dme-mir-318- 12- and 20-way alignments

dme-mir-318	chr3R:6234024-6234091 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 6234066-6234087
   star strand at position 6234030-6234051
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3R:6234009-6234106 +	GT-------------------CCTTCGGTTTCAGTTTA-----------------TGGGATACACACAGTTCAGTTTTGTCACAC-TTCAAGCATCACTGGGCTTTGTTTATCTCATGAG-AGCGAAATTTATTCA
droSim1	chr3R:15159142-15159239 -	GT-------------------CCTTCGGTTTCAGTTTA-----------------TGGGATACACACAGTTCAGTTTTGTCACAC-TTTAAGCATCACTGGGCTTTGTTTATCTCATGAG-AGCGAAATTTATTCA
droSec1	super_0:15709308-15709405 -	GT-------------------CCTTCGGTTTCAGTTTA-----------------TGGGATACACACAGTTCAGTTTTGTCACAC-TTCAAGCATCACTGGGCTTTGTTTATCTCATGAG-AGCGAAATTTATTCA
droYak2	chr3R:10262524-10262621 +	GT-------------------CCTCCGGTTTCAGTTTA-----------------TGGGATACACACAGTTCAGTTTTGTCGCAC-TACAAGCATCACTGGGCTTTGTTTATCTCATGAG-AGCGAAATTTGTTCA
droEre2	scaffold_4770:15383893-15383990 -	GT-------------------CCTCCGGTTTCAGTTTA-----------------TGGGATACACACAGTTCAGTTTTGTCACAC-TTCAAGCATCACTGGGCTTTGTTTATCTCATGAG-AGCGAAATTTGTTCA
droAna3	scaffold_13340:867199-867296 -	GT-------------------CCTCCGGTTTCAATTTG-----------------TGGGATACACACGGTTCAGTTGTGTCACTTTTGCGAGCATCACTGGGCTTTGTTTATCTCATAAG-ACTGAAATTTGTTC-
dp4	chr2:7233334-7233450 -	GTGCGTGTGAAACGTGTGCCTCTTTTGGTTTCAATTTA-----------------TGGGATGCACCAAGTTCAGTTTTGTCACAT-TTCGAGCATCACTGGGCTTTGTTTATCTCATAAG-AGCGAAATTGATTCA
droPer1	super_0:1094016-1094132 -	GTGCGTGCGAAACGTGTGCCTCTTTTGGTTTCAATTTA-----------------TGGGATGCACCAAGTTCAGTTTTGTCACAT-TTCGAGCATCACTGGGCTTTGTTTATCTCATAAG-AGCGAAATTGATTCA
droWil1	scaffold_181089:1480166-1480280 +	AA-------------------TTTTCGCTTTTTGTTTTGGCTCTACTGTTCTCGCTGCTGCACTTACACTTTGCTTTTTTCGCT--TTCGTTCGACACTGGGCTTTCTTTTACATTTTAGTTAAGCCatttattta
droVir3	scaffold_13047:1194318-1194415 +	GA--------------------TTTGGATTTCAATTTA-----------------TGGGATACACCAAGTTCAGTTTTGTCAGATGTCCAAGCATCACTGGGCTTTGTTTATCTCATAAG-AGTGAAATTTGTTCA
droMoj3	scaffold_6540:5225329-5225427 +	GA-------------------TTAAGGATTTCAATTTA-----------------TGGGATACACTAAGTTCAGTTTTGTCAGATGTCCAAGCATCACTGGGCTTTGTTTATCTCATAAG-AGCGAAATTTGTTCA
droGri2	scaffold_14906:5077291-5077389 -	GA-------------------TTTCGGATTTCAATTTA-----------------TGGGATACACCAAGTTCAGTTTTGTCAGATGTCCAAGCATCACTGGGCTTTGTTTATCTCATAAG-AGCGAAATTAGTTCA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:6234009-6234106 +	NA	G-------TCCTT-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------
droSim1	chr3R:15159142-15159239 -	2	G-------TCCTT-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--TAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------
droSec1	super_0:15709308-15709405 -	2	G-------TCCTT-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------
droYak2	chr3R:10262524-10262621 +	1	G-------TCCTC-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCGCACTA--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droEre2	scaffold_4770:15383893-15383990 -	1	G-------TCCTC-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droEug1	scf7180000409692:710233-710330 +	2	G-------ACCCC-----------TGGTTTCAGTTTATGGGATACACACAGCTCAGTCTTGTCACATGT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA---------------------------
