepare actual mapping commands
+            if options.paired == 'paired':
+                cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
+            else:
+                cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
+            # align
+            tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
+            with open(tmp, 'w') as tmp_stderr:
+                returncode = subprocess.call(args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno())
+            # get stderr, allowing for case where it's very large
+            stderr = ''
+            buffsize = 1048576
+            with open(tmp, 'r') as tmp_stderr:
+                try:
+                    while True:
+                        stderr += tmp_stderr.read(buffsize)
+                        if not stderr or len(stderr) % buffsize != 0:
+                            break
+                except OverflowError:
+                    pass
+            if returncode != 0:
+                raise Exception(stderr)
+            elif options.output_mapping_stats is not None:
+                # Write stderr (containing the mapping statistics) to a named file
+                with open(options.output_mapping_stats, 'w') as mapping_stats:
+                    mapping_stats.write( stderr )
+            # get suppressed and unmapped reads output files in place if appropriate
+            if options.paired == 'paired' and tmp_suppressed_file_name and \
+                    options.output_suppressed_reads_l and options.output_suppressed_reads_r:
+                try:
+                    left = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
+                    right = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
+                    shutil.move( left, options.output_suppressed_reads_l )
+                    shutil.move( right, options.output_suppressed_reads_r )
+                except Exception as e:
+                    sys.stdout.write( 'Error producing the suppressed output file.\n' )
+            if options.paired == 'paired' and tmp_unmapped_file_name and \
+                    options.output_unmapped_reads_l and options.output_unmapped_reads_r:
+                try:
+                    left = tmp_unmapped_file_name.replace( '.fastq', '_1.fastq' )
+                    right = tmp_unmapped_file_name.replace( '.fastq', '_2.fastq' )
+                    shutil.move( left, options.output_unmapped_reads_l )
+                    shutil.move( right, options.output_unmapped_reads_r )
+                except Exception as e:
+                    sys.stdout.write( 'Error producing the unmapped output file.\n' )
+            # check that there are results in the output file
+            if os.path.getsize( options.output ) == 0:
+                raise Exception('The output file is empty, there may be an error with your input file or settings.')
+        except Exception as e:
+            stop_err( 'Error aligning sequence. ' + str( e ) )
+    finally:
+        # clean up temp dir
+        if os.path.exists( tmp_index_dir ):
+            shutil.rmtree( tmp_index_dir )
+    stdout += 'Sequence file aligned.\n'
+    sys.stdout.write( stdout )
+
+
+if __name__ == "__main__":
+    __main__()
diff -r dfb484045b7e -r ba39548ca273 bowtie_genome_wrapper/bowtie_genomic_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie_genome_wrapper/bowtie_genomic_wrapper.xml	Mon Apr 04 14:07:23 2022 +0000
@@ -0,0 +1,968 @@
+<tool id="bowtie_genomic_wrapper" name="Align to the Genome with Bowtie" version="1.2.0">
+  <description></description>
+  <requirements>
+    <requirement type="package" version="1.2.0">bowtie</requirement>
+  </requirements>
+  <version_command>bowtie --version</version_command>
+  <command>
+    python '$__tool_directory__/bowtie_genomic_wrapper.py'
+      ## Set number of threads
+      --threads="\${GALAXY_SLOTS:-4}"
+      ## Outputs
+      --output="${output}"
+      #if str( $singlePaired.sPaired ) == "single"
+        #if $output_unmapped_reads_l
+          --output_unmapped_reads="${output_unmapped_reads_l}"
+        #end if
+        #if $output_suppressed_reads_l
+          --output_suppressed_reads="${output_suppressed_reads_l}"
+        #end if
+        --galaxy_input_format="${singlePaired.sInput1.ext}"
+      #else
+        #if $output_unmapped_reads_l and $output_unmapped_reads_r
+          --output_unmapped_reads_l="${output_unmapped_reads_l}"
+          --output_unmapped_reads_r="${output_unmapped_reads_r}"
+        #end if
+        #if $output_suppressed_reads_l and $output_suppressed_reads_l
+          --output_suppressed_reads_l="${output_suppressed_reads_l}"
+          --output_suppressed_reads_r="${output_suppressed_reads_r}"
+        #end if
+        --galaxy_input_format="${singlePaired.pInput1.ext}"
+      #end if
+      ## Inputs
+      --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper
+      --suppressHeader="${suppressHeader}"
+      --genomeSource="${refGenomeSource.genomeSource}"
+      #if $refGenomeSource.genomeSource == "history":
+        ##index already exists
+        #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ):
+          ##user previously built
+          --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"
+          --do_not_build_index
+        #else:
+          ##build index on the fly
+          --ref="${refGenomeSource.ownFile}"
+          --indexSettings="${refGenomeSource.indexParams.indexSettings}"
+          #if $refGenomeSource.indexParams.indexSettings == "indexFull":
+            --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}"
+            #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":
+              --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}"
+              --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}"
+              --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}"
+              --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}"
+            #end if
+            --inodc="${refGenomeSource.indexParams.nodc}"
+            --inoref="${refGenomeSource.indexParams.noref}"
+            --ioffrate="${refGenomeSource.indexParams.offrate}"
+            --iftab="${refGenomeSource.indexParams.ftab}"
+            --intoa="${refGenomeSource.indexParams.ntoa}"
+            --iendian="${refGenomeSource.indexParams.endian}"
+            --iseed="${refGenomeSource.indexParams.seed}"
+          #end if
+        #end if
+      #else
+        ##use pre-built index
+        --ref="${refGenomeSource.index.fields.path}"
+      #end if
+      --paired="${singlePaired.sPaired}"
+      #if $singlePaired.sPaired == "single":
+        --input1="${singlePaired.sInput1}"
+        --params="${singlePaired.sParams.sSettingsType}"
+        #if $singlePaired.sParams.sSettingsType == "full":
+          --skip="${singlePaired.sParams.sSkip}"
+          --alignLimit="${singlePaired.sParams.sAlignLimit}"
+          --trimH="${singlePaired.sParams.sTrimH}"
+          --trimL="${singlePaired.sParams.sTrimL}"
+          #if $singlePaired.sParams.alignModeOption.alignMode == 'nMode'
+            --mismatchSeed="${singlePaired.sParams.alignModeOption.sMismatchSeed}"
+            --mismatchQual="${singlePaired.sParams.alignModeOption.sMismatchQual}"
+            --seedLen="${singlePaired.sParams.alignModeOption.sSeedLen}"
+            --rounding="${singlePaired.sParams.alignModeOption.sRounding}"
+          #else
+            --maxMismatches="${singlePaired.sParams.alignModeOption.maxMismatches}"
+          #end if
+          --forwardAlign="${singlePaired.sParams.sForwardAlign}"
+          --reverseAlign="${singlePaired.sParams.sReverseAlign}"
+          --tryHard="${singlePaired.sParams.sBestOption.sTryHardOption.sTryHard}"
+          --allValAligns="${singlePaired.sParams.sAllValAlignsOption.sAllValAligns}"
+          #if $singlePaired.sParams.sAllValAlignsOption.sAllValAligns == "noAllValAligns"
