--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/orthologs/ucsb_hamster/lib/wisecfg/worm.gf	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,898 @@
+# Splice sites and intron regions information for GeneWise-21
+# Tue Jan 14 16:50:39 IST 1997
+# Created by Mor Amitai (mor@compugen.co.il)
+# dataset : C.Elegans data from the Sanger Centre. given by Ewan Birney
+# preliminary results. For Ewan's use only
+# Consensi are read from top down. The value, for a sequence,
+# is the number in the line of the first consensus that
+# matches the sequence.
+# Note: the set of sequences that are represented by a consensus
+# are all the sequences that match this consensus and none of the
+# previous consensi
+#
+# the numbers in types 5SS, 3SS, CDS, and the emissions are the number of
+# occurrences of each sequence in the database. 
+# In case of a consensus this is the number of occurrences of sequences 
+# that are represented by the consensus in the database divided by the 
+# number of sequences that are represented by the consensus.
+# *stay_prob is the probability of the transition from the state to itself.
+# No_Spacer_Prob is the probability of transition from Pyrimidine directly 
+# to 3SS (no spacer).
+type 5SS
+center 3
+phase all
+begin consensus
+AAAGTGAGTT 61
+GATGTAAGTT 51
+A-TGTAAGTT 28.25
+-AAGTGAGTT 28
+-AAGTAAGTT 24.75
+A-AGTGAGTT 22.3333
+AA-GTGAGTT 22
+TTGGT-AGTT 20.25
+AAGGTTTGT- 19.75
+-AGGTAATTT 19.25
+T-TGTAAGTT 19
+A-AGTAAGTT 18.3333
+AT-GTGAGTT 17
+GA-GTGAGTT 17
+-AGGTAAATT 16.75
+A-GGTTAGTT 16.75
+AAGGTAA-AA 13.5
+AAGGTAA-AT 13.25
+T--GTAAGTT 10.4
+-A-GTAAGTT 11.1429
+-T-GTAAGTT 10.3
+--GGTGAGTT 10.1667
+--AGTGAGTT 9.22222
+-C-GTAAGTT 8.8
+-T-GTGAGTT 8.33333
+--GGTTAGTT 8
+AA-GTAAG-A 7.73333
+-AGGTTTGT- 7.41667
+-AGGTGAG-A 7.0625
+CAGGTAA-A- 6.5625
+AA-GTA-GTT 6.5
+-A-GTTAGTT 6.41667
+-G-GTAAGTT 6.4
+-AGGTATTT- 6
+AA-GTAAG-T 5.54545
+-AGGTAAA-A 5.5
+-AAGTAAGT- 5.45455
+-A-GTAAGAA 5.36364
+--GGTATGTT 5.26667
+-TGGTGAGT- 5.25
+-AAGTGAGT- 5.16667
+-ATGTAAGT- 5.09091
+AAGGT-AGT- 5.09091
+-AGGTGAGA- 4.75
+-TGGTAAGT- 4.58333
+-AGGTAATT- 4.5
+-AGGTATGT- 4.41667
+--GGTAAGAT 4.28571
+--GGTAAGAA 4.25
+---GTGAGTT 4.2
+--GGTTGGTT 3.5625
+-AGGTTTGA- 3.4375
+A--GTAAGT- 3.28571
+AAGGTAT-A- 3.125
+-AGGT-AGT- 2.61111
+--GGTAA-TT 2.575
+T--GTAAGT- 2.5
