dme-mir-1013- 12- and 20-way alignments

dme-mir-1013	chr3R:26617358-26617418 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 26617358-26617380
   star strand at position 26617398-26617418
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3R:26617343-26617433 -	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAATAA--------------AAGTATGCCGAACTCGCAGGCGACGGATGCGCGA
droSim1	chr3R:26257486-26257576 -	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAATAA--------------AAGTATGCCGAACTCGCAGGCGACGGATGCGCGA
droSec1	super_4:5435200-5435290 -	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAATAA--------------AAGTTTGCCGAACTCGCAGGCGACGGATGCGCGA
droYak2	chr3R:27538983-27539073 -	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATTGGGACGGCCGTTAATAA--------------AAGTATGCCGAACTCGCAGGCGACGGATGCGCGA
droEre2	scaffold_4820:1381504-1381594 +	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATTGGAGCGGCCGTTAATAA--------------AAGTATGCCGAACTCGCAGGCGACGGATGCGCGA
droAna3	scaffold_12911:4366271-4366356 +	CACTGTGCTGGAGAGGTAATCTTTGAATAATTATCTGTGAGTTGTGGCATCTAATGA--------------TTGTT-----ATCTTCCAGACGTCGCATGCGTGA
dp4	chr2:577090-577184 +	CACTGTGCTGGAGCGGTAAGTC----------CATGAATTGCATCCCCCTTTGATTATTCTTTAATCTGGAAATCCCTGTGATCCCATAGACGACGGATGCGCGA
droPer1	super_7:3361274-3361368 +	CACTGTGCTGGAGCGGTAAGTC----------CATGAATTGCATCCCCCTTTGATTATTCTTTAATCTGGAAATCCCTGTGATCCCATAGACGACGGATGCGCGA
droWil1	scaffold_181130:10168431-10168520 -	AACTGTATTAGAAAGGTATAATGAATAAACCAATTTGAATAGC-AAACCATTAAATC--------------AATTTCCTTTTTTGTCTAGACGACGTATGCGTGA
droVir3	Unknown	CACAGTGCTGGAGAGGTCAGCTGCTTGA----------------TAACCATTTGTAA--------------ATGTAACTCGTTTGAACAGGCGACGCATGCGCGA
droMoj3	Unknown	CACAGTGCTGGAGAGGTAATTCCT----------------------------------------------------------TTGTACAGGCGGCGCATGCGCGA
droGri2	Unknown	CACAGTGCTGGAAAGGTAATCTTCTTAAATATTATT----------TTCGCTAATGC--------------TATTACTCGCTTTGATTAGGCGTCGCATGCGGGA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:26617343-26617433 -	NA	CACCGTGCTGGAGAGGTGAGTTTCGTACACTT----AATTAATA---GGA-------------T-----------------CGGC------C---GTTA-ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGC-GCGA
droSim1	chr3R:26257486-26257576 -	26	CACCGTGCTGGAGAGGTGAGTTTCGTACACTT----AATTAATA---GGA-------------T-----------------CGGC------C---GTTA-ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGC-GCGA
droSec1	super_4:5435200-5435290 -	23	CACCGTGCTGGAGAGGTGAGTTTCGTACACTT----AATTAATA---GGA-------------T-----------------CGGC------C---GTTA-ATAAAAGTTTGCCGAACTCG-------CAGGCGACGGATGC-GCGA
droYak2	chr3R:27538983-27539073 -	37	CACCGTGCTGGAGAGGTGAGTTTCGTACACTT----AATTAATT---GGG-------------A-----------------CGGC------C---GTTA-ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGC-GCGA
droEre2	scaffold_4820:1381504-1381594 +	7	CACCGTGCTGGAGAGGTGAGTTTCGTACACTT----AATTAATT---GGA-------------G-----------------CGGC------C---GTTA-ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGC-GCGA