+            --valAlign="${singlePaired.sParams.sAllValAlignsOption.sValAlign}"
+          #end if
+          --suppressAlign="${singlePaired.sParams.sSuppressAlign}"
+          --best="${singlePaired.sParams.sBestOption.sBest}"
+          #if $singlePaired.sParams.sBestOption.sBest == "doBest":
+            --strata="${singlePaired.sParams.sBestOption.sdStrata}"
+            #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
+              --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.sdMaxBacktracks}"
+            #end if
+          #else:
+            #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
+              --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.snMaxBacktracks}"
+            #end if
+          #end if
+          --offrate="${singlePaired.sParams.sOffrate}"
+          --seed="${singlePaired.sParams.sSeed}"
+        #end if
+      #else:
+        --input1="${singlePaired.pInput1}"
+        --input2="${singlePaired.pInput2}"
+        --maxInsert="${singlePaired.pMaxInsert}"
+        --mateOrient="${singlePaired.pMateOrient}"
+        --params="${singlePaired.pParams.pSettingsType}"
+        #if $singlePaired.pParams.pSettingsType == "full":
+          --skip="${singlePaired.pParams.pSkip}"
+          --alignLimit="${singlePaired.pParams.pAlignLimit}"
+          --trimH="${singlePaired.pParams.pTrimH}"
+          --trimL="${singlePaired.pParams.pTrimL}"
+          #if $singlePaired.pParams.alignModeOption.alignMode == 'nMode'
+            --mismatchSeed="${singlePaired.pParams.alignModeOption.pMismatchSeed}"
+            --mismatchQual="${singlePaired.pParams.alignModeOption.pMismatchQual}"
+            --seedLen="${singlePaired.pParams.alignModeOption.pSeedLen}"
+            --rounding="${singlePaired.pParams.alignModeOption.pRounding}"
+          #else
+            --maxMismatches="${singlePaired.pParams.alignModeOption.maxMismatches}"
+          #end if
+          --minInsert="${singlePaired.pParams.pMinInsert}"
+          --forwardAlign="${singlePaired.pParams.pForwardAlign}"
+          --reverseAlign="${singlePaired.pParams.pReverseAlign}"
+          --tryHard="${singlePaired.pParams.pBestOption.pTryHardOption.pTryHard}"
+          --allValAligns="${singlePaired.pParams.pAllValAlignsOption.pAllValAligns}"
+          #if $singlePaired.pParams.pAllValAlignsOption.pAllValAligns == "noAllValAligns"
+            --valAlign="${singlePaired.pParams.pAllValAlignsOption.pValAlign}"
+          #end if
+          --suppressAlign="${singlePaired.pParams.pSuppressAlign}"
+          --best="${singlePaired.pParams.pBestOption.pBest}"
+          #if $singlePaired.pParams.pBestOption.pBest == "doBest":
+            --strata="${singlePaired.pParams.pBestOption.pdStrata}"
+            #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
+              --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
+              --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pdMaxBacktracks}"
+            #end if
+          #else:
+            #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
+              --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
+              --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pnMaxBacktracks}"
+            #end if
+          #end if
+          --offrate="${singlePaired.pParams.pOffrate}"
+          --seed="${singlePaired.pParams.pSeed}"
+        #end if
+      #end if
+      #if $save_mapping_stats
+        --output_mapping_stats="$mapping_stats"
+      #end if
+  </command>
+  <inputs>
+    <conditional name="refGenomeSource">
+      <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
+          <options from_data_table="bowtie_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference genome" />
+        <conditional name="indexParams">
+          <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index">
+            <option value="indexPreSet">Default</option>
+            <option value="indexFull">Set your own</option>
+          </param>
+          <when value="indexPreSet" />
+          <when value="indexFull">
+            <conditional name="autoBehavior">
+              <param name="autoB" type="select" label="Choose to use automatic or specified behavior for some parameters (-a)" help="Allows you to set --packed, --bmax, --bmaxdivn, and --dcv">
+                <option value="auto">Automatic behavior</option>
+                <option value="set">Set values (sets --noauto and allows others to be set)</option>
+              </param>
+              <when value="auto" />
+              <when value="set">
+                <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)" help="Packed representation saves memory but makes indexing 2-3 times slower">
+                  <option value="unpacked">Use regular representation</option>
+                  <option value="packed">Use packed representation</option>
+                </param>
+                <param name="bmax" type="integer" value="-1" label="Maximum number of suffixes allowed in a block (--bmax)" help="-1 for not specified. Must be at least 1" />
+                <param name="bmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block as a fraction of the length of the reference (--bmaxdivn)" />
+                <param name="dcv" type="integer" value="1024" min="3" label="The period for the difference-cover sample (--dcv)" help="A larger period yields less memory overhead, but may make suffix sorting slower, especially if repeats are present" />
+              </when>
+            </conditional>
+            <param name="nodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (with a very repetitive reference)">
+              <option value="dc">Use difference-cover sample</option>
+              <option value="nodc">Disable difference-cover sample</option>
+            </param>
+            <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)">
+              <option value="ref">Build all index files</option>
+              <option value="noref">Do not build paired-end alignment index files</option>
+            </param>
+            <param name="offrate" type="integer" value="5" min="0" label="The indexer will mark every 2^n Burrows-Wheeler rows with their corresponding location on the genome (-o)" help="Marking more rows makes reference-position lookups faster, but requires more memory to hold the annotations at runtime" />
+            <param name="ftab" type="integer" value="10" min="1" label="The size of the ftab lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab size is 4^(n+1) bytes" />
+            <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)">
+              <option value="no">Do not convert Ns</option>
+              <option value="yes">Convert Ns to As</option>
+            </param>
+            <param name="endian" type="select" label="Endianness to use when serializing integers to the index file (--big/--little)" help="Little is most appropriate for Intel- and AMD-based architecture">
+              <option value="little">Little</option>
+              <option value="big">Big</option>
+            </param>
+            <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" />
+          </when>  <!-- indexFull -->
+        </conditional>  <!-- indexParams -->
+      </when>  <!-- history -->
+    </conditional>  <!-- refGenomeSource -->
+    <conditional name="singlePaired">
+      <param name="sPaired" type="select" label="Is this library mate-paired?">
+        <option value="single">Single-end</option>
+        <option value="paired">Paired-end</option>
+      </param>
+      <when value="single">
+        <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
+        <conditional name="sParams">
+          <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
+            <option value="preSet">Commonly used</option>
