dme-mir-4919- 12- and 20-way alignments

dme-mir-4919	chr2R:11833392-11833451 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 11833392-11833412
   star strand at position 11833431-11833451
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2R:11833377-11833466 +	TGGACATACTAAATGGTGAGTCTCT-----AGGGGATTA--GCAAGCTATAATTTC------------TC-ACTTAATCCCTGAA------------------CGACTTGCAGAGGCCGTTTTGGGTG
droSim1	chr2R:10571957-10572046 +	TGGACATACTAAATGGTGAGTCTCT-----AGGGGATTA--GCAAGCTATAATTCC------------TC-AATTAATCCCTGAA------------------CGACTTGCAGAGGCCGTTTTGGGTG
droSec1	super_1:9333409-9333498 +	TGGACATACTAAATGGTGAGTCTTT-----AGGGGATTA--GCAAGCCATAATTCC------------TC-ACTTAATCCCTGAA------------------CGACTTGCAGAGGCCGTTTTGGGTG
droYak2	chr2R:17148711-17148800 -	TGGACATACTGAATGGTGAGTCTCT-----AGGGGATTA--GCAAGCCATGATTCC------------TC-CCTTAATCCCTGAA------------------CGACTTGCAGAGGCCGTTTTGGGTG
droEre2	scaffold_4845:14024563-14024652 -	TGGACATACTAAATGGTGAGTCTCT-----AGGGGATTA--GCAAGCCATATTTCC------------AC-ACTTAATCCCTGAA------------------CGACTTGCAGAGGCCGTTTTGGGAG
droAna3	scaffold_13266:11891001-11891093 -	TGGACATACTGAATGGTGAGTTTACAAGTCGGC---ACTAAT---TTTTGAAGCGG------------GAATGTGAATATGAG-----------------CCGTAAATTGCAGAAGCGGTGCTGGGCG
dp4	chr3:18992460-18992549 -	TGGACATCTTAAATGGTGAGTCTTCCATTCCAG-------------------TTCCTTTGCGTTTTGTCC-ACTGATTCACTCAA------------------ACTTATACAGAGGCCGTTTTGGGTG
droPer1	super_242:24174-24263 -	TGGACATCTTAAATGGTGAGTCTTCCATTCCAG-------------------TTCCTTTGCGTTTTGTCC-ACTGATTCACTCAA------------------ACTTATACAGAGGCCGTTTTGGGTG
droWil1	Unknown	TGGATATATTGAATGGTAAGTCCC------------------------------------------------------------------------------------TTTAGAGGCTGTTTTGGGTG
droVir3	Unknown	TCGATGTGCTGAATGGTGAGCTTTG--CCTGAG---TG-------------GGTCC------------AC-ACCAAATCCTAATC------------------CCATTTGCAGAGGCTGTGCTGGGCG
droMoj3	Unknown	TCGATGTGCTAAATGGTAAGTCCC--ACTTCAGGCACTT--CTAATCT--------------------------GAATATTAATACTCTTTCTCTCTCTCTCCTGTCTTGCAGAGGCTGTACTTGGCG
droGri2	Unknown	TCGATGTTTTAAATGGTGCGTGCTTAACTTGAA---AGAGAT---CTCACAAATCC------------AA-TCTTAAT------T------------------AAGATTGCAGAGGCTGTTCTGGGTG

