dme-mir-1016- 12- and 20-way alignments

dme-mir-1016	chr2R:10120635-10120692 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 10120635-10120655
   star strand at position 10120668-10120692
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2R:10120620-10120707 -	CTCCAAGCTTTTCCAGTAAGTATAGAGAGGATGTGATTGGTAAAT------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droSim1	chr2R:8883298-8883385 -	CTCCAAGCTTTTCCAGTAAGTACAGAGATGATGTAATGCGTAAAT------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droSec1	super_1:7628246-7628333 -	CTCCAAGCTTTTCCAGTAAGTATAGAGAGGATGTAATGCGTATAT------TCCAAT----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droYak2	chr2R:10057668-10057755 -	CTCCAAGCTGTTCCAGTAAGTATAGAGGGGATGTGATGGGTAAAT------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droEre2	scaffold_4845:15723071-15723158 +	CTCCAAGCTGTTTCAGTAAGTATAGAGAGGATGTGATGGGCAAAA------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droAna3	scaffold_13266:5804278-5804360 +	CTCTAAACTTTTTCAGTGAGTACTTGTAATATA-AATCCATAAA--------TCAAA----------ACT-----------------CACTT-TTTCCA-AC-TTAGTCGCCGTGGTGTGAT
dp4	chr3:17369366-17369470 -	CTCAAAGCTCTTCCAGTGAGTACACAATTCAATTCCTCGGCAAGGCTATCGTCTGAAACTAATTTCCCTT-----------------CACTTATCCCTGCCCTGCAGTCGTCGCGGCGTCAT
droPer1	super_31:422912-423016 +	TTCAAAGCTCTTCCAGTGAGTACACAATTCAATTCCTCGGCAAGGCTATTGTCTGAAACTAATGTCCCTT-----------------CACTTATCCCTGCCCTGCAGTCGGCGCGGCGTCAT
droWil1	scaffold_180700:1839743-1839828 +	TTCCAAATTGTTCCAGTAAGTTAAAA-----TGATCTAAAATCAT------TTCAAA----------T-T----------GATT---CAATAATCTCTTCCA-TTAGTCGACGCGGTGTCAT
droVir3	scaffold_12875:17586457-17586541 +	TTCCAAACTATTTCAGTAAGTAGCA------GGTGCTGAGTGCAT------G----A----TTGTCTCTA----TATCTT--------GATT-----ATCTTTGCAGTCGACGCGGGGTTAT
droMoj3	scaffold_6496:11208550-11208642 +	TTCCAAGCTGTTTCAGTAAGTAGAGCACGCATTTCCAGTACCCAACTA----------------TTCGTTACTATATCTG--------TACA-----ATTTTTGTAGTCGACGCGGGGTTAT
droGri2	scaffold_15245:14096515-14096602 -	TTCCAAACTGTTTCAGTAAGTGGTAACACA-ACTACTATGTTTGT------GC-AAC----------ATT----------TAATGGACAG-T-----ATCTTTGCAGTCGACGGGGAGTTAT