droEug1	scf7180000409679:78776-78859 -	30	CACAGTGCTGGAAAGGTGAGT-TCATAGACTA----AATCAGTA---TGA-------------A-----------------AAGT------G---ACTA-AT------ATACCGAATTCG-------CAGGAGACGGATGC-GCGA
droBia1	scf7180000302113:733286-733375 +	14	CACCGTGCTGGAGCGGTGAGTTTCGTACACTT----AGTTAATT---CG--------------G-----------------AGGC------C---ATTA-ATAAAAGTATGCCGAACTCG-------CAGGCGGCGGATGC-GCGA
droTak1	scf7180000415367:120661-120751 +	13	CACTGTGCTGGAGAGGTGAGTTTCGTACACTT----AATTAATA---TGG-------------A-----------------AAGC------C---ATTA-ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGC-GCGA
droEle1	scf7180000491280:2970971-2971061 -	48	CACAGTGCTGGAGAGGTGAGTTTCGTACGCTT----AATTAATA---AAT-------------G-----------------AAGC------A---ATTA-ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGC-GCGA
droRho1	scf7180000774800:25017-25107 -	33	CACAGTGCTGGAGAGGTGAGTTTCGTACACTT----AATTAATA---AAG-------------G-----------------AAGC------C---ATTA-ATAAAAGTATGCCGAACTCG-------CAGGCGACGGATGC-GCGA
droFic1	scf7180000453782:677613-677706 +	3	CACGGTTCTGGAGCGGTGAGTTTCGTACACTT----AATTAATACAAGAA-------------G-----------------CGGG------G---ATTA-ATAAAAGTATGTCGAACTCG-------CAGGCGGCGGATGC-GCGA
droKik1	scf7180000302390:601160-601259 -	32	CACGGTGCTGGAAAGGCGAGTTTTGTATATTT----AATTAATT---TTC-------------A-----------------AAGTATCGTTCATAATTA-ATAAAAGTATGCTGAACTCG-------CAGGCGGCGAATGC-GCGA
droAna3	scaffold_12911:4366271-4366356 +	3	CACTGTGCTGGAGAGGTAATCTTTGAATAATT----ATCTGTGA---GTT-------------G-----------------TGGC------A---TCTA-ATGATTGTT-----ATCTTC-------CAGACGTCGCATGC-GTGA
droBip1	scf7180000396640:1207116-1207199 +	24	CACAGTGCTGGAGCGGTAAGTTGGAGGAAT------GCCTAT---GAGTCAC--------------------------------------------GTC-ATGTACTGATCTTTATCTTC-------CAGACGACGGATGC-GCGA
dp4	chr2:577090-577184 +	4	CACTGTGCTGGAGCGGTAAGTCC--------------ATGAATT---GCA---TCCCCCTTTGATTATTCTTT----A---AT-------------CTG---GAAATCCCTGTGATCCCA-------TAGACGACGGATGC-GCGA
droPer1	super_14:1306248-1306344 -	50	CACCATCCTGCATAGGGACATCAAGCCGGCGA----ACATATTC---TTG-------------GATG--------------CGGC------C---GGCAATGCCAAGCTCGGCGATTTCG-----GTCTGGCG-CGTATGCTGCGG
droWil1	scaffold_181130:10168431-10168520 -	30	AACTGTATTAGAAAGGTATAATGAATAAACCA----ATTTGAAT---AG--------------C-----------------AAAC------C---ATTA-AATCAATTTCCTTTTTTGTC-------TAGACGACGTATGC-GTGA
droVir3	scaffold_13047:11434928-11435028 -	29	CACAGTGCTGGAGAGGTGGGT-GCATCCACAT----CAGCTGCT---TG--------------ATAACCATTTGTAAATGTA----------------A-----ATCCTCCTTTAACTCG-TTTGAACAGGCGACGCATGC-GCGA
droMoj3	scaffold_6540:30312688-30312787 +	15	CACAGTGCTGGAGAGGTGGGA-GCATTGATTTCACCACCCAT---AAGACAC------------------ATTCTCACAGTT----------------T-----TTCTTGC-TTAATTCC-TTTGTACAGGCGGCGCATGC-GCGA
droGri2	scaffold_14624:1473562-1473665 -	17	CACAGTGCTGGAAAGGTGATTCAAATC------------CAT---AAGCCACAATCTTCTT-AAATATTATTT----T---CG-------------CTA-----ATGCTATTTGTACTCGCTTTGATTAGGCGTCGCATGC-GGGA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAATAA--------------AAGTATGCCGAACTCGCAGGCGACGGATGCGCGA