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:11833377-11833466 +	NA	TGGACATACTAAATGGTGAGTCTCT---AGGGG--ATTAGC-A-------------------AGCTATAATT----TCTCACT-TAATCCC----TGAAC-------------------------------------------GA-CTTGCAGAGGCCGTTTTGGGTG
droSim1	chr2R:10571957-10572046 +	14	TGGACATACTAAATGGTGAGTCTCT---AGGGG--ATTAGC-A-------------------AGCTATAATT----CCTCAAT-TAATCCC----TGAAC-------------------------------------------GA-CTTGCAGAGGCCGTTTTGGGTG
droSec1	super_1:9333409-9333498 +	15	TGGACATACTAAATGGTGAGTCTTT---AGGGG--ATTAGC-A-------------------AGCCATAATT----CCTCACT-TAATCCC----TGAAC-------------------------------------------GA-CTTGCAGAGGCCGTTTTGGGTG
droYak2	chr2R:17148711-17148800 -	37	TGGACATACTGAATGGTGAGTCTCT---AGGGG--ATTAGC-A-------------------AGCCATGATT----CCTCCCT-TAATCCC----TGAAC-------------------------------------------GA-CTTGCAGAGGCCGTTTTGGGTG
droEre2	scaffold_4845:14024563-14024652 -	32	TGGACATACTAAATGGTGAGTCTCT---AGGGG--ATTAGC-A-------------------AGCCATATTT----CCACACT-TAATCCC----TGAAC-------------------------------------------GA-CTTGCAGAGGCCGTTTTGGGAG
droEug1	scf7180000409672:743652-743740 +	19	TGGACATTCTAAATGGTGGGTCTCT---AGGGG--ATTTACTA-------------------AA--TTATTT----CCTTGTT-AAATCTC----TTAAC-------------------------------------------CA-TTTACAGAAGCCGTTTTGGGTG
droBia1	scf7180000302292:2006181-2006269 +	19	TGGACATACTAAATGGTGAGTCGCC---AGGGG--ATTTCCTA---------AAGGGTAGTAAGCTACA---------TCATT-TAAAC------------------------------------------------------CC-TTCGCAGAGGCCGTTCTGGGGG
droTak1	scf7180000415795:733158-733248 -	52	TGGATATACTAAATGGTGGGTCTCC---AAAGG--AATTTATA-------------------CCCATTATAT----CTCTACC-TAATCTT----TAAAC-------------------------------------------CC-CTTACAGAAGCCGTTTTGGGTG
droEle1	scf7180000491107:834450-834545 +	6	TGGACATACTTAATGGTGAGTCTTT---GAGGG--TCTAGC-AAGAAACTTGAT-------------AAGCT----CTTGAAT-AAATCCC----TAATC-------------------------------------------CG-CTTACAGAGGCCGTTTTGGGTG
droRho1	scf7180000779911:267592-267685 -	48	TGGACATTCTAAATGGTGAGTCTTT---AGGGG--ATTTCT-T-------------------A-CTGTAGTTTTCTCCTAAAT-AAACCCA----TACCC-------------------------------------------ACCTTAATAGAAGCTGTTTTGGGTG
droFic1	scf7180000453948:1083547-1083638 +	17	TGGACATACTAAATGGTGAGTCTCT---AGGAG--ATTTAT-A-------------------AGCCCCATTTCAATCCCTAA--TAATACT----TG-AC-------------------------------------------CA-TTTTTAGAGGCCGTTTTGGGTG
droKik1	scf7180000302385:1064069-1064163 +	10	TGGGCATACTAAATGGTGAGTCTCT---AGAGAGGATTAGT-T--------------------TCTCCTGGT----CATCAAC-TAACCTCTATATGACT-------------------------------------------TA-CCCACAGAGGCCGTTCTGGGCG
droAna3	scaffold_13266:11891001-11891093 -	48	TGGACATACTGAATGGTGAGTTTAC---AAG----------------------------------------T----CGGCAC--TAATTTT----TGAAGCGGGAATGTGAATATGAGC---------------------CGTAA-ATTGCAGAAGCGGTGCTGGGCG
droBip1	scf7180000396547:586641-586728 +	8	TGGACATACTGAATGGTGAGTCTGG---AGGTC--AATATT-G-------------------AATAAAGGAA----TCTGAA------------------------------TATCGAC---------------------CGTAACATTGCAGAAGCGGTGCTGGGCG
dp4	chr3:18992460-18992549 -	32	TGGACATCTTAAATGGTGAGTCTTC---CATTC---------CAGTTCCTTTGCGTTTT-----------------GTCCACT-GATTCAC----TCAAA-------------------------------------------CT-TATACAGAGGCCGTTTTGGGTG
droPer1	super_242:24174-24263 -	39	TGGACATCTTAAATGGTGAGTCTTC---CATTC---------CAGTTCCTTTGCGTTTT-----------------GTCCACT-GATTCAC----TCAAA-------------------------------------------CT-TATACAGAGGCCGTTTTGGGTG
droWil1	scaffold_181150:1332685-1332769 -	34	TGGACATAATAGCGGGTGAGTGAAA-----GAG--ATA-CG-A-------------------GATTACAATT------TGGATTACATTT-----TTGGT-------------------------------------------TG-GTCGCAGAAACGTCAATGGGTA
droVir3	scaffold_12875:17265801-17265883 +	14	TCGATGTGCTGAATGGTGAGCTTTGCCTGA-------G-----------------------------TGGGT----CCACACC-AAATCCTAATCCCATT-------------------------------------------TA-TTTGCAGAGGCTGTGCTGGGCG
droMoj3	scaffold_6496:10745157-10745258 -	24	TCGATGTGCTAAATGGTAAGTCCCACTTCAGGC--ACTTCT-A-------------------ATCT-------------GAA------------------------------TATTAATACTCTTTCTTTCTCTCTCTCTCCTGT-CTTGCAGAGGCTGTACTTGGCG
droGri2	scaffold_15245:16779329-16779419 +	28	TCGATGTTTTAAATGGTGCGTGCTT---AACTT--GAAAGAGA-------------------TCTCACAAAT----CCAATCT-TAATTAA----GTGAT-------------------------------------------TC-ATTGCAGAGGCTGTTCTGGGTG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TGGACATACTAAATGGTGAGTCTCT-----AGGGGATTA--GCAAGCTATAATTTC------------TC-ACTTAATCCCTGAA------------------CGACTTGCAGAGGCCGTTTTGGGTG