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:10120620-10120707 -	NA	CTCCAAGCTTTTCCAGTAAGTATAGAG---AG----GATGTGA-TT---GGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droSim1	chr2R:8883298-8883385 -	2	CTCCAAGCTTTTCCAGTAAGTACAGAG---AT----GATGTAA-TG---CGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droSec1	super_1:7628246-7628333 -	1	CTCCAAGCTTTTCCAGTAAGTATAGAG---AG----GATGTAA-TG---CGTA-----------------TA-T---------------TCCAATGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droYak2	chr2R:10057668-10057755 -	1	CTCCAAGCTGTTCCAGTAAGTATAGAG---GG----GATGTGA-TG---GGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droEre2	scaffold_4845:15723071-15723158 +	1	CTCCAAGCTGTTTCAGTAAGTATAGAG---AG----GATGTGA-TG---GGCA-----------------AA-A---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droEug1	scf7180000409462:2724067-2724155 +	1	CTCAAAGCTTTTCCAGTGAGTATAGAG---AG----GATGTGA-TGG--TGTA-----------------AT-T---------------GCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGTGGCGTTAT
droBia1	scf7180000301506:3144548-3144634 +	1	CTCAAAGCTCTTCCAGTGAGTATAAAG---AG----GACGTGA-TG----CCA-----------------AG-T---------------GCCAAAGTTTACCTGTCTCCA--TA-CTTAGTCGGCGCGGAGTTAT
droTak1	scf7180000414111:24446-24536 -	2	CTCCAAGCTTTTCCAGTGAGTATAGAG---AG----CATGTGA-TGCAAGGTA-----------------AT-G---------------GCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGGCGCGGAGTTAT
droEle1	scf7180000491349:753074-753164 +	1	CTCCAAGCTTTTTCAGTGAGTATCGAA---GG----CATATGC-AA---GATA-----------------T--------GA--T-GTATACTAAGATTAACCTCT--TTA--AA-CTTAGTCGTCGCGGAGTTAT
droRho1	scf7180000777200:436780-436870 -	1	CTCCAAGCTTTTCCAGTTAGTATCAAATTTAT----GATATGA-TT---GGTA-----------------AA-T---------------ACTTAAATTGACCTCTCTCCA--TT-CTTAGTCGTCGCGGAGTTAT
droFic1	scf7180000453948:312447-312534 +	1	TTCCAAGCTTTTCCAGTAAGTATAGAG---CA----GATGTGA-TG---GGTC-----------------AG-A---------------ACCAAACTTCACCTGCCTCTG--TA-CTTAGTCGTCGCGGAGTGAT
droKik1	scf7180000302366:807245-807331 -	1	CTCGAAGCTGTTCCAGTGAGTAACGAG---AA----AGGGGAG-TT---GGAA-----------------GC-C---------------ACATAAACTAACATGCATCC---TT-CGTAGTCGCCGAGGTGTGAT
droAna3	scaffold_13266:5804278-5804360 +	1	CTCTAAACTTTTTCAGTGAGTACTTGT---AA------TATAAATC---CATA-----------------A------------------ATCAAAACTCACTTT-TTCCA---A-CTTAGTCGCCGTGGTGTGAT
droBip1	scf7180000396372:418170-418256 +	1	CTCCAAACTGTTTCAGTGAGTACATGC---AA--TGGATATATGTA---CATA-----------------A--A---------------TCCA-GACTTACTT-TCTCC---TA-CTTAGTCGCCGTGGTGTGAT
dp4	chr3:17369366-17369470 -	1	CTCAAAGCTCTTCCAGTGAGTACACAA---TT----CAATTCC-TC---GGCAAGGCTATCGTCTGAAAC----TAATT----------TC---CCTTCACTTATCCCTG--CCCTGCAGTCGTCGCGGCGTCAT
droPer1	super_31:422912-423016 +	1	TTCAAAGCTCTTCCAGTGAGTACACAA---TT----CAATTCC-TC---GGCAAGGCTATTGTCTGAAAC----TAATG----------TC---CCTTCACTTATCCCTG--CCCTGCAGTCGGCGCGGCGTCAT
droWil1	scaffold_180700:1839743-1839828 +	1	TTCCAAATTGTTCCAGTAAGTTAAAAT---GA------T---C-TA---AAAT-----------------CATTTC------AA-----ATT--GATTCAATAATCTCTT--CC-ATTAGTCGACGCGGTGTCAT
droVir3	scaffold_12875:17586457-17586541 +	1	TTCCAAACTATTTCAGTAAGTAGCAGG---T----------GC-TG---AGTG-----------------CA-TGATTGTC--------TCTATATCTTGATTATC------T-TTGCAGTCGACGCGGGGTTAT
droMoj3	scaffold_6496:11208550-11208642 +	1	TTCCAAGCTGTTTCAGTAAGTAGAGCA---CG----CATTTCC-AG---TACCCAACTAT----------------TCGTT--------ACTATATCTGTACAATT------T-TTGTAGTCGACGCGGGGTTAT
droGri2	scaffold_15245:14096515-14096602 -	1	TTCCAAACTGTTTCAGTAAGTGGTAAC---ACAACTACTATGT-TT-------------------------G-TGC-----AACA----TTTAATG-------GACAGTATCT-TTGCAGTCGACGGGGAGTTAT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CTCCAAGCTTTTCCAGTAAGTATAGAGAGGATGTGATTGGTAAAT------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT

