dme-mir-4972- 12- and 20-way alignments

dme-mir-4972	chr2L:3636966-3637073 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 3636992-3637013
   star strand at position 3637030-3637049
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:3636951-3637088 -	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCACCTCG--------------G--------------CTTTACAGATATATATATATATATCGTGTATATATCTGTGCGATCGGGAT------------------TGAGACTGAGGTTGG-TCCGAGTACTTTTGTGGCCA---TTTACACC
droSim1	chr2L:3596396-3596533 -	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCAACTCG--------------G--------------CTTTATATATATGTATATATATCGTGTATATATATCTGAGAGATCGGGAT------------------TGAGACTGAGGTTGG-TCCGAGTACTTTTGTGGCCA---TTTACACC
droSec1	super_5:1737908-1738045 -	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCACCTCG--------------G--------------CTTTATATATATGTATATATATCGTGTATATATATCTGAGAGATCGGGAT------------------TGAGACTGAGGTTGG-TCCGAGTACTTTTGTGGCCA---TTTACACC
droYak2	chr2L:3630931-3631061 -	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCAACTCG--------------A--------------CTtTtTtTGTtTtTtTtTtTt-------TtTtTtTCTGTGAGATCGGGAT------------------TGAGACTGAGGTTGG-TCTCAGTACTTTTGTGGCCA---TTTACACC
droEre2	scaffold_4929:3675838-3675960 -	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCACCTCA--------------G--------------CTATATATATATGT---------------GTGTATCTGTGGGATCGGGAT------------------TGAGACTGAGGTTGG-TCTTAGTACTTTTGTGGCCA---TTTGCACC
droAna3	scaffold_12916:5691742-5691836 -	CACTTGCAAGGCATAAATCAAAAGCGCCGTAGGCCT-CCGCCACT-----------------------------------------------------------------------ATGAGTCT------------------GGAGTCTGGTGATGG-TGGAGTGCCTTTTGTGGCCA---TTGGCACC
dp4	chr4_group3:5095808-5095871 +	CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGAC---------------------------------------------------------------------------TT----------------------------------------TGGAGT-TTTTTGTGGC--------ACAGT
droPer1	super_1:6587322-6587385 +	CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGAC---------------------------------------------------------------------------TT----------------------------------------TGGAGT-TTTTTGTGGC--------ACAGT
droWil1	scaffold_180708:9512363-9512488 +	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTTCCACCTCTATATAGTATAATGTGTTCCACATACTCGAC------------------------------------------TTGGGA-----------------GTTGAATTCGAAGTTG--TCCATGT-CTTTTGTGGCCAAT-TTTACACC
droVir3	Unknown	CACTCGCGTGGCATAAATCAAATGCGTTGCAGGCCG-CCGGC-----------------GCTCCACGCACTCGAC--------------T---------------------------------------------------------------------CCTC---TACTTGCGGCTAGCAGCTCCACT
droMoj3	Unknown	CACTTGTGTGGCATAAATCAAATGCGCAGCAGGCCG-CCAGCTATACCCA---------G--------------C-------------------------------------------------------------------------------CAAGCCAAGTGGTCTTTGGGGCCA---TTTACACG
droGri2	Unknown	CACTTGCATGGCATAAATCAAATGCGCCGCGGGCCT-TTGCTACG-------------TGCCACATGCACTCGAC--------------T--CTCGCCTCTCAACACGACTGACCGAACA---TTGCAGCAGATCGGGGCATTCCACTC----------CAAGTGGTCTTTGAGGCCA---TTTGCACG