droBia1	scf7180000302402:8322956-8323053 +	1	G-------TCCCC-----------CGGTTTCAGTTTATGGGATACACACAGTTCAGTCGTGTCGCATTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droTak1	scf7180000415380:1406001-1406136 -	2	G-------TCCAGTTTAAGAAAAAGGATTTCAGTTTATGGGATATACACAGTTCAGTCTTGTCGCCTTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCAACAAGGGATATTTATTCAAACCCAAAA
droEle1	scf7180000490995:508430-508525 -	4	G-------ACTCT-----------CGGTTTCAATTTATGGGATACACACAGTTCAGTCTTGTCACATTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGA--GAAATTTGTTCA---------------------------
droRho1	scf7180000777158:16332-16429 -	2	G-------GACCC-----------CGGTTTCAATTTATGGGATACACACAGTTCAGTTTTGTCACATTT--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droFic1	scf7180000453800:2313678-2313775 +	1	G-------ATCCA-----------CGGTTTCAATTTATGGGATACACACAGTTCAGTTTTGTCACATTC--CAA---GCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA---------------------------
droKik1	scf7180000302475:1425888-1425985 +	1	T-------GCCCC-----------CGATTTCAATTTATGGGATACACACAGTTCAGTTTTGTCACATTTTTCGATCCTCATCACTGGGCTTTGTTTATCTCATAAAAGCGAAATTT--------------------------------
droAna3	scaffold_13340:867198-867296 -	3	G-------TCCTC-----------CGGTTTCAATTTGTGGGATACACACGGTTCAGTTGTGTCACTTTT-GCGA---GCATCACTGGGCTTTGTTTATCTCATAAGACTGAAATTTGTTCA---------------------------
droBip1	scf7180000394085:131950-132048 +	2	G-------TCCTC-----------CGGTTTCAAATTATGGGATACACACAGTTCAGTTTTGTCACTTTT-GCGA---ACATCACTGGGCTTTGTTTATCTCATAAGACTGAAATTTGTTCA---------------------------
dp4	chr2:7233334-7233438 -	2	CGTGTGCCTCTTT-----------TGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACATTT--CGA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCA---------------------------
droPer1	super_0:1094016-1094113 -	2	C-------TCTTT-----------TGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACATTT--CGA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCA---------------------------
droWil1	scaffold_181108:652-751 +	3	G-------TCAGA-----------CGGTTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCGCATTCCACGA---GCATCACTGGGCTTTGTTTATCTCATAAAGGAGAAATGAATACA---------------------------
droVir3	scaffold_13047:1194317-1194415 +	2	T-------GATTT-----------GGATTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCAGATGT-CCAA---GCATCACTGGGCTTTGTTTATCTCATAAGAGTGAAATTTGTTCA---------------------------
droMoj3	scaffold_6540:5225327-5225427 +	2	G-------TGATT---------AAGGATTTCAATTTATGGGATACACTAAGTTCAGTTTTGTCAGATGT-CCAA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTTGTTCA---------------------------
droGri2	scaffold_14906:5077291-5077389 -	1	G-------ATTTC-----------GGATTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCAGATGT-CCAA---GCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTAGTTCA---------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GT-------------------CCTTCGGTTTCAGTTTA-----------------TGGGATACACACAGTTCAGTTTTGTCACAC-TTCAAGCATCACTGGGCTTTGTTTATCTCATGAG-AGCGAAATTTATTCA