Size

Hit Count

Total Norm

droSim1

CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAATAA--------------AAGTATGCCGAACTCGCAGGCGACGGATGCGCGA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.....................................................ATAA--------------AAGTATGCCGAACTCG..................	20	1	275.00	2.00	211.00	41.00	21.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCA................	22	1	206.00	11.00	126.00	26.00	43.00
.....................................................ATAA--------------AAGTATGCCGAACTCGC.................	21	1	104.00	4.00	78.00	12.00	10.00
......................................................TAA--------------AAGTATGCCGAACTCGCAGT..............	23	1	100.00	4.00	18.00	10.00	68.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAG...............	23	1	78.00	48.00	12.00	2.00	16.00
.....................................................ATAA--------------AAGTATGCCGAACTC...................	19	1	24.00	0.00	21.00	2.00	1.00
......................................................TAA--------------AAGTATGCCGAACTCGCA................	21	1	22.00	1.00	14.00	4.00	3.00
.......................................................AA--------------AAGTATGCCGAACTCGCAGT..............	22	1	20.00	0.00	5.00	1.00	14.00
......................................................TAA--------------AAGTATGCCGAACTCGCAG...............	22	1	14.00	8.00	2.00	3.00	1.00
......................................................TAA--------------AAGTATGCCGAACTCGCAGC..............	23	1	13.00	0.00	3.00	2.00	8.00
......................................................TAA--------------AAGTATGCCGAACTCGC.................	20	1	12.00	0.00	8.00	3.00	1.00
......................................................TAA--------------AAGTATGCCGAACTCGCAGG..............	23	1	12.00	0.00	4.00	1.00	7.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCG................	22	1	11.00	0.00	4.00	4.00	3.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAGT..............	24	1	8.00	1.00	0.00	4.00	3.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCT................	22	1	6.00	0.00	6.00	0.00	0.00
..............................TTAATTAATAGGATCGGCC........................................................	19	1	5.00	0.00	5.00	0.00	0.00
.....................................................ATAA--------------AAGGATGCCGAACTCGCA................	22	1	4.00	1.00	2.00	0.00	1.00
.....................................................ATAA--------------AAGTATGCCGAACT....................	18	1	4.00	0.00	4.00	0.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAGC..............	24	1	4.00	0.00	1.00	0.00	3.00
........................GTACACTTAATTAATAGGATCGGCC........................................................	25	1	3.00	0.00	3.00	0.00	0.00
.............................CTTAATTAATAGGATCGGCC........................................................	20	1	3.00	0.00	3.00	0.00	0.00
....................................AATAGGATCGGCCGTTAATAA--------------..................................	21	1	3.00	0.00	3.00	0.00	0.00
.......................................................AA--------------AAGTATGCCGAACTCGCAGG..............	22	1	2.00	0.00	0.00	0.00	2.00
.....................................................ATAA--------------AATTATGCCGAACTCG..................	20	1	2.00	0.00	1.00	0.00	1.00
......................................................TAA--------------AATTATGCCGAACTCGC.................	20	1	2.00	0.00	2.00	0.00	0.00
.....................................ATAGGATCGGCCGTTAATAA--------------AAGT..............................	24	1	2.00	0.00	2.00	0.00	0.00
............................ACTTAATTAATAGGATCGGCC........................................................	21	1	2.00	0.00	2.00	0.00	0.00
......................................................TAA--------------AAGTATCCCGAACTCGCAGT..............	23	1	2.00	0.00	2.00	0.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTGG..................	20	1	2.00	0.00	0.00	2.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAGG..............	24	1	2.00	0.00	1.00	0.00	1.00
.....................TTCGTACACTTAATTAATAGGATC............................................................	24	1	2.00	0.00	2.00	0.00	0.00
...................................TAATAGGATCGGCCGTTAATAA--------------..................................	22	1	1.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AACTATGCCGAACTCGCA................	22	1	1.00	0.00	1.00	0.00	0.00
......................................................TAA--------------AAGTATGCCGAACTCGAC................	21	1	1.00	0.00	1.00	0.00	0.00
......................................................TAA--------------AAGTATGTCGAACTCGCAGT..............	23	1	1.00	0.00	0.00	0.00	1.00
........................................................................AGTATGCCGAACTCGCAGT..............	19	1	1.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTATACCGATCTCGCAG...............	23	1	1.00	1.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGTATGCTGAACTCG..................	20	1	1.00	0.00	1.00	0.00	0.00
...............................TAATTAATAGGATCGGCCGTTAA...................................................	23	1	1.00	0.00	1.00	0.00	0.00
......................................................TAA--------------AAGTATGCCGAACTC...................	18	1	1.00	0.00	1.00	0.00	0.00
......................................................TAA--------------AAGCATGCCGAACTCGCAGT..............	23	1	1.00	0.00	0.00	0.00	1.00
