dme-mir-4956- 12- and 20-way alignments

dme-mir-4956	chrX:6979769-6979886 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	CDS

Legend:

   mature strand at position 6979799-6979820
   star strand at position 6979836-6979857
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:6979754-6979901 -	GAGTGCCAACAATTTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATG------AACGATCCTCGGGCAAGCAACACCAACCTG
droSim1	chrX:5492772-5492919 -	GAGTGCCAACAATCTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAACCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATG------AACGATCCTCGGGCAAGCAACACCAACTTG
droSec1	super_24:199934-200081 -	GAGTGCCAACAATCTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGCGATGATCTCATG------AACGATCCTCGGGCAAGCAACACCAACTTG
droYak2	chrX:14374793-14374940 +	GAGTGCCAACAATCTGGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCATG------AACGATCCCCGGGCAAGCAACACCAACCTG
droEre2	scaffold_4690:15890244-15890391 -	GAGTGCCAATAATCTTGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCATG------AACGATCCCCGGGCAAGCAACACCAACCTG
droAna3	scaffold_13117:2326296-2326455 -	CAGTGCCAATTCCCTTGGCGGCGGCGGTGGCGGCAACATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGCTTAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGACGATCACATGCTT---AATGACCAGCGGCCGAGCAACACCAACCTG
dp4	chrXL_group1a:6391512-6391662 -	CAGTGCCAATAATCTTG------------GCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCGAGCAACACCAATCTG
droPer1	super_25:931278-931428 +	CAGTGCCAATAATCTTG------------GCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCCAGCAACACCAATCTG
droWil1	scaffold_180777:2984533-2984680 +	CAGTGCCAATTCCCTTGGCG---------GTGGCAATATGTGCAATATGCCACCGATGGCCAGTAACAATTCATTGAACAACCTGTGCGGTCTATCATTGGGCAGCGGCGGCAGCGATGATCTTATG------AACGATCATCGTCCGAGTAATACCAATTTG
droVir3	scaffold_12928:60655-60799 -	CAGCGCCAATTCCCTTG------------GCGGCAACATCTGCAATATGCCGCCAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATTGGCAGCGGCGGCAGCGATGATCACATG------AACGATCAGCGCAACAGCAACACCAATTTG
droMoj3	scaffold_6359:1380681-1380822 -	CAGCGCCAATTCCCTCG------------GCGGCAACATCTGCAACATG---CCAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATCGGCAGCGGCGGCAGCGATGATCTGATG------AACGATCAGCGCACAAGCAACACCAATTTG
droGri2	scaffold_14853:6692716-6692854 -	CAGCGCCAATTCACTCGGCG---------G---A---CTCTGCAACATG---CCGATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATAGGCAGCGGGGGCAGCGATGATCTTATG------AACGATCCACGCAACAGCAACACCAATTTG

