dme-mir-4944- 12- and 20-way alignments

dme-mir-4944	chr3R:6338726-6338855 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 6338757-6338778
   star strand at position 6338797-6338818
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3R:6338711-6338870 -	AGA-TG-CCCAGACAGCAA---AAGT----------------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTTTTCTGCTT--CT--GCCGCTGAGCAAGTTTTAAATATTACCGCTTAGTT-------ACAGCTGCAGG------------------------------AAG-AAAAGTTATAATTATGGACTACGTACATAAATATCTTGGCAAGTGT------TT
droSim1	chr3R:15041591-15041748 +	AGA-TG-CCCAGACAGCAA---AAGT----------------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTT--CTGCTC--CT--GCCGCCTAGCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGG------------------------------AAG-AAAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGT------TT
droSec1	super_0:15602732-15602889 +	AGA-TA-CCCAGACAGCAA---AAGC----------------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTT-TCTGCTC--CT--GCCGCCGAGCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGG------------------------------AAG--AAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGT------TT
droYak2	chr3R:10367066-10367225 -	AGA-TG-CCCAGACAGCAA---AAGT----------------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTTCGCTGCTC--CT--GCCGCCGAGCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGG------------------------------AAG-AAAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGT------TT
droEre2	scaffold_4770:15270440-15270598 +	AGA-TG-CCCAGACAGCAA---AAGT----------------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTT-GCTGCTT--CT--GCCGCCGAGCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGG------------------------------AAG-AAAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGT------TT
droAna3	scaffold_13340:761260-761417 +	AGA-TGGCCCAGACAGCAA---AAGT----------------------------------------------------------------------------------------------------------------------------------------AACTT-TGGTAATCGAAAAAGTTTCGCTTTCGT------TTTTTTCCATC-CCGAACAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTTCGGA------------------------------GAG-GAAAGTTATAATTATGGCCTAAGTACATAAATAACTCGCCAAATGT------TT
dp4	chr2:7128424-7128589 +	AGA-TG-G-CAGACGGCCC---AAGG----------------------------------------------------------------------------------------------------------------------------------------AACTT-TGGTAATCGAAAAAGTTTCGCTTTTTTCGC---TTTTTT--CTCAGTGGCCAAGTTTTAAATATTAACGCTTAGTTACTCCGTACAGCTGCAGA------------------------------AAGAAAAAGTTATAATTATGGCCTAAGTACATAAATAACTCGGCAAATGT------AC
droPer1	super_0:982713-982880 +	AGA-TG-G-CAGACGGCCC---AAGG----------------------------------------------------------------------------------------------------------------------------------------AACTT-TGGTAATCGAAAAAGTTTCGCTTTTTT-TTTGCTTTTTT--CTCAGTGGCCAAGTTTTAAATATTAACGCTTAGTTACTCCGTACAGCTGCAGA------------------------------AATAAAAAGTTATAATTATGGCCTAAGTACATAAATAACTCGGCAAATGT------AC
droWil1	scaffold_181108:125373-125548 -	AGA-TG-GG------GCAA---AAGTATGTCGACTGAGGAAAACCGGAGA---------------------------------------------------------------------------------G----------CA------------------AACTTGTAGTAATCGAAAAAGTTTCGGTTTGTT------------------GTAGCCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGAA--G---------------------------AGAAAAAGTTATAATTATGCCGTAAGTACATAAATAACACGGCAAATGTGACTTTTT
droVir3	scaffold_13047:1304911-1305088 -	AGA----ATAAGAAAGAAATGTTAGG-------------ACGGCTGGACA---------------------------------------------------------------------------------G----------GATTCAGTTTTGTTGCTGCTTACTG-CGGTAATCGAAAAAGTTTTGTT-----------------------GTAGCCAAGTTTTAAATATTAACGCTTACTT-------ACAGCTGCAGAGCTG--------------------------GAA-AAAAGTTATAATTATGGCGTAAGTACATAAATAACGCTGCAAATGT------GC
droMoj3	scaffold_6540:5375446-5375637 -	GGAATA-ATAAGAAAGAAATG----------------------CTGGAGAGGC---------------------------------------------------------------------ACAGGCACAGTCTGGCTTGAGATTCAGTT----TGCTGCTTACGG-CGGTAATCGAAAAAGTTTTCTGTT---------------------GTAGCCAAGTTTTAAATATTAACGCTTACTT-------ACAGCTGCAGAGCTG--------------------------GAA-AAAAGTTATAATTGTGGCGTAAGTACATAAATAACGCTGCAAATGC------GC
droGri2	scaffold_14906:4949937-4950217 +	AGA----ATAAGAAAGAAATGTAAGC-------------AACGCTCG------GtgtGtTtgtGtTtgtGtGtgtGtGggtGtGtgtGtGggtGtGtgGGtgtggGtttgTGtttgTGtGGgtCA-GCACAG---GACTTGAGATACAGTTTTGTTGCTG----CTG-CGGTAATCGAAAAAGTTTGGTT-----------------------GTAGCCAAGTTTTAAATATTAACGCTTACTT-------ACAGCTGCAGAGCAGAGCTAAGCAGAAAAAAAAAATAAATAAAA-GAAAGTTATAATTATGGCGTAAGTACATAAATAACGCTGCAAATGT------GC