Size

Hit Count

Total Norm

droSim1

GT-------------------CCTTCGGTTTCAGTTTA-----------------TGGGATACACACAGTTCAGTTTTGTCACAC-TTTAAGCATCACTGGGCTTTGTTTATCTCATGAG-AGCGAAATTTATTCA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..............................................................................................TCACTGGGCTTTGTTTATCTCA....................	22	1	255.00	6.00	129.00	33.00	87.00
..............................................................................................TCACTGGGCTTTGTTTATCTC.....................	21	1	219.00	1.00	145.00	43.00	30.00
..............................................................................................TCACTGGGCTTTGTTTATCT......................	20	1	21.00	1.00	14.00	2.00	4.00
..............................................................................................TCACTGGGCTTTGTTTATC.......................	19	1	8.00	0.00	5.00	3.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTCG....................	22	1	8.00	0.00	6.00	0.00	2.00
..............................................................................................TCGCTGGGCTTTGTTTATCTC.....................	21	1	2.00	0.00	1.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCTCAA...................	23	1	2.00	0.00	0.00	0.00	2.00
..............................................................................................TCACTGGGCTCTGTTTATCTCT....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTCTTTATCTCA....................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCTTTATTTATCTC.....................	21	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCACTAGGCTTTGTTTATCTCA....................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................CACTGGGCTTTGTTTATCTC.....................	20	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCCCTGGGCTTTGTTTATCTCA....................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTTCATCTCA....................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTCAAAA.................	25	1	1.00	1.00	0.00	0.00	0.00
................................................................................................CCTGGGCTTTGTTTATCTC.....................	19	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................ATCACTGGGCTTTGTTTATC.......................	20	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCTCT....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTGTGTTTATCTC.....................	21	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCACTGGACTTTGTTTATCTC.....................	21	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCACTGGGCCTTGTTTATCTCA....................	22	1	1.00	0.00	0.00	0.00	1.00

