sblock1267- 12- and 20-way alignments

sblock1267	chr2L:1163545-1163636 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 1163600-1163621
   star strand at position 1163556-1163579
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species	Coordinate	Alignment
dm3	chr2L:1163530-1163651 -	CGAATATGTCCAACCTACAGCAGA--AATCTCCGGGGAAATTGCGATGGC----------------------------------------------------------------------------------AA----------CTGGTCTTATTGTAATTTCGATTCGCCCTC------GCGAATTTCACTCGCTTATTT-CTGACCCAATTTCCCGAATGC
droSim1	chr2L:1135602-1135722 -	CGAATATGTTCAACCTACAGC-----AATCTCCGGGGAAATTGCGATGGC----------------------------------------------------------------------------------TACT-------ACTGGTCTTATTGTAATTTCGATTCGCCCTC------GCGAATTTCACTCGCTCAT-T-CTGACCCAATTTCCCGAATGC
droSec1	super_14:1123583-1123704 -	CGAATATGTTTAACGTACAGC-----AATCTCCGGGGAAATTGCGATGGC----------------------------------------------------------------------------------TACT-------ACTGGTCTTATTGTAATTTCGATTCGCCCTC------GCGAATTTCACTCGCTCATTT-CTGACCCAATTTCCCGAATGC
droYak2	chr2L:1142840-1142972 -	CGAATATATTCAACCTACAACCCAGTAATCTCCAGGAAAATTCCAACTTC----------------------------------------------------------------------------------TGCTCATTCACGTTGGCCTAATTGTAATTTTAATTCGC-CTC------GTA-AATTCACTCGCTTTTTTGCTGACCCAATTCCCTGAATGC
droEre2	scaffold_4929:1208206-1208337 -	CGAACATATTCAACCTACAACCTATTAATCTCGAGGGAAATTGCAATTCC----------------------------------------------------------------------------------TACCCATTCACGGTGGTCTTATTGTTATTTTAATTCGC-CTC------GTA-AATTCACTCGCTTATAG-CTGACCCCATTCCCTGAATGC
droAna3	scaffold_12916:4636831-4636950 -	TCA---------AACAATAACATATAT--ATACC----------------------------------------TAGACTTTTTTTATTGTTGATATTTT--------------------------------TA----------TTCATTAAAGTGTTGTTTTTAATGGC---C------GTTAAATTCACTCGCATATTT-CTGACCCAATTTCCCAGATAC
dp4	Unknown	AGCATCCTTATCAAC---------------------------------------AAATAATTCTCTCGTCAGCCTCGGTGT------------------------------------------------------------------------TTTTAATTTTTTTTCGTAAAT------AATAATTTCACTCGCATATTT-CTGACCCAATTTCCCGAATGC
droPer1	Unknown	AGCATTCGTAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------TAATAATTTCACTCGCATATTT-CTGACCCAATTTCCCGAATGC
droWil1	scaffold_181132:349232-349330 -	CAGATGTTTTGGGACCACAGCAAAAAA-----AA--AAAAAAGCAGAAATTCGCG-----------------------------------------------------------------------------TGCT-------AATGAACGTA-----AT-------------------TAAATTTTCCCTTTACATATTT-ATGACCCAATTTTG----TTT
droVir3	Unknown	ATAAGG-------------------------------ACATGTTATTAATTCACATGTTATGTTttTTttTGtttTtTttT----TTtttTttTttTttTtGTAATTGAACTTATTTACAATGTTCAGCTTGTG-------------------------------------CTCATTAAAAAGCATTTCCCTTGCTTATTT-CTGACCCAATTATCGCCCTGT
droMoj3	scaffold_6500:24978110-24978147 +	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTTCACTTACATATAT-CTGACCCAATTTCCTGCTTGC
droGri2	scaffold_15252:5770169-5770236 +	TTTTTTAAATCAGACTG-------------------------------------------------------------------------------------------------------------------TG---------------------------------CTCATTA------AAGCATTTCACTTGCATATTT-TTGACCCATTTTCCTTCTTTT