....................................AATAGGATCGGCCGTTAATAA--------------AA................................	23	1	1.00	0.00	1.00	0.00	0.00
.....................................................ATAA--------------AAGAATGCCGAACTCGCAGT..............	24	1	1.00	0.00	0.00	1.00	0.00
....................................................AATAA--------------AAGTATGCCGAACTC...................	20	1	1.00	0.00	0.00	0.00	1.00
......................................................TAA--------------AAGTATGCCGAACTCG..................	19	1	1.00	0.00	0.00	1.00	0.00
......................................................TAA--------------AAGTATGCCAAACTCGCAG...............	22	1	1.00	1.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGTTTGCAGAACTCGCAG...............	23	1	1.00	1.00	0.00	0.00	0.00
...............................TAATTAATAGGATCGGCC........................................................	18	1	1.00	0.00	1.00	0.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAC...............	23	1	1.00	0.00	1.00	0.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCT..................	20	1	1.00	0.00	1.00	0.00	0.00
.................................ATTAATAGGATTGGCCGTTAA...................................................	21	1	1.00	0.00	1.00	0.00	0.00
.....................................................ATAA--------------AAGTAAGCCGAACTCGC.................	21	1	1.00	0.00	1.00	0.00	0.00
......................................................TAA--------------AAGTATGCCGAACTCGCAGTT.............	24	1	1.00	0.00	0.00	0.00	1.00
.......................................................AA--------------AAGTATGCCGAACTCGCAGC..............	22	1	1.00	0.00	0.00	0.00	1.00
.................................ATTAATAGGATCGGCCGTTAAT..................................................	22	1	1.00	0.00	1.00	0.00	0.00
.....................................................ATAA--------------CAGTATGCCGAACTCGCAG...............	23	1	1.00	1.00	0.00	0.00	0.00
.....................................................ATCA--------------AAGTATGCCGAACTCG..................	20	1	1.00	0.00	1.00	0.00	0.00
....................................................AATAA--------------AAGxATGCCGTACTCGCAG...............	23	1	1.00	1.00	0.00	0.00	0.00
.....................................ATAGGATCGGCCGTTAATAA--------------AAG...............................	23	1	1.00	0.00	1.00	0.00	0.00
...................................TAATAGGATCGGCCGTTAAT..................................................	20	1	1.00	0.00	1.00	0.00	0.00
.........................................................................GTATGCCGAACTCGCAGT..............	18	1	1.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCC................	22	1	1.00	0.00	1.00	0.00	0.00
......................................................TAA--------------AAGTATGCCGTACTCGCA................	21	1	1.00	1.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGAATGCCGAACTCG..................	20	1	1.00	0.00	1.00	0.00	0.00
.....................................ATAGGATCGGCCGTTAATAA--------------AAGTAT............................	26	1	1.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCGT.................	21	1	1.00	0.00	1.00	0.00	0.00
......................................................TAA--------------AAGTATGCCGAACTCGCT................	21	1	1.00	0.00	1.00	0.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCC..................	20	1	1.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAT...............	23	1	1.00	1.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGTATACCGAACTCGCAGT..............	24	1	1.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGAATGCCGAACTCGCAG...............	23	1	1.00	1.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGGATGCCGAACTCGC.................	21	1	1.00	0.00	1.00	0.00	0.00
.....................................................ATAA--------------AAGTCTGCCGCACTCGCAG...............	23	1	1.00	1.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGTATGGCGAACTCG..................	20	1	1.00	0.00	1.00	0.00	0.00
......................................................TAA--------------AAATATACCGAACTCGCA................	21	1	1.00	1.00	0.00	0.00	0.00
....................................................AATAA--------------AAGTATGCCGAACTCGCAGC..............	25	1	1.00	0.00	0.00	1.00	0.00
......................................................TAA--------------AAGTATGCCGGACTCGCAGT..............	23	1	1.00	0.00	0.00	0.00	1.00
....................................AATAGGATCGGCCGTTAATAA--------------AAG...............................	24	1	1.00	0.00	1.00	0.00	0.00
.....................................ATAGGATCGGCCGTTAATAA--------------AA................................	22	1	1.00	0.00	1.00	0.00	0.00
.....................................................ATAA--------------AAGTATGCCGAAATCGCAG...............	23	1	1.00	1.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGGATGCCGAACTCG..................	20	1	1.00	0.00	1.00	0.00	0.00
.......................................................AA--------------AAGTATGCCGAACTCGCAG...............	21	1	1.00	1.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGTATGTCGAACTCGCA................	22	1	1.00	0.00	1.00	0.00	0.00
......................................TAGGATCGGCCGTTAATAA--------------AAGTATGC..........................	27	1	1.00	0.00	0.00	0.00	1.00