+--GGTT-GTT 2.42857
+-A-GTA-GTT 2.42424
+-AGGTAAG-- 2.23529
+---GTTAGTT 2.16667
+---GTAAGAT 2.04444
+A--GTGAGT- 1.97436
+A--GTA-GTT 1.9697
+-AGGTA--TT 1.84375
+-AGGTAA-A- 1.82143
+C--GTAAGT- 1.80556
+AA-GTGAG-- 1.7619
+AAGGTA---A 1.7234
+--GGTGAG-A 1.64286
+G--GTAAGT- 1.63889
+T--GTA-GTT 1.63636
+-TGGTAAG-- 1.625
+CAGGTA---A 1.54902
+--GGTGAG-T 1.54762
+AAGGTA---T 1.52632
+AAGGTT-G-- 1.46
+AA-GT-A-TT 1.45833
+CAGGTA---T 1.42857
+A--GTAAGA- 1.37838
+---GTGAGTG 1.35897
+-AGGTG-GT- 1.16667
+--GGTATG-A 1.07407
+-AGGTT-TT- 0.952381
+-A-GTAAG-- 0.794118
+-AGGTAA--- 0.790698
+--GGTA-GT- 0.734375
+-A-GT-AGT- 0.731183
+--GGT-AGT- 0.696629
+-AGGTA-G-- 0.66
+---GTAAG-A 0.643478
+-AGGT-AG-- 0.59375
+--GGTA-G-T 0.58871
+--GGTAA--A 0.583333
+AA-GTA-G-- 0.555556
+-AGGTAT--- 0.532787
+-A-GT--GTT 0.525
+--GGTT-GT- 0.515873
+-A-GTGAG-- 0.481481
+--GGTAA-A- 0.466667
+-AGGT-A-T- 0.466667
+-A-GTAA-T- 0.407407
+---GTGAG-A 0.4
+-AGGTTT--- 0.39
+A-GGTA--T- 0.362319
+---GTATGT- 0.326797
+---GTAAG-- 0.221854
+-AAGTA--A- 0.219298
+---GT--GTT 0.209402
+--GGTA-G-- 0.1875
+--GGT-AG-- 0.155556
+--GGTA--T- 0.15493
+-AGGT---A- 0.1375
+A--GTAA--- 0.116838
+-A-GTA--T- 0.109053
+---GTT-GT- 0.0944444
+-AAGT-A--- 0.0761905
+---GT--GAT 0.0670886
+-AGGT----- 0.0541575
+--GGTA---- 0.0411523
+---GTA-G-- 0.037037
+---GTAA--- 0.0363757
+---GT-A-T- 0.0309423
+A--GT----T 0.0201761
+---GTG-G-- 0.0192593
+---GT--G-- 0.00953471
+---GT---T- 0.0090535
+---GT----- 0.00283019
+end consensus
+type 5SS
+center 3
+phase 0
+begin consensus
+GATGTAAGTT 43
+AA-GTGAGTT 15.25
+A-TGTAAGTT 14.75
+AAGGTTTGT- 13.5
+GA-GTGAGTT 11.25
+AAGGTAA-TT 11
+CAGGTAA-TT 10.25
+A-AGTAAGTT 9.5
+-AGGTTAGTT 9
+-TGGTGAGTT 9
+AAGGTAA-AT 8.75
+GC-GTAAGTT 8.5
+T-TGTAAGTT 8.5
+-AGGTATTTT 7.75
+A--GTGAGTT 5.90909
+--GGTAAGTT 4.92308
+-A-GTAAGTT 5.25
+--GGTTAGTT 4.66667
+AAGGTAA--A 4.5
+-AGGTTTGT- 4.25
+--GGTGAGTT 4.125
+-A-GTAAGAA 3.73333
+AAGGTT-GT- 3.54545
+-AGGTGAGA- 3.5
+-ATGTAAGT- 3.41667
+--GGTATGTT 3.3125
+GAGGTAA-T- 3.26667
+CA-GT-AGTT 3.2
+-AGGTAAAA- 3.14286
+-TGGTGAGT- 2.75
+CAGGTAA--A 2.71429
+-AGGTGAG-A 2.66667
+-ATGTA-GTT 2.66667
+AAGGTAT-T- 2.5
+AAGGTT-GA- 2.4375
+CAGGTAT-T- 2.35714
+---GTAAGTT 2.29167
+--GGTAAGAT 2.26667
+---GTGAGTT 1.7
+-A-GT-AGTT 1.47619
+AA-GTAAG-- 1.40816
+-AGGTGAG-- 1.40625
+--TGTAAGT- 1.38889