+            <option value="full" selected="true">Full parameter list</option>
+          </param>
+          <when value="preSet" />
+          <when value="full">
+            <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
+            <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
+            <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
+            <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
+            <conditional name="alignModeOption">
+              <param name="alignMode" type="select" label="Alignment mode">
+                <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
+                <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
+              </param>
+              <when value="nMode">
+                <param name="sMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
+                <param name="sMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
+                <param name="sSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
+                <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)" help="Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way">
+                  <option value="round">Round to nearest 10</option>
+                  <option value="noRound">Do not round to nearest 10</option>
+                </param>
+              </when>
+              <when value="vMode">
+                <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
+              </when>
+            </conditional>
+            <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
+              <option value="forward">Align against the forward reference strand</option>
+              <option value="noForward">Do not align against the forward reference strand</option>
+            </param>
+            <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
+              <option value="reverse">Align against the reverse-complement reference strand</option>
+              <option value="noReverse">Do not align against the reverse-complement reference strand</option>
+            </param>
+            <conditional name="sBestOption">
+              <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option">
+                <option value="noBest">Do not use best</option>
+                <option value="doBest">Use best</option>
+              </param>
+              <when value="noBest">
+                <conditional name="sTryHardOption">
+                  <param name="sTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode">
+                    <option value="noTryHard">Do not try hard</option>
+                    <option value="doTryHard">Try hard</option>
+                  </param>
+                  <when value="noTryHard">
+                    <param name="snMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
+                  </when>
+                  <when value="doTryHard" />
+                </conditional>
+              </when>
+              <when value="doBest">
+                <param name="sdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)">
+                  <option value="noStrata">Do not use strata option</option>
+                  <option value="doStrata">Use strata option</option>
+                </param>
+                <conditional name="sTryHardOption">
+                  <param name="sTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode">
+                    <option value="noTryHard">Do not try hard</option>
+                    <option value="doTryHard">Try hard</option>
+                  </param>
+                  <when value="noTryHard">
+                    <param name="sdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
+                  </when>
+                  <when value="doTryHard" />
+                </conditional>
+              </when>
+            </conditional> <!-- bestOption -->
+            <conditional name="sAllValAlignsOption">
+              <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
+                <option value="noAllValAligns">Do not report all valid alignments</option>
+                <option value="doAllValAligns">Report all valid alignments</option>
+              </param>
+              <when value="noAllValAligns">
+                <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" />
+              </when>
+              <when value="doAllValAligns" />
+            </conditional>
+            <param name="sSuppressAlign" type="integer" value="1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" />
+            <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" />
+            <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
+            <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
+            <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
+          </when> <!-- full -->
+        </conditional> <!-- sParams -->
+      </when> <!-- single -->
+      <when value="paired">
+        <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
+        <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
+            <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
+               <column name="name" index="0"/>
+               <column name="value" index="0"/>
+               <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
+           </options>
+        </param>
+        <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
+        <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)">
+          <option value="fr">FR (for Illumina)</option>
+          <option value="rf">RF</option>
+          <option value="ff">FF (for SOLiD)</option>
+        </param>
+        <conditional name="pParams">
+          <param name="pSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
+            <option value="preSet">Commonly used</option>
+            <option value="full">Full parameter list</option>
+          </param>
+          <when value="preSet" />
+          <when value="full">
+            <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
+            <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />
+            <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
+            <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
+            <conditional name="alignModeOption">
+              <param name="alignMode" type="select" label="Alignment mode">
+                <option value="nMode" selected="true">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
+                <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
+              </param>
+              <when value="nMode">
+                <param name="pMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
+                <param name="pMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
+                <param name="pSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
+                <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)" help="Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way">
+                  <option value="round">Round to nearest 10</option>
+                  <option value="noRound">Do not round to nearest 10</option>
+                </param>
+              </when>
+              <when value="vMode">
+                <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
+              </when>
+            </conditional>
+            <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
+            <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
+              <option value="forward">Align against the forward reference strand</option>
+              <option value="noForward">Do not align against the forward reference strand</option>
+            </param>
+            <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
+              <option value="reverse">Align against the reverse-complement reference strand</option>