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:1163530-1163651 -	NA	CGAATATG-----T-CCAACCT----------ACAGC--AGAAA-----------TC-TCCGGGGA---------------AATTG-------------------------CGATGGCA---------------ACTGGTCTTATTGTAATTTCGA-------TTCGCCCTCG------CG------AATTT--CA-CTCGCTTATTT-CTGACCCAATTT----CCCGAATGC
droSim1	chr2L:1135602-1135722 -	1	CGAATATG-----T-TCAACCT----------ACAGC-----AA-----------TC-TCCGGGGA---------------AATTG-------------------------CGATGGCT------------ACTACTGGTCTTATTGTAATTTCGA-------TTCGCCCTCG------CG------AATTT--CA-CTCGCTCAT-T-CTGACCCAATTT----CCCGAATGC
droSec1	super_12247:184-305 -	2	CGAATATG-----T-TTAACGT----------ACAGC-----AA-----------TC-TCCGGGGA---------------AATTG-------------------------CGATGGCT------------ACTACTGGTCTTATTGTAATTTCGA-------TTCGCCCTCG------CG------AATTT--CA-CTCGCTCATTT-CTGACCCAATTT----CCCGAATGC
droYak2	chr2L:1142840-1142972 -	1	CGAATATA-----T-TCAACCT----------ACAACCCAGTAA-----------TC-TCCAGGAA---------------AATTCC-------A-ACTTCTGCTCATTCACGTTGGCCT---------A-------------ATTGTAATTTTAA-------TTCG-CCTCG------TA------AA-TT--CA-CTCGCTTTTTTGCTGACCCAATTC----CCTGAATGC
droEre2	scaffold_4929:1208206-1208337 -	1	CGAACATA-----T-TCAACCT----------ACAACCTATTAA-----------TC-TCGAGGGA---------------AATTGC-------A-ATTCCTACCCATTCACGGTGGTCT---------T-------------ATTGTTATTTTAA-------TTCG-CCTCG------TA------AA-TT--CA-CTCGCTTATAG-CTGACCCCATTC----CCTGAATGC
droEug1	scf7180000409005:43469-43592 +	1	TAAAAACA----AT-TCGG--------------------------------CCTATC-TTGAGACG---------------TTTTTA----TTAA---TTTTCTTTAATAAAAGCGGCTT---------TT--TA--------------ATTTTATTT-----TTTGCTCTCG------TA------AATTT--AA-ATCGCTTATTT-CTGACCCAATTT----CCTCAATGC
droBia1	scf7180000302188:691215-691325 +	1	AGATTT------------G--------------------------------CCTATC-TGGAGGCT---------------TTTTCG-------A-TTTCTTACTCATTAACGGTGGCGT---------TT--TT--------------AT------T-----TTCGCACTCG------TA------CATTT--CA-CTCGCTTATTT-CTGACCCAATTT----CCGCAATGC
droTak1	scf7180000415264:198414-198531 +	1	CAAATACA-----T-TCGC--------------------------------CCTATC-TTGGGAGA---------------TTTTCA-------A-TTTTTTACTCATTAACGGTGGCTT---------TT--T-----------------TTTAT-T-----TTTGCGCTCG------TA------AATTT--CA-CTTGCTTATTT-CTGACCCAATTT----CCTCAATGC
droEle1	scf7180000491273:2316499-2316606 +	2	TGTACAAG-----T-TCTG--------------------------------TCTATC-TTGAGACA---------------TTTTCA-------A-TTTTTTACTCATTAACGGTGGCAT---------TT--TT--------------TTTTTAA---------------------------------TTCCACG-CTCATTAATTT-CTGACCCAATTT----CCCCAATGC
droRho1	scf7180000766778:451-555 +	1	TGAATACA-----T-GATAGAC----------AGAA---------------CCTATC-TTGAGACA---------------TTTTCA-------A-TTTTGTACTCATTAACGGTGGCTT---------TT--T------------------------------CAA---------------------------CG-CTCGTTAATTT-CTGACCCAATTT----CCCCAATGC