+--GGTAAG-A 1.32075
+--GGTT-GTT 1.21429
+-A-GTGAGT- 1.16667
+--GGTAA-TT 1.12821
+AAGGTAT--- 1.125
+A--GTA-GTT 1.09756
+CAGGTA---T 1.05556
+AAGGTA---T 1
+CAGGT--GT- 1
+GAGGTA--T- 0.956522
+A-GGTA-GT- 0.871795
+AAGGT-A-T- 0.866667
+CAGGTA--A- 0.857143
+GA-GTAAG-- 0.829787
+-AGGTTTG-- 0.818182
+A--GTAAGA- 0.809524
+--GGTGAG-A 0.795455
+-A-GTGAGA- 0.75
+-TGGTA-G-T 0.74
+GAGGTAT--- 0.729167
+--GGT-AGTG 0.695652
+--AGTAAG-A 0.607843
+-AGGTTTT-- 0.546875
+---GT-AGTT 0.488095
+---GTAAGT- 0.45
+---GTA-GTT 0.415929
+---GTGAGT- 0.413793
+AAGGTA---- 0.40566
+CAGGTA---- 0.375
+GAGGTA---- 0.367188
+-AGGTT-G-- 0.337838
+--GGT-AG-T 0.289855
+-A-GT-A-TT 0.28655
+---GTAAG-T 0.282051
+--GGTAA-T- 0.264957
+--GGTATG-- 0.264368
+AA-GT--GT- 0.259887
+--GGTAA-A- 0.244186
+A--GTAA--A 0.212644
+-ATGTA-G-- 0.171123
+-A-GTGA--A 0.15493
+--GGT--GT- 0.107914
+-AGGTT---- 0.0951684
+--GGTA-G-- 0.0941176
+-A-GT-AG-- 0.0711297
+--GGTA--T- 0.0663812
+-AAGTA---- 0.0590164
+---GTT-GT- 0.0509259
+--TGTAA--- 0.0499376
+-AGGTG---- 0.0425532
+--GGTA---- 0.0223793
+---GT-AG-- 0.0221502
+---GTA-G-- 0.0173088
+---GT-A-T- 0.0157715
+A--GT----T 0.0103437
+---GT--G-- 0.00594251
+---GT---T- 0.00467836
+---GT----- 0.00116399
+end consensus
+type 5SS
+center 3
+phase 1
+begin consensus
+A-AGTGAGTT 9.25
+TT-GTAAGTT 9.25
+-TGGTGAGTT 8.25
+A-TGTAAGTT 8
+-T-GTAAGTT 5.09091
+--AGTGAGTT 4.33333
+A--GTAAGTT 3.66667
+--GGTTAGTT 3.125
+-AGGTAA-TT 2.66667
+TTGGTAAG-- 2.2
+--GGTTTGTT 2.1875
+CA-GTAAGT- 2.06667
+T--GTAAGTT 2.81818
+--GGTGAGTA 1.9375
+---GTGAGTT 1.70455
+-AGGTAA-A- 1.17188
+A--GTAAGT- 1.16667
+--AGT-AGTT 1
+-TGGTAAG-- 0.928571
+AA-GTAAG-- 0.909091
+--GGTA-GTT 0.884615
+---GTAAGTA 0.878049
+--GGTGAGA- 0.796875
+A--GTGAGT- 0.727273
+AAGGTAT--- 0.714286
+-TGGTT-GT- 0.696429
+--AGTA-GTT 0.6875
+---GTAAGAT 0.679245
+-AGGTT-GT- 0.660714
+---GTAAGT- 0.521739
+--GGTATG-A 0.516667
+-AGGTAA--- 0.403846
+--GGTGAG-- 0.342105
+--GGTA--TT 0.316384
+A--GT--GTT 0.283333
+---GTAAG-A 0.245283
+-AGGTA-G-- 0.228758
+-TGGTA-G-- 0.207317
+-A-GTGAG-- 0.19883
+-AGGTT-G-- 0.1875
+-TGGTAA--- 0.183333
+-AGGTG--T- 0.130802
+-AGGTA---- 0.109091
+---GT-AGT- 0.103792
+---GTAAG-- 0.103774
+---GT--GTT 0.0700637
+-A-GTA--T- 0.0614035
+-AGGTT---- 0.0442708
+---GTATG-- 0.0401554
+--GGTA---- 0.0193694
+--GGT--G-- 0.0173797
+A--GT-A--- 0.0144654
