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changeset 3:a4f602cc3aa9 draft

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v0.0.9, was missing mirabait. Adds tests for miraconvert
author peterjc
date Fri, 02 Oct 2015 06:12:23 -0400
parents 4eb32a3d67d1
children 1713289d9908
files test-data/U13small_m.mira4_de_novo.cstats.tabular test-data/U13small_m.mira4_de_novo.mira tools/mira4_0/README.rst tools/mira4_0/mira4_bait.xml tools/mira4_0/mira4_de_novo.xml tools/mira4_0/mira4_mapping.xml
diffstat 6 files changed, 890 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/U13small_m.mira4_de_novo.cstats.tabular	Fri Oct 02 06:12:23 2015 -0400
@@ -0,0 +1,4 @@
+# name              	length	av.qual	#-reads	mx.cov.	av.cov	GC%	CnIUPAC	CnFunny	CnN	CnX	CnGap	CnNoCov
+MIRA_rep_c1         	1530	61	11	9	4.46	36.08	0	0	0	0	3	0
+MIRA_rep_c2         	541	31	6	6	5.24	38.62	5	0	0	0	2	0
+MIRA_rep_c3         	454	42	6	6	4.46	35.81	10	0	0	0	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/U13small_m.mira4_de_novo.mira	Fri Oct 02 06:12:23 2015 -0400
@@ -0,0 +1,748 @@
+@Version	2	0
+@Program	MIRALIB
+@ReadGroup
+@RG	ID	1
+@RG	technology	Sanger
+@RG	strainname	StrainX
+@RG	segmentnaming	sanger
+@EndReadGroup
+CO	MIRA_rep_c1
+NR	11
+LC	1533
+CT	MIRA	1	5	=		.	Note=Assembled with MIRA
+CT	H454	175	175	=		.	Note=No edit. PL: 3 RS: 2 RL: 1 RWTS: 0 EL: 1
+CT	H454	664	664	=		.	Note=No edit. PL: 2 RS: 6 RL: 0 RWTS: 0 EL: 0
+CT	DGPc	1483	1483	=		.	Note=*: 1 T: 1  -  50%25
+CT	H454	1483	1483	=		.	Note=No edit. PL: 3 RS: 1 RL: 0 RWTS: 0 EL: 0
+CT	DGPc	1513	1513	=		.	Note=*: 1 A: 1  -  50%25
+CT	H454	1513	1513	=		.	Note=No edit. PL: 2 RS: 1 RL: 0 RWTS: 0 EL: 0
+CS	aaatttcataaaatttctcatttcaaaaacgagaaaattaaggccttgcggggttaaatcgttatcaagtaatcagtcggctcactgcccagtgtggacactggccaatattatggcaccagcctttgagaaaaggaaacctttttttgaatccatctccctgacctggggttt*gggttgggttttatcagcatagggtgacaggcaagttcaatctgattggatcctggatcccatcatggggtatctgttcctaaatcattccctgatcctcggtcagagcgagcgcttaggttcccgctgcagttaaacacctggttcatctgggcatactaaggttatgactttccacctgggagtccacgacaactgaaaaaactcaaaacttctttaagtagaagttgagcctgaagctgaggcagctgtttcagagaggaggaggaggaggagatagcaaatgtcaagggatttccatttctctttcaatgccaacatacttcagggcatcagcctggctgtatctgtaatcaaaaaacagttcttcgcaagtctggatggctctcctgacaaaaacacctatcctgtgatcaccattaaccatcataacttttgcatagcagtttggatttaccgaatgatttgcaaaacgaattttgttacccttgcaggttgcatccaccacaaaatcattgttcaagttgaacagaaagctgcacatgtatttatcacacactttccctcttccgtcagcttagcttcaggaacctcgagtactgtgggcaatttagaaaaagaaaatgccgtttgaaattctgaatttgcaaagtactataagaataatttatagcaatgagtttaaaactcaactttttattgccttctcaccagctgcaaagtgttttgtaccagtgaatttttgcaataatgcagtatggtatatttttcaactttgaataaagaatacttgaaattgaaaaaaaaaattgagtctgatgggtctagtgtgtttataaaatgacttaagatcccacagttattttaaagtaatacattactcaactggtattcattttgatgccattattttattttataaaactagtcatccttgcagaagtgtatctgattaactcttgacaactactttgcctattttattaacagctgcatttaacccacgtgacaggataactaatttctattgtttttgtatttttgcctcctccttccaagatagcagtagagtactgtgttaaatcttgcttcagaagagcttgtttaaaatagttataaagaaagtaaaatacatagaaaaacacgttataattttaaattaaaaaagaaaaaagatgtctactctgaataaattatgcatacatataaggtctgaacaaaaacatgaaaagatgggctctgagtatcaattttaaaaatctttaccagtataacattactcaaacaaaaattaaaatttaatataa*ttaagtacatattccaagacaacaaatgg*accttgactgttaattctgg
+CQ	76ABAAEDGJC??>?BCGCHDCCDCCCCB=:<:636?@@<A@==@ADEEA=CFBBCDCAD@EECDDCGED?AAAA?EBAB@?DECCCCBBGDECCAD=67@B@AEDFDDDCDDGGCCDCCDCKQNWNNOKLMJKMVJKPUb_`ff\W=LKLLRMXW\e`f[\URVSV^bcda`Y5cmea`eghb\b`__Y^Q`aadgja_aabefebbd]_ghfdfedldebcVVY\\^e_]_`_cfebfegjhg][__ec[Z`W\]dbbibbhadXc`\U^]aegjfgkde][b^Z^`dZ\bbaRRT[_ehggkkcfhbbdecdhcdfbbfebfeagbhdedgkiccegdebdehfgba]\]]aded]\X`]`bfgdckegejccebfaifkjffddddhijgigggffeffcdcbfaegc`bbbbdfg`cheefjhedffkfgfffeehdgkgghmceddbagjdgjgggjgieiddcafhf`dhgfifikgighmihggkjgidhdleghjdjiegigkhjefglgjhkheihhjiifkmkhjiidhljjjeiigdeedc^dkgf\]ecjififdeekjhieeeiihhhddhf`bbafdkefilgfkilioghmhjhhfhghhmegc[lfbhieibeec`cjcbeeccgkggghfifbeagfjifcdihdYhfgfhdhfacbhfhehehgkkgehgbhledfdeddcV`addcceeakjfhjemfikgfcgedfjfenlej`fh_defee`cefi`diic[c`egiee_b]c]`^d\^W]`jbhffleefhje^`H`caddcgcciffhfhmddee_egfge`cggfckjfddda]WZbh``]a[cZZed^j]\c`Y[V_f`ajffddf[\]\`cfgijaVW;SWP]^afcb\VT[X[]_^`^_\\jhkda`eea`fd`Z`U``ebeg]`hhgahfe]gb_f`QOPbcmihmd^c``[N[_`iggc_ab_g`daddecdfdbffkpjmkigecc`\VUQQW[X]XYPY]`gdcbclheecgjedaeYheac]b`_ddb^`ba[ahhigkidgddeccdddbhcRYG]^gdghbcdgghgh^ba`_fb[acWd`]efedfedVelklkde`a_cabc`cgfc[^b`_^Xd]a^]debgf\`b^^^_XPZU[c]bf`[`X`]]gdceba]hdecbabbdgc\S_S\[^``ac_`aX]]bfhgbcc`bb`bc_^cgbe__[YYa[_\X\ZY\_^__\]cciacd^_`gcdejg[fY]_\`__c``a``ZYW\````^]c]]QWRSbdfghbadaegffcabba_baaa_[_Y_]Z\YTV^abbd``_]_WXf[c[aa`dabcc`edbeadabaabbb``bYKXTMTUKSPZ\```]`bacb`^_RLRKHOPZYQHGL??CEO[YZ_[^YWOJY\fdVVMNQ?<C6OVXb_W[[VVR_SPMOQPQ[VYXZVNN9GLMYYca`a_Y_]XTNQLLRRRKQUONIIMPT[aTNRVWAbYXTQLGNGJENJSPJJHLJPGM=HOAC;/@OIQYTQISQ\XT>DHMJ>E
+\\
+RD	U13a03c03.t1
+RG	1
+RS	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTAACAAATCTCATGGTTTAAAAATTTCATAAAATTTCTCATTTCAAAAACGAGAAAATTAAGGCCTTGCGGGGTTAAATCGTTATCAAGTAATCAGTCGGCTCACTGCCCAGTGTGGACACTGGCCAATATTATGGCACCAGCCTTTGAGAAAAGGAAACCTTTTTTTGAATCCATCTCCCTGACCTGGGGTTT*GGGTTGGGTTTTATCACCATAGGGTGACAGGCAAGTTCAATCTGATTGGATCCTGGATCCCATCATGGGGTATCTGTTCCTAAATCATTCCCTGATCCTCGGTCAGAGCGAGCGCTTAGGTTCCCGCTGCAGTTAAACACCTGGTTCATCTGGGCATACTAAGGTTATGACTTTCCACCTGGGAGTCCACGACAACTGAAAAAACTCAAAACTTCTTTAAGTAGAAGTTGAGCCTGAAGCTGAGGCAGCTGTTTCAGAGAGGAGGAGGAGGAGGAGATaGCaaATGTCaAGGGATTTCCATTTCTCTTTCAATGCCAACATACTTCAGGGCATCAGCCTGGCTGTATCTGTAATCAAAAAACAgTTCTTCGCAAGTCTGGATGGCTCTCCCTGAACAAAAAACACCTATCCCTGGTTGAATCACCCCATTAAACCCAATCCCTAAACTTTTTGGCCATAAACCAATTTTTGGGGAATTTTTCTCCCAAAAATTGAATATTTTGCCCAAAAAACCGCAAAAATATTTGTTGTTTTTAACCCCCCTCTTTGTCCCCGAGGGTGTTTTGCCCTCTTCCCCATCCCCCTCTCTAAAAAAAATTCATTTCTTTGTTTTCTCCAAAAAGTTTTTTGATAAAAACAAGAAAAAAAAGCGCCCCGCCCCTCCTCATTTGTTTTTTTTTTTTTATTTTACAACCACACCCACACCTTTTTTTCTCCCCTCTCCTCTCTCTCCCCCTTCTTCACCCCCCTCTTTTTCTCTTTTTTTGGGGGGGGGGAGAGAGAGAGAAAAAAAAATTTTTTCTCCT
+RQ	!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!;8777==----61511EAAE,=>=>>>@AE@====>AAEAEAAAAAAABA83:*3.1=>>:?>8;>?AB@?8;;??8@599,BB<A@@DB?=???><C>?@><ACAAAA??D?B7887736?A???A?@<<=>AEEAAAAAAAAAAB826-8739:694?@F@ABBAAB???BEABABAABAD?@?BAA?AA?=?<988:8?;;?>@?A865.;63797564889C@?>C5;BBA?AAA????A??@?A=@@@@ABCAA:====?D@?@AB????B?AAAABAAAAAAA?C??D@B>D<;804*5178:9@245188548AED@>?A8@?:@A@>?D???A@BB=<<<@;A<=?<:A?@@@?AB@@G??;9:1::9=:86/6?4792;;;EAAAAAAAAA?AAAEABAAAABBDAC1;1)62.72>??@82183*4+02)3737?;=D?=8+-7-5-162730;98:;2::/8:!*+!!'+342!5.3;???A@@;8983545:;;?AA@;6/78;=;=>C0/,9/3++*)(40-<<>AA??D@@@@?ACA@BBC@A7:!67.4,*3*+..3153,*(+-5+/),,,5.*)),,,40,+)*,,)**20-,,.+**)***-88-+2-+.-2<=32-*+)3-:.3+,/0)*,,-(,..*/.*)(/,..0/3/7/142+)))).,/582,*)()))-))//,))))++3)))))*1.0*')&+'+%''*22+)(((()+38,,))*)(()))((+()).()+*,&)*(&)&&),1)++/0,6.+,(&%,.5:15,*())(()+(+))))*,,),+,0325-'.12.,**,+,04,*&*+**-5@D1.*)+++.*)(,+)),''+''),-0-./946?<>>,))*,))+)0))()()),)),.5+,./,,4+.((''/,...()(,),((11592(.,)'))(,,*+11,**,,-)*+,1==A2/+5.-0;;:11*())','+.3/78;>??</*...1+*+(()(
+TN	U13a03c03_1
+QL	63
+QR	627
+AO	1	236	1	236
+AO	238	608	237	607
+AO	609	1043	609	1043
+RT	HAF3	63	253	=	MIRA	.
+RT	HAF3	255	520	=	MIRA	.
+RT	HAF5	521	547	=	MIRA	.
+RT	HAF3	548	554	=	MIRA	.
+RT	KMRF	554	574	=	MIRA	.
+RT	HAF5	555	601	=	MIRA	.
+RT	KMRF	582	602	=	MIRA	.
+RT	HAF3	602	627	=	MIRA	.
+ER
+AT	1	565	63	627
+RD	U13a08f10.p2
+RG	1
+RS	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTAACAAATCATCAGTGGTTTAGAAATTTCATAAAATTTCTCATTTCAAAAACGAGAAAATTAAGGCCTTGCGGGGTTAAATCGTTATCAAGTAATCAGTCGGCTCACTGCCCAGTGTGGACACTGGCCAATATTATGGCACCAGCCTTTGAGAAAAGGAAACCTTTTTTTGAATCCATCTCCCTGACCTGGGGTTT*GGGTTGGGTTTTATCAGCATAGGGTGACAGGCAAGTTCAATCTGATTGGATCCTGGATCCCATCATGGGGTATCTGTTCCTAAATCATTCCCTGATCCTCGGTCAGAGCGAGCGCTTAGGTTCCCGCTGCAGTTAAACACCTGGTTCATCTGGGCATACTAAGGTTATGACTTTCCACCTGGGAGTCCACGACAACTGAAAAAACTCAAAACTTCTTTAAGTAGAAGTTGAGCCTGAAGCTGAGGCAGCTGTTTCAGAGAGGAGGAGGAGGAGGAGATAGCAAATGTCAAGGGATTTCCATTTCTCTTTCAATGCCAACATACTTCAGGGCATCAGCCTGGCTGTATCTGTAATCAAAAAACAGTTCTTCGCAAGTCTGGATGGCTCTCCTGACAAAAACACCTATCCTGTGATCACCATTAACCATCATAACTTTTGCATAGCAGTTTGGATTTACCGAATGATTTGCAAAACGAATTTTGTTACCCTTGCAGGTTGCATCCACCACAAAATCATTGTTCAAGTTGAACAGAAAGCTGCACATGTATTTATCACACACTTTCCCTCTTCCGTCAGTTTAGCTTCAGGAACCCCGAGTACTGTGGGAATTTAGAAAAGAAAATGCCGTTTGAAATTCTGAATTTGCAAAGTACTATTGAGATTATTTATCGCAATGAGTTTAAAACCCACT
+RQ	!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?;=;F@844AA4=@7AAAAAAAA@??@??B?<GA==4239==@@=:@:9;22;96:525:;896:;;;;??B;;AD??AAA?B???AAA??AA==>=?==@====?===>=??AAAAA?B;54/14=BACABBABA====@:=?<A=:CCABAA@@@@D??@@??ABBAAAA?A????AAAAAAAAAA??ECACB@@CGGEC@EEAAAA?A?:=>===AAAA?BAAA?AAA@======??>AAAB@8::==>F?>?DA?AAAAABBB???ACDFA@BAABB@>@>@DEEA@@?????AAAAAB<@;9=@A===;=AA=5====AAAAAAAAA???=@=>>?=;=???A?====??@C@>@@AAAAAAA??AA@====<C@A==8?==AAEA@D>@AG??:<61<<?>@@@@@@@AAAAAAAAAAAA?645/.5A=::87;?AB:=;::<AB??BBFBBBAABBEABFBBCG@@@A==BC;>D@?>??@8B?;331747?A=;==>E====@;A??E@?==8@=;;BA=>;=:9==44==;=??AA<:=9<6:???AAA;;841581/78;6;166:9?E?>@==9;98;9;=;92:/88====>==>?A:0575:;=====:EAA======AABAB62199==98===;544/6;6=4/3**35;5:;A9/()**0;0**,,-2;:?;;7-,+*-(,,,3555.*+-63;0+.,*(,+6892/.)*/),15?9-+))17=====@810(),-64-0/..**13*&(*,)(%)*--;3713-4.+(()),.,+/-+,*,,/389-'*)*(,)2A04,1./+,*/+)+)&&*.*)+)(()0/21**-.)((($(%)((++**+*-//(*())(((0(*(.*'%**))-++'
+TN	U13a08f10_2
+TS	1
+QL	66
+QR	816
+AO	1	239	1	239
+AO	241	931	240	930
+RT	HAF3	66	523	=	MIRA	.