+              <option value="noReverse">Do not align against the reverse-complement reference strand</option>
+            </param>
+            <conditional name="pBestOption">
+              <param name="pBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option">
+                <option value="noBest">Do not use best</option>
+                <option value="doBest">Use best</option>
+              </param>
+              <when value="noBest">
+                <conditional name="pTryHardOption">
+                  <param name="pTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode">
+                    <option value="noTryHard">Do not try hard</option>
+                    <option value="doTryHard">Try hard</option>
+                  </param>
+                  <when value="noTryHard">
+                    <param name="pMaxAlignAttempt" type="integer" value="100" min="1" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" />
+                    <param name="pnMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
+                  </when>
+                  <when value="doTryHard" />
+                </conditional>
+              </when>
+              <when value="doBest">
+                <param name="pdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)">
+                  <option value="noStrata">Do not use strata option</option>
+                  <option value="doStrata">Use strata option</option>
+                </param>
+                <conditional name="pTryHardOption">
+                  <param name="pTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode">
+                    <option value="noTryHard">Do not try hard</option>
+                    <option value="doTryHard">Try hard</option>
+                  </param>
+                  <when value="noTryHard">
+                    <param name="pMaxAlignAttempt" type="integer" value="100" min="1" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" />
+                    <param name="pdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
+                  </when>
+                  <when value="doTryHard" />
+                </conditional>
+              </when>
+            </conditional>
+            <conditional name="pAllValAlignsOption">
+              <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
+                <option value="noAllValAligns">Do not report all valid alignments</option>
+                <option value="doAllValAligns">Report all valid alignments</option>
+              </param>
+              <when value="noAllValAligns">
+                <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" />
+              </when>
+              <when value="doAllValAligns" />
+            </conditional>
+            <param name="pSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" />
+            <param name="pMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" />
+            <param name="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
+            <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
+            <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
+          </when> <!-- full -->
+        </conditional> <!-- pParams -->
+      </when> <!-- paired -->
+    </conditional> <!-- singlePaired -->
+    <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" />
+    <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" />
+  </inputs>
+  <outputs>
+    <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
+      <actions>
+        <conditional name="refGenomeSource.genomeSource">
+          <when value="indexed">
+            <action type="metadata" name="dbkey">
+              <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
+                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+              </option>
+            </action>
+          </when>
+          <when value="history">
+            <action type="metadata" name="dbkey">
+              <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+            </action>
+          </when>
+        </conditional>
+      </actions>
+    </data>
+    <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
+      <filter>save_mapping_stats is True</filter>
+    </data>
+    <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
+      <filter>((
+          singlePaired['sPaired'] == "single" and
+          singlePaired['sParams']['sSettingsType'] == "full" and
+          singlePaired['sParams']['sMaxFile'] is True
+        ) or (
+          singlePaired['sPaired'] == "paired" and
+          singlePaired['pParams']['pSettingsType'] == "full" and
+          singlePaired['pParams']['pMaxFile'] is True
+        ))
+      </filter>
+      <actions>
+        <conditional name="singlePaired.sPaired">
+          <when value="single">
+            <action type="format">
+              <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
+            </action>
+          </when>
+          <when value="paired">
+            <action type="format">
+              <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
+            </action>
+          </when>
+        </conditional>
+      </actions>
+    </data>
+    <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
+      <filter>singlePaired['sPaired'] == "paired"</filter>
+      <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
+      <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
+      <actions>
+        <conditional name="singlePaired.sPaired">
+          <when value="single">
+            <action type="format">
+              <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
+            </action>
+          </when>
+          <when value="paired">
+            <action type="format">
+              <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
+            </action>
+          </when>
+        </conditional>
+      </actions>
+    </data>
+    <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
+      <filter>
+        ((
+          singlePaired['sPaired'] == "single" and
+          singlePaired['sParams']['sSettingsType'] == "full" and
+          singlePaired['sParams']['sUnmappedFile'] is True
+        ) or (
+          singlePaired['sPaired'] == "paired" and
+          singlePaired['pParams']['pSettingsType'] == "full" and
+          singlePaired['pParams']['pUnmappedFile'] is True
+        ))
+      </filter>
+      <actions>
+        <conditional name="singlePaired.sPaired">
+          <when value="single">
+            <action type="format">
+              <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
+            </action>
+          </when>
+          <when value="paired">
+            <action type="format">
+              <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
+            </action>
+          </when>
+        </conditional>
+      </actions>
+    </data>
+    <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
+      <filter>singlePaired['sPaired'] == "paired"</filter>
+      <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
+      <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
+      <actions>
+        <conditional name="singlePaired.sPaired">
+          <when value="single">
+            <action type="format">
+              <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
+            </action>
+          </when>
+          <when value="paired">
+            <action type="format">
+              <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
+            </action>
+          </when>
+        </conditional>
+      </actions>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <!--
+      Bowtie command:
+      bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
+      sort bowtie_out6_u.sam > bowtie_out6.sam
+      -p is the number of threads. You need to replace the + with 2 dashes.