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:3636951-3637088 -	NA	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCTCG---------------------------GCTTTACAGATATATATA----------------TATAT-ATCGTGTATAT-----------------------ATCTGTG-------------------------------CGATCGGGATTGA-------GACTGAGG-TTGGTCC---------GAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droSim1	chr2L:3596396-3596533 -	1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------ACTCG---------------------------GCTTTATATATATGTATA----------------TATAT-CGTGTATATAT-----------------------ATCTGAG-------------------------------AGATCGGGATTGA-------GACTGAGG-TTGGTCC---------GAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droSec1	super_5:1737908-1738045 -	1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCTCG---------------------------GCTTTATATATATGTATA----------------TATAT-CGTGTATATAT-----------------------ATCTGAG-------------------------------AGATCGGGATTGA-------GACTGAGG-TTGGTCC---------GAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droYak2	chr2L:3630931-3631061 -	1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------ACTCG---------------------------ACTATATATGTATATA----------------TATATAT--------ATAT-----------------------ATCTGTG-------------------------------AGATCGGGATTGA-------GACTGAGG-TTGGTCT---------CAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droEre2	scaffold_4929:3675838-3675960 -	1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCTCA---------------------------GCTATATATATATGT--------------------------------GTGT-----------------------ATCTGTG-------------------------------GGATCGGGATTGA-------GACTGAGG-TTGGTCT---------TAG-----------------------------------T-ACTTTTGTGGCCA--TTTGCACC
droEug1	scf7180000409554:2446749-2446886 +	1	CACTTGCATGGCATAAATCAAAAGCGCCGTGGGCCT-CCA------CCTAG---------------------------GCTGTATATGTGTGTGCC----AA--------TATATATATGC-----T--------------------AG---ATCTGTA-------------------------------AGATCGGGATTGA-------GACTGAGC-TTGGTCT---------TGG-----------------------------------T-GCTTTTGTGGCCA--TTTACACC
droBia1	scf7180000302408:1936903-1937038 -	1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------ACTCG---------------------------GCTCCATACATATATACA----G------------------------ATAT-----------------------ATCTATG-------------------------------GGATCGGGATTGA-------AACCGAGG-CTGGTCAGCATTACTGCAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droTak1	scf7180000415399:625592-625728 -	1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------ACTCT---------------------------GCTATATATATACA------------------TATATATGCGT-----T--------------------AA---ATCTATG-------------------------------GGATCGGGATTGA-------GACTGAGG-TTGGTCAGTACT----CCG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droEle1	scf7180000490728:350554-350688 -	2	CACTTGCATGGCATAAATCAAAAGCGCCGCAGGCCT-CCA------CTACG---------------------------ATATACCACATATATA----------------TATATATTCATG-------------------------AA---GTCTATG-------------------------------GGATCGGGATTGA-------GACTGAGGCTTGGTCT---------CAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droRho1	scf7180000779523:343635-343767 -	3	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCACG--------------------------------ATATATATGTATA----GA--------TATATGTTCGTG-------------------------AA---ATCTATG-------------------------------GGATCGGGATTGA-------GTCTGGGG-TTGGTCA---------CAG-----------------------------------T-ACTTTTGTGGCCA--TTTACACC