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:6979754-6979901 -	NA	GAGTGCCAACAATTTAGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCA---TG------AACGATCCTCGGGCAAGCAACACCAACCTG
droSim1	chrX:5492772-5492919 -	6	GAGTGCCAACAATCTAGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAACCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCA---TG------AACGATCCTCGGGCAAGCAACACCAACTTG
droSec1	super_24:199934-200081 -	8	GAGTGCCAACAATCTAGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGCGATGATCTCA---TG------AACGATCCTCGGGCAAGCAACACCAACTTG
droYak2	chrX:14374793-14374940 +	3	GAGTGCCAACAATCTGGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCCCGGGCAAGCAACACCAACCTG
droEre2	scaffold_4690:15890244-15890391 -	6	GAGTGCCAATAATCTTGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCCCGGGCAAGCAACACCAACCTG
droEug1	scf7180000409095:320865-321012 -	2	TAGTGCCAACAATCTTGGAG---------------------------G---CGGCAACATGTGCCACCTACCGCCAATGGCCAGCAACAATTCGCTAAACAATCTGTGCGGTTTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCCAGGGCCAGTAACACCAACCTG
droBia1	scf7180000301760:1606806-1606953 +	1	TAGCGCCAACAACCTTGGCG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGACGATCTCA---TG------AACGATCCCCGGGCGAGCAACACCAACCTG
droTak1	scf7180000415873:625354-625510 -	7	CAGTGCCAACAATCTTGGCG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTATGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCAATATGATGATGAACGATCCGCGGGCGAGCAACACCAACCTG
droEle1	scf7180000491023:836960-837107 +	3	AAGTGCCAACAATCTTGGCG---------------------------G---TGGCAACATGTGCCACCTGCCTCCGATGGCCAGCAACAATTCGCTAAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCGCGGGCAAGCAACACCAACCTG
droRho1	scf7180000779514:332128-332275 +	3	GAGTGCCAACAATCTTGGCG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGACGATCTCA---TG------AACGATCCGCGGGCAAGCAACACCAACCTG
droFic1	scf7180000453927:1025569-1025716 +	3	TAGTGCCAACAACCTTGGCG---------------------------G---CGGCAACATGTGCCATCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCGCGGGCGAGCAACACCAACCTG
droKik1	scf7180000302230:43195-43339 +	1	TAGTGCCAACTCCCTTGG---------------------------------CGGCAACATTATCAACCTGCCGCCGATAACCAGCAACAATTCGCTGAACAATCTCTGCGGCCTGTCGTTAGGCAGCGGCGGCAGCGACGATCACC---TA------AACGATCCCAGGGCGAGCAACACCAACCTG
droAna3	scaffold_13117:2326296-2326455 -	8	CAGTGCCAATTCCCTTGGCGGCGGCG------------------GTGG---CGGCAACATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGCTTAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGACGATCACA---TGCTT---AATGACCAGCGGCCGAGCAACACCAACCTG
droBip1	scf7180000396696:795107-795284 +	4	CAGCGCCAATTCATTGGGCGGCGGCGGCGGTGGAGGCGGTGGCGGCGG---CGGCAATATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGTTGAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGATGATCACA---TGCTG---AACGATCAGCGGGCCAGCAATACCAACCTG
dp4	chrXL_group1a:6391512-6391662 -	5	CAGTGCCAATAATCTTGG---------------------------------CGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACA---TGATGATGCACGATCAGCGATCGAGCAACACCAATCTG
droPer1	super_25:931278-931428 +	1	CAGTGCCAATAATCTTGG---------------------------------CGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACA---TGATGATGCACGATCAGCGATCCAGCAACACCAATCTG
droWil1	scaffold_180777:2984533-2984680 +	1	CAGTGCCAATTCCCTTGGCG---------------------------G---TGGCAATATGTGCAATATGCCACCGATGGCCAGTAACAATTCATTGAACAACCTGTGCGGTCTATCATTGGGCAGCGGCGGCAGCGATGATCTTA---TG------AACGATCATCGTCCGAGTAATACCAATTTG
droVir3	scaffold_12928:60655-60799 -	2	CAGCGCCAATTCCCTTGG---------------------------------CGGCAACATCTGCAATATGCCGCCAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATTGGCAGCGGCGGCAGCGATGATCACA---TG------AACGATCAGCGCAACAGCAACACCAATTTG
droMoj3	scaffold_6359:1380681-1380818 -	5	C-----C---AATTCCCTCG---------------------------G---CGGCAACATCTGCAACATGC---CAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATCGGCAGCGGCGGCAGCGATGATCTGA---TG------AACGATCAGCGCACAAGCAACACCAATTTG
droGri2	scaffold_14853:6692716-6692854 -	4	CAGCGCCAATTCACTCGGCG---------------------------GACTCTGCAACAT------------GCCGATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATAGGCAGCGGGGGCAGCGATGATCTTA---TG------AACGATCCACGCAACAGCAACACCAATTTG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GAGTGCCAACAATTTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATG------AACGATCCTCGGGCAAGCAACACCAACCTG