+---GT-A--- 0.0048218
+---GT--G-- 0.00395005
+---GT----- 0.00155651
+end consensus
+type 5SS
+center 3
+phase 2
+begin consensus
+-AAGTGAGTT 17.25
+-AAGTAAGTT 13.75
+-GAGTGAGTT 8.5
+TG-GTAAGTT 7.75
+A--GTAAGTT 4.26667
+T--GTAAGTT 4.09091
+-A-GTGAGTT 3.58333
+T--GTGAGTT 3.09091
+-AAGTAAGT- 3.08333
+-AAGTGAGT- 3
+A--GTGAGTT 2.90909
+-A-GTTAGTT 2.6875
+-AGGTAA-TT 2.5
+-A-GTAAGAA 2.4375
+-A-GTAAGAT 2.1875
+-A-GTATGTT 2.125
+A--GTAAGT- 1.24444
+--TGTAAGT- 1.13636
+--AGT-AGTT 1.13158
+-AGGTGAG-- 1.03333
+-AGGTAA--A 0.983051
+-AGGTT-GT- 0.966667
+--CGT-AGTT 0.857143
+-G-GTA-GTT 0.7
+--GGTAAGA- 0.660714
+--GGTT-GTT 0.645833
+-AGGTA-TT- 0.642857
+T--GT-AGTA 0.581818
+---GTAAGT- 0.5
+---GTA-GTT 0.429688
+---GTGAGT- 0.427711
+-A-GTAAG-- 0.381944
+-AGGTAA--- 0.298387
+-AGGTA-G-- 0.272222
+A--GTAAG-- 0.25
+-A-GT--GTT 0.228571
+-AAGTA-G-- 0.2
+---GTAA-TT 0.194444
+---GTGAG-A 0.194444
+---GTTAGT- 0.19209
+-AGGTTT--- 0.158333
+---GT-AGAT 0.153488
+-AGGTA---- 0.100379
+---GTAAG-- 0.097561
+--GGTAA--- 0.0759259
+-A-GT-A-T- 0.0700549
+--GGT--GT- 0.0628019
+AA-GTA---- 0.052381
+---GTATG-- 0.0413437
+--GGT--G-- 0.0202815
+-A-GT-A--- 0.0149254
+---GT---TT 0.0146813
+---GT---T- 0.00532449
+---GTA---- 0.00401891
+---GT----- 0.00131086
+end consensus
+type 3SS
+center 3
+phase all
+begin consensus
+CAGAAA 372
+CAGATT 316
+CAGATG 290
+CAGATC 263
+CAGGAA 253
+CAGAAT 246
+CAGAAC 221
+CAGGTT 218
+CAGATA 215
+CAGAGA 200
+CAGGAT 175
+CAGAAG 167
+CAGACA 160
+CAGCAA 158
+CAGACT 151
+CAGGT- 148.667
+CAGGAG 139
+CAGCTC 129
+CAGAGT 127
+CAGGCT 125
+CAGGCA 124
+CAGCTT 116
+CAG-TC 115
+CAGAGC 112
+CAGGGA 112
+CAGACG 109
+CAGCCA 106
+CAG-TT 100
+CAGGAC 100
+CAGCTG 96
+CAGCAT 95
+CAGACC 90
+CAGTGA 89
+CAGCTA 85
+CAGGGT 85
+CAGCAC 80
+TAGAAA 80
+CAGGCC 77
+CAG-TG 73
+CAGAGG 72
+CAG-CA 70
+TAGGAA 66
+CAGGCG 65
+CAG-AC 62
+CAGTTA 62
+CAG-AT 61
+CAGTG- 60.3333
+CAGCGT 55
+TAGGTT 53
+TAGAAT 51
+CAGCCG 50
+TAGAT- 49.25
+CAGTC- 43
+TAGGT- 40.6667
+CAGC-- 37
+TAGG-T 32.3333
+TAGAC- 24.75
+TAG-AC 19.25
+TAG-CA 19
+TAG-GA 17.5
+TAGCT- 16
+-AGGGC 15
+AAGGT- 14.25
+TAG-A- 13
+AAGAT- 12.5
+TAG--T 10
+TAG--- 7.9375
+AAGA-- 5.25
+AAGG-- 4.63636
+AAG--- 1.84375
+-AG--- 1.60606
+end consensus
+type 3SS
+center 3
+phase 0
+begin consensus
+CAGAAA 167
+CAGATT 160
+CAGGTT 160
+CAGATG 145
+CAGATC 143
+CAGGAA 139
+CAGAAT 113