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:6338711-6338870 -	NA	AGA-TGC-CCAGACAGCAAAAGT-------------------------------------------------------------------------------------------------------------------AACTT----------------TCGTAATCGAAAAAGTTTCGCTTTTTT--------TTCTGCT---------TCTGCCGCTGAGCAAGT-TTTAAATATTACCGCTTAGTT-------ACAGCTGCAG-G------------------------------AAG-AAAAGTTATAATTATGGACTACGTACATAAATATCTT-GGCAAGTGT----------------------TT
droSim1	chr3R:15041591-15041748 +	1	AGA-TGC-CCAGACAGCAAAAGT-------------------------------------------------------------------------------------------------------------------AACTT----------------TCGTAATCGAAAAAGTTTCGCTTTTTT-C---------TGCT---------CCTGCCGCCTAGCAAGT-TTTAAATATTAACGCTTAGTT-------ACAGCTGCAG-G------------------------------AAG-AAAAGTTATAATTATGGGCTAAGTACATAAATAACTT-GGCAAGTGT----------------------TT
droSec1	super_0:15602732-15602889 +	1	AGA-TAC-CCAGACAGCAAAAGC-------------------------------------------------------------------------------------------------------------------AACTT----------------TCGTAATCGAAAAAGTTTCGCTTTTTTTC---------TGCT---------CCTGCCGCCGAGCAAGT-TTTAAATATTAACGCTTAGTT-------ACAGCTGCAG-G------------------------------AAG--AAAGTTATAATTATGGGCTAAGTACATAAATAACTT-GGCAAGTGT----------------------TT
droYak2	chr3R:10367066-10367225 -	1	AGA-TGC-CCAGACAGCAAAAGT-------------------------------------------------------------------------------------------------------------------AACTT----------------TCGTAATCGAAAAAGTTTCGCTTTTTT--------CGCTGCT---------CCTGCCGCCGAGCAAGT-TTTAAATATTAACGCTTAGTT-------ACAGCTGCAG-G------------------------------AAG-AAAAGTTATAATTATGGGCTAAGTACATAAATAACTT-GGCAAGTGT----------------------TT
droEre2	scaffold_4770:15270440-15270598 +	1	AGA-TGC-CCAGACAGCAAAAGT-------------------------------------------------------------------------------------------------------------------AACTT----------------TCGTAATCGAAAAAGTTTCGCTTTTTTGC---------TGCT---------TCTGCCGCCGAGCAAGT-TTTAAATATTAACGCTTAGTT-------ACAGCTGCAG-G------------------------------AAG-AAAAGTTATAATTATGGGCTAAGTACATAAATAACTT-GGCAAGTGT----------------------TT
droEug1	scf7180000409692:832659-832824 -	1	AGA-TGG-CCAGACAGCAAAAGT-------------------------------------------------------------------------------------------------------------------AACTT----------------TCGTAATCGAAAAAGTTTCGCTTTTTTTC---------TGCTGCTGCTGCTGCTGCTGCC--TCAAGT-TTTAAATATTAACGCTTAGTT-------ACAGCTGCAG-A------------------------------AGG-AAAAGTTATAATTATGGCCTAAGTACATAAATAACTC-GGCAAATGT----------------------TT
droBia1	scf7180000302402:8442381-8442527 -	1	AGA-TGG-CCAGACAGCAAAAGT-------------------------------------------------------------------------------------------------------------------AACTT----------------TCGTAATCGAAAAAGTTTCGCTTTTTT--------CTCT----------------------CGGAAGT-TTTAAATATTAACGCTTAGTT-------ACAGCTGCAG-A------------------------------GGG-AAAAGTTATAATTATGGCCTAAGTACATAAATAACTC-GGCAAATGT----------------------TT
droTak1	scf7180000415380:1278630-1278781 +	1	AGA-TGG-CCAGACAGCAGAAGT-------------------------------------------------------------------------------------------------------------------AACTT----------------TCGTAATCGAAAAAGTTTCGCTTTTCTTTT-----C---------------------CCCGAGCAAGT-TTTAAATATTAACGCTTAGTT-------ACAGCTGCAG-A------------------------------AGG-AAAAGTTATAATTATGGCCTAAGTACATAAATAACTCCCGCAAATGT----------------------TT
droEle1	scf7180000490995:395638-395791 +	1	AGA-TGG-CCAGACGGCAGAAGT-------------------------------------------------------------------------------------------------------------------AACTT----------------TCGTAATCGAAAAAGTTTCACTTTTTT--------C---------------CCTGCTGCCGAGTAAGT-TTTAAATATTACCGCTTAGTT-------ACAGCTGCAA-A------------------------------AAG-AAAAGTTATAATTATGGCCTAAGTACATAAATAACTT-GGCAAATGT----------------------TT
droRho1	scf7180000779224:47738-47897 +	4	AGA-TGG-CCAGACGGCACAAGT-------------------------------------------------------------------------------------------------------------------AACTT----------------TCGTAATCGAAAAAGT-TCGTTTTTTT--------TTTTGC----------CCTGCTGCCGAGCAAGTTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAAGA------------------------------AAG-AAAAGTTATAATTATGGCCTAAGTACATAAATAACTT-GGCAAATGT----------------------TT