Size

Hit Count

Total Norm

droSim1

GAGTGCCAACAATCTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAACCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATG------AACGATCCTCGGGCAAGCAACACCAACTTG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.....................................................CGATGGCCGGCAACAACTCGCT........................................................................................	22	1	6.00	0.00	6.00	0.00	0.00
.....................................................CGATGGCCAGCAACAACTCGCT........................................................................................	22	1	5.00	0.00	3.00	2.00	0.00
..........................................................................TGACTAACATCTGCGGAT.......................................................................	18	1	4.00	0.00	0.00	1.00	3.00
......................................................................................GCGGATTxTCGCTGGGCGG..........................................................	18	1	3.00	0.00	0.00	0.00	3.00
........................................................................................................................................CATCCTCGGGCAAGCAACAC.......	20	1	2.00	0.00	0.00	0.00	2.00
.....................................................................................................GCATCGGTGGTAGTGACGA...........................................	19	1	2.00	0.00	0.00	0.00	2.00
......................................................GATGGCCGGCAACAACTCGCTG.......................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
.........................................................................CTGAATAACCTCTGCGGCTTGTCGCT................................................................	26	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................G------AACGATCCTCGGGCAAGCAACACC......	25	1	1.00	0.00	0.00	1.00	0.00
...........................................................................GAATAACCTCTGCGGATTGTC...................................................................	21	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................AGTGATGATCTCATG------AAC...........................	18	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................AACGATCCTCGGGCAAGCAACACC......	24	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................................CCTCGGGCAAGCAACACC......	18	1	1.00	0.00	1.00	0.00	0.00
.........................................................................CTGAATAACCTCTGCGGATTGTCGCT................................................................	26	1	1.00	0.00	0.00	0.00	1.00
....................................................ACGATGGACAGCAACAAC.............................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.........................................................................CTGAATAACCTCTGCGGAT.......................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................AACGATCCTCGGGCAAGCAAC.........	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................CTGAATAACCTCTGCGGATTGTCGCTGGG.............................................................	29	1	1.00	0.00	0.00	1.00	0.00
.....................................................CGATGGCCAGCAACAACTCGCG........................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................G------AACGATCCTCGGGCAAGCAACAC.......	24	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................AACGATCCTCGGGCAAGC............	18	1	1.00	0.00	0.00	1.00	0.00
.........................................................................CTGAATATCCTCCGCGGA........................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................AACGATCCTCGGGAAAGCAAC.........	21	1	1.00	0.00	0.00	0.00	1.00
.......................................................ATGGCCATCAAGAACTCGC.........................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................TCTCATG------AACGATCCTCGGGCA...............	22	1	1.00	0.00	0.00	0.00	1.00
.........................................................................CTGAATAACCTCTGCGGATTGTCGCC................................................................	26	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................CGGATTGTCGCTGGGCAGCG........................................................	20	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................GATGATCTCATG------AACGATCCTCGGGCA...............	27	1	1.00	0.00	0.00	0.00	1.00
.....................................................CGATGGCCGGCAACAACTCGCC........................................................................................	22	1	1.00	0.00	1.00	0.00	0.00