+      chrM_base needs to be the base location/name of the index files.
+      -->
+      <param name="genomeSource" value="indexed" />
+      <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
+      <param name="index" value="equCab2chrM" />
+      <param name="sPaired" value="single" />
+      <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
+      <param name="sSettingsType" value="preSet" />
+      <param name="suppressHeader" value="true" />
+      <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True">
+        <metadata name="dbkey" value="equCab2" />
+      </output>
+    </test>
+    <test>
+      <!--
+      Bowtie command:
+      bowtie-build -f test-data/phiX.fasta phiX_base
+      bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 +best +un bowtie_out8_u.fastq phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out7_u.sam
+      sort bowtie_out7_u.sam > bowtie_out7.sam
+      sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
+      sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
+      Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
+      -p is the number of threads. You need to replace the + with 2 dashes.
+      The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
+      chrM_base is the index files' location/base name.
+      -->
+      <param name="genomeSource" value="history" />
+      <param name="ownFile" value="phiX.fasta" />
+      <param name="indexSettings" value="indexPreSet" />
+      <param name="sPaired" value="paired" />
+      <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
+      <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
+      <param name="pMaxInsert" value="1000" />
+      <param name="pMateOrient" value="ff" />
+      <param name="pSettingsType" value="full" />
+      <param name="pSkip" value="0" />
+      <param name="pAlignLimit" value="-1" />
+      <param name="pTrimH" value="0" />
+      <param name="pTrimL" value="0" />
+      <param name="alignMode" value="nMode" />
+      <param name="pMismatchSeed" value="2" />
+      <param name="pMismatchQual" value="70" />
+      <param name="pSeedLen" value="28" />
+      <param name="pRounding" value="round" />
+      <param name="pMinInsert" value="0" />
+      <param name="pMaxAlignAttempt" value="100" />
+      <param name="pForwardAlign" value="forward" />
+      <param name="pReverseAlign" value="reverse" />
+      <param name="pTryHard" value="noTryHard" />
+      <param name="pValAlign" value="1" />
+      <param name="pAllValAligns" value="noAllValAligns" />
+      <param name="pSuppressAlign" value="-1" />
+      <param name="pUnmappedFile" value="true" />
+      <param name="pMaxFile" value="false" />
+      <param name="pBest" value="doBest" />
+      <param name="pdMaxBacktracks" value="800" />
+      <param name="pdStrata" value="noStrata" />
+      <param name="pOffrate" value="-1" />
+      <param name="pSeed" value="-1" />
+      <param name="suppressHeader" value="true" />
+      <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
+      <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" />
+      <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" />
+    </test>
+    <!-- start testing of non-sanger variant fastq reads -->
+    <test>
+      <param name="genomeSource" value="history" />
+      <param name="ownFile" value="phiX.fasta" />
+      <param name="indexSettings" value="indexPreSet" />
+      <param name="sPaired" value="paired" />
+      <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" />
+      <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" />
+      <param name="pMaxInsert" value="1000" />
+      <param name="pMateOrient" value="ff" />
+      <param name="pSettingsType" value="full" />
+      <param name="pSkip" value="0" />
+      <param name="pAlignLimit" value="-1" />
+      <param name="pTrimH" value="0" />
+      <param name="pTrimL" value="0" />
+      <param name="alignMode" value="nMode" />
+      <param name="pMismatchSeed" value="2" />
+      <param name="pMismatchQual" value="70" />
+      <param name="pSeedLen" value="28" />
+      <param name="pRounding" value="round" />
+      <param name="pMinInsert" value="0" />
+      <param name="pMaxAlignAttempt" value="100" />
+      <param name="pForwardAlign" value="forward" />
+      <param name="pReverseAlign" value="reverse" />
+      <param name="pTryHard" value="noTryHard" />
+      <param name="pValAlign" value="1" />
+      <param name="pAllValAligns" value="noAllValAligns" />
+      <param name="pSuppressAlign" value="-1" />
+      <param name="pUnmappedFile" value="true" />
+      <param name="pMaxFile" value="false" />
+      <param name="pBest" value="doBest" />
+      <param name="pdMaxBacktracks" value="800" />
+      <param name="pdStrata" value="noStrata" />
+      <param name="pOffrate" value="-1" />
+      <param name="pSeed" value="-1" />
+      <param name="suppressHeader" value="true" />
+      <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
+      <output name="output_unmapped_reads_l" ftype="fastqillumina" file="bowtie_out8_1.fastqillumina.sorted" sort="True" />
+      <output name="output_unmapped_reads_r" ftype="fastqillumina" file="bowtie_out8_2.fastqillumina.sorted" sort="True" />
+    </test>
+    <test>