droSec1

CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAATAA--------------AAGTTTGCCGAACTCGCAGGCGACGGATGCGCGA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.....................................................ATAA--------------AAGTTTGCCGAACTCGC.................	21	1	172.00	7.00	142.00	23.00
.....................................................ATAA--------------AAGTTTGCCGAACTCGCAG...............	23	1	88.00	1.00	74.00	13.00
.....................................................ATAA--------------AAGTTTGCCGAACTCG..................	20	1	32.00	3.00	18.00	11.00
......................................................TAA--------------AAGTTTGCCGAACTCGCAGT..............	23	1	27.00	0.00	25.00	2.00
......................................................TAA--------------AAGTTTGCCGAACTCGCAG...............	22	1	25.00	2.00	21.00	2.00
.......................................................AA--------------AAGTTTGCCGAACTCGCAGT..............	22	1	20.00	2.00	16.00	2.00
.....................................................ATAA--------------AAGTTTGCCGAACTCGCA................	22	1	17.00	0.00	12.00	5.00
.....................................................ATAA--------------AAGTTTGCCGAACTCGCAGT..............	24	1	12.00	1.00	11.00	0.00
......................................................TAA--------------AAGTTTGCCGAACTCGCA................	21	1	7.00	1.00	4.00	2.00
.....................................................ATAA--------------AAGTTTGCCGAATTCGC.................	21	1	3.00	0.00	3.00	0.00
.......................................................AA--------------AAGTTTGCCGAACTCGCAG...............	21	1	3.00	0.00	2.00	1.00
.....................................................ATAA--------------AAGTTTGCCGAACTCGT.................	21	1	2.00	0.00	0.00	2.00
......................................................TAA--------------AAGTTTGCCGAACTCGC.................	20	1	2.00	0.00	1.00	1.00
.....................................................ATAA--------------AAGTTTGCCGAACTC...................	19	1	2.00	0.00	0.00	2.00
......................................................TAA--------------AAGTTTGCCGAACTCGCAGA..............	23	1	1.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTTTGCCAAACTCGC.................	21	1	1.00	0.00	0.00	1.00
.......................................................AA--------------AAGTTTGCCGAACTCGTAGT..............	22	1	1.00	0.00	1.00	0.00
.....................................................ATGA--------------AAGTTTGCCGAACTCG..................	20	1	1.00	0.00	1.00	0.00
.....................................................ATTA--------------AAGTTTGCCGAACTCG..................	20	1	1.00	0.00	1.00	0.00
......................................................TAA--------------AAGTTTGCCGAACTCGCAGTT.............	24	1	1.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGxTTGCCGAACTCGCGG...............	22	1	1.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTTTGCCGATCTCGC.................	21	1	1.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTTTGCCGAAGTCGCAG...............	23	1	1.00	0.00	1.00	0.00
.....................................................ATAT--------------AAGTTTGCCGAACTCG..................	20	1	1.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTTTGCCGAACCCGC.................	21	1	1.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTTTGCCGAACTCGGAG...............	23	1	1.00	0.00	1.00	0.00
......................................................TAA--------------AAGxTTGCCGAACTCGCAGT..............	22	1	1.00	0.00	1.00	0.00
.......................................................................AAGTTTGCCGAACTCGCAG...............	19	1	1.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAG...............	23	1	1.00	0.00	1.00	0.00
...............GTGAGTTTCGTACACTTAATT.....................................................................	21	1	1.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGxTTGCCGAACTCGC.................	20	1	1.00	0.00	1.00	0.00
.......................................................AA--------------AAGTTTGCCGAACTCGCGGT..............	22	1	1.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTTTGCCGAACTCAC.................	21	1	1.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTTTGCCGACCTCGCAG...............	23	1	1.00	0.00	0.00	1.00
......................................................TAA--------------AACTTTGCCGAACTCGCAG...............	22	1	1.00	0.00	1.00	0.00
.....................................ATAGGATCGGCCGTTAATAA--------------AAGTTTG...........................	27	1	1.00	1.00	0.00	0.00
.....................................................ATAA--------------AAGTTTGCCGAACTCGCT................	22	1	1.00	1.00	0.00	0.00
......................................................ATA--------------AAGTTTGCCGAACTCGCAG...............	22	1	1.00	0.00	1.00	0.00
....................................AATAGGATCGGCCGTTAA...................................................	18	1	1.00	0.00	0.00	1.00