droFic1	scf7180000454155:379877-379982 -	1	CGAATATA-----T-TCAG--------------------------------TCTATC-TTGAGGCG---------------T---------------TTATTACTCATTGATGGTGCCGT---------T-------------AT------------T-----TTTGCGCTCG------TA------AATTT--AA-CTCGCTTGTTT-CTGACCCAATTT----CCTCAATGC
droKik1	scf7180000302405:402582-402723 -	1	AAAATAGG-----T-TCAGGTTTTCATTC---TCTATGTATATA-----------TG-TATATGGG-------------G-TTTTCA-------A-TTCTTCGCTTATTAACTAGGGCAG---------TT--GA--------------TGTGCGATT-----TTTGAGCTCG------TA------AATTT--CATTTCGCATATTT-CTGACCCAATTT----CCCAAATGC
droAna3	scaffold_12916:4636831-4636951 -	1	TCAAAC---------------A----------ATAACATATATA-----------TA-CCTAGACT---------------TTTTTTATTGTTGATATTTTTATTCATTAAA-GTGTTGT---------TT--T------------------------------TAATGGCCG------TT------AAATT--CA-CTCGCATATTT-CTGACCCAATTT----CCCAGATAC
droBip1	scf7180000396737:128183-128307 +	1	AACAATAA-----A-ATTTTAT----------ACAA---------------ACAAGC-CTAGAACT---------------TTTTTTTTTATTGATATTTTTGCTCATTAAAAGTGTCGT---------TG--T------------------------------TTATGCCCG------T-------AATTT--CA-CTCGCATATTT-CTGACCCAATTT----CCCAGATGC
dp4	chr4_group3:9617618-9617737 -	1	AGCATCCT-----TATCAACAA----------ATA-------ATTCTCTCGTCA-GCCTCG-G-TG---------------TTTTTA-------ATTTTTTTACTCATTAGCGGTGA-----------------------------------------------------TCG------TAAATAATAATTT--CA-CTCGCATATTT-CTGACCCAATTT----CCCGAATGC
droPer1	super_8:811321-811439 -	1	AGCATCCT-----TATCAACAA----------ATA-------ATTCTCTCGTCA-GCCTCG--GTG---------------TTTTTA-------A-TTTTTTACTCATTAGCGGTGA-----------------------------------------------------TCG------TAAATAATAATTT--CA-CTCGCATATTT-CTGACCCAATTT----CCCGAATGC
droWil1	scaffold_181132:349232-349350 -	1	CAGATAAGGACATT-GTGT--------------------------------TTTGTT-TTGGGACCACAGCAAAAAAAAAAAAAAG-------------------------CA-----GAAATTCGCGT--GCTA-------------------------------------ATGAACGTAATTAAATTTTC--CC-TTTACATATTT-ATGACCCAATTT----TG----TTT
droVir3	scaffold_12963:5860254-5860409 +	1	AGGACATG-----T-TATTAAT-TCACATGTTATGTT-----AA-----------TT-AATGA------------------AATATA-------A-TTTAAATAA------TAATAATA------------GTAATTGAACACATTTTATTTACAATGTTCAGCTTGTGCTCA------TTAAAAAGCATTT--CC-CTTGCTTATTT-CTGACCCAATTATCGCCCTGTATTT
droMoj3	scaffold_6500:24978110-24978147 +	3	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTT--CA-CTTACATATAT-CTGACCCAATTT----CCTGCTTGC
droGri2	scaffold_15252:5770092-5770236 +	2	AGGACATA-----C-ATAGTAT----------TTATT--------ATTCCATTTATT-TGT--GTA---------------TATTTG-------T-TTTCTTTTTTAATAAAAATAAT------------------TGAAC-CGTTTTTTTTA-AA---TCAGACTGTGCTCATTAA--AG------CATTT--CA-CTTGCATATTT-TTGACCCATTTT----CCTTCTTTT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CGAATATGTCCAACCTACAGCAGA--AATCTCCGGGGAAATTGCGATGGC----------------------------------------------------------------------------------AA----------CTGGTCTTATTGTAATTTCGATTCGCCCTC------GCGAATTTCACTCGCTTATTT-CTGACCCAATTTCCCGAATGC