+      <param name="genomeSource" value="history" />
+      <param name="ownFile" value="phiX.fasta" />
+      <param name="indexSettings" value="indexPreSet" />
+      <param name="sPaired" value="paired" />
+      <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" />
+      <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" />
+      <param name="pMaxInsert" value="1000" />
+      <param name="pMateOrient" value="ff" />
+      <param name="pSettingsType" value="full" />
+      <param name="pSkip" value="0" />
+      <param name="pAlignLimit" value="-1" />
+      <param name="pTrimH" value="0" />
+      <param name="pTrimL" value="0" />
+      <param name="alignMode" value="nMode" />
+      <param name="pMismatchSeed" value="2" />
+      <param name="pMismatchQual" value="70" />
+      <param name="pSeedLen" value="28" />
+      <param name="pRounding" value="round" />
+      <param name="pMinInsert" value="0" />
+      <param name="pMaxAlignAttempt" value="100" />
+      <param name="pForwardAlign" value="forward" />
+      <param name="pReverseAlign" value="reverse" />
+      <param name="pTryHard" value="noTryHard" />
+      <param name="pValAlign" value="1" />
+      <param name="pAllValAligns" value="noAllValAligns" />
+      <param name="pSuppressAlign" value="-1" />
+      <param name="pUnmappedFile" value="true" />
+      <param name="pMaxFile" value="false" />
+      <param name="pBest" value="doBest" />
+      <param name="pdMaxBacktracks" value="800" />
+      <param name="pdStrata" value="noStrata" />
+      <param name="pOffrate" value="-1" />
+      <param name="pSeed" value="-1" />
+      <param name="suppressHeader" value="true" />
+      <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
+      <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" />
+      <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" />
+    </test>
+    <!-- end testing of non-sanger variant fastq reads -->
+    <test>
+      <!--
+      Bowtie command:
+      bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam
+      sort bowtie_out9_u.sam > bowtie_out9.sam
+      -p is the number of threads. You need to replace the + with 2 dashes.
+      chrM_base is the index files' location/base name.
+      -->
+      <param name="genomeSource" value="indexed" />
+      <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
+      <param name="index" value="equCab2chrM" />
+      <param name="sPaired" value="single" />
+      <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
+      <param name="sSettingsType" value="full" />
+      <param name="sSkip" value="0" />
+      <param name="sAlignLimit" value="-1" />
+      <param name="sTrimH" value="0" />
+      <param name="sTrimL" value="0" />
+      <param name="alignMode" value="nMode" />
+      <param name="sMismatchSeed" value="2" />
+      <param name="sMismatchQual" value="70" />
+      <param name="sSeedLen" value="28" />
+      <param name="sRounding" value="round" />
+      <param name="sForwardAlign" value="forward" />
+      <param name="sReverseAlign" value="reverse" />
+      <param name="sTryHard" value="doTryHard" />
+      <param name="sValAlign" value="1" />
+      <param name="sAllValAligns" value="noAllValAligns" />
+      <param name="sSuppressAlign" value="-1" />
+      <param name="sUnmappedFile" value="false" />
+      <param name="sMaxFile" value="false" />
+      <param name="sBest" value="noBest" />
+      <param name="sOffrate" value="-1" />
+      <param name="sSeed" value="-1" />
+      <param name="suppressHeader" value="true" />
+      <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True">
+        <metadata name="dbkey" value="equCab2" />
+      </output>
+    </test>
+    <test>
+      <!--
+      Bowtie command:
+      bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
+      bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam
+      sort bowtie_out10_u.sam > bowtie_out10.sam
+      -p is the number of threads. You need to replace the + with 2 dashes.
+      chrM_base is the index files' location/base name.
+      -->
+      <param name="genomeSource" value="history" />
+      <param name="ownFile" value="phiX.fasta" />
+      <param name="indexSettings" value="indexFull" />
+      <param name="autoB" value="auto" />
+      <param name="nodc" value="dc" />
+      <param name="noref" value="ref" />
+      <param name="offrate" value="5" />
+      <param name="ftab" value="10" />
+      <param name="ntoa" value="no" />
+      <param name="endian" value="little" />
+      <param name="seed" value="-1" />
+      <param name="sPaired" value="paired" />
+      <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
+      <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
+      <param name="pMaxInsert" value="1000" />
+      <param name="pMateOrient" value="ff" />
+      <param name="pSettingsType" value="preSet" />
+      <param name="suppressHeader" value="true" />
+      <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
+    </test>
+    <test>
+      <!--
+      Bowtie command:
+      bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
+      bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam
+      sort bowtie_out10_u.sam > bowtie_out10.sam
+      -p is the number of threads. You need to replace the + with 2 dashes.