droSec1

GT-------------------CCTTCGGTTTCAGTTTA-----------------TGGGATACACACAGTTCAGTTTTGTCACAC-TTCAAGCATCACTGGGCTTTGTTTATCTCATGAG-AGCGAAATTTATTCA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..............................................................................................TCACTGGGCTTTGTTTATCTCA....................	22	1	5745.00	1084.00	7.00	4654.00
..............................................................................................TCACTGGGCTTTGTTTATCTC.....................	21	1	659.00	151.00	0.00	508.00
..............................................................................................TCACTGGGCTTTGTTTATCT......................	20	1	161.00	38.00	0.00	123.00
................................................................................................ACTGGGCTTTGTTTATCTCA....................	20	1	32.00	4.00	0.00	28.00
..............................................................................................TCACTGGGCTTTGTTTATCTCAA...................	23	1	23.00	5.00	0.00	18.00
..............................................................................................TCACTGGGCTTTGTTTATTTCA....................	22	1	12.00	8.00	0.00	4.00
..............................................................................................TCACTGGGCTTTGTTTATATCA....................	22	1	10.00	9.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTCTATCTCA....................	22	1	9.00	0.00	0.00	9.00
..............................................................................................TCACTGGGCTTTGTTTATCCCA....................	22	1	9.00	3.00	0.00	6.00
..............................................................................................TCAATGGGCTTTGTTTATCTCA....................	22	1	8.00	1.00	0.00	7.00
...............................................................................................CACTGGGCTTTGTTTATCTCA....................	21	1	8.00	2.00	0.00	6.00
..............................................................................................TCACTGGCCTTTGTTTATCTCA....................	22	1	7.00	1.00	0.00	6.00
..............................................................................................TCACTGGTCTTTGTTTATCTCA....................	22	1	7.00	1.00	0.00	6.00
..............................................................................................TCACTGGGCTTTGTTTGTCTCA....................	22	1	7.00	1.00	0.00	6.00
..............................................................................................TCGCTGGGCTTTGTTTATCTCA....................	22	1	6.00	0.00	0.00	6.00
..............................................................................................TAACTGGGCTTTGTTTATCTCA....................	22	1	6.00	0.00	0.00	6.00
..............................................................................................TCACAGGGCTTTGTTTATCTCA....................	22	1	6.00	0.00	0.00	6.00
..............................................................................................TCACTGGGCTTTGTTTCTCTCA....................	22	1	6.00	1.00	0.00	5.00
..............................................................................................TCACTGGGCTTTTTTTATCTCA....................	22	1	6.00	0.00	0.00	6.00
..............................................................................................TCACTGGGCTTTGCTTATCTCA....................	22	1	6.00	1.00	0.00	5.00
..............................................................................................TCACTGGGCCTTGTTTATCTCA....................	22	1	6.00	1.00	0.00	5.00
..............................................................................................TCACTGGGCTTTGxTTATCTCA....................	21	1	5.00	0.00	0.00	5.00
..............................................................................................TCACTGGACTTTGTTTATCTCA....................	22	1	5.00	1.00	0.00	4.00
..............................................................................................TCACTGGGCTTTCTTTATCTCA....................	22	1	5.00	1.00	0.00	4.00
..............................................................................................CCACTGGGCTTTGTTTATCTCA....................	22	1	5.00	1.00	0.00	4.00
..............................................................................................TCACTGAGCTTTGTTTATCTCA....................	22	1	5.00	1.00	0.00	4.00
..............................................................................................TCACTTGGCTTTGTTTATCTCA....................	22	1	4.00	0.00	0.00	4.00
..............................................................................................TCACTGGGCTTTGTTTATGTCA....................	22	1	4.00	3.00	0.00	1.00
..............................................................................................TCACTAGGCTTTGTTTATCTCA....................	22	1	4.00	0.00	0.00	4.00
..............................................................................................TCACTGGGATTTGTTTATCTCA....................	22	1	4.00	0.00	0.00	4.00
..............................................................................................TCACTGGGCTTTGTTTATCTAA....................	22	1	4.00	2.00	0.00	2.00
..............................................................................................TCACTGGGCTTTGTTTACCTCA....................	22	1	4.00	1.00	0.00	3.00
..............................................................................................TCACTGGGTTTTGTTTATCTCA....................	22	1	4.00	0.00	0.00	4.00
..............................................................................................TCACTGGGCATTGTTTATCTCA....................	22	1	4.00	0.00	0.00	4.00
..............................................................................................TCACTGGGCTTTGTTTATATC.....................	21	1	4.00	4.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTCT....................	22	1	4.00	0.00	0.00	4.00
..............................................................................................TCACTGGGCTTTGTTTATCACA....................	22	1	4.00	0.00	0.00	4.00
..............................................................................................TCACTGCGCTTTGTTTATCTCA....................	22	1	3.00	1.00	0.00	2.00
..............................................................................................ACACTGGGCTTTGTTTATCTCA....................	22	1	3.00	1.00	0.00	2.00
..............................................................................................TCACTxGGCTTTGTTTATCTCA....................	21	1	3.00	0.00	0.00	3.00
..............................................................................................TCATTGGGCTTTGTTTATCTCA....................	22	1	3.00	1.00	0.00	2.00
..............................................................................................TCACTGGGCTTTGTTCATCTCA....................	22	1	3.00	2.00	0.00	1.00
................................................................................................ACTGGGCTTTGTTTATCTC.....................	19	1	3.00	1.00	0.00	2.00
..............................................................................................TCACTGGGCTTTGTTTATCTCG....................	22	1	3.00	0.00	0.00	3.00
..............................................................................................TCACTGGGCTTTGTTTATCTCC....................	22	1	3.00	1.00	0.00	2.00
..............................................................................................TCCCTGGGCTTTGTTTATCTCA....................	22	1	3.00	3.00	0.00	0.00
..............................................................................................GCACTGGGCTTTGTTTATCTCA....................	22	1	3.00	0.00	0.00	3.00
..............................................................................................TCACTGAGCTTTGTTTATCTC.....................	21	1	3.00	0.00	0.00	3.00
..............................................................................................TCACTGTGCTTTGTTTATCTCA....................	22	1	3.00	0.00	0.00	3.00
.............................................................................................CTCACTGGGCTTTGTTTATCTCA....................	23	1	3.00	1.00	0.00	2.00