+CAGGAT 111
+CAGAAC 100
+CAGGT- 86.3333
+CAGGCT 82
+CAGGCA 80
+CAGA-A 79.3333
+CAGCTT 79
+CAGGGA 79
+CAGGAG 77
+CAGCAA 75
+CAGCTC 72
+CAGACT 70
+CAGCCA 64
+CAGGGT 59
+CAGAAG 58
+CAG-TC 57
+CAGAGT 49
+CAG-AC 48.6667
+CAGGCC 48
+CAG-TT 45
+CAGACC 45
+TAGGAA 41
+CAGAGC 39
+CAGCAT 34
+CAGGCG 33
+CAGTTG 33
+TAGAAA 33
+TAGGAT 33
+TAGGT- 26.75
+CAG-TA 26
+TAGAT- 23.25
+CAGT-T 21.6667
+CAG-C- 19.7143
+CAG-GC 16.6667
+CAGC-- 15.2
+TAGAA- 14.6667
+TAGG-- 12.2
+TAGAC- 10
+AAGGT- 9.5
+TAG-T- 6.375
+TAG--A 5.85714
+CAG-GG 10
+TAG--T 4.57143
+AAGG-- 3.16667
+AAGA-- 2.875
+-AG--- 0.575221
+end consensus
+type 3SS
+center 3
+phase 1
+begin consensus
+CAGATG 88
+CAGAAA 86
+CAGGAA 80
+CAGGTG 60
+CAGAA- 56.6667
+CAGAT- 56.3333
+CAGCTG 55
+CAGACG 53
+CAGGAG 52
+CAGCAA 43
+CAGGAT 43
+CAG-TC 37.3333
+CAGACT 33
+CAG-T- 26.8571
+CAGT-A 23.6667
+CAG-CA 24.6667
+CAG-AT 24
+CAGAG- 22
+CAG-CG 21.3333
+CAGTG- 19.6667
+CAG-AC 19
+CAG-CT 15
+TAG-AA 12.75
+TAGAT- 12.5
+CAG-CC 11.25
+CAGCG- 11.75
+TAGGT- 9.25
+CAGGG- 8
+TAGA-- 6
+TAG-T- 4.375
+TAGG-- 4.27273
+-AGCA- 2.75
+TAG--- 2.10526
+-AG-A- 1.44
+AAG--- 0.875
+-AG--- 0.145833
+end consensus
+type 3SS
+center 3
+phase 2
+begin consensus
+CAGAAA 119
+CAGAGA 114
+CAGATT 100
+CAGAAT 79
+CAGAAC 76
+CAGAT- 66.3333
+CAGTGA 60
+CAGAG- 49
+CAGCAA 40
+CAGAAG 38
+CAGAC- 36.5
+CAG--A 23.1
+CAGTG- 24
+CAG--T 20
+TAGA-A 17.5
+CAG-TG 16.3333
+CAG--C 14.5455
+TAGA-T 12.5
+CAG--G 8.875
+TAGA-C 8.5
+TAGG-A 8.5
+TAG-T- 4.33333
+AAGA-- 2.5
+TAG--- 2.5
+AAG--- 0.6875
+-AG--- 0.15625
+end consensus
+type CDS
+phase all
+begin consensus
+AAA 84633.000000
+AAC 46592.000000
+AAG 60437.000000
+AAT 62516.000000
+ACA 46370.000000
+ACC 24553.000000
+ACG 26490.000000
+ACT 35930.000000
+AGA 58310.000000
+AGC 33692.000000
+AGG 25680.000000
+AGT 32467.000000
+ATA 28413.000000
+ATC 49079.000000
+ATG 55085.000000
+ATT 57612.000000
+CAA 70444.000000
+CAC 32088.000000
+CAG 36967.000000
+CAT 39211.000000
+CCA 41062.000000
+CCC 12109.000000
+CCG 20902.000000
+CCT 16745.000000
+CGA 38937.000000
+CGC 16213.000000
+CGG 19184.000000
+CGT 23512.000000
+CTA 19576.000000
+CTC 36258.000000
+CTG 35452.000000
+CTT 37193.000000
+GAA 78165.000000
+GAC 30372.000000
+GAG 41478.000000
+GAT 54272.000000
+GCA 33687.000000
+GCC 21235.000000
+GCG 14088.000000
+GCT 33925.000000
+GGA 53236.000000