+RT	HAF5	524	550	=	MIRA	.
+RT	HAF3	551	557	=	MIRA	.
+RT	KMRF	557	577	=	MIRA	.
+RT	HAF5	558	604	=	MIRA	.
+RT	KMRF	585	605	=	MIRA	.
+RT	HAF3	605	659	=	MIRA	.
+RT	KMRF	659	679	=	MIRA	.
+RT	HAF5	660	732	=	MIRA	.
+RT	HAF3	733	733	=	MIRA	.
+RT	HAF5	734	761	=	MIRA	.
+RT	HAF4	762	773	=	MIRA	.
+RT	HAF3	774	816	=	MIRA	.
+ER
+AT	1	751	66	816
+RD	U13a03e10.p2
+RG	1
+RS	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTGCAAATTCAGAATTTCAAACGGCATTTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAAGCTAAGCTGACGGAAGAGGGAAAGTGTGTGATAAATACATGTGCAGCTTTCTGTTCAACTTGAACAATGATTTTGTGGTGGATGCAACCTGCAAGGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCAAACTGCTATGCAAAAGTTATGATGGTTAATGGTGATCACAGGATAGGTGTTTTTGTCAGGAGAGCCATCCAGACTTGCGAAGAACTGTTTTTTGATTACAGATACAGCCAGGCTGATGCCCTGAAGTATGTTGGCATTGAAAGAGAAATGGAAATCCCTTGACATTTGCTATCTCCTCCTCCTCCTCCTCTCTGAAACAGCTGCCTCAGCTTCAGGCTCAACTTCTACTTAAAGAAGTTTTGAGTTTTTTCAGTTGTCGTGGACTCCCAGGTGGAAAGTCATAACCTTAGTATGCCCAGATGAACCAGGTGTTTAACTGCAGCGGGAACCTAAGCGCTCGCTCTGACCGAGGATCAGGGAATGATTTAGGAACAGATACCCCATGATGGGATCCAGGATCCAATCAGATTGAACTTGCCTGTCACCCTATGCTGATAAAACCCAACCCCAAACCCCAGGTCAGGGAGATGGATTCCAAAAAAGGTTTCCTTTTCTCAAAGGGCTGGTGCCATAAATATTGGGCCAGTGGTCCAACACTGGGCCAGTGAAGCCGACTGGATTACCTTTGATAAACGATTTAACCCCCGGAAAGGGCCTTAAATTTCCCCCCGTTTTTTGAAAATGGGGAAATTTTTTTAATGAAAATTTCTCAAAACCCCCTTGGAGGTTTTTGTTTAAAGCCCGTTTAAAAAAAAATTTCTCCTTGGTTAAAATAAAAGGAAGGGTTCTCTCCCGGGGGGAAAAT
+RQ	!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!>9;8:533752?C544;4148449@7<@@@;=866686AB@=====@==E==;;;@=>===B==@::;;:7ABB99?A??<AAA>==;==?????AB??????AA??AAA==A========AA?B???@??A??ADCA@EE@@AAAAA======@??D@???BD?AAAAAA@=?C>:=?AAAAA??A===B???????D?@==<<@?AA?A???AC@BBAECAAA@@@C@@G@A@B<?A???AAAEE@@@BACA@@AACAFE=?7337AAAAEBA@?DD@AAACC?CD@ACAA@C@AABAABAAA=:===A<???A??AAA?AAA???AAAAAAC@@B@CAAAAABAA??BDA;7;?A?AACAABA@@CAAA?AA???<?87*.*29AAAAAAAABBBA@@?AAAAA?A==;BB??@?ABA??????@@>@@B?????@AA@AC?=<52*/38@A??>B=====8=>A=B======AB=8=;>==>==C=>=A=B=>=BA??A??DAAAA??===B=9EEAA?=;<538A??<773766C?@@EEBA?A>=6;/3=?4;8689C<79251:378=9:8:@BEAAA?AA=:5*,85=89..43:5:G@AAAABA>====>=>=====E=?AA??>3;:8=8=D?=?=?E;17?=?@=73/3/268B=B844*+()*))49BB==:3.,*1,**,**,-*2,/2,3*,5./;;8==>56.2@6A===7681/.33*+-66632,(,*).**.31,)(&))*)**()*00.56.4.1/1/6C85526575,,0,,41-+((.8882//35BB2/,+,*)'+*/54)(0)+,**&).))&),*'%''))***)*.*(/,))1*)))%(%'')(,-,**),0,3,+*,*)%,/3&&&)844..+))'$))*****050/++*+)**%+***))**+*(+..**))+')()&
+TN	U13a03e10_2
+TS	1
+QL	47
+QR	748
+RT	HAF5	47	67	=	MIRA	.
+RT	KMRF	48	68	=	MIRA	.
+RT	HAF3	68	73	=	MIRA	.
+RT	KMRF	73	93	=	MIRA	.
+RT	HAF5	74	119	=	MIRA	.
+RT	KMRF	100	120	=	MIRA	.
+RT	HAF3	120	162	=	MIRA	.
+RT	HAF4	163	174	=	MIRA	.
+RT	HAF5	175	202	=	MIRA	.
+RT	HAF3	203	203	=	MIRA	.
+RT	HAF5	204	276	=	MIRA	.
+RT	KMRF	257	277	=	MIRA	.
+RT	HAF3	277	331	=	MIRA	.
+RT	KMRF	331	351	=	MIRA	.
+RT	HAF5	332	378	=	MIRA	.
+RT	KMRF	359	379	=	MIRA	.
+RT	HAF3	379	385	=	MIRA	.
+RT	HAF5	386	412	=	MIRA	.
+RT	HAF3	413	722	=	MIRA	.
+RT	HAF3	724	748	=	MIRA	.
+ER
+AT	824	123	47	748
+RD	U13a03e10.t1
+RG	1
+RS	CCTTGCATGCCTTGCAGGTCAACTCTAGAGGACCCCTGCAAATTCAGAATTTCAAACGGCATTTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAAGCTAAGCTGACGGAAGAGGGAAAGTGTGTGATAAATACATGTGCAGCTTTCTGTTCAACTTGAACAATGATTTTGTGGTGGATGCAACCTGCAAGGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCAAACTGCTATGCAAAAGTTATGATGGTTAATGGTGATCACAGGATAGGTGTTTTTGTCAGGAGAGCCATCCAGACTTGCGAAGAACTGTTTTTTGATTACAGATACAGCCAGGCTGATGCCCTGAAGTATGTTGGCATTGAAAGAGAAATGGAAATCCCTTGACATTTGCTATCTCCTCCTCCTCCTCCTCTCTGAAACAGCTGCCTCAGCTTCAGGCTCAACTTCTACTTAAAGAAGTTTTGAGTTTTTTCAGTTGTCGTGGACTCCCAGGTGGAAAGTCATAACCTTAGTATGCCCAGATGAACCAGGTGTTTAACTGCAGCGGGAACCTAAGCGCTCGCTCTGACCGAGGATCAGGGAATGATTTAGGAACAGATACCCCATGATGGGATCCAGGATCCAATCAGATTGAACTTGCCTGTCACCCTATGCTGATAAAACCCCAACCCCAAACCCCCAGGTGCAGGGGAGAAGGGATTCCAAAAAAAAGGGTTTCCCTTTTTCCTCCAAAAGGCCTGGGTGCCCATAAATTATTTGGGCCAAGTTGTTCCCACCACTTGGGGCCCGTTGGAACCCCGAACCTGAATTTAACTTTGAATTAAACGCAATTTTAACCCCCCCCCAAGAGACACCTT
+RQ	(')*14.-*0-0**1,).0.%-.1:9479)7)'11>AAA=A>A>=912-/5:?A@DBA;;;@@@AAAA??ADAAEDBAAAAAABA@???@==40-:16:=???@?>9?C?;;C8?55-1.*1198<AA@F?;4686=?AAABA9;79;>DBABD@@A@C@AA=B=<><C8<=@;=@@@A@A??=C56>CC?CC?@A>87=;/<?A????A?AAA@@@A@@ABBAAA???@?AEAAAACC????BBB???AB@@D@>>?BC?@@F@@?==:;769?B69<570266=CBC==;;><?78-688@A??A<<942?:=;@85:49??DBAC@???D;A======ABA@?>?>6::=A<?DBB??;:;:;????<?CAAAA?C<;4;96====?AAACDCA@@AAAAAAAAA????BAAABAAAAAAAAAAAAAA==9===AAAAAAAAAAA@A88678B@AAAAAAAAAAA@A8==5;;?EAC9B=A?@@@B???=;;;?::===??8:2768=<@?9@?<??B???@G@@AAAAC@@;;;,2--81576A?>??A?A@A>=11/000210<=@@>5;75:ABB@@AA=7/6361,188@=====>8728709418823=5>1:-04128=:;;537753?<@?<4.8988;9;==<??@=;5;;@B==:=====9=757226.-7?C;/,///:?E;:)/.)((,()2/,,,',-/304)-337;?E=6242/72/5*,21,(((,,.243,)3-),1,))*/+)()+)*334:8/3')))*5,-+/5*+0)**,1**//2+1,(,,/-(,*-,1.,-,)))*.,,47/,0*+.))-**>+'*').,4371-*+22**-*-1))*)(+'&+*+&
+TN	U13a03e10_1
+QL	37
+QR	680
+RT	HAF5	37	57	=	MIRA	.
+RT	KMRF	38	58	=	MIRA	.
+RT	HAF3	58	63	=	MIRA	.
+RT	KMRF	63	83	=	MIRA	.
+RT	HAF5	64	109	=	MIRA	.
+RT	KMRF	90	110	=	MIRA	.
+RT	HAF3	110	152	=	MIRA	.
+RT	HAF4	153	164	=	MIRA	.
+RT	HAF5	165	192	=	MIRA	.
+RT	HAF3	193	193	=	MIRA	.
+RT	HAF5	194	266	=	MIRA	.
+RT	KMRF	247	267	=	MIRA	.
+RT	HAF3	267	321	=	MIRA	.
+RT	KMRF	321	341	=	MIRA	.
+RT	HAF5	322	368	=	MIRA	.
+RT	KMRF	349	369	=	MIRA	.
+RT	HAF3	369	375	=	MIRA	.
+RT	HAF5	376	402	=	MIRA	.
+RT	HAF3	403	680	=	MIRA	.
+ER
+AT	824	181	37	680
+RD	U13a06d03.t1
+RG	1
+RS	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTTAAGTAGAAGTTGAGCCTGAAGCTGAGGCAGCTGTTTCAGAGAGGAGGAGGAGGAGGAGATAGCAAATGTCAAGGGATTTCCATTTCTCTTTCAATGCCAACATACTTCAGGGCATCAGCCTGGCTGTATCTGTAATCAAAAAACAGTTCTTCGCAAGTCTGGATGGCTCTCCTGACAAAAACACCTATCCTgTGATCACCATTAACCATCATAACTTTTGCATAGCATTTTGGATTTACCGAATGATTTGCAAAACGAATTTTGTTACCCTTGCAGGTTGCATCCACCACAAAATCATTGTTCAAGTTGAACAGAAAGCTGCACATGTATTTATCACACACTTTCCCTCTTCCGTCAGCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAAAAAAAGAAAATGCCGTTTGAAATTCTGAATTTGCAAAGTACTATAAGAATAATTTATAGCAATGAGTTTAAAACTCAACTTTTTATTGCCTTCTCACCAGCTGCAAAGTGTTTTGTACCAGTGAATTTTTGCaaTAATGCAGTATGGTATATTTTTCaACTTTGAATAAAGAATACTTGAAaTTGAAAAAAAAAATTGAGTCTGAtGGGTCTAGTGTGTTTATAAAATGACCTTAGGAACCCCCCGTTATTTTAAAGTTAGACCTTTACCTCCACTGGGTATTCCTTTTTGAAAGCCATTTATTTTATTTTTAAAAAAACCTAGTTTCTCCTTTGGCCGAAATGTTTTCTGAAATAAACCCTTTGAACCACTTTCTTTTGCCCTTTTTATTGTTAACCCGCCCGCCTTTTAACCCCACCGTTTAACACGGGAAACA
+RQ	!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!@A???>??893;5.8;?B?C;=;====;88;=CAAA==961/9.5.5=7::>=8:=75:6/34-6;?A@??;<,6625777:5:4:C;?DAAAAAAAADAAACDB@@EAF@A>??EDBBFDGCAAAAF@DA@B?=AC?DAACCC@?@@AAEEEDAAA@@A;;>7==?=@==A=>==A?AAEB@??;???CC?32!*).66/8??AAABAC@EAAA=ACBAAB??AAA?97+799B@=?=A?@==B;=====?EA@@@?B@=B=A@A?A?AABAABB??A????BAA?B??=BB?::8:=9DD:=9:?5:838<@@?;??;AAACD?FACEA??AAACC@@CF?D?CA?CD?@A??;6??BBA>==6??A?B======>@<;4:=A:=====?<AA997+;????>???AAAAAA?6:=63*3?9>/86:??B?8??>?9A>=B16;9:=?>DA?D@A?C<6<=C==AAAAAA?BB89448=C=AAABD@?A???CAAAC@95778;?CABCA6.5--2+*3,495;></93!!.567?;++9-,0//23==DB33.!+4.66553?=>==51+*.()+.+!57;?AAAA@AA@@8/1((21/32!*51345514*)(21./3/00+/,-))),-*,0))11:87?6941355)),'*)))'*,(*()-*),)+-*,+)((+,+1.::42+.-(+.,6*-+(*+53-.3.,.(*(+)6.+)**,**)(,,2*+5+(*)).*'0**1+*(*,+-2-01/)*)))-+)))(),()*,).,2)+,.03.+)$')'-2*..-)*+)()-+0056))*-6+))))))))/..(++*-))&&
+TN	U13a06d03_1
+QL	33
+QR	662
+AO	1	588	1	588
+AO	590	867	589	866
+RT	HAF3	33	100	=	MIRA	.
+RT	HAF5	101	127	=	MIRA	.
+RT	HAF3	128	134	=	MIRA	.
+RT	KMRF	134	154	=	MIRA	.
+RT	HAF5	135	181	=	MIRA	.
+RT	KMRF	162	182	=	MIRA	.
+RT	HAF3	182	236	=	MIRA	.
+RT	KMRF	236	256	=	MIRA	.
+RT	HAF5	237	262	=	MIRA	.
+RT	HAF3	263	263	=	MIRA	.
+RT	HAF5	264	309	=	MIRA	.
+RT	HAF3	310	310	=	MIRA	.
+RT	HAF5	311	338	=	MIRA	.
+RT	HAF4	339	350	=	MIRA	.
+RT	HAF3	351	393	=	MIRA	.
+RT	KMRF	393	413	=	MIRA	.
+RT	HAF5	394	430	=	MIRA	.
+RT	HAF3	431	445	=	MIRA	.
+RT	KMRF	445	474	=	MIRA	.
+RT	HAF5	446	473	=	MIRA	.
+RT	HAF3	474	505	=	MIRA	.
+RT	HAF5	506	580	=	MIRA	.
+RT	KMRF	561	613	=	MIRA	.
+RT	HAF3	581	581	=	MIRA	.
+RT	HAF5	582	610	=	MIRA	.
+RT	HAF4	611	611	=	MIRA	.
+RT	HAF3	612	662	=	MIRA	.