droFic1	scf7180000453924:1625288-1625423 -	1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------GCTCG----------------------------CTATATAC--------A----GA--------TATATATGCGTG-------------------------AA---GTCTATG-------------------------------GGATCGGGACTGAGAACTGGGACCGAGG-TTGGTCG---------CAG-----------------------------------T-ACTTTTGTGGCCA--TTTGCACC
droKik1	scf7180000302270:976219-976364 +	1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCA------CCGCCGACA--CCGCCAGATATTAT----------GTATATATATATATATATATA--------TAT------------ATATACTTGACAG---------AA---ATCTATG-------------------------------GGATCGGGATCGA-------AACTGAGG-TTGG------------------------------------------------------------GTCCA-TTTTACAC-
droAna3	scaffold_12916:5691742-5691836 -	2	CACTTGCAAGGCATAAATCAAAAGCGCCGTAGGCCT-CCG------CCACT---------------------------------------------------------------------------------------------------------------------------------------------ATGAGTCTGGA-------GTCTGGTG-ATGGTGG---------AGT-----------------------------------G-CCTTTTGTGGCCA--TTGGCACC
droBip1	scf7180000396568:1147600-1147682 +	1	CACTTGCATGGCATAAATCAAAAGCGCCATAGGCCT-CCA------C----------------------------------------------------------------------------------------------------------------------------------------------------AGACTACA-------GGCCAGTG-TTGGTGT--------------------------------------------------CATTTGTGGCCA--TTTGCACC
dp4	chr4_group3:5095808-5095886 +	2	CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGACTTTG------GAGTT--------------TTTTGTGGCACAGTGTGTGTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTG
droPer1	super_1:6587322-6587402 +	2	CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGACTTTG------GAGTT--------------TTTTGTGGCACAGTGTGTGTATG----------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG
droWil1	scaffold_180708:9512363-9512488 +	1	CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTTCCA------CCTCT------------------------------ATATA-----GTATA------ATGTGTTC--------------CACATACTCGAC---------------------------------------------------------TTGGGA------GTTGAATTCGAAG-TTG-TCC---------ATG-----------------------------------T--CTTTTGTGGCCAATTTTACACC
droVir3	scaffold_12963:15108661-15108745 +	2	CACTCGCGTGGCATAAATCAAATGCGTTGCAGGCCG-CCG------GCGCT--------------------CCACG-------TTG------------------------------------------CACTCGAC----------------------------------------------------------------------------------------TC---------CTC-----------------------------------T-A--CTTGCGGCTA--GCAGCTCC
droMoj3	scaffold_6500:18077427-18077576 +	2	CACTTGTGTGGCATAAATCAAATGCGCAGCAGGCCG-CCA------GCTGA--CG--C-----------------------------------TGA------CCGTGTTG------------------CACTCGAGTCGAG------------------------T-----------------------------------------------TGAGT-GGAGTCAACTCG----CCGCAGCTTTTCATTCGCATATACCCAGCCAAGCCAAGTGGTCTTTGGGGCCA--TTTACACG
droGri2	scaffold_15126:4287105-4287265 -	2	CACTTGCATGGCATAAATCAAATGCGCCGCGGGCCT-TTG------CTACG---------------------------------TGC---------------------CA--------------CATGCACTCGACTCTCGCCTCTCAACACGACTGACCGAACATTGGCTGGACAAGCCAAGCTGCAGCAGATCGGGGC-----ATTCC-----------ACTCC---------AAG-----------------------------------TGGTCTTTGAGGCCA--TTTGCACG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCACCTCG--------------G--------------CTTTACAGATATATATATATATATCGTGTATATATCTGTGCGATCGGGAT------------------TGAGACTGAGGTTGG-TCCGAGTACTTTTGTGGCCA---TTTACACC