+      chrM_base is the index files' location/base name.
+      -->
+      <param name="genomeSource" value="history" />
+      <param name="ownFile" value="phiX.fasta" />
+      <param name="indexSettings" value="indexFull" />
+      <param name="autoB" value="auto" />
+      <param name="nodc" value="dc" />
+      <param name="noref" value="ref" />
+      <param name="offrate" value="5" />
+      <param name="ftab" value="10" />
+      <param name="ntoa" value="no" />
+      <param name="endian" value="little" />
+      <param name="seed" value="-1" />
+      <param name="sPaired" value="paired" />
+      <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
+      <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
+      <param name="pMaxInsert" value="1000" />
+      <param name="pMateOrient" value="ff" />
+      <param name="pSettingsType" value="preSet" />
+      <param name="suppressHeader" value="true" />
+      <param name="save_mapping_stats" value="true" />
+      <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
+      <output name="mapping_stats" ftype="txt" file="bowtie_out11.txt" sort="True" />
+    </test>
+  </tests>
+
+  <help>
+
+**What it does**
+
+Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
+
+.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
+
+------
+
+**Know what you are doing**
+
+.. class:: warningmark
+
+There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
+
+ .. __: http://bowtie-bio.sourceforge.net/index.shtml
+
+------
+
+**Input formats**
+
+Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
+
+------
+
+**A Note on Built-in Reference Genomes**
+
+The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
+
+------
+
+**Outputs**
+
+The output is in SAM format, and has the following columns::
+
+    Column  Description
+  --------  --------------------------------------------------------
+   1 QNAME  Query (pair) NAME
+   2 FLAG   bitwise FLAG
+   3 RNAME  Reference sequence NAME
+   4 POS    1-based leftmost POSition/coordinate of clipped sequence
+   5 MAPQ   MAPping Quality (Phred-scaled)
+   6 CIGAR  extended CIGAR string
+   7 MRNM   Mate Reference sequence NaMe ('=' if same as RNAME)
+   8 MPOS   1-based Mate POSition
+   9 ISIZE  Inferred insert SIZE
+  10 SEQ    query SEQuence on the same strand as the reference
+  11 QUAL   query QUALity (ASCII-33 gives the Phred base quality)
+  12 OPT    variable OPTional fields in the format TAG:VTYPE:VALUE
+
+The flags are as follows::
+
+    Flag  Description
+  ------  -------------------------------------
+  0x0001  the read is paired in sequencing
+  0x0002  the read is mapped in a proper pair
+  0x0004  the query sequence itself is unmapped
+  0x0008  the mate is unmapped
+  0x0010  strand of the query (1 for reverse)
+  0x0020  strand of the mate
+  0x0040  the read is the first read in a pair
+  0x0080  the read is the second read in a pair
+  0x0100  the alignment is not primary
+
+It looks like this (scroll sideways to see the entire example)::
+
+  QNAME	FLAG	RNAME	POS	MAPQ	CIAGR	MRNM	MPOS	ISIZE	SEQ	QUAL	OPT
+  HWI-EAS91_1_30788AAXX:1:1:1761:343	4	*	0	0	*	*	0	0	AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG	hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
+  HWI-EAS91_1_30788AAXX:1:1:1578:331	4	*	0	0	*	*	0	0	GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG	hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
+
+-------
+
+**Bowtie settings**
+
+All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.
+
+------
+
+**Bowtie parameter list**
+
+This is an exhaustive list of Bowtie options:
+
+For indexing (bowtie-build)::
+
+  -a                 No auto behavior. Disable the default behavior where bowtie automatically 
+                     selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according 
+                     to the memory available. [off]
+  --packed           Packing. Use a packed representation for DNA strings. [auto] 
+  --bmax INT         Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
+  --bmaxdivn INT     Suffix maximum fraction. The maximum number of suffixes allowed in a block 
+                     expressed as a fraction of the length of the reference. [4]
+  --dcv INT          Difference-cover sample. Use INT as the period for the difference-cover 
+                     sample. [1024]
+  --nodc INT         No difference-cover sample. Disable the difference-cover sample. [off]
+  -r                 No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions 
+                     of the index. Used only for paired-end alignment. [off]
+  -o                 Offrate. How many Burrows-Wheeler rows get marked by the indexer. The 
+                     indexer will mark every 2^INT rows. The marked rows correspond to rows on 
+                     the genome. [5]
+  -t INT             The ftab lookup table used to calculate an initial Burrows-Wheeler range 
+                     with respect to the first INT characters of the query. Ftab size is 4^(INT+1) 
+                     bytes. [10]
+  --ntoa             N conversion. Convert Ns to As before building the index. Otherwise, Ns are 
+                     simply excluded from the index and Bowtie will not find alignments that 
+                     overlap them. [off]
+  --big              Endianness. Endianness to use when serializing integers to the index file. [off]
+  --little           Endianness. [--little]
+  --seed INT         Random seed. Use INT as the seed for the pseudo-random number generator. [off]
+
+For aligning (bowtie)::
+
+  -s INT             Skip. Do not align the first INT reads or pairs in the input. [off]
+  -u INT             Align limit. Only align the first INT reads/pairs from the input. [no limit]
+  -5 INT             High-quality trim. Trim INT bases from the high-quality (left) end of each 
+                     read before alignment. [0]
+  -3 INT             Low-quality trim. Trim INT bases from the low-quality (right) end of each 
+                     read before alignment. [0]
+  -n INT             Mismatch seed. Maximum number of mismatches permitted in the seed (defined 
+                     with seed length option). Can be 0, 1, 2, or 3. [2]
+  -e INT             Mismatch quality. Maximum permitted total of quality values at mismatched 
+                     read positions. Bowtie rounds quality values to the nearest 10 and saturates 
+                     at 30. [70]
+  -l INT             Seed length. The number of bases on the high-quality end of the read to 
+                     which the -n ceiling applies. Must be at least 5. [28]
+  --nomaqround       Suppress Maq rounding. Values are internally rounded to the nearest 10 and 
+                     saturate at 30. This options turns off that rounding. [off] 
+  -v INT             Maq- or SOAP-like alignment policy. This option turns off the default 
+                     Maq-like alignment policy in favor of a SOAP-like one. End-to-end alignments 
+                     with at most INT mismatches. [off]
+  -I INT             Minimum insert. The minimum insert size for valid paired-end alignments. 