+ER
+AT	391	1020	33	662
+RD	U13e07f02.t2
+RG	1
+RS	ACATGCTGCAGTCGATCTAGAGGATCCCATGTCAAGGGATTTCCATTTCTCTTTCAATGCCAACATACTTCAGGGCATCAGCCTGGCTGTATCTGTAATCAAAAAACAGTTCTTCGCAAGTCTGGATGGCTCTCCTGACAAAAACACCTATCCTGTGATCACCATTAACCATCATAACTTTTGCATAGCAGTTTGGATTTACCGAATGATTTGCAAAACGAATTTTGTTACCCTTGCAGGTTGCATCCACCACAAAATCATTGTTCAAGTTGAACAGAAAGCTGCACATGTATTTATCACACACTTTCCCTCTTCCGTCAGCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAAAAAAAGAAAATGCCGTTTGAAATTCTGAATTTGCAAAGTACTATAAGAATAATTTATAGCAATGAGTTTAAAACTCaACTTTTTATTGCCTTCTCACCAGCTGCAAAGTGTTTTGTACCAGTGAATTTTTGCAAtAATGCAGTATGGTaTATTTTTCAACTTTGAATAAAGAATACTTGTAAATTGAAAAAAAAAATTGGAGTTCTGGATGGGTCTACGTGGTGTTTATAAAATAACCTAACGCATCGCCCCATCCAGCTTTTTTTCTGAGAGAGTACAGATACCAGCCACTCCCGCGGGGTTGTTTCGATCTTGCAATGCCCCGCCAACTTTTTAATTTTTAGCAGAAAACCCCAGGTTCTAGCTCCCATTGACCAGAAAAATTGTTTATCCTCGGAAATACAAACGCCCTGTTGGAACCACAACTCATGCCTCTCTGCGCCCCTCAAGTTCGTGTAAATGTGAAAACCAGCGCCCCGCCCCGAGTTTTAGAAACGCCCGCCCCGCCTTGTGGAAGCCTTAGGGGAAGTATAACGCCCAGCGACGTTCTGCTCTCCTGGACAGCGTCGGCGTATGGTATCTGACGGTCTAAACATACGTCACGTAACGGGAGCCCCCCTCTTCCGCATCTCTCCCCACTATTTGTGGCTAGCAGAAGAGAAATAATAAGCCGCAGCGTATCTGATGAGGAGCAGACGTTATCACGCTCTGCGGTGGCGGTCTTTAGAACACAAAATTTCGCTGTTGTCGCGCCCTTCTCCGACGGAAAAGAGAAAAAACCCTCTCTGTCTTTTCTATTAAAATAAGTAATTGGTGGGTTTTTTCTGCTGCCTTCTGACGACGACCGAAGAGAAACGCGGGTTTTGTATAACGCAGATATCACATCGCGCGCCCTCCGCGTCCG
+RQ	*'-,,*55(,++/)''..912.-')).3ABAABAA=02-633===ABBAAA?A?A@AECAAAABADAA<>225*5/.6=?AADDAAAAABB???C?AAAAAEE?AA?A@AAAA??=@;:;77:9=B=>AABCA??B??A?AAAAAAAAAACCA=8<;C==@@@@A?AA?A?AAAAADAAAAADA::>67:5A==????=?9965?>9>?>>ADAAAB39*776??DC?<<?A<??88;69;>;A59A@?@@AAAAA@A?=AC@AC@8A18094130.9525;7;>;=77>>5;@@?=A8:?@>>==A;??>>?@@A<;<7;9-*1(//,0577;231.,+828=92;;@@;?@?A84:197138.705AA@@A@@88889....02;?@>=:?@99>A@@AD=6:6=7395577A;=B84*-)2/8FB@@@<13.!/8=@@??;98181215<<;:=9/.***(++*+),*/2571-65*7/8944/3,0*&+!),28;2*0*.000!/,.7>=>5.1.1389B83;.3.2,(2-())&,)01/.318=84-,**((+)/)22-**,.*+2-+(()(,,**.2659.+-+),,%-)))*())(((,,,)(,,+**)(()*(**)+%*()&*'')'')+)))(+**))')(),*)&+%)-,*-)**,.))**+,,*-.*)-,,)(((()(()*-++*)*-**,)*((((),-,))(()('))((())**)*)+)*+*,.22-),+*++*++**,)*..2-)(+***+&('(+&((()+**,*,)***))())))+,(,.((,*-.***(*)((''('('(*(*)))*,*(%$)(()((().3+(((*-**'%)))+++)+*,*)*+--**)*,(*,&&)%%+-1,+*-)+*''('(')*))()+)++))'())))))*)))*-,*,,)))))(*)(((-)***+,*)(*+-*)&()''*.).('&)'*)-))()++30*+**%***(,))),))-,0))(++***((())*1,-64/2,./.-/()).*)))))(('')++).++,))--))-)6'(''''(-,//,/)%)((+((''***()/*())*+*0'+)*+**),*))+'((&(+**,-+*)+-:;.,*,**)+()'+2-192-*+(+(*$$+$)'))0+,*,2*)-).+'+''*)(+*,))*&*++')(++(+(()+))($(&(*+().'*+)))+)'-))+)&*))))**))*)()*+)*,+))))'+)+/12,)(')+$'*()(*
+TN	U13e07f02_2
+QL	29
+QR	538
+RT	HAF5	29	55	=	MIRA	.
+RT	HAF3	56	62	=	MIRA	.
+RT	KMRF	62	82	=	MIRA	.
+RT	HAF5	63	109	=	MIRA	.
+RT	KMRF	90	110	=	MIRA	.
+RT	HAF3	110	164	=	MIRA	.
+RT	KMRF	164	184	=	MIRA	.
+RT	HAF5	165	237	=	MIRA	.
+RT	HAF3	238	238	=	MIRA	.
+RT	HAF5	239	266	=	MIRA	.
+RT	HAF4	267	278	=	MIRA	.
+RT	HAF3	279	321	=	MIRA	.
+RT	KMRF	321	341	=	MIRA	.
+RT	HAF5	322	358	=	MIRA	.
+RT	HAF3	359	373	=	MIRA	.
+RT	KMRF	373	402	=	MIRA	.
+RT	HAF5	374	401	=	MIRA	.
+RT	HAF3	402	433	=	MIRA	.
+RT	HAF5	434	508	=	MIRA	.
+RT	KMRF	489	529	=	MIRA	.
+RT	HAF3	509	509	=	MIRA	.
+RT	HAF5	510	538	=	MIRA	.
+ER
+AT	459	968	29	538
+RD	U13a05b10.t1
+RG	1
+RS	ACTTCCCTTGCCGCTGCAGGTCGACCTAACAGGATCCCTGGCTGTATCTGTAATCAAAAAACAGTTCTTCGCAAGTCTGGATGGCTCTCCTGACAAAAACACCTATCCTGTGATCACCATTAACCATCATAACTTTTGCATAGCAGTTTGGATTTACCGAATGATTTGCAAAACGAATTTTGTTACCCTTGCAGGTTGCATCCACCACAAAATCATTGTTCAAGTTGAACAGAAAGCTGCACATGTATTTATCACACACTTTCCCTCTTCCGTCAGCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAGAAAAAGAAAATGCCGTTTGAAATTCTGAATTTGCAAAGTACTATAAGAATAATTTATAGCAAGGAGTTTAAAACTCAACTTTTTATTGCCTTCTCACCaGCTGCAAAGTGTTTTGTACCAgTGAATTTTTGCAATAATGCAGTATGGTATATTTTTCAACTTTGAaTAAAGAATACTTGAAAtTGAAAAAAAAAATTGAGTCtGATGGGTCTAGTGTGTTTATAAAATGACTTAAGATCCCACAGTTATTTTAAAGTAATACATTACACCACTGGTATTCATTTTGATGCCATTTTTTTATTTTAAAAAACTAGTCATCCTTGCAGAAGTGTATCTGATTAACTCTTGACAACTACTTTGCCATATTTTATTACCAGCTGCATTTCCCCCCGTGACAGGATAACTAATTTCTATTGTTTTTGTATTTTTGCCGCCACCTTCCAAGATAGCCCTAGGAGTACTGTGTGAAATCCTTGCATCAGAAAGACCTGCTTTAAAATAGTCATAAAGAAAGTAAGAATACATTCAAAAACTCCTTT
+RQ	(+/+*&)))+)))+)+10/79:*-))*.*(.,.***-6====A=>@E==A=>87;:BC<863)*;:A@?=7=CA??:746;BC?????;@=>=A>A993578@@=A?AAA==::=A=@@==?B=>=AAEAAAAB@>?AA?@FAC@BD?;;;??=@@===D==::4-6,25<=8;2<79@@B?;6;>==?984106<>??=0.+*/-/67AB@;5*.37:9==@?=.00*3.5;;;?@@;>4:==????CA;;.,,*-<2,+2,.2245===?A?9=?;>A6>6/669==B=?=<6853*708;873>39?.*)(1-2==:A9=:=?A@@=9<@@<9????>@@AA?;@5<?9@7:9=::305.32.2.95;?A5-))2,*729**608??23???CAC98+.8;>A?@@@-2!)23.664<AAA?:2.>>C@:4!.0465=<12;>56;4*+,3/*C;8@A???>><=CBA:8://01.!,(*<1823...167,,!(21=28677551137943,!)2.2-0>??+/;16;;GAA=1-,+.:<6964626497?7:0084;9AC?AAAAA;;85>-53-1+77?:?;@C;???@7898;;=6::***,)*0/5+.463/.6774,1-8:?@AA=@;A-*4.84.37.,0).1(1;9@</-*,.)**,/5*-663-3-042,,23-,,.024,2::20/,-38/1/34355-1+).++)*//-*2-2+2,-46:>;:,(1**314,+,+)25,*))-+*/--**((+(0//*---*(*++)01--1*,(()(),-?311'+.))'(()17:6-++(+*%,19-(**)*-&'+*..(+**((,*,0))+)()0/
+TN	U13a05b10_1
+QL	37
+QR	676
+AO	1	373	1	373
+AO	374	437	375	438
+AO	438	478	440	480
+AO	479	480	482	483
+AO	481	504	485	508
+AO	505	539	510	544
+AO	540	853	546	859
+RT	HAF5	37	64	=	MIRA	.
+RT	KMRF	45	65	=	MIRA	.
+RT	HAF3	65	119	=	MIRA	.
+RT	KMRF	119	139	=	MIRA	.
+RT	HAF5	120	192	=	MIRA	.
+RT	HAF3	193	193	=	MIRA	.
+RT	HAF5	194	221	=	MIRA	.
+RT	HAF4	222	233	=	MIRA	.
+RT	HAF3	234	276	=	MIRA	.
+RT	KMRF	276	296	=	MIRA	.
+RT	HAF5	277	322	=	MIRA	.
+RT	KMRF	303	323	=	MIRA	.
+RT	HAF3	323	328	=	MIRA	.
+RT	KMRF	328	357	=	MIRA	.
+RT	HAF5	329	356	=	MIRA	.
+RT	HAF3	357	388	=	MIRA	.
+RT	R454	372	373	=	MIRA	.
+RT	HAF5	389	463	=	MIRA	.
+RT	R454	436	437	=	MIRA	.
+RT	KMRF	444	496	=	MIRA	.
+RT	HAF3	464	464	=	MIRA	.
+RT	HAF5	465	493	=	MIRA	.
+RT	R454	477	478	=	MIRA	.
+RT	HAF4	494	494	=	MIRA	.
+RT	HAF3	495	581	=	MIRA	.
+RT	HAF3	585	608	=	MIRA	.
+RT	HAF3	621	676	=	MIRA	.
+ER
+AT	512	1151	37	676
+RD	U13a04c06.t1
+RG	1
+RS	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXATTTTAAACAACCTCTTCTGAAGCAAGATTTAACACAGTACTCTACTGCTATCTTGGAAGGAGGAGGCAAAAATACAAAAACAATAGAAATTAGTTATCCTGTCACGTGGGTTAAATGCAGCTGTTAATAAAATAGGCAAAGTAGTTGTCAAGAGTTAATCAGATACACTTCTGCAAGGATGACTAGTTTTATAAAATAAAATAATGGCATCAAAATGAATACCAGTTGAGTAATGTATTACTTTAAAATAACTGTGGGATCTTAAGTCATTTtATAAACACACTAGACCCATCAGACTCAATTTTTTTTTTCAATTTCAAGTATTCTTTATTCAAAGTTGAAAAATATACCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCTGGTGAGAAGGCCATAAAAAGTTGAGTTTTAAACTCATTGCTATAAATTATTCTTATAGTACTTTGCAAATTCAGAATTTCAAACGGCATTTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAAGCTAAGCTGACGGAAGAGGGAAAGTGTGTGATAAATaCATGTGCAGCTTTCTGTTCAACTTGAACAATGATTTTGTGGTGGATGCAACCTGCA*GGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCaAACTGCTATGCAAAAgTTATGATGGTTAATGGTGATCACAGGATAGGTGTTTTTGTCAGGAGAACCCCCCCAGAATTGCGAAAGAAACTGTTTTTTTTGAATTACCGAATACCAGCCCAGGGCCGAATGCCCATGAAAATTATGTTTGGGCCTTTGAAAAAGAAAAAAATGGGGAAAATCCCCTTTGGACCATTTT
+RQ	!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!@@=B@:6;2@=,?647<>>ADB??:0,1..53392=A2711?AAABAAAAAAAAAB==;667.88,367;=9===867:AAB=A52)..0;;?@CC@???>AAC>@9@;;9>4:>@=8??@;?>>9>@BA??;;;9@;AD@8;5,75<@9/2*777<>A<4,*736AAAB=;;9;86:4:7187ABCDD?=?/*8;AAA:=:@859:?>AAA=B??@@@@@A@??49:5;=C<@=?????>???AAAAD=9>?;;?@==;;6586@8@???34!---58>@@B?:7-837::3+/29;;?C:9.977??7:;;?@>@@AAB?@??>?AA@B684-8@@@?@DAAA>>,*0;?>AB>B>A>A??86@@@B?@=???CGAAC@@@@EBB75;;=;:8415138=?D=78,/.*32:B>>@?;8888C@@@@@A????<6;>9;C=@?87:9:?ADD;74;<AAAAA@@>AB?>@EBBB@A@AAA@;CA=C?7;578?@@@@=@@@@A:;4+486<7/--/2/.5/49?AAA;>7)99?>::7/41./1.75C?<AAAA@@A=8>=0.!*-9BBAAADE@AAAAAA?????9;;;2;8==:<6=A?==:C<677=;==DA?1./*,.1=:,024*,/285CCAA@@65543-)(/-/4=7/,).1!/,,-2)(.().+48.!1**031;8==?<=002-*-./.71.976/.;;;BAB?<7-()(+,)+)+.+()12:*0*(2+,*-0156522/111;5;;=7//,)*(,*,/-+*+1'+09<0),)*()1-(('(,'++10.+61/3--+)+/./,*-*.376588773?:88*-11::515,20,,-+*(()(-+33A<
+TN	U13a04c06_1
+QL	51
+QR	764
+AO	1	660	1	660
+AO	662	897	661	896
+RT	HAF3	51	355	=	MIRA	.
+RT	KMRF	354	406	=	MIRA	.
+RT	HAF4	356	356	=	MIRA	.
+RT	HAF5	357	385	=	MIRA	.
+RT	HAF3	386	386	=	MIRA	.
+RT	HAF5	387	448	=	MIRA	.
+RT	HAF3	449	493	=	MIRA	.
+RT	KMRF	493	522	=	MIRA	.
+RT	HAF5	494	521	=	MIRA	.
+RT	HAF3	522	527	=	MIRA	.
+RT	KMRF	527	547	=	MIRA	.
+RT	HAF5	528	573	=	MIRA	.
+RT	KMRF	554	574	=	MIRA	.
+RT	HAF3	574	616	=	MIRA	.
+RT	HAF4	617	628	=	MIRA	.
+RT	HAF5	629	656	=	MIRA	.
+RT	HAF3	657	659	=	MIRA	.
+RT	HAF5	660	730	=	MIRA	.
+RT	KMRF	711	731	=	MIRA	.
+RT	HAF3	731	764	=	MIRA	.