Size

Hit Count

Total Norm

droSim1

TGGACATACTAAATGGTGAGTCTCT-----AGGGGATTA--GCAAGCTATAATTCC------------TC-AATTAATCCCTGAA------------------CGACTTGCAGAGGCCGTTTTGGGTG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................................................................TAATCCCTGAA------------------CGACTTGCAG...............	21	1	1761.00	8.00	806.00	600.00	347.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGT..............	22	1	772.00	9.00	288.00	200.00	275.00
..........................................................................TAATCCCTGAA------------------CGACTTGCA................	20	1	301.00	0.00	177.00	108.00	16.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGA..............	22	1	275.00	0.00	103.00	92.00	80.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGG..............	22	1	116.00	0.00	35.00	38.00	43.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGC..............	22	1	69.00	0.00	40.00	13.00	16.00
..........................................................................TAATCCCTGAA------------------CGACTTGC.................	19	1	60.00	0.00	36.00	22.00	2.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAT...............	21	1	36.00	0.00	13.00	11.00	12.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAC...............	21	1	36.00	0.00	22.00	7.00	7.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGTT.............	23	1	26.00	0.00	14.00	10.00	2.00
.........................................................................TTAATCCCTGAA------------------CGACTTGCAG...............	22	1	17.00	0.00	7.00	5.00	5.00
..........................................................................TAATCCCTGAA------------------CGACTTGCGG...............	21	1	17.00	0.00	2.00	11.00	4.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGTA.............	23	1	15.00	0.00	7.00	6.00	2.00
...............GTGAGTCTCT-----AGGGGATTA--GC.....................................................................................	21	1	14.00	7.00	2.00	4.00	1.00
.........................................................................TTAATCCCTGAA------------------CGACTTGCA................	21	1	11.00	0.00	9.00	2.00	0.00
...........................................................................AATCCCTGAA------------------CGACTTGCAGT..............	21	1	10.00	2.00	7.00	1.00	0.00
..........................................................................TAATCCCTGAA------------------CGACTTGCG................	20	1	10.00	0.00	3.00	5.00	2.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAA...............	21	1	8.00	0.00	4.00	2.00	2.00
...........................................................................AATCCCTGAA------------------CGACTTGCAG...............	20	1	7.00	0.00	3.00	4.00	0.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGAA.............	23	1	6.00	0.00	3.00	3.00	0.00
........................................................................ATTAATCCCTGAA------------------CGACTTGCAG...............	23	1	5.00	0.00	3.00	2.00	0.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGAAA............	24	1	5.00	0.00	1.00	2.00	2.00
..........................................................................TAATCCCTGAA------------------CGACTTGCATT..............	22	1	4.00	0.00	0.00	0.00	4.00
............................................................................ATCCCTGAA------------------CGACTTGCAG...............	19	1	4.00	0.00	3.00	1.00	0.00
.........................................................................TTAATCCCTGAA------------------CGACTTGCAGT..............	23	1	4.00	0.00	1.00	2.00	1.00
..........................................................................TAACCCCTGAA------------------CGACTTGCAG...............	21	1	4.00	0.00	2.00	1.00	1.00
............................................................................ATCCCTGAA------------------CGACTTGCAGA..............	20	1	3.00	0.00	2.00	1.00	0.00
..........................................................................TAATCCCCGAA------------------CGACTTGCAG...............	21	1	3.00	0.00	1.00	2.00	0.00
...........................................................................AATCCCTGAA------------------CGACTTGCAGA..............	21	1	3.00	0.00	1.00	2.00	0.00
.......................................................................AATTAATCCCTGAA------------------CGACTTGCAG...............	24	1	3.00	0.00	2.00	0.00	1.00
...........................................................................AATCCCTGAA------------------CGACTTGCAGTT.............	22	1	3.00	0.00	1.00	2.00	0.00