droSec1

GAGTGCCAACAATCTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGCGATGATCTCATG------AACGATCCTCGGGCAAGCAACACCAACTTG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..........................................................................................ATTGTCGCTGGGCAGCGGTGG....................................................	21	1	2.00	1.00	0.00	1.00
.............................................................................ATAATCTCTGCGGATTGTC...................................................................	19	1	2.00	0.00	2.00	0.00
.........................................................................................GATTGTCGCTGGGCAGCGGTG.....................................................	21	1	1.00	0.00	1.00	0.00
.........................................................................CTGAATAATCTCTGCGGATT......................................................................	20	1	1.00	0.00	1.00	0.00
..........................................................................................ATTGTCGCTGGGCGGCGGTGGT...................................................	22	1	1.00	1.00	0.00	0.00
.....................................................................................................................................GACGATCCTCGGGCAAGA............	18	1	1.00	1.00	0.00	0.00
................................................................AACAACGCGCTGAATGAT.................................................................................	18	1	1.00	0.00	1.00	0.00
.......................................................................................CGGATTGTCGCTGGGCAGCGGT......................................................	22	1	1.00	1.00	0.00	0.00
............................................................................................................................ATG------AACGAxxCTCGGGCAAG.............	18	1	1.00	0.00	1.00	0.00
.........................................................................................GATTGTCGCTGGGCAGCGGTGGT...................................................	23	1	1.00	1.00	0.00	0.00
..................................................................CAACTCGCTGAATAATCTCT.............................................................................	20	1	1.00	0.00	1.00	0.00
.......................................................................................CGGATTGTCGCTGGGCAGCGGTT.....................................................	23	1	1.00	1.00	0.00	0.00
................................................................................................GCTGGGCAGCGGTGGTAGT................................................	19	1	1.00	0.00	1.00	0.00
..............................................................................................................................G------AACGATCCTCGGGCAAGC............	19	1	1.00	0.00	1.00	0.00
...................................................................................TCTGCGGATTATCGGTGG..............................................................	18	1	1.00	0.00	1.00	0.00
.......................................................................................................................ATCTCATG------AACGATCCTCGGGC................	22	1	1.00	0.00	1.00	0.00

droYak2

GAGTGCCAACAATCTGGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCATG------AACGATCCCCGGGCAAGCAACACCAACCTG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
............................................................................................................................................CCCGGGCxGGCAACACCA.....	17	1	2.00	0.00	0.00	0.00	2.00	0.00
.......AACAATCTGGCGG---------GCAGC.................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
....................................................................................CTGCGGACTGTCGCTGGGCAG..........................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................CTGAATAACCTCTGCGGACT......................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................CTGAATAACCTCTGCGGACTGTCGCT................................................................	26	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................TCTGCGGACTGTCGCTGGGCAGCGGC......................................................	26	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................................GACGGTCGCxGGGCAGC.........................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................ATAACCTCTGCGGACTGTCGCT................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................TGCGGACTGTCGCTGGGCAGC.........................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................................................................CGGACTGTCGCTGGGCAGCGGCT.....................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
...........ATCTGGGCG---------GCGGCAC...............................................................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................GATGGCCAGCCACAGTTCGCT........................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
...................................................................................TCTGCGGACTGTCGCTGGGCAGA.........................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
............................................................................................................................ATG------AACGATCCCCGGGCAAG.............	20	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................................................................................G------AACGATCCCCGGGCAAGCAACACCA.....	26	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

GAGTGCCAATAATCTTGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCATG------AACGATCCCCGGGCAAGCAACACCAACCTG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
....................................................................................CTGCGGACTGTCGCTGGGCAG..........................................................	21	1	3.00	0.00	1.00	0.00	2.00
..........................................................................................ACTGTCGCTGGGCAGCGGTT.....................................................	20	1	1.00	0.00	0.00	0.00	1.00
...............................AGCAACATGTxCCACCTGC.................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
....................................................................................CTCCGGACTGTCGCTGGGCAG..........................................................	21	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................CGGACTGTCGCTGGGCAGCGGC......................................................	22	1	1.00	1.00	0.00	0.00	0.00
...................................................................................................................GATGATATCATG------AACGAAC.......................	19	1	1.00	1.00	0.00	0.00	0.00
............TCTTGGGG---------GCGGCAACATGTGC........................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
..........................................................................................ACTTTCGCTGGGCAGCGGCG.....................................................	20	1	1.00	0.00	0.00	0.00	1.00
........................................................................................................................................GATCCCCGGGCAAGCAACACCA.....	22	1	1.00	1.00	0.00	0.00	0.00
......................................TGTGCCACCTACCGCCGTTG.........................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.........................................................................CTGAATAACCTCTGCGGACT......................................................................	20	1	1.00	0.00	0.00	0.00	1.00
....................................................................................CTGCGGACTGTCCCTGGGCAG..........................................................	21	1	1.00	0.00	0.00	0.00	1.00