+ER
+AT	1274	561	51	764
+RD	U13a08f11.t1
+RG	1
+RS	GGGAGTGCACTCGATCTAGAGGACCCTATTTATCACACACTTTCCCTCTTCCGTCAGCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAGAAAAAGAAAATGCCGTTTGAAATTCTGAATTTGCAAAGTACTATAAGAATAATTTATAGCAAGGAGTTTAAAACTCAACTTTTTATTGCCTTCTCACCAGCTGCAAAGTGTTTTGTACCAGTGAATTTTTGCAATTAATGCAGGTATGGTTATATTTTTTCAACCTTTGAATCAAAGGAATACTTTGCAAATCTGGAAACAATAACTATACTTTAAGTCTGAAACTCTGTTCCTGGATGTCGTTTTAATAAAAATATGGACCTTCAACGAATCCCCCACATAGCTTTAATTTTTAAGAAGTTTAAGATACAACATCTTCGACCTTCAAAACTGGGTTAGATATCTCTATTCTTTGGATGGCCCACTTATATTGTCTCTCAGATCTTCTTCTATTACATAACTAATAGCGTCCGGTTCTCACTCTCTCTCTCGACCAGCGAAGGTATGCTGTGCCCTGGAATTGAATACCTCCTTTCGGAACACTACACTGCTACTTTATGGCCCTTATACTTATATAATCTTATATCACTATGAGCCTGGCCATATCTTACACCGCGCGCAGACGGTTGAGAACAGACGATAAGACCACTACACATCTATTCTCATAGATTTGTTTCTATCTGAGTATGATATCTTCTCTGAGCCTCTCCACTCTCCCTTCTCCGAATGAGGCAATATAGCGCACGATGCTCAGAGAAGCGTAGTCGCGTGGTTGGTTTCTCGATAGATCCTCTTCGCCCTCTCTCATGACAAAAGCGAAGCACTCTTGTTCTCTGAACGAGAGTCTAGCTGTCTTTACCAGAGACGGAAATGAGTTGTACTAAATTATACTCTACTCTCGTCCATAAGCATCAGCCGCGCCGTCTCTTATCGCACATCTCTGCTCTCTCAATAGCTATCGTGCATGTATACACAGAGAATAGATCATGCATGTACTCGTATATACGTTATGTCATCACTCTCTCTGCGTAACACATGACGATATCTGCTGATCTGCGCGATCATCTCTCTATTCATATATCATGATAGGGTCGTCTGTGAACACATCACATACTCATCTTATCGCGAGAA
+RQ	''$&'&-&((,/,')68;=2.+&(*.1=:9==9:@@?A?9::=::=BAA???AAAA@@=>==AAC?=>:489/-1(22/===BAAG@????<7;397498/730????A=D??@;<@?>=A8?884/37>@AAC=A::2.2.744??:>;982:A8)'03/97=@?<@@?@A@B@@?::>:;;@=B;95;76886==@C=:?8?:A;5;:7/,/-*20233623-<:6*))*)),,*-*+74596.2//5/.*7:32,/,/2/<,+*)*+/-*2/,-2*-2+--**)+**,-,*++++)()+)())))(,,()(((,,)*),))+)&()))*+'+())&**,3//5+)*((+)*())'((++%()2+:@/-,***(.*,+./)**,.6-))*+***./*,**-1&**((*())+)(,+)*+)*-*+*+/,-.((()(512,)),.,+,*(*+*+/5),'')'0+)()((((..3))*'(()*-,*0(+/+(*))*(()))-))*,'((*,/*))')))*++,*,*()(,(()+((+*,,**)*),&()*.,--3+(+,))(*(+/(,,)*()())((,)+.,)),'''1)+*(*)*0/.-*)+),)(('//(*-+1..*0*.-.+/-4+*))))*/.)+++*),,)))+))+('+))))(()*)))-+4''))''()))))-/0.0+.81/*+*,*+)+,)/,1,,*/,))+,***-)))))+)()))))-0,,+)))('-)*(*++)-62,*)))()++))+-')**.,./)+*()+)))))))()***11.1))''+()+)1)),,))*,,,)*15.*+1***+)+)).&****,,.3*/.-+)),/-**))),)))(+**))+),0*)(($*)()))%.+*+/*)*,+*&)')*0()+()+*)-)(()))))'()'''(()2/,.))-/+-,1+(-'+'')+)))(()),,*)))).)/--)()(-+)()))*,+3-0..-*+()*.++')++')')))%**.6456**,*+))(,(..713+0*,.1))(,)+*)(1())))*,.)*0,)++,+/76,,,,))-)+)+,),(),***,)(*.,,.:,+*+1(((,,)**%,*,)))+*)*5/:/0+(((&))&()))())+*)))(***.02*,())),()*(++*+)))('
+TN	U13a08f11_1
+QL	27
+QR	230
+RT	HAF3	27	57	=	MIRA	.
+RT	KMRF	57	77	=	MIRA	.
+RT	HAF5	58	103	=	MIRA	.
+RT	KMRF	84	104	=	MIRA	.
+RT	HAF3	104	109	=	MIRA	.
+RT	KMRF	109	138	=	MIRA	.
+RT	HAF5	110	137	=	MIRA	.
+RT	HAF3	138	169	=	MIRA	.
+RT	HAF5	170	230	=	MIRA	.
+ER
+AT	721	924	27	230
+RD	U13e07d02.t2
+RG	1
+RS	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXATTTTATACTTTTAGGCACTACTGGTCAAAGTATTTGGGATCTTTTCCAGAATTAACAGTCAAGGT*CCATTTGTTGTCTTGGAATATGTACTTAA*TTATATTAAATTTTAATTTTTGTTTGAGTAATGTTATACTGGTAAAGATTTTTAAAATTGATACTCAGAGCCCATCTTTTCATGTTTTTGTTCAGACCTTATATGTATGCATAATTTATTCAGAGTAGACATCTTTTTTCTTTTTTAATTTAAAATTATAACGTGTTTTTCTATGTATTTTACTTTCTTTATAACTATTTTAAACAAGCTCTTCTGAAGCAAGATTTAACACAGTACTCTACTGCTATCTTGGAAGGAGGAGGCAAAAATACAAAAACAATAGAAATTAGTTATCCTGTCACGTGGGTTAAATGCAGCTGTTAATAAAATAGGCAAAGTAGTTGTCAAGAGTTAATCAGATACACTTCTGCAAGGATGACTAGTTTTATAAAATAAAATAATGGCATCAAAATGAATACCAGTTGAGTAATGTATTACTTTAAAATAACTGTGGGATCTTAAGTCATTTTATAAACACACTAGACCCATCAGACTCAATTTTTTTTTTCAATTTCAAGTATTCTTTATTCaAAGTTGAAAAATATaCCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCtGGTGAGAAGGCCATAAAAAgTTGAGTTTTAAACTCATTGCTATAAATTATTCTTATAGTaCTTTGCAAaTTCagAATTTCAAACGGCaTTTTCTTTTTCTAAATTGCCCACCGTTTCCCGAAGGTTCCTGAAACCAAACTGAACGGAAGAAGGGAAAGTGTGTGAATAACTC
+RQ	!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!=9=;49.-,,66,2(*18=56--1A;CEC?4787<?A;;;A:=BBAA=@@992;A>@D?EAEB894/+75??BD?AAAAA??@=B=@?A??B???AABBEAAAABA@@@?CCFBBBAC@A>???>;AA@ACA?;8817AA?=;8;58?DDBAAAC???>CC93.*9.8CAAABAEDA@>D????A@??5:94>?:@BAA=??A?CDA@CCAB@AADC??97176/6;1?ADABAAAAAADAAAAEAAAAAAAAAAAAD??@??@DDAAA??8===?AAAAAAAADAAABABBBCAADAADDFAD@?CADDD?=A<5;2686==AAAC@AA@DDFCAFD??;;:8AA=>@:=9:==>>=88:+363?=;?@@EDFAAAAA?AA?AA??AAA===C?;<?@??=844.97?A@?:9A97B;;=>>AD9::646+6>2>806669>@??;8@???@=<<;@;E@D@AABAD>=>>=@===AAAEFFAAAAAAA??59?=@?20)),.7<@DC>==9=>A@;6532748?@@;<5<==A;==8==61**0-12173>@<@=A@2935<EBAA??AA??B>81..2988:61*25:<B@CCAADDEAAA??B?AA61-+34/836ADAA@98!8:55-397BD:1+,!.2,.**/+--0?<8-,2*-24=;;5?>/5+,*24.,.+(+))*(-*(,!)-(-*(9,,,,(*.6@AA>!/-/(()+23;67>61)()(*()****,5:>A8;-,-*()!))))),-,!+*,!!5*43,+)))*-3+!,65,*++,/-((+,.36-4,+)+((0,())+&3*.)*++**)/4(5/(3..*)-/0453315702**-*14*-+/+(+.*((++
+TN	U13e07d02_2
+QL	126
+QR	882
+AO	1	145	1	145
+AO	147	175	146	174
+AO	177	721	175	719
+AO	723	773	720	770
+AO	774	797	772	795
+AO	798	833	797	832
+AO	834	836	834	836
+AO	837	855	838	856
+AO	856	869	858	871
+AO	870	943	873	946
+RT	HAF3	153	689	=	MIRA	.
+RT	KMRF	688	740	=	MIRA	.
+RT	HAF4	690	690	=	MIRA	.
+RT	HAF5	691	719	=	MIRA	.
+RT	HAF3	720	720	=	MIRA	.
+RT	HAF5	721	782	=	MIRA	.
+RT	R454	773	774	=	MIRA	.
+RT	HAF3	783	827	=	MIRA	.
+RT	KMRF	827	856	=	MIRA	.
+RT	HAF5	828	855	=	MIRA	.
+RT	HAF3	856	861	=	MIRA	.
+RT	R454	857	858	=	MIRA	.
+RT	KMRF	861	881	=	MIRA	.
+RT	HAF5	862	882	=	MIRA	.
+RT	CRMr	870	870	=	MIRA	.
+ER
+AT	1533	777	126	882
+RD	U13a03g02.t1
+RG	1
+RS	XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTGCAAAGTACTATAAGAATAATTTATAGCAATGAGTTTAAAACTCAACTTTTTATTGCCTTCTCACCAGCTGCAAAGTGTTTTGTACCAGTGAATTTTTGCAATAATGCAGTATGGTATATTTTTCAACTTTGAATAAAGAATACTTGAAATTGAAAAAAAAAATTGAGTCTGATGGGTCTAGTGTGTTTATAAAATGACTTAAGATCCCACAGTTATTTTAAAGTAATACATTACTCAACTGGTATTCATTTTGATGCCATTATTTTATTTTATAAAACTAGTCATCCTTGCAGAAGTGTATCTGATTAACTCTTGACAACTACTTTGCCTATTTTATTAACAGCTGCATTTAACCCACGTGACAGGATAACTAATTTCTATTGTTTTTGTATTTTTGCCTCCTCCTTCCAAGATAGCAGTAGAGTACTGTGTTAAATCTTGCTTCAGAAGAGCTTGTTTAAAATAGTTATAAAGAAAGTAAAATACATAGAAAAACACGTTATAATTTTAAATTAAAAAAGAAAAAAGATGTCTACTCTGAATAAATTATGCATACATATAAGGTCTGAACAAAAACATGAAAAGATGGGCTCTGAGTATCAATTTTAAAAATCTTTACCAGTATAACATTACTCAAACAAAAATTAAAATTTAATATAATTTAAGTACATATTCCAAGACAACCAATGGAACCTTGACTGTTAATTCTGGGAAAAGATCCC
+RQ	!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!DEEEAA=2?777;42;/73E;;=@=@@?@AA>==>=;?BB@@@AA?ABAAABAAAA@AEABAB?A==?@AEEBAAAAADBECCA========?7=3==AABDEEEEDADFA????DB?AAAAAAAE@=@==@@@@=BB==:@@>E?A?AAA?@@A=AAEFBEFE@?==@>;AA???;B==??A?A????AFCABCCDC?A?DAA@????DAA@DAAAAABABEEAAAABAAAA@@CD@BC@ED@A?>?@CBA?B=>>:@EEAAAACAAAAAABBAAABACD?AAA?????@A???8:=5:6;A@DA?AAAECAAA==>=:9ADABC@@==>>DAAAAABABAEEEAAAAABEDA?A:@=<@>A?===8==?ACEAAAAAABAA<<??<?>>;;;ABAAAABA>@@AAAAEEE?AA;=>EAAAD?8A39:<==?????CCDAAB@@=:<=>880424?DADEBAAAEEEEBAABA??AAA?;?9??>@==8@ABBA=AA?@9:C;C;AA@DABCC@ADBEAAABAABBA@=B;;>????;=8<>>=@=AAAA@A><0.2-*30:82/)/,'*11=::A=@;42+99BD56-./(/+-BD@@=:==842?3/*,39=A??<<6.8)053;9AAAA??B?:611-*211*,3-0**.03;A4..56@B;:60.).)+)-.42,*(,*0)*&*1--1+-72054-+02?8:-,0.+,9(+22..'(,10
+TN	U13a03g02_1
+QL	44
+QR	757
+RT	HAF3	44	87	=	MIRA	.
+RT	HAF5	88	162	=	MIRA	.
+RT	KMRF	143	195	=	MIRA	.
+RT	HAF3	163	163	=	MIRA	.
+RT	HAF5	164	192	=	MIRA	.
+RT	HAF4	193	193	=	MIRA	.
+RT	HAF3	194	730	=	MIRA	.
+ER
+AT	820	1533	44	757
+//
+EC
+CO	MIRA_rep_c2
+NR	6
+LC	543
+CT	MIRA	1	5	=		.	Note=Assembled with MIRA
+CT	IUPc	22	22	=		.	Note=Strain 'StrainX': W
+CT	H454	32	32	=		.	Note=No edit. PL: 1 RS: 2 RL: 0 RWTS: 0 EL: 0
+CT	IUPc	42	42	=		.	Note=Strain 'StrainX': Y
+CT	IUPc	173	173	=		.	Note=Strain 'StrainX': K
+CT	IUPc	209	209	=		.	Note=Strain 'StrainX': R
+CT	H454	431	431	=		.	Note=No edit. PL: 3 RS: 4 RL: 0 RWTS: 0 EL: 0
+CT	H454	444	444	=		.	Note=No edit. PL: 5 RS: 4 RL: 0 RWTS: 0 EL: 0
+CT	H454	455	455	=		.	Note=No edit. PL: 2 RS: 4 RL: 0 RWTS: 0 EL: 0
+CT	DGPc	464	464	=		.	Note=G: 3 *: 2  -  40%25
+CT	H454	464	464	=		.	Note=No edit. PL: 1 RS: 3 RL: 0 RWTS: 0 EL: 0
+CT	DGPc	469	469	=		.	Note=A: 3 *: 2  -  40%25
+CT	H454	469	469	=		.	Note=No edit. PL: 3 RS: 3 RL: 0 RWTS: 0 EL: 0
+CT	DGPc	475	475	=		.	Note=T: 3 *: 2  -  40%25
+CT	H454	475	475	=		.	Note=No edit. PL: 4 RS: 3 RL: 0 RWTS: 0 EL: 0
+CT	DGPc	480	480	=		.	Note=T: 3 *: 2  -  40%25
+CT	H454	480	480	=		.	Note=No edit. PL: 1 RS: 3 RL: 1 RWTS: 0 EL: 1
+CT	IUPc	481	481	=		.	Note=Strain 'StrainX': W
+CT	H454	490	490	=		.	Note=No edit. PL: 4 RS: 3 RL: 1 RWTS: 0 EL: 1
+CT	H454	506	506	=		.	Note=No edit. PL: 1 RS: 2 RL: 0 RWTS: 0 EL: 0
+CT	DGPc	520	520	=		.	Note=*: 1 C: 1  -  50%25
+CT	H454	520	520	=		.	Note=No edit. PL: 2 RS: 1 RL: 0 RWTS: 0 EL: 0
+CS	gcaatatcgtgacgatatgtawgataaatacatgtgcagctytctgttcaacttgaacaatgattttgtggtggatgcaacccgcaagggtaacaaaattcgttttgcaaatcattcggtaaatccaaactgctatgcaaaagttatgatggttaacggtgatcacaggatakgtatttttgccaagagagccatccagactggcgaaragctgttttttgattacagatacagccaggctgatgccctgaagtatgtcggcatcgaaagagaaatggaaatcccttgacatctgctacctcctccccctcctctgaaacagctgccttagcttcaggaacctcgagtactgtgggcaatttaaaaaaagaacatgcagtttgaaattctgaatttgcaaagtactgtaagaataatttatagtaatgagtttaaaaatcaactttttattgccttctcaccagctgcaaagtgttttgtwccagtgaa*ttttgcaataatgcagtatggtacatttt*cactttgaataaagaatacttga
+CQ	+&-,(,)+))*(/)0*,120--3??@CC@@@5??@GED:>5,;BFGFGABCC@5???>C@DGF??EHEHDGEHEDACD@ABFDE<67:9>CBBCGEGEBBGIJEHDEHDIFHHHDBDEEDEIIHDEIDHHDEEEDDFGEFEEFFDEGB@?@GADDDDHCCGDBEIF?<E83/*878GGIFFHEEC::=23<CGDEA>;:==<GDFB=<+7/;FHHIIHFJGEFAEB>ACGCHIEDDEJJDDFCCEDGDDFC=2@??=>>6>?DEBDC>;040?CCCCEDHEIDFEDGFAAFEEJHDDDDEEHHEEEEEDFEDHGEHAEFCDEHIGIHGFHHEE@?=69979;=EAD3:/0::?CA?DCEDD??CDDCHG>C?@CBDDDGDDFFBAFFDDG??@AEDCCAHDDDDDDFE><9?=:GDDEDEDHDEDC>A<79C?ACHHDG?DED+HHFDDDDCBB9@B??C?<?1CBB>.CB>??+?HB;9<(5)/C8@<)?HB7=CD@:BHB?>3,>66777BBC;<G5343@7G5<76:47400,-.62++,
+\\
+RD	230375b.t7
+RG	1
+RS	ACGAGCAATATCGTGACGATATGTAAGATAAATACATGTGCAGCTCTCTGTTCAACTTGAACAATGATTTTGTGGTGGATGCAACCCGCAAGGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCAAACTGCTATGCAAAAGTTATGATGGTTAACGGTGATCACAGGATAGGTATTTTTGCCAAgAGTGCCATCCAgACTGGCGAAAAGCTGTTTTTTGATTACAGATACAGCCAGGCTGATGCCCTGAAGTATGTCGGCATCGAAAGAGAAATGGAAATCCCTTGACATCTGCTACCTCCTCCCCCTCCTCTGAAACAGCTGCCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAAAAAAAGAACATGCAGTTTGAAATTCTGAATTTGCAAAGTACTGTAAGAATAATTTATAGTAATGAGTTTAAAAATCCACCTTTTAATGCCTTCCCACCACGCTGCAAAGTTTTGTTGTTCCACTGAAATTTTTGCCATAAATGCCGTAATGTTCATTTTTCCCCCTTGAAAAAAAAGAACTTTGAACTTGGAGCCGGTCGCCGTGGCTTAAGATTTTTTTTTAACCGGCCGCGAAGCCTTATTCCCCTTTAATTGAGGGGGTTTATTTTTAAACTTGGGCCCTTGGCCCCCCCTTTTTACAAACCTTCTTAAATTGGGAAAAAACCCTGGGTTTTCCCCAACTCTTAACCGCCTTGGAAAGCAAATCCCCCCTTTTCCCCCCAGTGGGGGTTTATTACCAGAATAAAGCCGCCCCCCAATTCCCCTCCCCAAAATTTTTCCCCCCCTAATTGCAAATTGGAACCCCCCTGTTACGGCCCTTTAACCCCCGCGGGTGTTTGTGGTTCCCCCCCGTTAACCTAACTTTCCAGCCCCCAACCCCCCCCTTTCCTTTCTCCCTCCCTCCCCCCCTTTCGCGGGTTCCCCTCAACCCTAAATGGGGGCCCTTTG
+RQ	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
+TN	230375b_7
+QL	5
+QR	444
+RT	HAF3	5	25	=	MIRA	.