Size

Hit Count

Total Norm

droSim1

CGAATATGTTCAACCTACAGC-----AATCTCCGGGGAAATTGCGATGGC----------------------------------------------------------------------------------TACT-------ACTGGTCTTATTGTAATTTCGATTCGCCCTC------GCGAATTTCACTCGCTCAT-T-CTGACCCAATTTCCCGAATGC

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

CGAATATGTTTAACGTACAGC-----AATCTCCGGGGAAATTGCGATGGC----------------------------------------------------------------------------------TACT-------ACTGGTCTTATTGTAATTTCGATTCGCCCTC------GCGAATTTCACTCGCTCATTT-CTGACCCAATTTCCCGAATGC

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

CGAATATATTCAACCTACAACCCAGTAATCTCCAGGAAAATTCCAACTTC----------------------------------------------------------------------------------TGCTCATTCACGTTGGCCTAATTGTAATTTTAATTCGC-CTC------GTA-AATTCACTCGCTTTTTTGCTGACCCAATTCCCTGAATGC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...................................................................................................................................................................AATTCGC-TTC------GGA-AATTC..................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
.......................................ATTCCAACTTC----------------------------------------------------------------------------------GGCTCCT....................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

CGAACATATTCAACCTACAACCTATTAATCTCGAGGGAAATTGCAATTCC----------------------------------------------------------------------------------TACCCATTCACGGTGGTCTTATTGTTATTTTAATTCGC-CTC------GTA-AATTCACTCGCTTATAG-CTGACCCCATTCCCTGAATGC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...................................................................................................................................................................AATTCGC-CTC------GTT-AATTCC.................................	19	1	1.00	1.00	0.00	0.00	0.00

droAna3

TCA---------AACAATAACATATAT--ATACC----------------------------------------TAGACTTTTTTTATTGTTGATATTTT--------------------------------TA----------TTCATTAAAGTGTTGTTTTTAATGGC---C------GTTAAATTCACTCGCATATTT-CTGACCCAATTTCCCAGATAC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
....................................................................................ATATTGTTGATGTTTT--------------------------------TA----------...............................................................................	18	1	1.00	0.00	0.00	0.00	1.00
TCA---------CAxAATAACATATAT--A.................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

dp4

AGCATCCTTATCAAC---------------------------------------AAATAATTCTCTCGTCAGCCTCGGTGT------------------------------------------------------------------------TTTTAATTTTTTTTCGTAAAT------AATAATTTCACTCGCATATTT-CTGACCCAATTTCCCGAATGC

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

AGCATTCGTAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------TAATAATTTCACTCGCATATTT-CTGACCCAATTTCCCGAATGC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...ATTCGGAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------TAATAAATTC..................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................................AATGTCACTTGCATATTT-CT...................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................T	19	20	0.05	0.05	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................T	23	8	0.13	0.00	0.00	0.00	0.00	0.13