droSec1

TGGACATACTAAATGGTGAGTCTTT-----AGGGGATTA--GCAAGCCATAATTCC------------TC-ACTTAATCCCTGAA------------------CGACTTGCAGAGGCCGTTTTGGGTG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..........................................................................TAATCCCTGAA------------------CGACTTGCAGT..............	22	1	226.00	134.00	70.00	22.00
...............GTGAGTCTTT-----AGGGGATTA--GC.....................................................................................	21	1	39.00	19.00	18.00	2.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAG...............	21	1	38.00	24.00	8.00	6.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGA..............	22	1	17.00	14.00	3.00	0.00
...........................................................................AATCCCTGAA------------------CGACTTGCAGT..............	21	1	14.00	7.00	5.00	2.00
..........................................................................TAATCCCTGAA------------------CGACTTGCA................	20	1	7.00	4.00	0.00	3.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGTT.............	23	1	4.00	3.00	0.00	1.00
...........................................................................AATCCCTGAA------------------CGACTTGCAG...............	20	1	3.00	1.00	1.00	1.00
...............GTGAGTCTTT-----AGGGGATTA--G......................................................................................	20	1	3.00	2.00	0.00	1.00
..........................................................................TAATCCCTGAA------------------CGACTTGCGGT..............	22	1	2.00	1.00	1.00	0.00
..........................................................................TAATTCCTGAA------------------CGACTTGCAGT..............	22	1	2.00	1.00	1.00	0.00
...........................................................................AATCCCTGAA------------------CGACTTGCAGTT.............	22	1	2.00	0.00	2.00	0.00
...............GTGAGTCTTT-----AGGGGATTA--GCA....................................................................................	22	1	2.00	0.00	2.00	0.00
...............GTGAGTCTTT-----AGGGGATTA--CC.....................................................................................	21	1	1.00	1.00	0.00	0.00
...........................................................................AATCCCTGAA------------------CGACTTGCAGTA.............	22	1	1.00	1.00	0.00	0.00
..........................................................................TAATCCCTGAA------------------CGATTTGCAGT..............	22	1	1.00	0.00	1.00	0.00
...............GTGAGTCTTT-----AGGGGATTA--GCT....................................................................................	22	1	1.00	1.00	0.00	0.00
............................................................................ATCCCTGAA------------------CGACTTGCAGAGA............	22	1	1.00	1.00	0.00	0.00
..........................................................................TAATCCCTGAA------------------CGACTTGTAGA..............	22	1	1.00	1.00	0.00	0.00
...........................................................................TATCCCTGAA------------------CGACTTGCAGT..............	21	1	1.00	0.00	0.00	1.00
............................................................................ATCCCTGAA------------------CGACTTGCAGAT.............	21	1	1.00	0.00	0.00	1.00
...................................................ATTCC------------TC-ACTTAATCCCTGAA------------------CGACTTG..................	28	1	1.00	0.00	1.00	0.00
..........................................................................CAATCCCTGAA------------------CGACTTGCAGT..............	22	1	1.00	1.00	0.00	0.00
..........................................................................TAATCCCTGAA------------------CGGCTTGCAG...............	21	1	1.00	0.00	1.00	0.00
...............GTGAGTCTTT-----AxGGGATTA--GC.....................................................................................	20	1	1.00	0.00	1.00	0.00
.........................................................................TTAATCCCTGAA------------------CGACTTGCAG...............	22	1	1.00	1.00	0.00	0.00
............................................................................ATCCCTGAA------------------CGACTTGCAGT..............	20	1	1.00	0.00	1.00	0.00
..........................................................................TAATCCCTGAA------------------CGACTTGTAGT..............	22	1	1.00	1.00	0.00	0.00
..........................................................................TAATCACTGAA------------------CGACTTGCAGT..............	22	1	1.00	0.00	0.00	1.00
.........................................................................TTAATCCCTGAA------------------CGACTTGCAGT..............	23	1	1.00	0.00	1.00	0.00
..........................................................................TAATCTCTGAA------------------CGACTTGCAGT..............	22	1	1.00	0.00	1.00	0.00
...............GTGAGTCTTT-----AGGGGATT..........................................................................................	18	1	1.00	0.00	1.00	0.00
............................................................................ATCCCTGAA------------------CGACTTGCAGTT.............	21	1	1.00	0.00	0.00	1.00
...............GTGAGTCTTT-----AGGGGATTC--G......................................................................................	20	1	1.00	1.00	0.00	0.00
...............GTGAGTCTTT-----AGGGGATTA--.......................................................................................	19	1	1.00	0.00	0.00	1.00
..........................................................................TAATCCCTGAA------------------CGACTTGGAGT..............	22	1	1.00	1.00	0.00	0.00
..........................................................................TAATCCCTGAA------------------TGACTTGCAGT..............	22	1	1.00	0.00	1.00	0.00
..........................................................................TAATCCCTGAA------------------CGACTTGAAG...............	21	1	1.00	1.00	0.00	0.00
.........................................................................TTAATCCCTGAA------------------CGACTTG..................	19	1	1.00	0.00	0.00	1.00
..........................................................................TAATCCCTGAA------------------CGACTTTCAGT..............	22	1	1.00	0.00	0.00	1.00
...............GTGAGTCTTT-----AGGGGATTA--GCC....................................................................................	22	1	1.00	0.00	1.00	0.00
..........................................................................TAATCCCTGAA------------------CAACTTGCAGT..............	22	1	1.00	0.00	1.00	0.00