+RT	HAF4	47	58	=	MIRA	.
+RT	HAF5	59	86	=	MIRA	.
+RT	HAF3	87	87	=	MIRA	.
+RT	HAF5	88	160	=	MIRA	.
+RT	KMRF	141	161	=	MIRA	.
+RT	HAF3	161	215	=	MIRA	.
+RT	KMRF	215	235	=	MIRA	.
+RT	HAF5	216	262	=	MIRA	.
+RT	KMRF	243	263	=	MIRA	.
+RT	HAF3	263	269	=	MIRA	.
+RT	HAF5	270	296	=	MIRA	.
+RT	HAF3	297	318	=	MIRA	.
+RT	HAF4	319	330	=	MIRA	.
+RT	KMRF	330	350	=	MIRA	.
+RT	HAF5	331	367	=	MIRA	.
+RT	HAF3	368	368	=	MIRA	.
+RT	SRMr	368	368	=	MIRA	.
+RT	HAF5	369	436	=	MIRA	.
+RT	KMRF	382	411	=	MIRA	.
+RT	HAF4	437	444	=	MIRA	.
+ER
+AT	1	440	5	444
+RD	230375a.t7
+RG	1
+RS	TTCGAAGGCAATATCGTGACGATATGTATGATAAATAC*TGTGCAGCTTTCTGTTCAACTTGAACAATGATTTTGTGGTGGATGCAACCCGCAAGGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCAAACTGCTATGCAAAAGTTATGATGGTTAACGGTGATCACAGGATAGGTATTTTTGCCAAGAGTGCCATCCAGACTGGCGAAAAGCTGTTTTTTGATTACAGATACAGCCAGGCTGATGCCCTGAAGTATGTCGGCATCGAAAGAGAAATGGAAATCCCTTGACATCTGCTACCTCCTCCCCCTCCTCTGAAACAGCTGCCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAAAAAAAGAACATGCAGTTTGAAATTCTGAATTTGCAAAGTACTGTAAGAATAATTTATAGTAATGAG*TTAAAAATCAACTTTTTATTGCC*TCTCACCA*CTGC*AAGTG*TTTGTCCAGTGAATTTTGCATAATGCATATGTACATTTCACTTGATAAAATTCTGACTTGAAAAAAAAAAAAAAATTTATACGCCACTACCTTATAGTATTACTGCCGCCTTCACTTAGGAACTGGTACATACCTCACACACCTCCCTGGTATACAAGCGCCATGCCTCACATGCCCTTATGGATGGACCCCTTCGCCTTACCGCGGGTTTGTGTACCCATTACGTACTTGCCACCCTAACCCCGCTCCTTCCTTTTTCCTCTTCCCCCCATTCCGGGTTTCCCTAACTCTAAAGTGGGGGCCCTTG
+RQ	'%)&=995+)+(+)+))*(.).*+//0,.2===;9/3*,/67A@A8;4.:?DD=====A>9====@>>:C:=AABAAAB===68>::>>=?:-.44:????B==::8=@CAA<A?@A?AAAA>===A=AAAAAAAAA?AAAAAAAA@@@AC@BA======A@@===:=@=>A@;:C3/-*326?@@AAEA>81'.%&*,5;<884)937==A@;:,6,6?AABEEAGB@@;;:94=A;AFAAABGG??>===@DAAC@;1;6965:19::B<?A75/1/5A?AAAAAAFAA@===:=8@?EAAAAA?B=>@=AA??BA@E??E<=9<8?BBBEEAAAAAA=:3377268;;;;/8+.584;;4==@>A==:==??9:3376;====A@=?====??===>?==@==E@?A?7;C?<5*7249@?BAAAA?AA?<?73699;?AE@==?A@AAAAA@A;<,,*(+,0@6.21103***.+3666601-)+/8@;:==E@==>?<;9772,341::30,14:64))0-820,*,,()'(..-.,4:?9931/52*))*,)))*-*14,*(01(*./1,++/36522<89.*-.,-*&2**(**/1.,++)-.-+,.,,(%++1+%+--,,(.,(00/+&+0.+3,,*+(.+,,-03/.,++)((,0,+1..+622*,-)(+*+1+++-++('.0*),&()*/.(*+)*))0(),,*((-++)+('02*//.--)(%((*,2/1..-,8),/-*((,+*,*2.+*(+1+.20-.,,)+))*5..0*-+,/*'
+TN	230375a_7
+QL	8
+QR	487
+AO	1	38	1	38
+AO	40	437	39	436
+AO	439	461	437	459
+AO	463	470	460	467
+AO	472	475	468	471
+AO	477	481	472	476
+AO	483	789	477	783
+RT	HAF3	8	28	=	MIRA	.
+RT	HAF3	40	49	=	MIRA	.
+RT	HAF4	50	61	=	MIRA	.
+RT	HAF5	62	89	=	MIRA	.
+RT	HAF3	90	90	=	MIRA	.
+RT	HAF5	91	163	=	MIRA	.
+RT	KMRF	144	164	=	MIRA	.
+RT	HAF3	164	218	=	MIRA	.
+RT	KMRF	218	238	=	MIRA	.
+RT	HAF5	219	265	=	MIRA	.
+RT	KMRF	246	266	=	MIRA	.
+RT	HAF3	266	272	=	MIRA	.
+RT	HAF5	273	299	=	MIRA	.
+RT	HAF3	300	321	=	MIRA	.
+RT	HAF4	322	333	=	MIRA	.
+RT	KMRF	333	353	=	MIRA	.
+RT	HAF5	334	370	=	MIRA	.
+RT	HAF3	371	371	=	MIRA	.
+RT	SRMr	371	371	=	MIRA	.
+RT	HAF5	372	440	=	MIRA	.
+RT	KMRF	385	414	=	MIRA	.
+RT	HAF4	441	463	=	MIRA	.
+RT	HAF3	464	487	=	MIRA	.
+ER
+AT	1	480	8	487
+RD	230375c.t7
+RG	1
+RS	ATGCGAGCAAGATGGGACGATATGTGGGATAAATACATGTGCAGCTTTCTGTTCAACTTGAACAATGATTTTGTGGTGGATGCAACCCGCAAGGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCAAACTGCTATGCAAAAGTTATGATGGTTAACGGTGATCACAGGATATGTATTTTTGCCAAGAgAGCCATCCAgACTGGCGAAAAGCTGTTTTTTGATTACAGATACAGCCAGGCTGATGCCCTGAAGTATGTCGGCATCGAAAGAGAAATGGAAATCCCTTGACATCTGCTACCTCCTCCCCCTCCTCTGAAACAGCTGCCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAAAAAAAgAACATGCAGTTTGAAATTCTGAATTTGCAAAGTACTGTAAGAaTAATTTATAGTAATGAgTTTAAAAATCAACTTTTTATTGCCTTCTCACCAGCTGCAAAgTgTTTTGTTACAGTGAA*TTTTGCAATAATGCAGTATGGTACCTTTTTCCACCTTTGAATAAAGAAAACTTGAACTTGAGGGACCCCCCGGGGCCGGGTCTACTTTCTTTTTTTTATGCCGGGCGCAAACCTTAACCCCCTTAATTGAGGGGTTTAATTTTAACCTTGGGCCCTGGGCCCTTCTTTTTTACAACCTTCCTTGACGTGGGAAAAACCCCTGGGCGTTTCCCCCACCTCTAATTCCCCCTGGGGGAACATATCCCCCCTTTCCGCCCAACTTTGGGTTTTTTTACCAAAAGAAAGGCCCCCCCCCGATATTCCCCCTCTCCCAACATTTTTGCCCCCCCCTTAATTGGGAAAATTGGGACCCCCCCCTTTTCCGGGCCCTTTATACCCCCGGGGGGTTTTTTGGTTTTCCCCCCCCCTTTACCCCCTTCCATTGTCCAAGGCCCCTTAGGCCCCCCCCCTTCCCCTTCTCTCCCCTTCCTTTCCCCCCCATATTGCCCGGTTCCCCTTATAACTTCTTAATTTGGGGGCCCCTTTGGG
+RQ	'&$).35,1-%-)/)'*,(-/++3-,+*2.=9489;:;=>DAA17***9<@CC?@=;3+/174@:=;?::BAAAAAAD??;@7/1:9?A915256;::@;BDB??AAGAAABEACCAAAA>@A=:?5>AA@F@?D@AAAA@CDA><5*873?9====?A>?;9;5?===@C:0:1..)566DCCCC??8A8./!0,4?97212!3.6@==956*/.6CCAEEE=@??;88241:=?BCA??A<AA5:@>B@DAAA?;.<4334.,1469:5709,3,3:<====>=F@CB?D==55BBGA??????AAABB???C???CB>5848>>CCDAC>8.10*)12/7767958,1&&..48,*22=:A?A==;=@@?E!7::9?=<=AA>9=/.-+*+1/6377801.06<0,1*)(1*).!&.4?A84,*(/3.4*-!133.++*+)***1139544,/**+'*(&0-27(&,)'-*2*!+!*343((.)-*-+*3:51..('),1/,+*))(%)'+(**(+(,534(),))+596-/2,20<041)+-,2)-+)+()*&&(*.*,-&&&&$$&&&%%&&)*&'),*122*,-0*.&*(*.+()*(*-)+,,**)*643()0*,-***/0/4.+-++,39<4+,**)024,,,)+-,,0-()*(756,+)()+(')***-(()))+++--2365.1/,+++))'+-+(-33*-'),')),)+,,17-.+,+(()%$)()+)+/?D<,0.(++50++%),()22+&-3.*-*))+)-00,0-,,+*+-,2-571(*.)**08-+)))))()**)+,+3,,**64A8984-/1++-+,++1+*-(+0)**.5664-+3-0+*-,,-*..,/*,)+*/77-2,1))))+*2.*))**+(*..24-*+*,,--****(*''''),)('(*(&()+)))&.(),356;886-4.,.)))'(*,)+,***(112*))),*),(%.&,*)))(,/09./,*(()+..)&)*)(***)%,**-****(,,*)**
+TN	230375c_7
+QL	28
+QR	519
+AO	1	401	1	401
+AO	402	476	403	477
+AO	478	494	478	494
+AO	496	1023	495	1022
+RT	HAF3	28	47	=	MIRA	.
+RT	HAF4	48	59	=	MIRA	.
+RT	HAF5	60	87	=	MIRA	.
+RT	HAF3	88	88	=	MIRA	.
+RT	HAF5	89	161	=	MIRA	.
+RT	KMRF	142	162	=	MIRA	.
+RT	HAF3	162	216	=	MIRA	.
+RT	KMRF	216	236	=	MIRA	.
+RT	HAF5	217	263	=	MIRA	.
+RT	KMRF	244	264	=	MIRA	.
+RT	HAF3	264	270	=	MIRA	.
+RT	HAF5	271	297	=	MIRA	.
+RT	HAF3	298	319	=	MIRA	.
+RT	HAF4	320	331	=	MIRA	.
+RT	KMRF	331	351	=	MIRA	.
+RT	HAF5	332	368	=	MIRA	.
+RT	HAF3	369	369	=	MIRA	.
+RT	SRMr	369	369	=	MIRA	.
+RT	HAF5	370	437	=	MIRA	.
+RT	KMRF	383	412	=	MIRA	.
+RT	R454	398	399	=	MIRA	.
+RT	HAF4	438	443	=	MIRA	.
+RT	HAF5	444	485	=	MIRA	.
+RT	HAF3	486	494	=	MIRA	.
+RT	HAF5	496	518	=	MIRA	.
+RT	KMRF	499	519	=	MIRA	.
+RT	HAF3	519	519	=	MIRA	.
+ER
+AT	23	514	28	519
+RD	122533a.t7
+RG	1
+RS	GTTCGAGCAATATCCCTACGATCAACTAGAACAATGATTTTGTGGTGGATGCAACCCGCAAGGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCAAACTGCTATGCAAAAGTTATGATGGTTAACGGTGATCACAGGATAGGTATTTTTGCCAAGAGAGCCATCCAGACTGGCGAAGAGCTGTTTTTTGATTACAGATACAGCCAGGCTGATGCCCTGAAGTATGTCGGCATCGAAAGAGAAATGGAAATCCCTTGACATCTGCTACCTCCTCCCCCTCCTCTGAAACAGCTGCCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAAAAAAAGAACATGCAGTTTGAAATTCTGAATTTGCAAAGTACTGTAAGAATAATTTATAGTAATGAG*TTAAAAATCAAC*TTTTATTGCCTTCtCACCA*CTGC*AAGTG*TTTG*TACCGTGAA*TTTTGCAATAATGCCATATGGTACATTTTCCACTTTGAATAAAGAATACTTGAGCTTGAAAAAAAAAAAAAAAAAAGATTCTTTATTTAAGCGGCCGCGAGCTTTTCCCTTTAATAGGGTTAATTTAACTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
+RQ	&&&,1/?/,/(+)+'('+)(1.+*+,0**1-1574=====EBAABA=:=56;6879=>7-025<???@BA>>>;?ACBA?A?AAAEBEA?ABAA=FF@@??AA?@AA?A=@=A<<ACAAAD?==>@==@=@E=@@A@=A@;2:22-&623@DFBAABB=59;/888B?B?<72;;:@==84.)1,9AAEEFECB???;B?<>??;BCBAAAAAA?==>=@DA??;7.<8<524/37AA??><.,1.87====AEB@AAA===869BA@?=@=?AAAABBABBABAAAAAC==A??ABBBEEDAEEBA97:053064:A7;)2,,2.63:5==>=@:::A@;A=7A==A?AAA?A=9====??=D====B@@=:E=A@AAA?;4:6=64==?AABAB05**33/,.116>E@==9=:=;:?@=:A=466,-)!*..--./12310627:636668;.,*(1,9976E<6;5@=8=@8-(/))..033AAA:992/2/>674;65936400,-.62++,$**-8;34.**)118''4.**)+)))).11,**..-(.()+*))+$)$+')12,02*,.-,+*(,6*)*)1)(..8'!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+TN	122533a_7
+QL	27
+QR	517
+AO	1	404	1	404
+AO	406	417	405	416
+AO	419	431	417	429
+AO	433	437	430	434
+AO	439	442	435	438
+AO	444	448	439	443
+AO	450	453	444	447
+AO	455	463	448	456
+AO	465	968	457	960
+RT	HAF3	27	28	=	MIRA	.