droAna3

CAGTGCCAATTCCCTTGGCGGCGGCGGTGGCGGCAACATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGCTTAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGACGATCACATGCTT---AATGACCAGCGGCCGAGCAACACCAACCTG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
................GGCGGTGGCAGTGGCGGC.................................................................................................................................	18	1	5.00	0.00	5.00	0.00	0.00
................GGCGGTGGTGGTGGCGGC.................................................................................................................................	18	2	1.50	0.00	1.50	0.00	0.00
................GGTGGCGGTGGTGGCGGC.................................................................................................................................	18	3	1.00	0.00	1.00	0.00	0.00
...............TGGTGGCGGTGGTGGCGGC.................................................................................................................................	19	3	1.00	0.00	1.00	0.00	0.00
................GGCGGTGGAGGTGGCGGC.................................................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
..................CGGCGGCGAAGGCGGCAAC..............................................................................................................................	19	1	2.00	1.00	1.00	0.00	0.00
................GGCGGTGGCGGTGGCGGC.................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.............GTTGGCGGTGGCGGTGGC....................................................................................................................................	18	2	0.50	0.50	0.00	0.00	0.00
................GGAGGCGGTGGTGGCGGC.................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
..................................................................................CTGTGCGGCCTGTCGCTGGGCAGCGGCG.....................................................	28	1	1.00	1.00	0.00	0.00	0.00
................GGCAGCGACGGTGGCGGC.................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................GGCGGCGGAGGAGGCGGC.................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...................GGCGGCGAAGGCGGCAAC..............................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............TGGCGCCGGCGGTAGCGGC.................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
................GGCGGTGGCGGTGGCGGT.................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
..................................................................................................TAGGCATCGGCGGCAGC................................................	17	1	1.00	0.00	0.00	1.00	0.00
................................GCAACATGTGCGACCTGCCGCCCATGACC......................................................................................................	29	1	1.00	0.00	1.00	0.00	0.00
................GGCGGCGGCGGTGGTGGT.................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.................GCGGCGGCGGTGGTGGCGA...............................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............AGGCGGCGGCGGTGGAGGCA................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................AGCGGAGGCAGTGACGA...........................................	17	1	1.00	0.00	0.00	1.00	0.00
..................CGGTGGCGATGGCGGCAAC..............................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...................GGTGGCGGAGGCGGCAA...............................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................................CGCGGAGGCAGCGACGA...........................................	17	1	1.00	0.00	0.00	1.00	0.00
.................GAGGCGGCGGTGGCGGCAAG..............................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................GGGGAGGCAGCGACGA...........................................	16	1	1.00	0.00	0.00	1.00	0.00
..............TTGGAGGCGGTGGTGGCGGC.................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............GTGGCGGTGGCGGTGGCG...................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
................GGTGGCGGCGGCGGCGGC.................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................GCTGGGCAACGGCGGAA..................................................	17	1	1.00	0.00	0.00	1.00	0.00
.................GCGGCGGCGGTGGTGGCTA...............................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............................................................................AATCTGTGCGGCCTGTCGCT................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...................................................................................................GGGCAGCGGGGGCAACG...............................................	17	1	1.00	0.00	0.00	1.00	0.00
.................GCGGCGGTGGTGGCGGAAA...............................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
..................AGGCGGTGGTGGCGGCAAC..............................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...................GGTGGCGGAGGCGGCAAC..............................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.............AATGGCGGCGGCGGTGGC....................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00