droYak2

TGGACATACTGAATGGTGAGTCTCT-----AGGGGATTA--GCAAGCCATGATTCC------------TC-CCTTAATCCCTGAA------------------CGACTTGCAGAGGCCGTTTTGGGTG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..........................................................................TAATCCCTGAA------------------CGACTTGCAG...............	21	1	48.00	0.00	3.00	5.00	0.00	40.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGT..............	22	1	24.00	4.00	0.00	8.00	2.00	10.00
..........................................................................TAATCCCTGAA------------------CGACTTGCA................	20	1	8.00	0.00	0.00	1.00	0.00	7.00
.........................................................................TTAATCCCTGAA------------------CGACTTGCAG...............	22	1	6.00	0.00	0.00	0.00	0.00	6.00
...............GTGAGTCTCT-----AGGGGATTA--GC.....................................................................................	21	1	5.00	3.00	0.00	2.00	0.00	0.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGTT.............	23	1	5.00	1.00	0.00	2.00	0.00	2.00
............................................................................ATCCCTGAA------------------CGACTTGCAG...............	19	1	3.00	0.00	0.00	0.00	0.00	3.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGA..............	22	1	3.00	0.00	1.00	0.00	0.00	2.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAC...............	21	1	3.00	0.00	0.00	0.00	0.00	3.00
............................................................................ATCCCTGAA------------------CGACTTGCAGT..............	20	1	3.00	0.00	0.00	1.00	0.00	2.00
...........................................................................AATCCCTGAA------------------CGACTTGCAGT..............	21	1	3.00	0.00	0.00	2.00	0.00	1.00
........................................................................CTTAATCCCTGAA------------------CGACTTGCAG...............	23	1	2.00	0.00	0.00	0.00	0.00	2.00
...............GTGAGTCTCT-----AGGGGATTA--.......................................................................................	19	1	2.00	0.00	0.00	2.00	0.00	0.00
...........................................................................AATCCCTGAA------------------CGACTTGCAGTT.............	22	1	2.00	0.00	0.00	0.00	0.00	2.00
.........................................................................CTAATCCCTGAA------------------CGACTTGC.................	20	1	2.00	0.00	0.00	0.00	0.00	2.00
.....ATACTGAATGGTGAGTCTCT-----AGGGGATT..........................................................................................	28	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................TAATCCCTGAA------------------CGACTTGC.................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................................CTTAATCCCTGAA------------------CGACTTGCAGT..............	24	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................AATCCCTGAA------------------CGACTTGCAG...............	20	1	1.00	0.00	0.00	0.00	0.00	1.00
....................................................................TC-CCTTAATCCCTGAA------------------CGACTTGC.................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................................................................CCTTAATCCCTGAA------------------CGACTTGC.................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................C-CCTTAATCCCTGAA------------------CGACTTGCCGA..............	26	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGC..............	22	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................................TAATCCCTGAA------------------CGACTTGCC................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GGGAGTCTCT-----AGGGGTTT..........................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................................................CCTTAATCCCTGAA------------------CGACTTGCAG...............	24	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................ATCCCTGAA------------------CGACTTGCAGTT.............	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................................CTTAATCCCTGAA------------------CGACTTGC.................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGG..............	22	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GTGAGTCTCT-----AGGGGATT..........................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................ATCCCTGAA------------------CGACTTGCAGTA.............	21	1	1.00	0.00	0.00	0.00	0.00	1.00