Size

Hit Count

Total Norm

droSim1

CTCCAAGCTTTTCCAGTAAGTACAGAGATGATGTAATGCGTAAAT------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...............................................................................................TCCATAC-TTAGTCGTCGAGGG.....	21	1	2.00	0.00	0.00	0.00	2.00
..........................................................................................CTCTCxAGATAC-TTAGTCG............	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

CTCCAAGCTTTTCCAGTAAGTATAGAGAGGATGTAATGCGTATAT------TCCAAT----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
....................................................................TT-----------------CACCTCTCTCCATAC-TTAGT..............	22	1	8.00	2.00	3.00	3.00
...............GTAAGTATAGAGAGGATGTAATGC...................................................................................	24	1	3.00	2.00	0.00	1.00
...............GTAAGTATAGAGAGGATGTAATG....................................................................................	23	1	2.00	1.00	1.00	0.00
...............GTAAGTATAGAGAGGATG.........................................................................................	18	1	2.00	0.00	0.00	2.00
................TAAGTATAGAGAGGATGTAAT.....................................................................................	21	1	1.00	1.00	0.00	0.00
...............GTAAGTATAGAGAGGATGT........................................................................................	19	1	1.00	1.00	0.00	0.00
...............GTAAGTATCGAGAGGATGTAATGC...................................................................................	24	1	1.00	1.00	0.00	0.00
...............GTAAGTATAGAGAGGATGTAATGCGT.................................................................................	26	1	1.00	1.00	0.00	0.00
................TAAGTATAGAGAGGATGTAATG....................................................................................	22	1	1.00	0.00	1.00	0.00
...............GTAAGTATAGAGAGGATGTAATGCG..................................................................................	25	1	1.00	1.00	0.00	0.00
.....................................................................T-----------------CACCTCTCTCCATAC-TTAGTT.............	22	1	1.00	0.00	1.00	0.00
...............GTAAGTATAGAGAGGATGTAAA.....................................................................................	22	1	1.00	0.00	1.00	0.00