droWil1

CAGATGTTTTGGGACCACAGCAAAAAA-----AA--AAAAAAGCAGAAATTCGCG-----------------------------------------------------------------------------TGCT-------AATGAACGTA-----AT-------------------TAAATTTTCCCTTTACATATTT-ATGACCCAATTTTG----TTT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
........................AAA-----AA--AAAAGAACAGAAA..............................................................................................................................................................................	18	7	0.43	0.00	0.43	0.00	0.00
.....................AAAAAA-----AA--AAAAAAGAAGA................................................................................................................................................................................	19	34	0.09	0.00	0.09	0.00	0.00
.......................AAAA-----AA--AAAAGAACAGAA...............................................................................................................................................................................	18	6	0.33	0.00	0.33	0.00	0.00
.............AAAACAGCAAAAAA-----AA--AA.........................................................................................................................................................................................	18	15	0.13	0.00	0.13	0.00	0.00
.....................AAAACA-----AA--AAAAAAGCAG.................................................................................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
.......................AAAA-----AA--AAAAGAGCCGAA...............................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......................AAAA-----AA--AAAAGAGCACAA...............................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................ATTGCAAAAAA-----AA--AAAAA......................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................AAA-----AA--AAAGAAACAGAAA..............................................................................................................................................................................	18	6	0.17	0.00	0.17	0.00	0.00
.................CAGAAAAAAA-----AA--ACAAAAG....................................................................................................................................................................................	19	3	0.33	0.00	0.00	0.33	0.00
.............AACACAGGAAAAAA-----AA--AAAA.......................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
........................AAA-----AA--ACAAAAGCAGAAAG.............................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
......................AAAAA-----AA--AAAAAAGAACAAA..............................................................................................................................................................................	20	28	0.04	0.00	0.04	0.00	0.00
......................AAAAA-----AA--AAAAAGGAAGA................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
..............CCACAGGAAGAAA-----AA--AAA........................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
...............AACAGCGAAAAA-----AA--AAAA.......................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.....................AAAAAA-----AA--AAAAAAGAACAAA..............................................................................................................................................................................	21	25	0.04	0.00	0.04	0.00	0.00
......................AAAAA-----AA--AAAAAAGCAAAAA..............................................................................................................................................................................	20	27	0.04	0.00	0.04	0.00	0.00
....................CAAAAAA-----AA--AAAGAAGAA..................................................................................................................................................................................	18	9	0.11	0.00	0.11	0.00	0.00
.....................................................................................................................................................................................................ATTT-ATGAACCAATTGTG----TT.	20	1	1.00	0.00	1.00	0.00	0.00
................................AA--AAAAAAGCAGAAAAAC...........................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
......................AAAAA-----AA--AACAAAGGAGA................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......................AAAAA-----AA--AAAAAAGAAGACA..............................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
.....................AAAAAA-----AA--ACAAAAGAAGA................................................................................................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
.................CCCCAAAAAA-----AA--AAAAAA.....................................................................................................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25
........................AAA-----AA--AAAAAAGAAGAAG..............................................................................................................................................................................	18	8	0.13	0.00	0.13	0.00	0.00
.....................AAAAAA-----AA--AAAAAGGAAGA................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.........................AA-----AA--AAAAAAGCAAAAAA.............................................................................................................................................................................	18	44	0.02	0.00	0.02	0.00	0.00
.....................AAAAAA-----AA--ACAAAAGAAG.................................................................................................................................................................................	18	8	0.13	0.00	0.13	0.00	0.00
.........................AA-----AA--AAAACAGAAGAAAT.............................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.......................AAAA-----AA--AAAAGAGAAGAAA..............................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00
........................AAA-----AA--AAAAAAGGAGAAAAT............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.....................AAAAAA-----AA--AAAAAAACCGAA...............................................................................................................................................................................	20	7	0.14	0.00	0.14	0.00	0.00
.......................AAAA-----AA--AAAAAAAGAGAA...............................................................................................................................................................................	18	43	0.02	0.02	0.00	0.00	0.00
.......................AAAA-----AA--AAAAAAGGAAAAA..............................................................................................................................................................................	19	29	0.03	0.00	0.03	0.00	0.00
......................AAAAA-----AA--AAAAACCCAGAA...............................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............CACAGCACAAAA-----AA--ACAAAA.....................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.......................AAAA-----AA--AAAAAACAAGAA...............................................................................................................................................................................	18	43	0.02	0.00	0.02	0.00	0.00
......................AATAA-----AA--AAAAAAGAAGAAA..............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
........................AAA-----GA--AAAAGAGCAGAAATT............................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............AACAGCAAAAAA-----AG--AAAA.......................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.......................AAAA-----AA--AAAAAAGAACAA...............................................................................................................................................................................	18	46	0.02	0.00	0.02	0.00	0.00
........................AAA-----AA--AAAAAAGAATAAA..............................................................................................................................................................................	18	40	0.03	0.00	0.03	0.00	0.00
......................AAAAA-----AA--AAAAAAGGAGC................................................................................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
................ACAGCCAAACA-----AA--AAAAAA.....................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
..................AACAAAAAA-----AA--AAAAAAGA...................................................................................................................................................................................	19	41	0.02	0.00	0.02	0.00	0.00
..................AACAAAAAA-----AC--AAAAAAG....................................................................................................................................................................................	18	12	0.08	0.00	0.08	0.00	0.00
.AGATATTTTGGGACCAGA............................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......................AAAAA-----CA--AAAAAAGAAGAA...............................................................................................................................................................................	19	6	0.17	0.00	0.17	0.00	0.00
.....................AAAAAA-----AA--AAAGAAGAAG.................................................................................................................................................................................	18	8	0.13	0.00	0.13	0.00	0.00
.......................CAAA-----AA--AAAAAAGAAGAA...............................................................................................................................................................................	18	9	0.11	0.00	0.11	0.00	0.00
......................AAAAA-----CA--AAAAAAGCAGGA...............................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
......................AAAAA-----GA--AAAAAAGCAAAA...............................................................................................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
...............TACAGCAAAAAA-----AA--AAAA.......................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
...................TCAAAAAA-----AA--AAAAAAGAA..................................................................................................................................................................................	19	6	0.17	0.00	0.17	0.00	0.00
........................AAA-----AA--AAAAAGGAAGAAA..............................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
......................AAAAA-----AA--AAAAGAACAGA................................................................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
.....................AAAAAA-----AA--AGAAAAGGAG.................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............AACAGCCAAAAA-----AA--AAAA.......................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......................AAAAA-----AA--AAAAAAGCAAAA...............................................................................................................................................................................	19	37	0.03	0.00	0.03	0.00	0.00
......................AAAAA-----AA--AAAAAAAGAGAA...............................................................................................................................................................................	19	36	0.03	0.00	0.03	0.00	0.00
.................CATGAAAAAA-----AA--AAAAAA.....................................................................................................................................................................................	18	9	0.11	0.00	0.11	0.00	0.00
.................CAGCGAAAAA-----AA--AAGAAA.....................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.....................AAAAAA-----AA--AACAAAGAAGAA...............................................................................................................................................................................	20	5	0.20	0.00	0.20	0.00	0.00
.....................AAAAAA-----AA--AGAAAAGCAGA................................................................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
......................AAAAA-----AA--AAAAAAAGAGA................................................................................................................................................................................	18	47	0.02	0.00	0.02	0.00	0.00
..................AGCAAATAA-----AA--GAAAAAG....................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......................AAAAA-----CA--AAAAAGGCAGA................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.................CGGAAAAAAA-----AA--AAAAAA.....................................................................................................................................................................................	18	7	0.14	0.00	0.00	0.00	0.14
......................AAAAA-----AA--AAAAAAGAATAA...............................................................................................................................................................................	19	29	0.03	0.00	0.03	0.00	0.00