+GGC 16915.000000
+GGG 11380.000000
+GGT 18746.000000
+GTA 18214.000000
+GTC 27126.000000
+GTG 28827.000000
+GTT 37436.000000
+TAA 21016.000000
+TAC 24215.000000
+TAG 11205.000000
+TAT 34251.000000
+TCA 57624.000000
+TCC 32884.000000
+TCG 36367.000000
+TCT 41910.000000
+TGA 53826.000000
+TGC 36079.000000
+TGG 43985.000000
+TGT 36905.000000
+TTA 24513.000000
+TTC 56201.000000
+TTG 51452.000000
+TTT 46581.000000
+end consensus
+type CDS
+phase 0
+begin consensus
+AAA 29214.000000
+AAC 14368.000000
+AAG 21430.000000
+AAT 23711.000000
+ACA 15287.000000
+ACC 7556.000000
+ACG 6113.000000
+ACT 15236.000000
+AGA 13083.000000
+AGC 6073.000000
+AGG 2390.000000
+AGT 9505.000000
+ATA 5289.000000
+ATC 14308.000000
+ATG 19502.000000
+ATT 24404.000000
+CAA 23759.000000
+CAC 6982.000000
+CAG 11123.000000
+CAT 11541.000000
+CCA 22932.000000
+CCC 2834.000000
+CCG 6380.000000
+CCT 7320.000000
+CGA 9565.000000
+CGC 4160.000000
+CGG 2879.000000
+CGT 10219.000000
+CTA 5048.000000
+CTC 11747.000000
+CTG 8079.000000
+CTT 18194.000000
+GAA 35701.000000
+GAC 13432.000000
+GAG 19257.000000
+GAT 31475.000000
+GCA 16802.000000
+GCC 10031.000000
+GCG 5651.000000
+GCT 20774.000000
+GGA 28462.000000
+GGC 4276.000000
+GGG 2708.000000
+GGT 9185.000000
+GTA 7376.000000
+GTC 10825.000000
+GTG 10041.000000
+GTT 20526.000000
+TAA 0.000000
+TAC 10158.000000
+TAG 0.000000
+TAT 12776.000000
+TCA 16414.000000
+TCC 7520.000000
+TCG 9109.000000
+TCT 14215.000000
+TGA 0.000000
+TGC 6122.000000
+TGG 7942.000000
+TGT 8393.000000
+TTA 6535.000000
+TTC 18524.000000
+TTG 15014.000000
+TTT 14468.000000
+end consensus
+type CDS
+phase 1
+begin consensus
+AAA 27124.000000
+AAC 17085.000000
+AAG 28251.000000
+AAT 16214.000000
+ACA 16360.000000
+ACC 5893.000000
+ACG 13413.000000
+ACT 9274.000000
+AGA 18727.000000
+AGC 12003.000000
+AGG 12559.000000
+AGT 8521.000000
+ATA 16240.000000
+ATC 19315.000000
+ATG 28352.000000
+ATT 15596.000000
+CAA 24103.000000
+CAC 13923.000000
+CAG 18346.000000
+CAT 15063.000000
+CCA 10417.000000
+CCC 4057.000000
+CCG 9508.000000
+CCT 3959.000000
+CGA 9972.000000
+CGC 4083.000000
+CGG 7638.000000
+CGT 5560.000000
+CTA 8897.000000
+CTC 15780.000000
+CTG 22899.000000
+CTT 9969.000000
+GAA 18216.000000
+GAC 8305.000000
+GAG 14912.000000
+GAT 9677.000000
+GCA 6876.000000
+GCC 4330.000000