+RT	HAF5	29	56	=	MIRA	.
+RT	HAF3	57	57	=	MIRA	.
+RT	HAF5	58	130	=	MIRA	.
+RT	KMRF	111	131	=	MIRA	.
+RT	HAF3	131	185	=	MIRA	.
+RT	KMRF	185	205	=	MIRA	.
+RT	HAF5	186	232	=	MIRA	.
+RT	KMRF	213	233	=	MIRA	.
+RT	HAF3	233	239	=	MIRA	.
+RT	HAF5	240	266	=	MIRA	.
+RT	HAF3	267	288	=	MIRA	.
+RT	HAF4	289	300	=	MIRA	.
+RT	KMRF	300	320	=	MIRA	.
+RT	HAF5	301	337	=	MIRA	.
+RT	HAF3	338	338	=	MIRA	.
+RT	SRMr	338	338	=	MIRA	.
+RT	HAF5	339	407	=	MIRA	.
+RT	KMRF	352	381	=	MIRA	.
+RT	HAF3	408	422	=	MIRA	.
+RT	HAF3	430	455	=	MIRA	.
+RT	HAF5	496	516	=	MIRA	.
+RT	HAF4	517	517	=	MIRA	.
+ER
+AT	53	543	27	517
+RD	122533c.t7
+RG	1
+RS	ACTGAGCAAATCGTTACGATCAATAGAACAATGATTTTGTGGTGGATGCAACCCGCAAGGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCAAACTGCTATGCAAAAGTTATGATGGTTAACGGTGATCACAGGATATGTATTTTTGCCAAGAGAGCCATCCAGACTGGCGAAGAGCTGTTTTTTGATTACAGATACAGCCAGGCTGATGCCCTGAAGTATGTCGGCATCGAAAGAGAAATGGAAATCCCTTGACATCTGCTACCTCCTCCCCCTCCTCTGAAACAGCTGCCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAAAAAAAGAACATGCAGTTTGAAATTCTGAATTTGCAAAGTACTGTAAGAATAATTTATAGTAATGAGTTTAAAAATCAACTTTTTATTGCCTTCTCACCAGCTGCAAAGTGTTTTG*TACAGTGAA*TTTTGCAATAATGCA*TATGGTACATTTT*CACTTTGAATAAAAATACTTGACTTGAAAAAAAAAAAAAAAAATCTTAATAACGGCGCAGCTATCCTTATGAGGTATTTACTGGCCGGCGTCTTACACTCTGATGGAACCTGCTACCACTACGCTGCACACCCCTTCCACTGCTATACAGAGCCACATCCTCCCATGCCACGATGCATGACCCGTCGCCTACCGCGTTGTGTCCCCTACTAATCACCCACCGCCTCTCTCTCTCCCTCCGTCCTACCATGGGCTAGTCATTCTCGCCACAAATATGTA
+RQ	''&$),-0.,&'&)('))--(('(('..1874E;8;=AAAAAA;9A99<1849;>6*/24<;:6=>;9474;?BBA@AE@AAAEAA?ABBA=@@@@?AAEEAA@@>=@===<=AAABA?>====?AAAA@@@A=AA@=:<5-++..-?@ABBAA?:2,7-736B;?892.9:7?==66/)1+3?@EEEEA@D@@;B>8=@D?AF@?AA?A=AA?A?AA??<:6,;6=6661994<=:99.,3,97:=:====?@B??=C>5C@?EE??A?A?AAABBABAAAAADAD??C@AAEFBAEAAAAAA==;520/05.@9@23.+658;;5=8?<;:=:@@9<4*55::=AAADA?;??>CCA?B====BA?A?AAAAAAAAB9:7<88>==AA@<AABA25.1,76=??CB?D<ABABAEAAAAAA@@@>?=;@=8=4;33431..89@=E>100(*1.A7>135,*46AA>8=E;22,,,,,,/-4250:E433273E-30/200*23+1/,+),+*/1=77+*659<2758.,,)*.*)(&'(',+2+.,*.*(.(/.2-8/*-3-3-1=4;:0+.***033-/+,/*0)2.+,)&),,6,/,0%-//33..)))+86.-),(*5133//.+02%-1/9+01+-,*,))*)+,.))).)),-*(26;+3--1,.((,+-/--7//7,0,*8.70*6-%.*)))(+,1)102),)(),,-,28@9<*),1**<=96,***(/36,-+(/9+,,*(+)*0.9;56++-,+.)
+TN	122533c_7
+QL	24
+QR	504
+AO	1	450	1	450
+AO	452	460	451	459
+AO	462	476	460	474
+AO	478	490	475	487
+AO	492	769	488	765
+RT	HAF3	24	25	=	MIRA	.
+RT	HAF5	26	53	=	MIRA	.
+RT	HAF3	54	54	=	MIRA	.
+RT	HAF5	55	127	=	MIRA	.
+RT	KMRF	108	128	=	MIRA	.
+RT	HAF3	128	182	=	MIRA	.
+RT	KMRF	182	202	=	MIRA	.
+RT	HAF5	183	229	=	MIRA	.
+RT	KMRF	210	230	=	MIRA	.
+RT	HAF3	230	236	=	MIRA	.
+RT	HAF5	237	263	=	MIRA	.
+RT	HAF3	264	285	=	MIRA	.
+RT	HAF4	286	297	=	MIRA	.
+RT	KMRF	297	317	=	MIRA	.
+RT	HAF5	298	334	=	MIRA	.
+RT	HAF3	335	335	=	MIRA	.
+RT	SRMr	335	335	=	MIRA	.
+RT	HAF5	336	403	=	MIRA	.
+RT	KMRF	349	378	=	MIRA	.
+RT	HAF4	404	409	=	MIRA	.
+RT	HAF5	410	454	=	MIRA	.
+RT	HAF3	455	476	=	MIRA	.
+ER
+AT	53	533	24	504
+RD	122533b.t7
+RG	1
+RS	CCGAGCAATATCCCCACGATCACTAGAAAATGATTTTGTGGTGGATGCAACCCGCAAGGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCAAACTGCTATGCAAAAGTTATGATGGTTAACGGTGATCACAGGATATGTATTTTTGCCAAGAGAGCCATCCAGACTGGCGAAGAGCTGTTTTTTGATTACAGATACAGCCAGGCTGATGCCCTGAAGTATGTCGGCATCGAAAGAGAAATGGAAATCCCTTGACATCTGCTACCTCCTCCCCCTCCTCTGAAACAGCTGCCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAAAAAAAGAACATGCAGTTTGAAATTCTGAATTTGCAAAGTACTGTAAGAATAATTTATAGTAATGAGTTTAAAAATCAACTTTTTATTGCCTTCTCACCAGCTGCAAAGTGTTTTGTACCAGTGAATTTTTGCAATAATGCAGTATGGTACATTTTCAACTTTGAGATAAAGAATACTTGAGCTTGAAAACAAAAATGTATCTTTATTAAAGCGGCGCAACCTATATCCCTTTTAAGTGAGGGGTTAATTTTAACTTTGGGCCCTGGCCCTCCTTTTTTACCAACCTTCTTTGAACTGGGGAAAAACACCTGGGCTTTTACCCAACCTTTATATCCGCCTTTGGGCAAACAAAATTCCCCCTTTTTTCCGCCAAAGCGGGGGGTTTTTTTTTTACCCAAAAAAAAAGGGCCCGCCCACCCCCTATATTTGCCGCCCCTCTCCTCCCCAAAACAATTTTTCCGCCCCCCCCCCCTTTAAAATTTTTGGGCGCCAAAAAATGTGGGGGGGAAACCCCCCCCCCCCCCTTTTTTTTCCCCCGGCGCGCCCCATATTTTTAAAAACCCCCCCCCCCCGGGGGGTGGTTTTTTTTGTTGGGGGTTTTCCCCCCCCCCCCCCCCCCCACCCTTTTTTTTAAAAACCCCCCTCTATTTTAAAACATCTTTTTGTTGGCCCAAAGACCCCCCCCCCCCCTATTAATAAACCCCCCCCCCCCCCCCCCCCCTTTTTTTGCCCCCTTTTTTCTCCTCTCTCCCCCCCCCCCTTCCCCCCCCTTTTTTCCCCCCCCCCCCCCCCCCATTTTTTTTTTTTTTTTTCCCCGCCCGGGGTGTTTTTCTCCCCCCCCCCCCCTTTTTTAAAAAAAAAACCCTCTCTCTAAAAAAAAAAATTGCGGGGGGGGGGGGGGGCCCCCCCCCCCTTTAGGGGGGGGTTTCTCCCAAAAAATTTTTATTTTTTTCTTTTTTAGGGGGGGCCCTCCCCCCCCCCCCCCCCCCCAAAAAAAAAAATTTTTTTGTTTTTTGGGGGGGG
+RQ	'$(-,-4-)'()**'/4+7*+**,()8)(4/16458AAEAD?368/1:14489>5*-13;@::8D>>>>8>BABB@AAAF?AAA?=@BBA=??A@AAAAAAAABA=@=:=<AAAABA?==>D>?AAAA@=@@=BF@=8<6+,(../@ACBBEAA>44718:ADA@;;99:7:DBC650)2+7AAAFFAA????<;?<??C@@@@??A?A=<==8=AB@?C:6,>==;<<5<=AA?A<<..3,78@==B===@AAAAA@???@AA??A?ABAEEAABBBA?A?A=@@<;9@?ABFBFEBBAAAB>;9453054;B?A05..87=A?=AABAA9:A?A;E6<<9>==AAABAAAA???CAA?=====??=>@=<<8;?=A9:3;;7EAABABAEAAA566:69A==@@EAA=@==@EDCAAAA>====?====:=AAAA==B@===>=@@9:=541.52371=E@4;;9;4@>@>=@?=55666)*,(),--/@;?@120,*)-**./:11(*(++')'.+)'&&&&&'''+)*)+')01-04**(,-2,,**-,.*./52./62722--++,)-(*.2+()+---3//1**2986.0-3-+.-*''()-',.((%(,%*,))))))))*42/05<-24*%+(..*+0+**.62,011+))*+,+-,)*+.-,,())),+)('))*,**))1201.)/52.**+'.-*)))')).40***562/,,,)000,07:DBC0/,,+,))+&-),())).)*+++)+'(&.&.-0>66,*-)1++'-+)*(*+14.,))*(*.),-1772***%*.2,,*&&&%,(()()(,+-**)()*,,7463)*&)*+-.:17DD3+)))))))))*(**'()&&))&&*)(%)()1/*./-'*%(,+2.)&...+)))'+*'&&)))()*1,-)(+(+**,.+))&&'+)*))2.-.2*.**-('))&))**2+,*)&+((()))-))%))&))))))))))$$--0)))')'&)***&)+((((-114*2-+*))$)),(),(&**086><6.-*,)+65=D76),*16/)))+*'*(+*59/.())**.++$--1DE5/-,-)+)(*,,0+,.3)+*+)&&**+**-,-/*./+((()%&++988A8A774.*(&'(+()))-)*0,%(***-.*2-02<BB>94*())))')(')41+/****&))'+'++,*)&(+,,=/-)(()+-()),2A@ED5<A0;2*(.*)53@;23,*-*%)))3285,+**,),**)(*(((,***.&*),,-**%1289,(&-*.*)**,,.%*..3-)+*,+)))*)).0*&*,/5..*)*'*(-,))))))*)0))**,)-.6
+TN	122533b_7
+QL	29
+QR	489
+RT	HAF5	29	52	=	MIRA	.
+RT	HAF3	53	53	=	MIRA	.
+RT	HAF5	54	126	=	MIRA	.
+RT	KMRF	107	127	=	MIRA	.
+RT	HAF3	127	181	=	MIRA	.
+RT	KMRF	181	201	=	MIRA	.
+RT	HAF5	182	228	=	MIRA	.
+RT	KMRF	209	229	=	MIRA	.
+RT	HAF3	229	235	=	MIRA	.
+RT	HAF5	236	262	=	MIRA	.
+RT	HAF3	263	284	=	MIRA	.
+RT	HAF4	285	296	=	MIRA	.
+RT	KMRF	296	316	=	MIRA	.
+RT	HAF5	297	333	=	MIRA	.
+RT	HAF3	334	334	=	MIRA	.
+RT	SRMr	334	334	=	MIRA	.
+RT	HAF5	335	402	=	MIRA	.
+RT	KMRF	348	377	=	MIRA	.
+RT	HAF4	403	408	=	MIRA	.
+RT	HAF5	409	483	=	MIRA	.
+RT	KMRF	464	484	=	MIRA	.
+RT	HAF3	484	489	=	MIRA	.