droFic1	scf7180000453800:2435844-2436003 -	1	AGA-TGG-CCAGACAGCAGAAGT-------------------------------------------------------------------------------------------------------------------AACTT----------------TCGTAATCGAAAAAGTTTCGCTTTTTTTC---------TGCTC--------CCCGCTGCCAAGCAAGT-TTTAAATATTAACGCTTAGTT-------ACAGCTGCAG-A------------------------------AAG-AAAAGTTATAATTATGGCGTAAGTACATAAATAACTC-GGCAAATGT----------------------TT
droKik1	scf7180000302475:1550156-1550292 -	1	AGA-TGG-CCAGACAGCAGAAGT-------------------------------------------------------------------------------------------------------------------AACTTT---------------TGGTAATCGAAAAAGTTTCACTTTCTT-------------------------------GCGA-GAACT-TTTAAATATTAACGCTTAGTT-------ACAGCTGCAG-A------------------------------TGG-AAAAGTTATAATTATGGCCTAAGTACATAAATAACTC-GG-------------------------------
droAna3	scaffold_13340:761260-761417 +	1	AGA-TGGCCCAGACAGCAAAAGT-------------------------------------------------------------------------------------------------------------------AACTT----------------TGGTAATCGAAAAAGTTTCGCTTTCGTTTTTTT--C---------------C--A-TCCCGAACAAGT-TTTAAATATTAACGCTTAGTT-------ACAGCTTCGG-A------------------------------GAG-GAAAGTTATAATTATGGCCTAAGTACATAAATAACTC-GCCAAATGT----------------------TT
droBip1	scf7180000394085:232688-232843 -	1	AGA-TGGCCCAGACAGCAAAAGT-------------------------------------------------------------------------------------------------------------------AACTT----------------TGGTAATCGAAAAAGTTTCGCTTTCGT------CT-----TT---------TTTAT-CCCGAACAAGT--TTAAATATTAACGCTTAGTT-------ACAGCTCCAG-A------------------------------AAG-AAAAGTTATAATTATGGCCTAAGTACATAAATAACTC-GGCAAATGT----------------------TT
dp4	chr2:7128424-7128589 +	1	AGA-TGG--CAGACGGCCCAAGG-------------------------------------------------------------------------------------------------------------------AACTT----------------TGGTAATCGAAAAAGTTTCGCTTTTTTCG----CT-----TT---------TTTCTCAGTGGCCAAGT-TTTAAATATTAACGCTTAGTTACTCCGTACAGCTGCAG-A------------------------------AAGAAAAAGTTATAATTATGGCCTAAGTACATAAATAACTC-GGCAAATGT----------------------AC
droPer1	super_0:982713-982880 +	1	AGA-TGG--CAGACGGCCCAAGG-------------------------------------------------------------------------------------------------------------------AACTT----------------TGGTAATCGAAAAAGTTTCGCTTTTTTTTTG--CT-----TT---------TTTCTCAGTGGCCAAGT-TTTAAATATTAACGCTTAGTTACTCCGTACAGCTGCAG-A------------------------------AATAAAAAGTTATAATTATGGCCTAAGTACATAAATAACTC-GGCAAATGT----------------------AC
droWil1	scaffold_181108:125373-125548 -	2	AGA-TGG-G------GCAAAAGT-ATGTCGACTGAGGAAAACC-GGA--------------------------------------------------------------GAG----------------------CA--AACTT---------------GTAGTAATCGAAAAAGTTTCGGTTTGTT-------------------------------GTAGCCAAGT-TTTAAATATTAACGCTTAGTT-------ACAGCTGCAG-AA-----------------------------GAGAAAAAGTTATAATTATGCCGTAAGTACATAAATAACAC-GGCAAATGTGAC--------TT---T-----TT
droVir3	scaffold_13047:1304900-1305088 -	2	AGA-A---TAAGAAA------GAAATG-----TTAGGACGGCT-GGA--------------------------------------------------------------CAG----------------------GATTCAGTTTTGTTGCTGCTTACTGCGGTAATCGAAAAAGTTTTGTTG------------------------------------TAGCCAAGT-TTTAAATATTAACGCTTACTT-------ACAGCTGCAG-AGCTG--------------------------GAA-AAAAGTTATAATTATGGCGTAAGTACATAAATAACGC-TGCAAATGTGCC------GCTTTTCT-----TT
droMoj3	scaffold_6540:5375448-5375637 -	3	GGAATAA-TAAGAAA------GAAATG--------------CT-GGA--------------------------------------------------------------GAGGCACAGGCACAGTCTGGCTTGAGATTCAGTT----TGCTGCTTACGGCGGTAATCGAAAAAGTTTTCTGTT----------------------------------GTAGCCAAGT-TTTAAATATTAACGCTTACTT-------ACAGCTGCAG-AGCTG--------------------------GAA-AAAAGTTATAATTGTGGCGTAAGTACATAAATAACGC-TGCAAATGC------------------------
droGri2	scaffold_14906:4949937-4950239 +	1	AGA-A---TAAGAAA------GAAATG-----TAAGCAACGCTCGGACAGATACAGATACAGAGACAGAGCCAGAGACAGAGCCAGAGACGGACACCGAAACTGAAACTGAGGCACA-GCACAG---GACTTGAGATACAGTTTTGTTGCTGC----TGCGGTAATCGAAAAAGTTTGGTTGT------------------------------------AGCCAAGT-TTTAAATATTAACGCTTACTT-------ACAGCTGCAG-AGCAGAGCTAAGCAGAAAAAAAAAATAAATAAAA-GAAAGTTATAATTATGGCGTAAGTACATAAATAACGC-TGCAAATGTGCCAGAGTGGGGTTGGTAGGAGTT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