droYak2

CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATTGGGACGGCCGTTAATAA--------------AAGTATGCCGAACTCGCAGGCGACGGATGCGCGA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.....................................................ATAA--------------AAGTATGCCGAACTCGCA................	22	1	232.00	19.00	10.00	6.00	41.00	156.00
.....................................................ATAA--------------AAGTATGCCGAACTCG..................	20	1	139.00	2.00	0.00	14.00	21.00	102.00
.....................................................ATAA--------------AAGTATGCCGAACTCGC.................	21	1	130.00	14.00	6.00	14.00	35.00	61.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAG...............	23	1	60.00	18.00	11.00	1.00	23.00	7.00
......................................................TAA--------------AAGTATGCCGAACTCGCAGT..............	23	1	33.00	9.00	1.00	2.00	4.00	17.00
......................................................TAA--------------AAGTATGCCGAACTCGCA................	21	1	29.00	5.00	0.00	5.00	7.00	12.00
......................................................TAA--------------AAGTATGCCGAACTCGCAG...............	22	1	20.00	4.00	1.00	1.00	10.00	4.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCT................	22	1	18.00	0.00	1.00	0.00	1.00	16.00
......................................................TAA--------------AAGTATGCCGAACTCGC.................	20	1	17.00	0.00	1.00	2.00	0.00	14.00
.......................................................AA--------------AAGTATGCCGAACTCGCAGT..............	22	1	14.00	5.00	3.00	2.00	1.00	3.00
.....................................................ATAA--------------AAGTATGCCGAACTC...................	19	1	13.00	1.00	0.00	0.00	0.00	12.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCC................	22	1	11.00	0.00	0.00	0.00	0.00	11.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAGT..............	24	1	5.00	2.00	0.00	2.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCG................	22	1	4.00	0.00	0.00	0.00	0.00	4.00
......................................................TAA--------------AAGTATGCCGAACTCG..................	19	1	4.00	0.00	0.00	0.00	0.00	4.00
......................................................TAA--------------AAGTATGCCGAACTCGCAGC..............	23	1	4.00	0.00	0.00	0.00	1.00	3.00
.......................................................AA--------------AAGTATGCCGAACTCGCAG...............	21	1	3.00	1.00	0.00	1.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAA...............	23	1	2.00	0.00	0.00	0.00	2.00	0.00
......................................................TAA--------------AAGTATGCCGAACTCGCAA...............	22	1	2.00	1.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGTATGCCGAACTCGT.................	21	1	2.00	0.00	0.00	1.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAT...............	23	1	2.00	0.00	0.00	0.00	0.00	2.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCCG...............	23	1	2.00	0.00	0.00	0.00	2.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTAGC.................	21	1	2.00	2.00	0.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGTATTCCGAACTCGC.................	21	1	2.00	0.00	0.00	0.00	0.00	2.00
.....................................................ATAA--------------AAGGATGCCGAACTCGCA................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................................AGTATGCCGAACTCGCAGT..............	19	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATGA--------------AAGTATGCCGAACTCGCCG...............	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGTATGCTGAACTCG..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AGGTATGCCGAACTCGCA................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGTATACCGAACTCGCAG...............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................TAA--------------AAGTATGCCGAACTCGCAGA..............	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGTATGCCAAACTC...................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................TAA--------------AAGTATGCCGAACTAGCAG...............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGGGTTTCGTACACTTAATT.....................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGACCTCG..................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTTTGCCGAACTCGCAG...............	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGGAGGCCGAACTCGC.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................AATAA--------------AAGTATGCCGAACTCGCAGT..............	25	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................TAA--------------AAGTATxCCGAACTCGCCG...............	21	1	1.00	1.00	0.00	0.00	0.00	0.00
...............GTGAGTTTCGTACACTTAATTAATTGGGAC............................................................	30	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................ATAA--------------AAGTATGCCAAACTCGCA................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGGATGCCGAACTA...................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................TAA--------------AGGTATGCCGAACCCGCAGG..............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAC...............	23	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGTATGCCGAACTCTC.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCT..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AATTATGCCGAACTCGCA................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................A--------------AAGGATGCCGAACTCGCAGT..............	21	1	1.00	1.00	0.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACGCGCT................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------ACGTATGCCGACCTCGC.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAATATGCCGAACTCGC.................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGTCTGCCGAACTCGCA................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGTCTGCCGAACTCG..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGTATGCCGAACT....................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