+ER
+AT	59	519	29	489
+//
+EC
+CO	MIRA_rep_c3
+NR	6
+LC	454
+CT	MIRA	1	5	=		.	Note=Assembled with MIRA
+CT	IUPc	23	23	=		.	Note=Strain 'StrainX': W
+CT	H454	240	240	=		.	Note=No edit. PL: 2 RS: 5 RL: 0 RWTS: 0 EL: 0
+CT	IUPc	279	279	=		.	Note=Strain 'StrainX': R
+CT	IUPc	286	286	=		.	Note=Strain 'StrainX': Y
+CT	IUPc	292	292	=		.	Note=Strain 'StrainX': Y
+CT	IUPc	295	295	=		.	Note=Strain 'StrainX': W
+CT	IUPc	325	325	=		.	Note=Strain 'StrainX': M
+CT	IUPc	352	352	=		.	Note=Strain 'StrainX': M
+CT	IUPc	370	370	=		.	Note=Strain 'StrainX': K
+CT	IUPc	381	381	=		.	Note=Strain 'StrainX': V
+CT	IUPc	397	397	=		.	Note=Strain 'StrainX': Y
+CS	gcgttattaaagacttttttttwtttttttttcaagttcaagtattctttattcaaagttgaaaaatgtaccatactgcattattgcaaaaattcactggtacaaaacactttgcagctggtgagaaggcaataaaaagttgatttttaaactcattactataaattattcttacagtactttgcaaattcagaatttcaaactgcatgttctttttctaaattgcccacagtactcgaggttcctgaagctaaggcagctgtttcagaggagggggargaagtaycaaatytcwagggatttccatttctctttccatgccgamatacttcagggcatcagcctgactgtmtctgtaatcaaaaaacakctcttcgccavtctggatggctctctyggcaaaaatacctatcctgtgatcaccgttaaccatcataacttttgcatagcattt
+CQ	&(*(70+=9;3)+(*.?DDH::**BbhPORHOPYY\]\]ZUJIJNY_b]WTST]YO[b_Z^b]a__]`b[[^\c`eggfddeZ^UZ\]^`Y\\UVVMWaWf`dbfaaaaac^^ge_^LOW[aadYZ]W]_cekdffgfl_\cagcdaegfebbdhcieecfefgebb]WVY]Pee`db`b`^\ge__de_b`Z`[_\]j]gddddgb]UQSCU^W\^N]^gijfffeec_]RPPHXUCK(?GFSXXVRSG[WLSXTMS\NT]Wc^d[(\JRRFWVTYB-.7,/0-*3-;27*58.0/42:<:@GBBDB=;32-64=);*9>><;/;AA@><864=<AE>>/0;=2>*4:3=,7<:3D7+<=7817G@6)3@A@@8<-<;3*79/<4213739;7:9/452<;??A:99734.68/06/1/178A?H4?@><5:>7<65:7?@AAC441%**,01
+\\
+RD	122533c.t3
+RG	1
+RS	CTTGCGTTATTAAAGACTTTTTTTTTGGTTTTTTTCAAGTTCAAGTATTCTTTATTCAAAGTTGAAAAaTGTACCATACTGCATTATTGCAAAAATTCACTGGTACAAAAcACTTTGCAGCTGGTGAGAAGGCAATAAAAAGTTGATTTTTAAACTCATTACTATAAATTATTCTTACAGTACTTTGCAAATTCAGAATTTCAAACTGCATGTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAACCTAAGGGCAGCTGTTTCTGAGGATGGGGAGAAAGTACAAATCTCTGAGGATTTCCATTTCTCCTCCCACCTCTAAATACTCCGCGGCATCTTCCTGAATGTCATATGTTGTGGGCAACTTCTCTTCACAACTCTGGATGGGTCTCTCTGAAAAAATACCTTTCCGTTGAAACTCCGTTAACCTTCTTATTTTTTGCATCCCCGTTTGGATGCCCCCACCTCATCGCCAAACTATTTTTTTTCCCCCTAACTGGTTGCAACCACCCAAAAACTTTGTTCCACTACCCGAACCAATAACTTCGCCCCTATGGCCAATCCCTAAAATGATTCTTTTTTTTCCGGCCCCGTCCTACCCCCCCCTGTTGTGGATTTGGTTTTCCGCTCGCAATTCCCCCTCGTTTTAAACCTGAAACACTGAGGTATAACCCCGGGGGTTCCCAAATTAATTACCTCTCCCACATTAACCCCTTTCCCCCCCACTGCCCGTTTTCCAGTAAAAAAACCCTTTCCTATCCCCCCTCCCCAATAAATTCCCCCCCCCCCCGGGAAAAAGACGGATACCTTCTTTTGGCCCCTCCCCCTCTTCCCCCCCCGTGTGTTATTGTTTGTTCTCCCGCCTTTCTGGCCCGGAAAACTGTGTTTAAACTCCCTCTAGAGAGGCGGTCATTAGGGTTTCCCCACATTCCGGGGTAATCCCCGGTAAAAAAACTTTTCCCCGGCGCGCCCCTAAGGGGGGAGAGAGCCCCAAGGGCGTTTCTCACAGTGTTTTCTCTTAGGCCCCCCCCCCAAAAAAATAATTTGGGTTT
+RQ	&&$)2*(1/*532-))&(.7AAE72&*,&49AA>;=@;AAABA636166?A34566;:57<?::@74(!+53857=DAC=@@AAED@>B??;;<???@A@@D@@C@A81)!*,64=?A;/>>>??9=.0.*.17:=@=@?;;818;??@A?CDDAACF@>=9??ACA<C?C@<C?:>@@@@;?73/88.07C9;/2618?ADAC@@AADA>7>+8;7A<7:4?C@@B@CDDA98*.34A643057698-+24,/*-.),*)((()'+933((1*0,),1191)()212//---*(/)%(),*+.0.222.-211****----*%,&..//-**%*)%4:05993-;7<23)(*11,)))++))*(,/*,.,10.2.()1*(*/)***,.42*-)(3*-<,*,-,*52,*4.-/,(-**)*0))'+$)/,.;:0-4+,-*,,*0421/-,+5,(*)%..+0*+/(),5/33*)(+*(()),)**(+,,5:9*(**)**-,*))*(.*,.**)))**,,**9>7+**)**+.*)'')%(),)++.-*+()(,**)*,+,3.-3//464=4-79)/5;.*)***(++.((/,,3..559/+)(*,*++*,))(-**)**+,)))(-))*/-*,,*,)*+),--2+***,*+)&2731-7/,-*)*-*-/*))**(**-,-9-01*,-+**)/53*-,-***.-))*(+**+,)++++)()*01*0+*-1.-+*))*+*+,)*.0**,(%**)))+--)*.&*++,(()())27+*++*(*,*+++**+,;4/*-53,0()((*+6++*(())(+)(,')-)))(*)(/,,)))++*+*0+*1156-*(((.-****+1)**+**))'+))**+*-,)()-47776;30.),00,+))0*()(*)+++,+(*+*))++*)%*(&%1**,/1,**).**),*)),**+))**13,+)))),***)%*.1:8;;)*..5551-/-,.,-,+)*-33-*)))),**-),10*())*))))*0+*)-001/*,)*+,+20>;::950526/)**-))*+*()*,,,
+TN	122533c_3
+QL	4
+QR	259
+RT	HAF3	4	40	=	MIRA	.
+RT	KMRF	39	91	=	MIRA	.
+RT	HAF4	41	41	=	MIRA	.
+RT	HAF5	42	70	=	MIRA	.
+RT	HAF3	71	71	=	MIRA	.
+RT	HAF5	72	146	=	MIRA	.
+RT	HAF4	147	152	=	MIRA	.
+RT	HAF5	153	252	=	MIRA	.
+RT	KMRF	178	207	=	MIRA	.
+RT	KMRF	212	232	=	MIRA	.
+RT	CRMr	221	221	=	MIRA	.
+RT	HAF3	253	259	=	MIRA	.
+ER
+AT	1	256	4	259
+RD	122533a.t3
+RG	1
+RS	ACGCGTTATTAAAGACTTTTTTTTTGGTTTTTTTCAAGTTCAAGTATTCTTTATTCAAAGTTGAAAaATGTACCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCTGGTGAGAAGGCAATAAAAAGTTGATTTTTAAACTCATTACTATAAATTATTCTTACAGTACTTTGCAAATTCAGAATTTCAAACTGCATGTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAAGCTAAGGCAGCTGTTTCATAGGAGGGGGAAGAAGTATCAAATCTCTTGGGATTTCCATTTCTCTTTCCATGCCGACATACTTCAGGGCATCTTCCTGACTGTCTCTTTTTTCGGGAAACTTCTCTTCGCCAATCTGGATGGCTCTCTCGGCAAAAATACCTATCCTGTGATCACCGTTAACCATCATAACTTTTGCATACCACTTTGGATTTACCACCGATATGCCACAACGATTTTTGTTACCCTTGCAGGTTGCACCACCCAAAATCGTTGTTCTTTTGCCCTTGCCAAATTCTGGGCCCCAAGGGCCAATTCCCCAAAATTAATCCTTTTAATTTCGTGGGCCGCGTTCCAGCTGTCCCCCTTGTTGAAGGTTTTTTTTCGCCCCCCGGCTCTCCCCCCCCCTTTTTAAACCCCGTAAACCATTATAGTTGGTTAAACCCCCGGGGGGTTCCCCCTTGTAAATTTTACCCCCCCCTCTCCCCCATTTAAAAATATGTGCCCTTTTTCTCCCCCCCACTGGGCCCGGGGTTTTCTCCTATTCCGGGGAAAGAAAAACCCTGTTTTCTCTTCGCCAAAATACTCCCCCCCCCCTTTTTATAAAAAAAAAAAAAACTTGGGGGCCCCCACCCCCCCCCGGGGGGGAAAAAAAAAAGCGCGGGGTTTTTGCGCGTTTTTTTTGGGGGGGGGGGGGTTTCTTTTCCCCCCCTTTTTTCCTTCCCCCCCAAAGGAGAAAAAATCTTTTTTGTTGGGGCGCCTCCCGGCGCCCCTCCCGGGGTTGGCGCGGCGAAAACGCGGTTTTTCCCCCCCCCCCAAAGGGGGGGGCGCAGATACCGCGTTTACTCCCCATAAATACTCCGGGGGGGAATAACATCCCGGGAAAAAAAAATTTTATATCTATATATGGGGCCTCCCAAAAAGGGGCATAAAACACGGAGAAACCGGCGCCCTTGTGTGGGCGTTTTTCTCTCAATGGGCGCCCCCCCCCTCAACAAAAATAAAAA
+RQ	'%+2*(6.+;8:2)+(*).1AA88(-,(88AA=;==99@;BC21-,,-8?91695?=5:7?;11,)!*-55==@:BABBAEABABA?BA??;<?<7AAAA?A<<B=9:620576:;@;4>>;@;;7*0/*22;@BCCBE@F?<??DACAAABDAACD?=<B?BB@DA@?B@<@=9B>@??8??678>0,6?9@>8>;?CAEAD??>@DEA>?4>A?C?8;7:A?ACCAADB>=-5;3>:/6-3:6@A4597->58:6318=B?DAA?72*/+.1)01771-.1.+/+).(610)-7-(,0-8968?:/A/4928,))-+1))21/1-6??>9:3-572629.)2510-+,,/5,3,*+.)*.)*+/.7>-..00,+.40:82+68.;2/,-.)+.-+*)**)626;?988623-37./5/1))78@>G<??>;5:>7:/--68;8?A40/,.1--.5:768.4))(())(+%)))+*))**((+(*(*0*--/;::2,+()))++)**,--:2**2/2(*)+,*))+((0-,/*))*+)*+-2+()++/**,,*-=751,,)((*25;(,,2),(-.(*,-+1-.,,./-%.%*1,,'()+)+('%.*)*))0,&(+(),),+++,/*./*,*,))))*)(%%%+-%**,3.+)0**202%-0,,20*/(*,*++))(0())()'(+))17:84.)+1.)))+))41,)$'''))'*0))&),3-,))++-)*+..*',,),+.+.((.**+++),*+,)%(.,/51+()''),.,*/--+(002/((,&+&*,*,+,,,*)*),*)-))*+*%.***,(+))$'&+%)*-'%*0.*+***///+.,,*)*),-*267<;30-(%)**(,1456;63)*,*,+=759.3-.342-*-+0())'))**,)200,)025))++++(*/466,',$))12*&///,)()*)/)+-),2-,**,*1.1.,***,)/,22-*%)),*&/)+',,++)/,**)((()))*,%(*)+)))(*&)).03&1;5:22))+))'.-))+&+/+)))((+*+,33=36-,,3//,+)+)),./+,)*+))*(*)))))%)),)$'+)+,*&)+++,-))**++7702&**1+)-*(*-+)+*)))/1.0.+,-)*)(**.*)**')'')$*.-)42)**00),+*)))%*,)).+.-.****(()(+)-)(()*.())((-*,(++//+,1*.-()/31/8/,/47;7,+(),324)*))(**0C@
+TN	122533a_3
+QL	3
+QR	450
+RT	HAF3	3	39	=	MIRA	.
+RT	KMRF	38	90	=	MIRA	.
+RT	HAF4	40	40	=	MIRA	.
+RT	HAF5	41	69	=	MIRA	.
+RT	HAF3	70	70	=	MIRA	.
+RT	HAF5	71	145	=	MIRA	.
+RT	HAF4	146	151	=	MIRA	.
+RT	HAF5	152	257	=	MIRA	.
+RT	KMRF	177	206	=	MIRA	.
+RT	KMRF	211	231	=	MIRA	.
+RT	SRMr	220	220	=	MIRA	.
+RT	KMRF	238	258	=	MIRA	.
+RT	HAF4	258	269	=	MIRA	.
+RT	HAF3	299	359	=	MIRA	.
+RT	HAF3	400	427	=	MIRA	.
+RT	KMRF	427	447	=	MIRA	.
+RT	HAF5	428	450	=	MIRA	.
+ER
+AT	1	448	3	450
+RD	122533b.t3
+RG	1
+RS	ACGCGTTATTAAAGATTTTTTTTTTGGTTTTTTTCAAGTTCAAGTATTCTTTATTCAAAGTTGAAAAATGTACCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCTGGTGAGAAGGCAATAAAAAGTTGATTTTTAAACTCATTACTATAAATTATTCTTACAGTACTTTGCaaATTCAGAATTTCAAACTGCATGTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAACCTAAGGCAGCTGTTTCAGAGGAGGGGGAGAAAGTATCAAATCTCTAGGGATTTCCATTTCTCTTTCCACGCCGAAATACTTCACGGCATCTTCCTGACTGTCTCTTTATTCGGGCAACATCTCTTCACCACTCTGGATGGCTCTCTCGGCATAAATACCTTTCCGGTGATCTCCGTTAAACTTCTTAATTTTTTGGCATCCCCGTTTGGGATGTACCGCACTGAATTGCAAAAACTAATTTTTGTTTACCCCTTGACGGGTTGCCATCCCACCCCAAAAATCCTTTGTTTCAAATTTGCCTCCGTGACCAAAATAACCTTGGGCCCCCCTAATGGGCCAAATTTCCCCTCATTAGTTTGAATTTCCTTTTTAAATTTTCCCTTGGTCCGCGTTTCCTAAACTCCCTCCCCCCGGTGTTGAGGGTTTGGTTTTTCCCGCCTCGGCAAATTCCCCCCCCTCACTTTTTAAAAACCCCTGTAAACCCACTTGGGTTTTTAAACCCCCTGGGGGGTGTCCCAAAATTTAAAGTTTAACCCAATCCCCACACATTAACTTCCCTTTTCCCCCCCCCTGGCCCGTTTTCTCCTTTCGGGAGAAACCCGTTCTGTTCCCCCCCTCCCTTAAAAAAAATTCCCCCCACCCCCCAGGGAAAAAGCGGTTATATCCTCCTTGGGGCCTCTCCCCCTCTCCCCCCCCCGAGTATATCTTTGGTGTCCCCGGCGCCTTTTTGCCCGGAAAATGTGTTATGCCCCTATAAAGGGGGGTCTATGGGGTTTCCCCCACACCCGGGTTCCCCCGTAATAAACCTTTTTCTCCCCGGCCCCCAGGGCGGAAGCCCCAAGGGGGGTTTCTCATGTTTTTTCATGGGCCCCCCCCCAAAAAATAAAAATTAG
+RQ	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
+TN	122533b_3
+QL	17
+QR	403
+RT	HAF3	17	39	=	MIRA	.
+RT	KMRF	38	90	=	MIRA	.
+RT	HAF4	40	40	=	MIRA	.
+RT	HAF5	41	69	=	MIRA	.
+RT	HAF3	70	70	=	MIRA	.
+RT	HAF5	71	145	=	MIRA	.
+RT	HAF4	146	151	=	MIRA	.
+RT	HAF5	152	251	=	MIRA	.
+RT	KMRF	177	206	=	MIRA	.
+RT	KMRF	211	231	=	MIRA	.
+RT	SRMr	220	220	=	MIRA	.
+RT	HAF3	252	281	=	MIRA	.
+RT	HAF5	298	318	=	MIRA	.
+RT	HAF3	319	320	=	MIRA	.
+RT	HAF3	337	359	=	MIRA	.