AGA-TG-CCCAGACAGCAA---AAGT----------------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTTTTCTGCTT--CT--GCCGCTGAGCAAGTTTTAAATATTACCGCTTAGTT-------ACAGCTGCAGG------------------------------AAG-AAAAGTTATAATTATGGACTACGTACATAAATATCTTGGCAAGTGT------TT

Size

Hit Count

Total Norm

droSim1

AGA-TG-CCCAGACAGCAA---AAGT----------------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTT--CTGCTC--CT--GCCGCCTAGCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGG------------------------------AAG-AAAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGT------TT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................................................................................................................................................................................CACTTTTTT--CTGCTC--CT--G............................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................................................AGAT-------ACAGCTGCAGG------------------------------ATG-......................................................	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

AGA-TA-CCCAGACAGCAA---AAGC----------------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTT-TCTGCTC--CT--GCCGCCGAGCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGG------------------------------AAG--AAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGT------TT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
............................................................................................................................................................................................................................................................................................................................................................TG	18	4	0.25	0.00	0.00	0.25
..................................................................................................................................................................................................................................................................................................................................ATAAATAAGTTAGCAAGT..........	18	1	1.00	0.00	1.00	0.00

droYak2

AGA-TG-CCCAGACAGCAA---AAGT----------------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTTCGCTGCTC--CT--GCCGCCGAGCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGG------------------------------AAG-AAAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGT------TT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
....................................................................................................................................................................................................................................................................................................................................AAATAACTTGGCGAGTGA------T.	19	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................GCTGCTC--CA--GCCGCCGAGT...................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