droYak2

GT-------------------CCTCCGGTTTCAGTTTA-----------------TGGGATACACACAGTTCAGTTTTGTCGCAC-TACAAGCATCACTGGGCTTTGTTTATCTCATGAG-AGCGAAATTTGTTCA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..............................................................................................TCACTGGGCTTTGTTTATCTCA....................	22	1	2538.00	1.00	208.00	328.00	297.00	1704.00
..............................................................................................TCACTGGGCTTTGTTTATCTC.....................	21	1	1004.00	0.00	21.00	37.00	36.00	910.00
..............................................................................................TCACTGGGCTTTGTTTATCT......................	20	1	46.00	0.00	8.00	7.00	4.00	27.00
..............................................................................................TCACTGGGCTTTGTTTATCTCG....................	22	1	24.00	0.00	0.00	0.00	0.00	24.00
..............................................................................................TCACTGGGCTTTGTTTATC.......................	19	1	11.00	0.00	0.00	0.00	0.00	11.00
................................................................................................ACTGGGCTTTGTTTATCTCA....................	20	1	10.00	0.00	3.00	2.00	3.00	2.00
..............................................................................................TCACTGGGCTTTGTTTATCTCC....................	22	1	9.00	0.00	2.00	0.00	7.00	0.00
..............................................................................................TCACTGGGCTTTGTTTCTCTCA....................	22	1	7.00	0.00	4.00	0.00	3.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCC......................	20	1	6.00	0.00	0.00	0.00	0.00	6.00
..............................................................................................TCACTGGGCTTTGTTTACCTCA....................	22	1	4.00	0.00	1.00	1.00	2.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTCAT...................	23	1	4.00	0.00	0.00	0.00	0.00	4.00
..............................................................................................TCACGGGGCTTTGTTTATCTCA....................	22	1	4.00	0.00	0.00	0.00	3.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCTCT....................	22	1	4.00	0.00	0.00	0.00	4.00	0.00
..............................................................................................CCACTGGGCTTTGTTTATCTC.....................	21	1	3.00	0.00	0.00	0.00	0.00	3.00
..............................................................................................TCACTGGACTTTGTTTATCTCA....................	22	1	3.00	0.00	0.00	0.00	2.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCTCAA...................	23	1	3.00	0.00	0.00	1.00	2.00	0.00
..............................................................................................TCACTGGGCTTTGGTTATCTC.....................	21	1	3.00	0.00	0.00	0.00	1.00	2.00
..............................................................................................TCACCGGGCTTTGTTTATCTCA....................	22	1	3.00	0.00	0.00	1.00	0.00	2.00

droEre2

GT-------------------CCTCCGGTTTCAGTTTA-----------------TGGGATACACACAGTTCAGTTTTGTCACAC-TTCAAGCATCACTGGGCTTTGTTTATCTCATGAG-AGCGAAATTTGTTCA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..............................................................................................TCACTGGGCTTTGTTTATCTCA....................	22	1	27.00	2.00	2.00	4.00	19.00
..............................................................................................TCACTGGGCTTTGTTTATCT......................	20	1	6.00	0.00	2.00	1.00	3.00
..............................................................................................TCACTTGGCTTTGTTTATCTCA....................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCTC.....................	21	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCTCAA...................	23	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCTCT....................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCTAA....................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTAGGCTTTGTTTATCTCA....................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGGTTATCTC.....................	21	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCCCA....................	22	1	1.00	0.00	0.00	1.00	0.00