droEre2

TGGACATACTAAATGGTGAGTCTCT-----AGGGGATTA--GCAAGCCATATTTCC------------AC-ACTTAATCCCTGAA------------------CGACTTGCAGAGGCCGTTTTGGGAG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..........................................................................TAATCCCTGAA------------------CGACTTGCAGT..............	22	1	9.00	0.00	0.00	0.00	9.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAG...............	21	1	7.00	1.00	0.00	0.00	6.00
...............GTGAGTCTCT-----AGGGGATTA--GC.....................................................................................	21	1	5.00	0.00	1.00	0.00	4.00
...............GTGAGTCTCT-----AGGGGATT..........................................................................................	18	1	3.00	0.00	0.00	0.00	3.00
...............GTGAGTCTCT-----AGGGGATTA--.......................................................................................	19	1	2.00	2.00	0.00	0.00	0.00
...........................................................................AATCCCTGAA------------------CGACTTGCAGT..............	21	1	2.00	0.00	0.00	0.00	2.00
....................................................................AC-ACTTAATCCCTGAA------------------CGACTTG..................	23	1	1.00	0.00	1.00	0.00	0.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGTT.............	23	1	1.00	0.00	0.00	0.00	1.00
..........................................................................TAATCCCTGAA------------------CGACTTGCAGA..............	22	1	1.00	0.00	1.00	0.00	0.00
..........................................................................TAATCCCTGAA------------------CGACTTGCA................	20	1	1.00	0.00	0.00	0.00	1.00
..........................................................................TAATCCCTGAA------------------AGACTTGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
......................TCT-----AGGGGATTA--GCAAGCCA...............................................................................	20	1	1.00	0.00	0.00	0.00	1.00
..........................................................................TAATCCCTGAA------------------CGACTTGAAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
...............GTGAGTCTCT-----AGTGGATTA--GC.....................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................TTAATCCCTGAA------------------CGACTTGCAG...............	22	1	1.00	0.00	0.00	0.00	1.00
............................................................................ATCCCTGAA------------------CGACTTGCAGT..............	20	1	1.00	0.00	0.00	0.00	1.00

droAna3

TGGACATACTGAATGGTGAGTTTACAAGTCGGC---ACTAAT---TTTTGAAGCGG------------GAATGTGAATATGAG-----------------CCGTAAATTGCAGAAGCGGTGCTGGGCG

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

TGGACATCTTAAATGGTGAGTCTTCCATTCCAG-------------------TTCCTTTGCGTTTTGTCC-ACTGATTCACTCAA------------------ACTTATACAGAGGCCGTTTTGGGTG

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TGGACATCTTAAATGGTGAGTCTTCCATTCCAG-------------------TTCCTTTGCGTTTTGTCC-ACTGATTCACTCAA------------------ACTTATACAGAGGCCGTTTTGGGTG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
....................................................TTCCTTTCCGTTTTGTGC-.........................................................	18	1	3.00	0.00	0.00	0.00	0.00	3.00
...............................AT-------------------TTCCTTTCCGTTTTGT............................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

TGGATATATTGAATGGTAAGTCCC------------------------------------------------------------------------------------TTTAGAGGCTGTTTTGGGTG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.....TTATTGAATGGGAAGTCCC------------------------------------------------------------------------------------....................	19	1	1.00	0.00	1.00	0.00	0.00
..TATATATTGAATGGTACG............................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..TATATATTGAATGGTAAA............................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................TTTGGAGGCTGTTTCGGG..	18	1	1.00	1.00	0.00	0.00	0.00

droVir3

TCGATGTGCTGAATGGTGAGCTTTG--CCTGAG---TG-------------GGTCC------------AC-ACCAAATCCTAATC------------------CCATTTGCAGAGGCTGTGCTGGGCG

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TCGATGTGCTAAATGGTAAGTCCC--ACTTCAGGCACTT--CTAATCT--------------------------GAATATTAATACTCTTTCTCTCTCTCTCCTGTCTTGCAGAGGCTGTACTTGGCG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
............................................................................ATATCAATAxTCTTTCTCTCT...............................	20	1	1.00	0.00	0.00	1.00	0.00

droGri2

TCGATGTTTTAAATGGTGCGTGCTTAACTTGAA---AGAGAT---CTCACAAATCC------------AA-TCTTAAT------T------------------AAGATTGCAGAGGCTGTTCTGGGTG

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