droYak2

CTCCAAGCTGTTCCAGTAAGTATAGAGGGGATGTGATGGGTAAAT------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
....................................................................TT-----------------CACCTCTCTCCATAC-TTAGT..............	22	1	168.00	41.00	52.00	11.00	60.00	4.00
...............GTAAGTATAGAGGGGATGTGATG....................................................................................	23	1	11.00	1.00	2.00	8.00	0.00	0.00
.....................................................................T-----------------CACCTCTCTCCATAC-TTAGTT.............	22	1	7.00	7.00	0.00	0.00	0.00	0.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTAG...............	21	1	6.00	1.00	0.00	0.00	4.00	1.00
.....................................................................T-----------------CACCTCTCTCCATAC-TTAGT..............	21	1	3.00	1.00	0.00	0.00	2.00	0.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTATT..............	22	1	3.00	0.00	1.00	0.00	2.00	0.00
....................................................................TT-----------------CACCTCTCTCCCTAC-TTAGT..............	22	1	3.00	0.00	1.00	0.00	2.00	0.00
...............GTAAGTATAGAGGGGATGTGATGG...................................................................................	24	1	3.00	0.00	0.00	3.00	0.00	0.00
....................................................................TT-----------------CACCTCTCTCCATCC-TTAGT..............	22	1	2.00	0.00	1.00	0.00	1.00	0.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTA................	20	1	2.00	0.00	2.00	0.00	0.00	0.00
........................................................................................ACCTCTCTCCATAC-TTAGT..............	19	1	2.00	1.00	0.00	0.00	1.00	0.00
....................................................................TT-----------------CACCTCTCTCAATAC-TTTGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTAAGTATAGAGGGGATGTGA......................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTAGA..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
....................................................................TG-----------------CACCTCTCTCCATAC-TGAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................TT-----------------CACCTCTCTCCTTGC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................TT-----------------CACCTCTCTCCATAT-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTAT...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................TT-----------------CAACTCTCTCCATAC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................TT-----------------CAACTCTCTCCCTAC-TTAGT..............	22	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................................................TT-----------------CACCTATCTCCCTAC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................TT-----------------CACCTCTCTCCATAC-TT.................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................TT-----------------CACTTATCTCCATAC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................TT-----------------CACCTCTCTTCATAC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................TT-----------------CACCTCTCTCCGTAC-TTAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................................................................ACCTCTCTCCCTAC-TTAGT..............	19	1	1.00	0.00	1.00	0.00	0.00	0.00
...............GTAAGTATAGAGGGGATGTG.......................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
...............GTAAGTATAGAGGGGATGGGCT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................TT-----------------CATCTCTCTCCATAC-TTAGT..............	22	1	1.00	1.00	0.00	0.00	0.00	0.00
.....................................................................T-----------------CACCTCTCTCCATCC-TTAGTT.............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................TT-----------------CAACTCTCTCCATTC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTAAGTATAGAGGGGATG.........................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................T-----------------CACCCCTCTCCATAC-TTAGTT.............	22	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................................................TT-----------------CACCGCTCTCCGTAC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................TT-----------------CATCTCTCTCCATCC-TTAGT..............	22	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................................................CT-----------------CACCTCTCTCCATAC-TTAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00