droAna3

GT-------------------CCTCCGGTTTCAATTTG-----------------TGGGATACACACGGTTCAGTTGTGTCACTTTTGCGAGCATCACTGGGCTTTGTTTATCTCATAAG-ACTGAAATTTGTTC-	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..............................................................................................TCACTGGGCTTTGTTTATCTCA....................	22	1	17.00	4.00	8.00	3.00	2.00
..............................................................................................TCACTGGGCTTTGTTTATCTC.....................	21	1	7.00	2.00	4.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCT......................	20	1	7.00	3.00	4.00	0.00	0.00
..............................................................................................TCACTGGGCTTCGTTTATCT......................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGCTTATCT......................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGCGCTTTGTTTATCTGA....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGTTTTTGTTTATCT......................	20	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGAGCTTTGTTTATCT......................	20	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATC.......................	19	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCACTGGGATTTGTTTATCT......................	20	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTAA....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCGCTGGGCTTTGTTTATCTCA....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTCTCTCA....................	22	1	1.00	0.00	0.00	1.00	0.00

dp4

GTGCGTGTGAAACGTGTGCCTCTTTTGGTTTCAATTTA-----------------TGGGATGCACCAAGTTCAGTTTTGTCACAT-TTCGAGCATCACTGGGCTTTGTTTATCTCATAAG-AGCGAAATTGATTCA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..............................................................................................TCACTGGGCTTTGTTTATCTCA....................	22	1	106.00	67.00	10.00	12.00	17.00
..............................................................................................TCACTGGGCTTTGTTTATCTC.....................	21	1	36.00	16.00	1.00	4.00	15.00
..............................................................................................TCACTGGGCTTTGTTTATCT......................	20	1	21.00	17.00	0.00	2.00	2.00
..............................................................................................TCACTGGGCTTTGTTTATCTCT....................	22	1	2.00	0.00	0.00	0.00	2.00
................................................................................................ACTGGGCTTTGTTTATCTCA....................	20	1	2.00	1.00	1.00	0.00	0.00
..............................................................................................TCACTGGGTTTTGTTTATCTCA....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCTCTGGGCTTTGTTTATCTCT....................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCTCTGGGCTTTGTTTATCTC.....................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCGCTGGGCTTTGTTTATCTCA....................	22	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................CACTGGGCTTTGTTTATCTCA....................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCxTTGTTTATCTCA....................	21	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................CTCACTGGGCTTTGTTTATCTC.....................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTTTCTCA......................	20	1	1.00	1.00	0.00	0.00	0.00

droPer1

GTGCGTGCGAAACGTGTGCCTCTTTTGGTTTCAATTTA-----------------TGGGATGCACCAAGTTCAGTTTTGTCACAT-TTCGAGCATCACTGGGCTTTGTTTATCTCATAAG-AGCGAAATTGATTCA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..............................................................................................TCACTGGGCTTTGTTTATCTCA....................	22	1	74.00	6.00	0.00	14.00	15.00	39.00
..............................................................................................TCACTGGGCTTTGTTTATCTC.....................	21	1	33.00	8.00	0.00	5.00	8.00	12.00
..............................................................................................TCACTGGGCTTTGTTTATCT......................	20	1	15.00	5.00	0.00	6.00	4.00	0.00
..............................................................................................TCACTGGGCTTTCTTTATCTCA....................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCGTTGTTTTTCTC.....................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTAACTCA....................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCTCAA...................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................................................TAACTGGGCTTTGTTTATCTCA....................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGTTTTGTTTATCTC.....................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................................................GTTCAGTTTTGTCGCTT-TT................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................ACGCTGGGCTTTGTTTATCTCA....................	22	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

AA-------------------TTTTCGCTTTTTGTTTTGGCTCTACTGTTCTCGCTGCTGCACTTACACTTTGCTTTTTTCGCT--TTCGTTCGACACTGGGCTTTCTTTTACATTTTAGTTAAGCCatttattta