.......................................................AA--------------AAGTATGCCGAACTCGC.................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACGCGC.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................AATTGGGACGGCCGTTAATAA--------------AAGTATGC..........................	29	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................ATAA--------------AAGTATACCGAACTCG..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................TAA--------------AAGTATGCTGAACTCGCAGT..............	23	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................TAA--------------AAGTATGCCTAACTGG..................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGGATACCGAACT....................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTGG..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................TAA--------------AAGTATGCCGAACTCGCAGG..............	23	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................A--------------AAGTATGCCGAACTCGCAGTA.............	22	1	1.00	0.00	0.00	1.00	0.00	0.00
................................GATTAATAGGGACGGCCG.......................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................TAA--------------AAGGATGCCGAACTCGCAGT..............	23	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGTATCCCGAACTCGC.................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATGA--------------AAGTATGCCGAACTCGA.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AGGTATGCCGAACTCG..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGTATACCGAACTCGCT................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................GTATGCCGAACTCGCCGT..............	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTACGCCGAACTCG..................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGTATGCCGAGCTCGCA................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.....................................................ATAA--------------AAGTATGCCGCACTCGC.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------ACGTATGCCGAACTCG..................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................TAA--------------AAGTATGCCCAACTCGCAGA..............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAC--------------AAGTCTGCCGAACTCG..................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACGCTCA................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTATTCCGAACTCGCA................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGTATGCCGAACTCAC.................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................ATAA--------------AAGTATGCCGAACACGC.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................AATAA--------------AAGAATGCCGAACTCG..................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGAGTTTCGTACACTTAATT.....................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGAACTCCC.................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
......................................................TAA--------------CAGTATGCCGCACTCGCAG...............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..CCGTGxTGGAGAGGAGAG.....................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................TAA--------------AAGTATGCCGTACTCGCAG...............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................ATAA--------------AAGTATGCCGACCTCGC.................	21	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATTGGAGCGGCCGTTAATAA--------------AAGTATGCCGAACTCGCAGGCGACGGATGCGCGA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.....................................................ATAA--------------AAGTATGCCGAACTCGCA................	22	1	431.00	11.00	18.00	0.00	402.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAG...............	23	1	269.00	5.00	14.00	0.00	250.00
.....................................................ATAA--------------AAGTATGCCGAACTCGC.................	21	1	215.00	8.00	13.00	0.00	194.00
.....................................................ATAA--------------AAGTATGCCGAACTCG..................	20	1	94.00	2.00	9.00	0.00	83.00
......................................................TAA--------------AAGTATGCCGAACTCGCAG...............	22	1	48.00	3.00	3.00	0.00	42.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCT................	22	1	25.00	0.00	3.00	0.00	22.00
......................................................TAA--------------AAGTATGCCGAACTCGCAGT..............	23	1	10.00	1.00	0.00	0.00	9.00
......................................................TAA--------------AAGTATGCCGAACTCGCA................	21	1	6.00	0.00	0.00	0.00	6.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAT...............	23	1	6.00	0.00	0.00	0.00	6.00
.....................................................ATAA--------------AAGTATGCCTAACTCGCAG...............	23	1	5.00	0.00	0.00	0.00	5.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAGA..............	24	1	5.00	0.00	0.00	0.00	5.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAA...............	23	1	4.00	0.00	0.00	0.00	4.00
.....................................................ATAA--------------AAGTATGCCGAACTCTCA................	22	1	4.00	0.00	0.00	0.00	4.00
......................................................TAA--------------AAGTATGCCGAACTCGCAGA..............	23	1	4.00	1.00	0.00	0.00	3.00
.....................................................ATAA--------------AAGTATGCCGAACTCGCAGT..............	24	1	3.00	0.00	0.00	0.00	3.00
.....................................................ATAA--------------AAGTATGACGAACTCGCAG...............	23	1	3.00	0.00	0.00	0.00	3.00
.....................................................ATAA--------------AAGTATGCCGAACTCGT.................	21	1	3.00	0.00	1.00	0.00	2.00
.....................................................ATAA--------------AAGTATGCCTAACTCGCA................	22	1	3.00	0.00	0.00	0.00	3.00
.....................................................ATAA--------------AAGTATGCCGAACTAGCAG...............	23	1	3.00	0.00	0.00	0.00	3.00
.....................................................ATAA--------------AAGTATGCCGAACTCGA.................	21	1	3.00	0.00	1.00	0.00	2.00
.....................................................ATAA--------------AAGTATGCCGAACTC...................	19	1	3.00	0.00	0.00	0.00	3.00
.....................................................ATAA--------------AAGTATGCAGAACTCGCA................	22	1	3.00	0.00	0.00	0.00	3.00