droEre2

CTCCAAGCTGTTTCAGTAAGTATAGAGAGGATGTGATGGGCAAAA------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
....................................................................TT-----------------CACCTCTCTCCATAC-TTAGT..............	22	1	866.00	21.00	58.00	0.00	787.00
.....................................................................T-----------------CACCTCTCTCCATAC-TTAGT..............	21	1	58.00	1.00	5.00	0.00	52.00
.....................................................................T-----------------CACCTCTCTCCATAC-TTAGTT.............	22	1	36.00	3.00	4.00	0.00	29.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTAG...............	21	1	22.00	0.00	1.00	0.00	21.00
...............GTAAGTATAGAGAGGATGTGATGG...................................................................................	24	1	12.00	0.00	0.00	0.00	12.00
...............GTAAGTATAGAGAGGATGTGA......................................................................................	21	1	11.00	0.00	1.00	0.00	10.00
....................................................................TT-----------------CACCTCTCTCAATAC-TTAGT..............	22	1	9.00	0.00	0.00	0.00	9.00
...............GTAAGTATAGAGAGGATGTGATGGGC.................................................................................	26	1	8.00	0.00	0.00	0.00	8.00
...............GTAAGTATAGAGAGGATGTGATG....................................................................................	23	1	7.00	0.00	1.00	0.00	6.00
....................................................................TT-----------------CACATCTCTCCATAC-TTAGT..............	22	1	7.00	0.00	0.00	0.00	7.00
....................................................................TT-----------------CACCTCTATCCATAC-TTAGT..............	22	1	6.00	0.00	0.00	0.00	6.00
....................................................................TT-----------------CACCTATCTCCATAC-TTAGT..............	22	1	6.00	0.00	0.00	0.00	6.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTA................	20	1	5.00	0.00	1.00	0.00	4.00
....................................................................TT-----------------AACCTCTCTCCATAC-TTAGT..............	22	1	4.00	0.00	0.00	0.00	4.00
...............GTAAGTATAGAGAGGATGTGATGGG..................................................................................	25	1	4.00	1.00	0.00	0.00	3.00
....................................................................TT-----------------CACCTCTCTCCATAC-TT.................	19	1	4.00	0.00	0.00	0.00	4.00
....................................................................TT-----------------CACCTCTCTACATAC-TTAGT..............	22	1	3.00	0.00	0.00	0.00	3.00
....................................................................TT-----------------CACCTCTCTCCATAA-TTAGT..............	22	1	3.00	0.00	0.00	0.00	3.00
....................................................................TT-----------------CACCTCTCTCCATAC-CTAGT..............	22	1	3.00	0.00	0.00	0.00	3.00
........................................................................................ACCTCTCTCCATAC-TTAGT..............	19	1	3.00	1.00	1.00	0.00	1.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTAGA..............	22	1	3.00	0.00	1.00	0.00	2.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTATT..............	22	1	2.00	0.00	0.00	0.00	2.00
.....................................................................T-----------------CACCTCTCTCCATAC-TTAGTA.............	22	1	2.00	0.00	0.00	0.00	2.00
....................................................................TT-----------------CACCTCTTTCCATAC-TTAGT..............	22	1	2.00	0.00	1.00	0.00	1.00
....................................................................TT-----------------CAACTCTCTCCATAC-TTAGT..............	22	1	2.00	0.00	0.00	0.00	2.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTGGT..............	22	1	2.00	1.00	0.00	0.00	1.00
....................................................................TT-----------------CACCCCTCTCCATAC-TTAGT..............	22	1	2.00	0.00	0.00	0.00	2.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTAGTT.............	23	1	2.00	0.00	0.00	0.00	2.00
....................................................................TT-----------------CACCTCTCTCCATCC-TTAGT..............	22	1	2.00	0.00	0.00	0.00	2.00
...................................................................CTT-----------------CACCTCTCTCCATAC-TTAGT..............	23	1	2.00	0.00	1.00	0.00	1.00
....................................................................TT-----------------CGCCTCTCTCCATAC-TTAGT..............	22	1	2.00	0.00	1.00	0.00	1.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTAGC..............	22	1	2.00	0.00	0.00	0.00	2.00
...............GTAAGTATAGAGAGGATGTGATCGGC.................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
...............TTAAGTATAGAGAGGATGTG.......................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------CACCTCTCTCTATAC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------CACCTCTCTCCCTAC-TTAGT..............	22	1	1.00	0.00	1.00	0.00	0.00
................TAAGTATAGAGAGGATGTGATG....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.....................................................................T-----------------CACCTCTCTCCATAC-TTAGTAA............	23	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTATAGAGAGGATGT........................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
......................................................AAA----------GTT-----------------CACCTCTCTCCATAC-T..................	22	1	1.00	1.00	0.00	0.00	0.00
.....................................................................T-----------------CACCTCTCTCCCTAC-TTAGT..............	21	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------CACCTCTCTCCATCC-TTCGT..............	22	1	1.00	0.00	1.00	0.00	0.00
...............GTAAGTATAGAGATGATGT........................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTAGCA.............	23	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTATAGAGAGGATGTG.......................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTATAGAGAGGATGTGAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...................................................................GTT-----------------CACCTCTCTCCATAC-TTAGT..............	23	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------CAACTCTCTCAATAC-TT.................	19	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------CACCTCTCTACATAA-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------CACACCTCTCCATAC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................CT-----------------CACCTCTCTCCATAC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
.................AAGTATAGAGAGGATGTGATGGGC.................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................CACCTCTCTCCATAC-TTAGT..............	20	1	1.00	0.00	0.00	0.00	1.00
.....................................................................T-----------------CACCTCTCTCCATAA-TTAGT..............	21	1	1.00	0.00	0.00	0.00	1.00
.....................................................................T-----------------AACCTCTCTCCATAC-TTAGT..............	21	1	1.00	0.00	0.00	0.00	1.00
.....................................................................T-----------------CACCTCTCTCCATAC-TTAGTGT............	23	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------CACCTCTCTCCATAC-TTAGG..............	22	1	1.00	0.00	0.00	0.00	1.00
.....................................................................T-----------------CACCTCTCTCCATAC-TTAG...............	20	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------GACCTCTCTCCATAC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTATAGAGAGGATTTGATGGGC.................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
...............TTAAGTATAGAGAGGATGCGA......................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------CAGCTCTCTCCATAC-TTAGT..............	22	1	1.00	0.00	1.00	0.00	0.00
.....................................................................T-----------------CACATCTCTCCATAC-TTAGTT.............	22	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTATAGAGAGGATGTGATC....................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTATAGAGAGGATGTCAT.....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.....................................................................T-----------------CACCTATCTCCATAC-TTAGT..............	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................CCTCTCTCCATAC-TTAGT..............	18	1	1.00	0.00	0.00	0.00	1.00
.....................................................................T-----------------CACCTCTCTCCATAC-TTAGAT.............	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------CACCTCTCTGCATAC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------CACCTCTCxCCATAC-TTAGT..............	21	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------CACCTCTCTCCACAC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................GT-----------------CAACTCTCTCCATAC-TTAGT..............	22	1	1.00	1.00	0.00	0.00	0.00
....................................................................TT-----------------CACATCTCTACATAC-TTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
....................................................................TT-----------------CACCTGTCTCCATGC-TTAGT..............	22	1	1.00	1.00	0.00	0.00	0.00
.....................................................................T-----------------CACCTCTCTCCATAC-TTATT..............	21	1	1.00	1.00	0.00	0.00	0.00
.....................................................................T-----------------CACCTTTCTCCATAC-TTAGTT.............	22	1	1.00	0.00	0.00	0.00	1.00
...................................................................CTT-----------------CACCTCTCTCCATAC-TTAG...............	22	1	1.00	0.00	0.00	0.00	1.00