Size

Hit Count

Total Norm

droSim1

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCAACTCG--------------G--------------CTTTATATATATGTATATATATCGTGTATATATATCTGAGAGATCGGGAT------------------TGAGACTGAGGTTGG-TCCGAGTACTTTTGTGGCCA---TTTACACC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.......................................................................................................................GGGAC------------------TGAGGCTGAGGTTG.................................	19	1	2.00	1.00	0.00	0.00	1.00

droSec1

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCACCTCG--------------G--------------CTTTATATATATGTATATATATCGTGTATATATATCTGAGAGATCGGGAT------------------TGAGACTGAGGTTGG-TCCGAGTACTTTTGTGGCCA---TTTACACC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................................................................ATATAGATCGTGTGTATA...................................................................................	18	1	1.00	0.00	1.00	0.00
...............................................................................................................GAGAGATCGGGAG------------------CGAGA..........................................	18	1	1.00	0.00	1.00	0.00

droYak2

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCAACTCG--------------A--------------CTtTtTtTGTtTtTtTtTtTt-------TtTtTtTCTGTGAGATCGGGAT------------------TGAGACTGAGGTTGG-TCTCAGTACTTTTGTGGCCA---TTTACACC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
................................................................................TTTTTTTTTTTTTTT-------TTTTTT.................................................................................	21	40	0.20	0.00	0.00	0.00	0.00	0.20
...................................................................................TTTTTTTTTTTT-------TTTTTTTTT..............................................................................	21	40	0.20	0.00	0.00	0.00	0.00	0.20
...............................................................................TTTTTTTTTTTTTTTT-------TTTTT..................................................................................	21	40	0.20	0.00	0.00	0.00	0.00	0.20
............................................................................TTTTTTTTTTTTTTTTTTT-------TT.....................................................................................	21	40	0.20	0.00	0.00	0.00	0.00	0.20
...........................................................................TTTTTTTTTTTTTTTTTTTT-------T......................................................................................	21	40	0.20	0.00	0.00	0.00	0.00	0.20
.............................................................................TTTTTTTTTTTTTTTTTT-------TTT....................................................................................	21	40	0.20	0.00	0.00	0.00	0.00	0.20
.................................................................................TTTTTTTTTTTTTT-------TTTTTTT................................................................................	21	40	0.20	0.00	0.00	0.00	0.00	0.20
..............................................................................TTTTTTTTTTTTTTTTT-------TTTT...................................................................................	21	40	0.20	0.00	0.00	0.00	0.00	0.20
.............................................................................TTTTTTTTTTTTTTTTTT-------TTTT...................................................................................	22	33	0.21	0.00	0.00	0.00	0.00	0.21
..............................................................................TTTTTTTTTTTTTTTTT-------TTTTT..................................................................................	22	33	0.21	0.00	0.00	0.00	0.00	0.21
............................................................................TTTTTTTTTTTTTTTTTTT-------TTT....................................................................................	22	33	0.21	0.00	0.00	0.00	0.00	0.21
...............................................................................TTTTTTTTTTTTTTTT-------TTTTTT.................................................................................	22	33	0.21	0.00	0.00	0.00	0.00	0.21
...........................................................................TTTTTTTTTTTTTTTTTTTT-------TT.....................................................................................	22	33	0.21	0.00	0.00	0.00	0.00	0.21
................................................................................TTTTTTTTTTTTTTT-------TTTTTTT................................................................................	22	33	0.21	0.00	0.00	0.00	0.00	0.21
.................................................................................TTTTTTTTTTTTTT-------TTTTTT.................................................................................	20	46	0.13	0.00	0.00	0.00	0.00	0.13
....................................................................................TTTTTTTTTTT-------TTTTTTTTT..............................................................................	20	46	0.13	0.00	0.00	0.00	0.00	0.13
................................................................................TTTTTTTTTTTTTTT-------TTTTT..................................................................................	20	46	0.13	0.00	0.00	0.00	0.00	0.13
...............................................................................TTTTTTTTTTTTTTTT-------TTTT...................................................................................	20	46	0.13	0.00	0.00	0.00	0.00	0.13
...........................................................................TTTTTTTTTTTTTTTTTTTT-------.......................................................................................	20	46	0.13	0.00	0.00	0.00	0.00	0.13
............................................................................TTTTTTTTTTTTTTTTTTT-------T......................................................................................	20	46	0.13	0.00	0.00	0.00	0.00	0.13
..................................................................................TTTTTTTTTTTTT-------TTTTTTT................................................................................	20	46	0.13	0.00	0.00	0.00	0.00	0.13
...................................................................................TTTTTTTTTTTT-------TTTTTTTT...............................................................................	20	46	0.13	0.00	0.00	0.00	0.00	0.13
.............................................................................TTTTTTTTTTTTTTTTTT-------TT.....................................................................................	20	46	0.13	0.00	0.00	0.00	0.00	0.13