droAna3

CACTGTGCTGGAGAGGTAATCTTTGAATAATTATCTGTGAGTTGTGGCATCTAATGA--------------TTGTT-----ATCTTCCAGACGTCGCATGCGTGA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...................................TGTGGGTTGGGGCATCT.....................................................	17	1	1.00	0.00	0.00	1.00	0.00
...................................TGTGGGTTGTGGGATCT.....................................................	17	1	1.00	0.00	0.00	1.00	0.00
....................CTTGGAATAATTATCTGGGA.................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.....................TTGGAATAATTATCGGTG..................................................................	18	1	1.00	0.00	0.00	1.00	0.00

dp4

CACTGTGCTGGAGCGGTAAGTC----------CATGAATTGCATCCCCCTTTGATTATTCTTTAATCTGGAAATCCCTGTGATCCCATAGACGACGGATGCGCGA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
....................................GATCGCATCCCCCTTTGA...................................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

CACTGTGCTGGAGCGGTAAGTC----------CATGAATTGCATCCCCCTTTGATTATTCTTTAATCTGGAAATCCCTGTGATCCCATAGACGACGGATGCGCGA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..............................................................................GTGAGCCCATAGxCGACGGA.......	19	1	7.00	7.00	0.00	0.00	0.00	0.00

droWil1

AACTGTATTAGAAAGGTATAATGAATAAACCAATTTGAATAGC-AAACCATTAAATC--------------AATTTCCTTTTTTGTCTAGACGACGTATGCGTGA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...................................TGAATAxC-AAACCATGAAA..................................................	18	1	2.00	0.00	2.00	0.00	0.00
...................AATAAATAAATCAATTTG....................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

CACAGTGCTGGAGAGGTCAGCTGCTTGA----------------TAACCATTTGTAA--------------ATGTAACTCGTTTGAACAGGCGACGCATGCGCGA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.....................................................................................AGCAxGCGACGCATGCGCG.	18	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

CACAGTGCTGGAGAGGTAATTCCT----------------------------------------------------------TTGTACAGGCGGCGCATGCGCGA

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CACAGTGCTGGAAAGGTAATCTTCTTAAATATTATT----------TTCGCTAATGC--------------TATTACTCGCTTTGATTAGGCGTCGCATGCGGGA

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