+                     Does checking on untrimmed reads if -5 or -3 is used. [0]
+  -X INT             Maximum insert. The maximum insert size for valid paired-end alignments. 
+                     Does checking on untrimmed reads if -5 or -3 is used. [250]
+  --fr               Mate orientation. The upstream/downstream mate orientations for a valid 
+                     paired-end alignment against the forward reference strand. [--fr]
+  --rf               Mate orientation. [off]
+  --ff               Mate orientation. [off]
+  --pairtries INT    Maximum alignment attempts for paired-end data. [100] 
+  --nofw             No forward aligning. Choosing this option means that Bowtie will not attempt 
+                     to align against the forward reference strand. [off]
+  --norc             No reverse-complement aligning. Setting this will mean that Bowtie will not 
+                     attempt to align against the reverse-complement reference strand. [off]
+  --un FILENAME      Write all reads that could not be aligned to file [off]
+  --max FILENAME     Write all reads with a number of valid alignments exceeding the limit
+                     set with the -m option to file [off]
+  --maxbts INT       Maximum backtracks. The maximum number of backtracks permitted when aligning 
+                     a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
+  -y                 Try hard. Try as hard as possible to find valid alignments when they exist, 
+                     including paired-end alignments. [off]
+  --chunkmbs INT     Thread memory. The number of megabytes of memory a given thread is given to 
+                     store path descriptors in --best mode. [32]
+  -k INT             Valid alignments. The number of valid alignments per read or pair. [off] 
+  -a                 All valid alignments. Choosing this means that all valid alignments per read 
+                     or pair will be reported. [off]
+  -m INT             Suppress alignments. Suppress all alignments for a particular read or pair 
+                     if more than INT reportable alignments exist for it. [no limit]
+  --best             Best mode. Make Bowtie guarantee that reported singleton alignments are 
+                     "best" in terms of stratum (the number of mismatches) and quality values at 
+                     mismatched position. [off]
+  --strata           Best strata. When running in best mode, report alignments that fall into the 
+                     best stratum if there are ones falling into more than one. [off]
+  -o INT             Offrate override. Override the offrate of the index with INT. Some row 
+                     markings are discarded when index read into memory. INT must be greater than 
+                     the value used to build the index (default: 5). [off]
+  --seed INT         Random seed. Use INT as the seed for the pseudo-random number generator. [off]
+  --snpphred INT     Use INT as the SNP penalty for decoding colorspace alignments. True ratio of 
+                     SNPs per base in the subject genome. [see --snpfrac]
+  --snpfrac DEC      Use DEC as the estimated ratio of SNPs per base when decoding colorspace 
+                     alignments. [0.001]
+  --col-keepends     Keep the extreme-end nucleotides and qualities when decoding colorspace 
+                     alignments. [off]
+
+    </help>
+    <citations>
+        <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
+    </citations>
+</tool>
diff -r dfb484045b7e -r ba39548ca273 bowtie_genome_wrapper/tool-data/bowtie_indices.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie_genome_wrapper/tool-data/bowtie_indices.loc.sample	Mon Apr 04 14:07:23 2022 +0000
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
+#
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/bowtie/hg18/,
+#then the bowtie_indices.loc entry would look like this:
+#
+#hg18	hg18	hg18	/depot/data2/galaxy/bowtie/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 hg18.3.ebwt
+#...etc...
+#
+#Your bowtie_indices.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+hg18canon			hg18	hg18 Canonical	/depot/data2/galaxy/bowtie/hg18/hg18canon
+hg18full			hg18	hg18 Full		/depot/data2/galaxy/bowtie/hg18/hg18full
+/orig/path/hg19	hg19	hg19			/depot/data2/galaxy/bowtie/hg19/hg19
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r dfb484045b7e -r ba39548ca273 bowtie_genome_wrapper/tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie_genome_wrapper/tool_data_table_conf.xml.sample	Mon Apr 04 14:07:23 2022 +0000
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of indexes in the Bowtie mapper format -->
+    <table name="bowtie_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="/home/jack/projects/tools_for_Galaxy/ribogalaxy-toolshed/tools/bowtie_genome_wrapper/tool-data/bowtie_indices.loc.sample" />
+    </table>
+</tables>