..............................................................................TTTTTTTTTTTTTTTTT-------TTT....................................................................................	20	46	0.13	0.00	0.00	0.00	0.00	0.13
............................................................................TTTTTTTTTTTTTTTTTTT-------.......................................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
...............................................................................TTTTTTTTTTTTTTTT-------TTT....................................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
....................................................................................TTTTTTTTTTT-------TTTTTTTT...............................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
..............................................................................TTTTTTTTTTTTTTTTT-------TT.....................................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
................................................................................TTTTTTTTTTTTTTT-------TTTT...................................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
.....................................................................................TTTTTTTTTT-------TTTTTTTTT..............................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
.............................................................................TTTTTTTTTTTTTTTTTT-------T......................................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
...........................................................................TTTTTTTTTTTTTTTTTTT...............................................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
..................................................................................TTTTTTTTTTTTT-------TTTTTT.................................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
.................................................................................TTTTTTTTTTTTTT-------TTTTT..................................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
...................................................................................TTTTTTTTTTTT-------TTTTTTT................................................................................	19	51	0.10	0.04	0.00	0.00	0.00	0.06
...............................................................................TTTGTTTTTTTTTTTA-------TTTGT..................................................................................	21	4	0.75	0.25	0.00	0.50	0.00	0.00
...............................................................................TTTGTTTTTTTTTTAT-------TTGT...................................................................................	20	4	0.75	0.00	0.00	0.75	0.00	0.00
............................................................................TTTTTTGTTTTTTTTTTTT-------TTT....................................................................................	22	6	0.33	0.00	0.00	0.00	0.00	0.33
...............................................................................TATTTTTTTTTTTTTT-------TTTTTTT................................................................................	23	34	0.03	0.00	0.00	0.00	0.00	0.03
........................................TCTCG--------------A--------------CTTTTTTTGTTT.......................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.................................................................................TATTTTTTTTTTTT-------TTTTTTTTT..............................................................................	23	34	0.03	0.00	0.00	0.00	0.00	0.03
.............................................................................TATTTTTTTTTTTTTTTT-------TTTTT..................................................................................	23	34	0.03	0.00	0.00	0.00	0.00	0.03
...........................................................A--------------CTTTTTTTTTTTTTTTTTTTT-------TTTTTTTTTG.............................................................................	32	2	0.50	0.50	0.00	0.00	0.00	0.00
................................................................................TTGTTTTTTTTTTGT-------TGTT...................................................................................	19	5	0.20	0.00	0.00	0.20	0.00	0.00
...........................................................................TTCTTGTGTTTTTTTTTTTT-------TTTT...................................................................................	24	6	0.17	0.00	0.17	0.00	0.00	0.00
..............................................................................TATTTTTTTTTTTTTTT-------TTTTTT.................................................................................	23	34	0.03	0.00	0.00	0.00	0.00	0.03
.............................................................................TTCTTGTGTTTTTTTTTT-------TTTTTT.................................................................................	24	6	0.17	0.00	0.17	0.00	0.00	0.00
...........................................................................................................ATCTGTGAGATCGGGAT------------------TGAGACT........................................	24	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................TTTTGTTTTTTCTTTGT-------TTTTT..................................................................................	22	4	0.25	0.25	0.00	0.00	0.00	0.00
................................................................................TTGTTTTTTTTTTTT-------TGTA...................................................................................	19	6	0.17	0.00	0.00	0.17	0.00	0.00
............................................................................TATTTTTTTTTTTTTTTTT-------TTTT...................................................................................	23	34	0.03	0.00	0.00	0.00	0.00	0.03
........................................................................................TTTTTTT-------TTTTTTTCAGG............................................................................	18	4	0.25	0.25	0.00	0.00	0.00	0.00
............................................G--------------C--------------CATTTTTTGTTTTTTTTTTTT-------.......................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................................................TATTTTTTTTTTTTTTTTTT-------TTT....................................................................................	23	34	0.03	0.00	0.00	0.00	0.00	0.03