droVir3

ATAAGG-------------------------------ACATGTTATTAATTCACATGTTATGTTttTTttTGtttTtTttT----TTtttTttTttTttTtGTAATTGAACTTATTTACAATGTTCAGCTTGTG-------------------------------------CTCATTAAAAAGCATTTCCCTTGCTTATTT-CTGACCCAATTATCGCCCTGT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.........................................................................TTTTTTTT----TTTTTTTTTTTTT.............................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
.....................................................................TTTTTTTTTTTT----TTTTTTTTT.................................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
..............................................................................TTT----TTTTTTTTTTTTTTTTTT........................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
....................................................................TTTTTTTTTTTTT----TTTTTTTT..................................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
...........................................................................TTTTTT----TTTTTTTTTTTTTTT...........................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
............................................................................TTTTT----TTTTTTTTTTTTTTTT..........................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
..........................................................................TTTTTTT----TTTTTTTTTTTTTT............................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
.................................................................TTTTTTTTTTTTTTTT----TTTTT.....................................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
..................................................................TTTTTTTTTTTTTTT----TTTTTT....................................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
.......................................................................TTTTTTTTTT----TTTTTTTTTTT...............................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
...............................................................TTTTTTTTTTTTTTTTTT----TTT.......................................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
........................................................................TTTTTTTTT----TTTTTTTTTTTT..............................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
...................................................................TTTTTTTTTTTTTT----TTTTTTT...................................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
................................................................TTTTTTTTTTTTTTTTT----TTTT......................................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
......................................................................TTTTTTTTTTT----TTTTTTTTTT................................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
.............................................................................TTTT----TTTTTTTTTTTTTTTTT.........................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
..............................................................TTTTTTTTTTTTTTTTTTT----TT........................................................................................................................................	21	47	0.13	0.02	0.00	0.00	0.02	0.09
...............................................................TTTTTTTTTTTTTTTTTT----TTTTTTTTTTTTTTTTTT........................................................................................................................	36	14	0.21	0.00	0.07	0.14	0.00	0.00
............................................................TTTTTTTTTTTTTTTTTTTTT----TTTTTTTTTTTTTTT...........................................................................................................................	36	14	0.21	0.00	0.07	0.14	0.00	0.00
..............................................................TTTTTTTTTTTTTTTTTTT----TTTTTTTTTTTTTTTTT.........................................................................................................................	36	14	0.21	0.00	0.07	0.14	0.00	0.00
.............................................................TTTTTTTTTTTTTTTTTTTT----TTTTTTTTTTTTTTTT..........................................................................................................................	36	14	0.21	0.00	0.07	0.14	0.00	0.00

droMoj3

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTTCACTTACATATAT-CTGACCCAATTTCCTGCTTGC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TTTTTTAAATCAGACTG-------------------------------------------------------------------------------------------------------------------TG---------------------------------CTCATTA------AAGCATTTCACTTGCATATTT-TTGACCCATTTTCCTTCTTTT

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image