+ER
+AT	15	401	17	403
+RD	230375a.t3
+RG	1
+RS	GTCTCTTTTTTAGAAATTTTTTTTTCAAGTTCCAGTATTCTTTATTCAAAGTTGAAAAATGTACCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCTGGTGAGAAGGCAATAAAAAGTTGATTTTTAAACTCATTACTATAAATTATTCTTACAGTACTTTGCAAATTCAGAATTTCAAACTGCATGTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAAGCTAAGGCAgCTGTTTCAAAGGAGGGGGAGGAGGTACCAAATTTCAAGGGATTTCCATTTCTTTTTCGATGCCGACATACTTCAGGGCATCAGCCTGGCTGTATCTGTAATCAAAAAACAGCTCTTCGCCAGTCTGGATGGCTCTCTTGGCAAAAATACCTATCCTGTGATCACCGTCAACCATCATAACTTTTGCATAGCATTTGGATTTTCCGAATTATTTGCTAAACGAATTTTTTACCCCTGGCGGTTTGCATCCACCACCAAAATCATTGTTTCATTTTGAACAGAAAACCGCACATTTTTTTTTTCATTACAACCCCCTTCCCAAATTCTGGGCCCCAAAGGGCAAAATCCCCAAAAATTGAATTCCTTTTTAAATTTCCCTAACCCCTTTTCTAAACTTGTTTCCCTTTTTTTAAAAATTGTTTATCCCCCCCCTCATTTCCTCCCCCACCCTTTTGAAAACCCGGAAAACCTTAAATTTTTTTAAACCCCTGGGGGTTCCCCCAAAAATTGTTAACCCCACCCCTCCCCTTAAAATTGCGCTTGTGTGCGCCCCCCACATGCCCCCCCTTTTCTTAATCGGGAAAGAACCTTTTTTTTCACCACTCTTCCTTTTATAATAAAAAAAATCCGCCCCACCCCCCCCCGGGAAAAAAAAAGGGGGTTTTCTTTTTTTGGGGGGCGCCTCTTCCCCTTTTCTCCTCCCTCCACAAAAAATCTCCTGTGTGCCCCTCGGGTGTCTTTTCGGGGGTGGGGGAAAAAAAAGGTGTTTCTCTCCTCCCCCCCCCCACAAGAGGGGGGGGGGTAAAAATAGGGGTTTTTCCCCCAAAAAATATCTGGGGGGGAGTAATAAAACCCCCCGGGAAAAAAAAAAAAATTTTTTTTTTCATCAAAAGAGGGCGCCGCTCCACAACAAGGGGGCGCAAAAAAAAAACTCTTATAAAAAGGGCGGCGCCT
+RQ	$&&+&)&))+)('+'$&.3AAAA??==736).*()1244=A@8;.&028=@A6:@;?==;>=:5==?AA?A?@A@DG<AAE?===:8DA@???D===@?AAA??==CBA???A@;<</752:=@AAAA=@;2;52@?@AAAA@@@@CEBAAAAAAAAAACAA9?@>AACC????:;@<<<CD5;:*:7:??AAAAA??D??@AAA@AA@@@@DDAAA@A@@?::>8;788*/*461@96/725;>9<=,+-!+*,B=>A97<)1.*7640/),/*./,)2--16,41/6.315:8>D@AAA;9/()533*/39==;:12866<775886?C;;8A8;13-192;,6;9?C>4;=@B@@E8553????7:059/+/-,,,.02638:6931342::==811,.,2,5/,-2)*/1**0,,)*.*,**)*55494=>?65*31%**,017535/-%*/.5/*,,*2,*,%+++2&-)*+1)+50746.**2,,/*+2***2/-*5*)*+05201,))1+))%()$.2.)0.1-%12;00-*,*7**028<6:8,2-()())))(**+0/6/66>B52..-*55;71.-*)0/,-*+5++*1**'*,51**)+&++***,.=503-,*(3+)25).5/,)++,'%))))(+)++2,,+((),,0+)))))(((,)()))).1/./0*-/,4**,,0/6+,())),.,)$**+/37-1,.))(+)')/+*..00+)(.-).22*%0642**.+33+**)),+)**/(**,*))),+)+*-,+()+(*+1+))))(,-++$(-++)+.1*)))(&*)++,+*+032*-(%)&*(*,,,)+$))))*..6/.+))$+)%(&/&*),+.+),,)))'(,*(**)(++*2*+).)),9@A1,)****,****+))&)')%+-/20,034/+)-1-/++,--)20-1)**)(1--+-(')+*+$)),)+240,,-+-+*+))1)*))*,*).+,+*-+,200--5))++))694-10760-)++)*-0-*+)(-+(**--/*)**))')))+0))**+'+**)'''&*-,*+*&)**+-//1-*++/+*,***-+-,202+))./1**2),+,39;52,,*+)))+)/65*))''))7797-**(*()**-,--//2/***..*79,&*&(($)--+.,*,*---30C*))()))+(*)+)(&)*())))***2
+TN	230375a_3
+QL	16
+QR	447
+RT	HAF3	17	33	=	MIRA	.
+RT	HAF5	34	60	=	MIRA	.
+RT	KMRF	41	81	=	MIRA	.
+RT	HAF3	61	61	=	MIRA	.
+RT	HAF5	62	136	=	MIRA	.
+RT	HAF4	137	142	=	MIRA	.
+RT	HAF5	143	248	=	MIRA	.
+RT	KMRF	168	197	=	MIRA	.
+RT	KMRF	202	222	=	MIRA	.
+RT	SRMr	211	211	=	MIRA	.
+RT	KMRF	229	249	=	MIRA	.
+RT	HAF4	249	260	=	MIRA	.
+RT	HAF3	306	316	=	MIRA	.
+RT	KMRF	316	336	=	MIRA	.
+RT	HAF5	317	363	=	MIRA	.
+RT	KMRF	344	364	=	MIRA	.
+RT	HAF3	364	419	=	MIRA	.
+RT	HAF5	421	444	=	MIRA	.
+RT	HAF3	445	447	=	MIRA	.
+ER
+AT	23	454	16	447
+RD	230375b.t1
+RG	1
+RS	CAATGGATCCTTGAATCTTCTACACCTCCCCCTCCTCTGAAACAGCTGCCTTAGCTTCAGGAAC*TCGAGTACTGTGGGCAATTTAGAAAAAgAACATGCAGTTTGAAATTCTGAATTTGCAAAGTACTGTAAGAATAATTTATAGTAATGAGTTTAAAAATCAACTTTTTATTGCCTTCTCACCAGCTGCAAAGTGTTTTGTACCAGTGAATTTTTGCAATAATGCAGTATGGTACATTTTTCAACTTTGAATAAAGAATACTTGAACTTGAAAAAAAAATAAAAAACCAAAAGATCTTTATTTAACCGGCCGCAAGCTTATTCCCTTTAGTGAGGGTTAATTTTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
+RQ	''*,32+,1/4(&)(033,.51,(*01B=@@=AA?@@BB>=383*>8<A:628<=;6<<3..'*,//86*443=????AAAA@A8;,;82;2!2.4:;AAAAAA:C:7??ABAA?????EE@@?????;BA1;4948==AAAA@@ABG?@????@A@>??A<A==DA@BA?D@@AAAA@@??>84.+;<AA@@CA>?>>C<@;@4;3*305:;;@=696554>@@?CC@==>===DAAAAAA@C><A=6;==98?<?>>1426==8:::<8-,'+,.A=92/-+39;+,*'2&))152435/8B?76)516>=B?>??C>>?BABEEAAAA4:33;=9@?A@=<43!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+TN	230375b_1
+QL	25
+QR	282
+AO	1	64	1	64
+AO	66	1235	65	1234
+RT	HAF3	25	37	=	MIRA	.
+RT	HAF4	38	63	=	MIRA	.
+RT	HAF5	64	155	=	MIRA	.
+RT	KMRF	76	96	=	MIRA	.
+RT	SRMr	87	87	=	MIRA	.
+RT	KMRF	101	130	=	MIRA	.
+RT	HAF4	156	161	=	MIRA	.
+RT	HAF5	162	236	=	MIRA	.
+RT	KMRF	217	269	=	MIRA	.
+RT	HAF3	237	237	=	MIRA	.
+RT	HAF5	238	266	=	MIRA	.
+RT	HAF4	267	267	=	MIRA	.
+RT	HAF3	268	279	=	MIRA	.
+ER
+AT	280	23	25	282
+RD	230375b.t3
+RG	1
+RS	CCGCGTTAATAAAGGCCTTTTTTAGGATTTTTTTTTTCAAGTTCCAGTATTcttTATtCAAAgTTGAAAAATGTACCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCTGGTGAGAAGGCAATAAAAAGTTGATTTTTAAACTCATTACTATAAATTATTCTTACAGTACTTTGCAAATTCAGAATTTCAAACTGCATGTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAAgCTAAGGCAGCTGTTTCACATGAAGGGGAAGAATGTACCAAATTTCATGGAATCCATTTCCCCTTCCAATGCCAAATAACTCCGAGGGCTCCACCCTGCCTTTTCTCTGTATCCAAAAAACCCCTCTCGCCCCCTCTCGGAATGGGCTCTCGTGGAAAAAAAACCATCCTCCTGTAATATCCCCGGTAAACCCATTAAAAATTTTCGGCAAAAACTTTGGTGGGATTTCCACGAAATATTTTGCAACAACCAATTTTTTGTCCCCCCCGGCGTGGTCTGCCCCCCACCCAAAACATCCCTTGCTCCTTGTTAAAAAAAAAACGCCCCCCCTTTTTTTTTTCCAACCCCCCCTCCCCTGCCCAAAATCCTGGGCCTCCGGAGAGGGCGCAAAACTCCCCCAAAGAGATAATAGATTCTTTTTAAATTTCCGTAAATCCCTTTTTCACACCTGTGTCTCCCTCGTTTTAAAAAGGGTTTACCCCCCCCACAATTTCTCCCCCCCTCCCTTTCTAAAAACCGGAAAACCCTATAATTTTTTAAACCCCGGGGGGGTGTCCCCAAAGTAGATTTTAACACTCACACCCCCCATTTAAATTGTGCCTTTGCCCCACACTGGGCCCGCCTCTTTCCAATTCGGGAAAAAACCTTTCTTTCCCCCCCCCTATTAATATGAATCCCGCCCACACCCCCGCGGGGAAAAAGAGAGAGGGTGTGGTGCAGTCTTTTGGGGCCCCCCTCCCCTCTCTCTCCCCCCACATAGAAATCCCCTGCGGCGCTCTGCGTGCTCTCTGGTGGCGGGAAAAGGTGTATACTCTCTCTCCTCCTCAAGGGGGGATATCGCACGTGTGTCCCCCTAATCTGCGGAGAGATACCCCGAGAGAGAATAAATTTATACATCATCAGGGGCCCCAATGGGGCAAACACGCCTATAGGGCGC
+RQ	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
+TN	230375b_3
+QL	29
+QR	272
+RT	HAF3	29	45	=	MIRA	.
+RT	HAF5	46	72	=	MIRA	.
+RT	KMRF	53	93	=	MIRA	.
+RT	HAF3	73	73	=	MIRA	.
+RT	HAF5	74	148	=	MIRA	.
+RT	HAF4	149	154	=	MIRA	.
+RT	HAF5	155	260	=	MIRA	.
+RT	KMRF	180	209	=	MIRA	.
+RT	KMRF	214	234	=	MIRA	.
+RT	SRMr	223	223	=	MIRA	.
+RT	KMRF	241	261	=	MIRA	.
+RT	HAF4	261	272	=	MIRA	.
+ER
+AT	24	267	29	272
+//
+EC
--- a/tools/mira4_0/README.rst	Wed Sep 02 07:46:29 2015 -0400
+++ b/tools/mira4_0/README.rst	Fri Oct 02 06:12:23 2015 -0400
@@ -105,6 +105,8 @@
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
         - MIRA 4.0.2 dependency now declared via dedicated Tool Shed package.
 v0.0.8  - Renamed folder now have a MIRA 4.9.x wrapper (internal change only).
+v0.0.9  - Additional unit tests now covering ``miraconvert``.
+        - Was missing ``mirabait`` wrapper since move to using Planemo.
 ======= ======================================================================
 
 
@@ -112,23 +114,23 @@
 ==========
 
 Development is on a dedicated GitHub repository:
-https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_4_0
+https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0
 
 For pushing a release to the test or main "Galaxy Tool Shed", use the following
 Planemo commands (which requires you have set your Tool Shed access details in
 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mira4_0/
+    $ planemo shed_update -t testtoolshed --check_diff tools/mira4_0/
     ...
 
 or::
 
-    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/mira4_0/
+    $ planemo shed_update -t toolshed --check_diff tools/mira4_0/
     ...
 
 To just build and check the tar ball, use::
 
-    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/mira4_0/
+    $ planemo shed_upload --tar_only tools/mira4_0/
     ...
     $ tar -tzf shed_upload.tar.gz 
     test-data/U13small_m.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira4_0/mira4_bait.xml	Fri Oct 02 06:12:23 2015 -0400
@@ -0,0 +1,126 @@
+<tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.9">
+    <description>Filter reads using kmer matches</description>
+    <requirements>
+        <requirement type="binary">mirabait</requirement>
+        <requirement type="package" version="4.0.2">MIRA</requirement>
+    </requirements>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <version_command interpreter="python">mira4_bait.py --version</version_command>
+    <command interpreter="python">
+mira4_bait.py $input_reads.ext $output_choice $strand_choice $kmer_length $min_occurence "$bait_file" "$input_reads" "$output_reads"
+    </command>
+    <inputs>
+        <param name="bait_file" type="data" format="fasta,fastq,mira" required="true" label="Bait file (what to look for)" />
+        <param name="input_reads" type="data" format="fasta,fastq,mira" required="true" label="Reads to search" />
+        <param name="output_choice" type="select" label="Output positive matches, or negative matches?">
+            <option value="pos">Just positive matches</option>
+            <option value="neg">Just negative matches</option>
+        </param>
+        <param name="strand_choice" type="select" label="Check for matches on both strands?">
+            <option value="both">Check both strands</option>
+            <option value="fwd">Just forward strand</option>
+        </param>
+        <param name="kmer_length" type="integer" value="31" min="1" max="32"
+               label="k-mer length" help="Maximum 32" />
+        <param name="min_occurence" type="integer" value="1" min="1"
+               label="Minimum k-mer occurence"
+               help="How many k-mer matches do you want per read? Minimum one" />
+    </inputs>
+    <outputs>
+        <data name="output_reads" format_source="input_reads" metadata_source="input_reads"
+	      label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
+            <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <output name="output_reads" file="tvc_mini_bait_pos.fastq" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
+            <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <param name="kmer_length" value="32" />
+            <param name="min_occurence" value="50" />
+            <output name="output_reads" file="tvc_mini_bait_strict.fastq" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
+            <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <param name="output_choice" value="neg" />
+            <output name="output_reads" file="tvc_mini_bait_neg.fastq" ftype="fastqsanger" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Runs the ``mirabait`` utility from MIRA v4.0 to filter your input reads
+according to whether or not they contain perfect kmer matches to your
+bait file. By default this looks for 31-mers (kmers or *k*-mers where
+the fragment length *k* is 31), and only requires a single matching kmer.
+
+The ``mirabait`` utility is useful in many applications and pipelines
+outside of using the main MIRA tool for assembly or mapping.
+
+.. class:: warningmark
+
+Note ``mirabait`` cannot be used on protein (amino acid) sequences.
+
+**Example Usage**
+
+To remove over abundant entries like rRNA sequences, run ``mirabait`` with
+known rRNA sequences as the bait and select the *negative* matches.
+
+To do targeted assembly by fishing out reads belonging to a gene and just
+assemble these, run ``mirabait`` with the gene of interest as the bait and
+select the *positive* matches.
+
+To iteratively reconstruct mitochondria you could start by fishing out reads
+matching any known mitochondrial sequence, assembly those, and repeat.
+
+
+**Notes on paired read**
+
+.. class:: warningmark
+
+While MIRA 4.0 is aware of many read naming conventions to identify paired read
+partners, this version of the ``mirabait`` tool considers each read in isolation.
+Applying it to paired read files may leave you with orphaned reads.
+
+The version of ``mirabait`` included in MIRA 4.9.5 onwards is pair-aware.
+
+
+**Citation**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
+Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
+Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
+http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
+    </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="bibtex">@ARTICLE{Chevreux1999-mira3,
+        author = {B. Chevreux and T. Wetter and S. Suhai},
+        year = {1999},
+        title = {Genome Sequence Assembly Using Trace Signals and Additional Sequence Information},
+        journal = {Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)}
+        volume = {99},
+        pages = {45-56},
+        url = {http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html}
+        }</citation>
+    </citations>
+</tool>
--- a/tools/mira4_0/mira4_de_novo.xml	Wed Sep 02 07:46:29 2015 -0400
+++ b/tools/mira4_0/mira4_de_novo.xml	Fri Oct 02 06:12:23 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.8">
+<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.9">
     <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
     <requirements>
         <requirement type="binary">mira</requirement>
@@ -177,12 +177,10 @@
             <param name="type" value="none" />
             <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" />
             <param name="maf_wanted" value="true"/>
-            <param name="bam_wanted" value="true"/>
+            <param name="bam_wanted" value="false"/>
             <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
-            <output name="out_bam" file="empty_file.dat" compare="contains" />
-            <!-- TODO: Suggest startswith as a compare method? -->
-            <output name="out_maf" file="header.mira" compare="contains" />
-            <output name="out_log" file="empty_file.dat" compare="contains" />
+            <output name="out_maf" file="U13small_m.mira4_de_novo.mira" ftype="mira" />
+            <output name="out_log" file="empty_file.dat" compare="contains" ftype="txt" />
         </test>
         <!-- Simple assembly based on MIRA's minidemo/solexa1 example
              Note we're using just one repeat group,
@@ -196,7 +194,7 @@
             <param name="maf_wanted" value="false"/>
             <param name="bam_wanted" value="false"/>
             <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" />
-            <output name="out_log" file="empty_file.dat" compare="contains" />
+            <output name="out_log" file="empty_file.dat" compare="contains" ftype="txt" />
         </test>
     </tests>
     <help>
--- a/tools/mira4_0/mira4_mapping.xml	Wed Sep 02 07:46:29 2015 -0400
+++ b/tools/mira4_0/mira4_mapping.xml	Fri Oct 02 06:12:23 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.8">
+<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.9">
     <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
     <requirements>
         <requirement type="binary">mira</requirement>