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

GA--------------------TTTGGATTTCAATTTA-----------------TGGGATACACCAAGTTCAGTTTTGTCAGATGTCCAAGCATCACTGGGCTTTGTTTATCTCATAAG-AGTGAAATTTGTTCA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..............................................................................................TCACTGGGCTTTGTTTATCTCA....................	22	1	653.00	11.00	93.00	4.00	43.00	502.00
..............................................................................................TCACTGGGCTTTGTTTATCTC.....................	21	1	545.00	2.00	17.00	0.00	41.00	485.00
..............................................................................................TCACTGGGCTTTGTTTATCT......................	20	1	41.00	3.00	11.00	1.00	4.00	22.00
..............................................................................................TCACTGGGCTTTGTTTATC.......................	19	1	16.00	0.00	2.00	0.00	1.00	13.00
..............................................................................................TCACTGGGCTTTGTTTATCTCG....................	22	1	13.00	0.00	0.00	0.00	0.00	13.00
..............................................................................................TCACTGGGCTTTGTTTATCTCAT...................	23	1	6.00	0.00	0.00	0.00	0.00	6.00
..............................................................................................CCACTGGGCTTTGTTTATCTC.....................	21	1	3.00	0.00	1.00	0.00	0.00	2.00
..............................................................................................TCACTGGGCTTTGTTTATCTCT....................	22	1	3.00	0.00	0.00	0.00	1.00	2.00
..............................................................................................TCACTGGGCTTTGTTTATCTCC....................	22	1	3.00	0.00	0.00	0.00	2.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCTCAA...................	23	1	3.00	2.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCTAA....................	22	1	2.00	0.00	1.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGCTTATCTCA....................	22	1	2.00	0.00	0.00	0.00	0.00	2.00
..............................................................................................TCACTGGGCCTTGTTTATCTCA....................	22	1	2.00	0.00	2.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCGATGTTTATCTCA....................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................TCACCGGGCTTTGTTTATCTCA....................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGCGCTTTGATTATCTCA....................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTGTTTTATCTC.....................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCGTTGTTTAGCTCA....................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTTTCTC.....................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTAGGCTTTGTTTATC.......................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCTT.....................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCC......................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTTTTTATCTCA....................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCG......................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTGTTTCTC.....................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGCTTATCTC.....................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGCTTATCT......................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................ACTGGGCTTTGTTTATCTC.....................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
............................................................................................TCTCACTGGGCTTTGTTTATCTCA....................	24	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTATTTATCTCA....................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................CCACTGGGCTTTGTTTATCTCA....................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGCGCTTTGTTTCTCTCA....................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGTTTTGTTTATCTC.....................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCGTTGTTTATCTC.....................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGGTTATCTC.....................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCCCA....................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................CTCACTGGGCTTTGTTTATCTCA....................	23	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