+GCG 5051.000000
+GCT 4374.000000
+GGA 5662.000000
+GGC 3760.000000
+GGG 3721.000000
+GGT 2776.000000
+GTA 6705.000000
+GTC 9254.000000
+GTG 14905.000000
+GTT 6438.000000
+TAA 7340.000000
+TAC 4898.000000
+TAG 5780.000000
+TAT 6230.000000
+TCA 20217.000000
+TCC 9131.000000
+TCG 15798.000000
+TCT 10258.000000
+TGA 18951.000000
+TGC 9200.000000
+TGG 15809.000000
+TGT 8676.000000
+TTA 11663.000000
+TTC 21772.000000
+TTG 29546.000000
+TTT 14611.000000
+end consensus
+type CDS
+phase 2
+begin consensus
+AAA 28295.000000
+AAC 15139.000000
+AAG 10756.000000
+AAT 22591.000000
+ACA 14723.000000
+ACC 11104.000000
+ACG 6964.000000
+ACT 11420.000000
+AGA 26500.000000
+AGC 15616.000000
+AGG 10731.000000
+AGT 14441.000000
+ATA 6884.000000
+ATC 15456.000000
+ATG 7231.000000
+ATT 17612.000000
+CAA 22582.000000
+CAC 11183.000000
+CAG 7498.000000
+CAT 12607.000000
+CCA 7713.000000
+CCC 5218.000000
+CCG 5014.000000
+CCT 5466.000000
+CGA 19400.000000
+CGC 7970.000000
+CGG 8667.000000
+CGT 7733.000000
+CTA 5631.000000
+CTC 8731.000000
+CTG 4474.000000
+CTT 9030.000000
+GAA 24248.000000
+GAC 8635.000000
+GAG 7309.000000
+GAT 13120.000000
+GCA 10009.000000
+GCC 6874.000000
+GCG 3386.000000
+GCT 8777.000000
+GGA 19112.000000
+GGC 8879.000000
+GGG 4951.000000
+GGT 6785.000000
+GTA 4133.000000
+GTC 7047.000000
+GTG 3881.000000
+GTT 10472.000000
+TAA 13676.000000
+TAC 9159.000000
+TAG 5425.000000
+TAT 15245.000000
+TCA 20993.000000
+TCC 16233.000000
+TCG 11460.000000
+TCT 17437.000000
+TGA 34875.000000
+TGC 20757.000000
+TGG 20234.000000
+TGT 19836.000000
+TTA 6315.000000
+TTC 15905.000000
+TTG 6892.000000
+TTT 17502.000000
+end consensus
+type Intron_Corr_Term
+phase all
+ 93.3478
+type Intron_Corr_Term
+phase 0
+ 194.143
+type Intron_Corr_Term
+phase 1
+ 362.18
+type Intron_Corr_Term
+phase 2
+ 357.052
+type Intron_emission
+begin consensus
+A 572525.000000
+C 267017.000000
+G 250100.000000
+T 588809.000000
+end consensus
+type Pyrimidine_emission
+begin consensus
+A 0.000000
+C 0.000000
+G 0.000000
+T 22799.000000
+end consensus
+type Spacer_emission
+begin consensus
+A 117.000000
+C 183.000000
+G 73.000000
+T 172.000000
+end consensus
+type Central_Intron_Stay_Prob
+ 0.994723
+type Pyrimidine_Stay_Prob
+ 0.719098
+type No_Spacer_Prob
+ 0.687177
+type Spacer_Stay_Prob
+ 0.163615