droEre2

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCACCTCA--------------G--------------CTATATATATATGT---------------GTGTATCTGTGGGATCGGGAT------------------TGAGACTGAGGTTGG-TCTTAGTACTTTTGTGGCCA---TTTGCACC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...........................................................................TATATATATATGT---------------GAGTGT................................................................................	19	1	2.00	0.00	0.00	0.00	2.00
..................................................................................ATATGT---------------GTGTATATGTGT..........................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................GTxTTGCTGTGGGATCGGGA..................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..........................................................................ATATATATGTATGT---------------GTGT..................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
..............................................................................ATATGTGTGT---------------GTGTATCTGT............................................................................	20	1	1.00	0.00	0.00	1.00	0.00
...................................................................................TATGT---------------GxGGATCTGTGGGA........................................................................	18	1	1.00	1.00	0.00	0.00	0.00
................................................................................ATATATGT---------------GTGTGTGTGT............................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...................................................................................TATGT---------------GGGTAACTGTGGGA........................................................................	19	1	1.00	0.00	0.00	1.00	0.00
............................................A--------------x--------------xTATTCATATATGT---------------GTGT..................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...........................................................................TATATATATATGT---------------GGGTGT................................................................................	19	1	1.00	0.00	0.00	0.00	1.00

droAna3

CACTTGCAAGGCATAAATCAAAAGCGCCGTAGGCCT-CCGCCACT-----------------------------------------------------------------------ATGAGTCT------------------GGAGTCTGGTGATGG-TGGAGTGCCTTTTGTGGCCA---TTGGCACC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.........................................................................................................................GCT------------------GGACTCTGGTGATGG-T..............................	19	1	3.00	1.00	2.00	0.00	0.00
...........................................................................................................................................................GG-TGGAGAGCCTTTTTTG...............	18	1	2.00	0.00	2.00	0.00	0.00
...............................................................................................................................................GAGTCTGGTGATGG-GGC............................	17	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................................GAGCTGG-TGGAGTGCCT.....................	17	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................................................CTGGTxATGG-TGGACTGC.......................	17	1	1.00	0.00	0.00	1.00	0.00

dp4

CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGAC---------------------------------------------------------------------------TT----------------------------------------TGGAGT-TTTTTGTGGC--------ACAGT

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGAC---------------------------------------------------------------------------TT----------------------------------------TGGAGT-TTTTTGTGGC--------ACAGT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..............................AGGACT-GAxAC---------------------------------------------------------------------------TT----------------------------------------TGGAGT-.......................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................AGGACT-GAxAC---------------------------------------------------------------------------TT----------------------------------------TGGAGT-T......................	19	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTTCCACCTCTATATAGTATAATGTGTTCCACATACTCGAC------------------------------------------TTGGGA-----------------GTTGAATTCGAAGTTG--TCCATGT-CTTTTGTGGCCAAT-TTTACACC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...............AATCACAAGCGACGTAGGCCT.........................................................................................................................................................	21	1	196.00	8.00	1.00	0.00	187.00
..............AAATCACAAGCGACGTAGGCC..........................................................................................................................................................	21	1	28.00	6.00	1.00	2.00	19.00
..............AAATCACAAGCGACGTAGGCCT.........................................................................................................................................................	22	1	15.00	1.00	1.00	1.00	12.00
................ATCACAAGCGACGTAGGCCT.........................................................................................................................................................	20	1	11.00	1.00	0.00	0.00	10.00
..............AAATCACAAGCGACGTAGGC...........................................................................................................................................................	20	1	4.00	4.00	0.00	0.00	0.00
..............AAATCACAAGCGACGTAGG............................................................................................................................................................	19	1	4.00	3.00	0.00	1.00	0.00
...............AATCACAAGCGACGTAGGCC..........................................................................................................................................................	20	1	2.00	1.00	0.00	0.00	1.00
.................TCACAAGCGACGTAGGCCT.........................................................................................................................................................	19	1	2.00	0.00	0.00	0.00	2.00
.................TCACAAGCGACGTAGGCC..........................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	2.00
.............................................................................................................................................TTGAATTCGAAGCTG--TGC............................	18	1	2.00	0.00	0.00	0.00	2.00
................ATCACAAGCGACGTAGGCC..........................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................TGGA-----------------GTTGAATTCCAAGTT..................................	19	1	1.00	0.00	1.00	0.00	0.00
...............AATCACAAGCGACGTAGGC...........................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
............................................................................................................................................GTTGAATTCGAAGTTG--TCCATGT-.......................	23	1	1.00	1.00	0.00	0.00	0.00

droVir3

CACTCGCGTGGCATAAATCAAATGCGTTGCAGGCCG-CCGGC-----------------GCTCCACGCACTCGAC--------------T---------------------------------------------------------------------CCTC---TACTTGCGGCTAGCAGCTCCACT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
............................GCAGGCCG-xCGTC-----------------GCTCCACGC.........................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00

droMoj3

CACTTGTGTGGCATAAATCAAATGCGCAGCAGGCCG-CCAGCTATACCCA---------G--------------C-------------------------------------------------------------------------------CAAGCCAAGTGGTCTTTGGGGCCA---TTTACACG

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CACTTGCATGGCATAAATCAAATGCGCCGCGGGCCT-TTGCTACG-------------TGCCACATGCACTCGAC--------------T--CTCGCCTCTCAACACGACTGACCGAACA---TTGCAGCAGATCGGGGCATTCCACTC----------CAAGTGGTCTTTGAGGCCA---TTTGCACG

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