GA-------------------TTAAGGATTTCAATTTA-----------------TGGGATACACTAAGTTCAGTTTTGTCAGATGTCCAAGCATCACTGGGCTTTGTTTATCTCATAAG-AGCGAAATTTGTTCA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..............................................................................................TCACTGGGCTTTGTTTATCTCA....................	22	1	1063.00	901.00	88.00	67.00	7.00
..............................................................................................TCACTGGGCTTTGTTTATCTC.....................	21	1	208.00	157.00	23.00	28.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCT......................	20	1	163.00	97.00	29.00	37.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTCAT...................	23	1	22.00	17.00	2.00	3.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATC.......................	19	1	7.00	3.00	3.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTCT....................	22	1	6.00	4.00	1.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTCAA...................	23	1	5.00	4.00	1.00	0.00	0.00
..............................................................................................TCACTGGGATTTGTTTATCTCA....................	22	1	3.00	1.00	1.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTAT........................	18	1	2.00	1.00	1.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTCTCT......................	20	1	2.00	0.00	0.00	2.00	0.00
..............................................................................................TCACTGGGCTTTGCTTATCTCA....................	22	1	2.00	2.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGCTTATCT......................	20	1	2.00	0.00	1.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTACCTCA....................	22	1	2.00	1.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTGTCTCA....................	22	1	2.00	1.00	1.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTCTATCTCA....................	22	1	2.00	1.00	0.00	0.00	1.00
..............................................................................................TCACTGGGCTTTGTTTATCTCG....................	22	1	2.00	2.00	0.00	0.00	0.00
..............................................................................................TCACTGTGCTTTGTTTATCTCA....................	22	1	2.00	1.00	1.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTCC....................	22	1	2.00	0.00	0.00	1.00	1.00
..............................................................................................TCGCTGGGCTTTGTTTATCTCA....................	22	1	2.00	1.00	0.00	1.00	0.00
..............................................................................................GCACTGGGCTTTGTTTATCTC.....................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................GCACTGGGCTTTGTTTATCT......................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................ACACTGGGCTTTGTTTATCTC.....................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATATCA....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCAATGGGCTTTGTTTATCTC.....................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACCGGGCTTTGTTTATCTC.....................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTTTCTC.....................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TAACTGGGCTTTGTTTATCTCA....................	22	1	1.00	0.00	1.00	0.00	0.00
................................................................................................ACTGGGCTTTGTTTATCTCA....................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTCGGCTGTGTTTATCTCA....................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTCGGCTTTGTTTATCTC.....................	21	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TTACTGGGCTTTGTTTATCTCA....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGxTTATCTC.....................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTTGGCTTTGTTTATCTCA....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTCTGTTTATCT......................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGTCTTTGTTTATCTCA....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTCGGCTTTGTTTATCT......................	20	1	1.00	0.00	0.00	1.00	0.00
...............................................................................TCAGATGTCCAAGCATCACTGGGC.................................	24	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTCAAA..................	24	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGCTTATCTCC....................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCTTTTTTTATCTC.....................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATATC.....................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCAATGGGCTTTGTTTATCT......................	20	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................CCACTGGGCTTTGTTTATCT......................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGCCCTTTGTTTATCTCA....................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCCCA....................	22	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................CTCACTGGGCTTTGTTTATCTCA....................	23	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCAATGGGCTTAGTTTATCTCA....................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCACTGGGCTCTGTTTATCTCA....................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCTTCGTTTGTCTC.....................	21	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCAGTGGGCTTTGTTTATCTCA....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTxTTTATC.......................	18	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTAGGCTTTGTTTATCAC.....................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTTA....................	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................................ACTGGGCTTTGTTTATCTCATT..................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTTTTTATCTTA....................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGATTATCTCA....................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTCATT..................	24	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCxTTGTTTATCTCA....................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTTTCTCA....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCGTTGTTTAGCTCA....................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCACTGGGCCTTGTTTATCTC.....................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCCA.....................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATGTCA....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATAT......................	20	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTCGGCTTTGTTTATCTCA....................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACGGGGCTTTGTTTATCTC.....................	21	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TCACTGTGCTTTGTTTATCTC.....................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGAGCTTTGTTTCTCTCA....................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................CCACTGGGCTTTGTTTATCTCA....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTCTCTCA....................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTAA....................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCTTTGTTTATCTCAAT..................	24	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................TCACTGGGCGTTGTTTATCT......................	20	1	1.00	0.00	0.00	1.00	0.00

droGri2

GA-------------------TTTCGGATTTCAATTTA-----------------TGGGATACACCAAGTTCAGTTTTGTCAGATGTCCAAGCATCACTGGGCTTTGTTTATCTCATAAG-AGCGAAATTAGTTCA	Size	Hit Count	Total Norm	V109 Male body
..............................................................................................TCACTGGGCTTTGTTTATCTCA....................	22	1	2.00	2.00
..............................................................................................TCACTGGGCTTTGTTTATCTCT....................	22	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