droAna3

CTCTAAACTTTTTCAGTGAGTACTTGTAATATA-AATCCATAAA--------TCAAA----------ACT-----------------CACTT-TTTCCA-AC-TTAGTCGCCGTGGTGTGAT

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

CTCAAAGCTCTTCCAGTGAGTACACAATTCAATTCCTCGGCAAGGCTATCGTCTGAAACTAATTTCCCTT-----------------CACTTATCCCTGCCCTGCAGTCGTCGCGGCGTCAT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
......................................................................................................TGCAGTGGTCGGGGCGTC..	18	1	1.00	0.00	0.00	1.00	0.00

droPer1

TTCAAAGCTCTTCCAGTGAGTACACAATTCAATTCCTCGGCAAGGCTATTGTCTGAAACTAATGTCCCTT-----------------CACTTATCCCTGCCCTGCAGTCGGCGCGGCGTCAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...................................CTAGGCAAGGCTGTTGTCTGAA.................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

TTCCAAATTGTTCCAGTAAGTTAAAA-----TGATCTAAAATCAT------TTCAAA----------T-T----------GATT---CAATAATCTCTTCCA-TTAGTCGACGCGGTGTCAT

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

TTCCAAACTATTTCAGTAAGTAGCA------GGTGCTGAGTGCAT------G----A----TTGTCTCTA----TATCTT--------GATT-----ATCTTTGCAGTCGACGCGGGGTTAT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
....AAACGATTTCxGTAAGTAGC..................................................................................................	19	1	9.00	9.00	0.00	0.00	0.00	0.00
.....AACGATTTCxGTAAGTAGC..................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00

droMoj3

TTCCAAGCTGTTTCAGTAAGTAGAGCACGCATTTCCAGTACCCAACTA----------------TTCGTTACTATATCTG--------TACA-----ATTTTTGTAGTCGACGCGGGGTTAT

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TTCCAAACTGTTTCAGTAAGTGGTAACACA-ACTACTATGTTTGT------GC-AAC----------ATT----------TAATGGACAG-T-----ATCTTTGCAGTCGACGGGGAGTTAT	Size	Hit Count	Total Norm	V109 Male body
................................................................................TAATGGACAG-T-----ATCTTTGCAG...............	21	1	1.00	1.00

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