dp4

CAGTGCCAATAATCTTG------------GCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCGAGCAACACCAATCTG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
............................................................................AGCAATCTATGCGGACTGTCGCT................................................................	23	1	3.00	1.00	2.00	0.00	0.00
.....................................................................................TGCGGACTGTCGCTGGGCAGC.........................................................	21	1	1.00	0.00	0.00	1.00	0.00
......................................................................................GCGGTCTGTCGCTGGGCATC.........................................................	20	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................TGCGGACTGTCGCTGGGCAGCG........................................................	22	1	1.00	0.00	0.00	1.00	0.00
..................................................................................................................................ATGCACGATxGGCGATCGAG.............	19	1	1.00	1.00	0.00	0.00	0.00
......................................................................................GCGGTCTGTCGCTGGGCA...........................................................	18	1	1.00	0.00	0.00	1.00	0.00
..........................................................................TTAGCAATCTATGCGGACTGTCGCT................................................................	25	1	1.00	0.00	0.00	0.00	1.00
..........................................................................TTAGCAATCTATGCGGACT......................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...........................................................................TAGCAATCTATGCGGACTGTCG..................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................GATGAGTACATGATGATG..............................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

CAGTGCCAATAATCTTG------------GCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCCAGCAACACCAATCTG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
............................................................................AGCAATCTATGCGGACTGTCGCT................................................................	23	1	10.00	0.00	0.00	0.00	0.00	10.00
.................................................................................TCTATGCGGACTGTCGCT................................................................	18	1	3.00	0.00	0.00	0.00	0.00	3.00
..........................................................................TTAGCAATCTATGCGGACT......................................................................	19	1	3.00	0.00	0.00	0.00	0.00	3.00
...............................................................................AATCTATGCGGACTGTCGCT................................................................	20	1	3.00	0.00	0.00	0.00	0.00	3.00
...............................................................................AATCTACGCGGACTGTCGC.................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
.................................CAACATGTGCAACCTGCTG...............................................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................................TTAGCAATCTATGCGGACTGTCGCC................................................................	25	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................ATCTATGCGGACTGTCGCT................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................GCTGGGCAGCGGCGGCGGC................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................AGCAATCTATGCGGACTGTCGCC................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
....................................................................................ATGCGGACTGTCGCTGGGCAGCG........................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................AATCTATGCGGACTGTCGC.................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................AATGACCAGCAACAATTCGCTT.......................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

CAGTGCCAATTCCCTTGGCG---------GTGGCAATATGTGCAATATGCCACCGATGGCCAGTAACAATTCATTGAACAACCTGTGCGGTCTATCATTGGGCAGCGGCGGCAGCGATGATCTTATG------AACGATCATCGTCCGAGTAATACCAATTTG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
....................................................................................................GGCAGCGGCGGCGGCGGT.............................................	18	2	0.50	0.00	0.50	0.00	0.00
............................................................................................................CGGCAGCGATGATCTTATG------AAC...........................	22	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................GCAGCGGCGGCAGCGATGAT..........................................	20	1	1.00	1.00	0.00	0.00	0.00

droVir3

CAGCGCCAATTCCCTTG------------GCGGCAACATCTGCAATATGCCGCCAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATTGGCAGCGGCGGCAGCGATGATCACATG------AACGATCAGCGCAACAGCAACACCAATTTG	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
......................................................................................................CAGCAGCAGCAGCGATGA...........................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
............................................ATATGCCGCCAATGGCCAGCA..................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

CAGCGCCAATTCCCTCG------------GCGGCAACATCTGCAACATG---CCAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATCGGCAGCGGCGGCAGCGATGATCTGATG------AACGATCAGCGCACAAGCAACACCAATTTG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...........................................................................................................................GATG------AACGATCAGCGCACAAGCAACACC......	28	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................ATCGATxGGCAGCTGCGGC...................................................	18	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................AGCGATGATCTGATG------AACGAT........................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................GCCTATCGATCGGCAGCGGCGGCAGCG...............................................	27	1	1.00	1.00	0.00	0.00	0.00
...........................................................................................CTATCGATCGGCAGCGGCGGCAGCGAT.............................................	27	1	1.00	1.00	0.00	0.00	0.00

droGri2

CAGCGCCAATTCACTCGGCG---------G---A---CTCTGCAACATG---CCGATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATAGGCAGCGGGGGCAGCGATGATCTTATG------AACGATCCACGCAACAGCAACACCAATTTG

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