AGA-TG-CCCAGACAGCAA---AAGT----------------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTT-GCTGCTT--CT--GCCGCCGAGCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGG------------------------------AAG-AAAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGT------TT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..........AGAAGGCAA---AAGT----------------------------------------------------------------------------------------------------------------------------------------AACTT-......................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	2.00

droAna3

AGA-TGGCCCAGACAGCAA---AAGT----------------------------------------------------------------------------------------------------------------------------------------AACTT-TGGTAATCGAAAAAGTTTCGCTTTCGT------TTTTTTCCATC-CCGAACAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTTCGGA------------------------------GAG-GAAAGTTATAATTATGGCCTAAGTACATAAATAACTCGCCAAATGT------TT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
................................................................................................................................................................................GAAAAAGCTTCGCTTTCTT------.....................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................TTCGT------TTTTATCCATG-CC.......................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

dp4

AGA-TG-G-CAGACGGCCC---AAGG----------------------------------------------------------------------------------------------------------------------------------------AACTT-TGGTAATCGAAAAAGTTTCGCTTTTTTCGC---TTTTTT--CTCAGTGGCCAAGTTTTAAATATTAACGCTTAGTTACTCCGTACAGCTGCAGA------------------------------AAGAAAAAGTTATAATTATGGCCTAAGTACATAAATAACTCGGCAAATGT------AC

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

AGA-TG-G-CAGACGGCCC---AAGG----------------------------------------------------------------------------------------------------------------------------------------AACTT-TGGTAATCGAAAAAGTTTCGCTTTTTT-TTTGCTTTTTT--CTCAGTGGCCAAGTTTTAAATATTAACGCTTAGTTACTCCGTACAGCTGCAGA------------------------------AATAAAAAGTTATAATTATGGCCTAAGTACATAAATAACTCGGCAAATGT------AC

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

AGA-TG-GG------GCAA---AAGTATGTCGACTGAGGAAAACCGGAGA---------------------------------------------------------------------------------G----------CA------------------AACTTGTAGTAATCGAAAAAGTTTCGGTTTGTT------------------GTAGCCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGAA--G---------------------------AGAAAAAGTTATAATTATGCCGTAAGTACATAAATAACACGGCAAATGTGACTTTTT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
........................TTATGTCGGCTGAGGAAA....................................................................................................................................................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	2.00
.........................TATGTCGGCTGAGGAAAG...................................................................................................................................................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	2.00
..............................................................................................................................................................................................................................................TTAGTG-------ACTGCTGCAGAA--G---------------------------A........................................................	20	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................................................................................................G-------AAAGCTGCAGAA--G---------------------------AGAA.....................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

AGA----ATAAGAAAGAAATGTTAGG-------------ACGGCTGGACA---------------------------------------------------------------------------------G----------GATTCAGTTTTGTTGCTGCTTACTG-CGGTAATCGAAAAAGTTTTGTT-----------------------GTAGCCAAGTTTTAAATATTAACGCTTACTT-------ACAGCTGCAGAGCTG--------------------------GAA-AAAAGTTATAATTATGGCGTAAGTACATAAATAACGCTGCAAATGT------GC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.................................................................................................................................................................................................................................................................GCACAGCTG--------------------------GAC-AAAAGT................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................ATATTAATGCTTGCTT-------AC.................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
...........................................CTGGACA---------------------------------------------------------------------------------G----------GATTGAGTTATG....................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00

droMoj3

GGAATA-ATAAGAAAGAAATG----------------------CTGGAGAGGC---------------------------------------------------------------------ACAGGCACAGTCTGGCTTGAGATTCAGTT----TGCTGCTTACGG-CGGTAATCGAAAAAGTTTTCTGTT---------------------GTAGCCAAGTTTTAAATATTAACGCTTACTT-------ACAGCTGCAGAGCTG--------------------------GAA-AAAAGTTATAATTGTGGCGTAAGTACATAAATAACGCTGCAAATGC------GC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.........................................................................................................................................................................................................................................................................................................AAAGTTATAATCGGGGCG...................................	18	1	2.00	2.00	0.00	0.00	0.00

droGri2

AGA----ATAAGAAAGAAATGTAAGC-------------AACGCTCG------GtgtGtTtgtGtTtgtGtGtgtGtGggtGtGtgtGtGggtGtGtgGGtgtggGtttgTGtttgTGtGGgtCA-GCACAG---GACTTGAGATACAGTTTTGTTGCTG----CTG-CGGTAATCGAAAAAGTTTGGTT-----------------------GTAGCCAAGTTTTAAATATTAACGCTTACTT-------ACAGCTGCAGAGCAGAGCTAAGCAGAAAAAAAAAATAAATAAAA-GAAAGTTATAATTATGGCGTAAGTACATAAATAACGCTGCAAATGT------GC	Size	Hit Count	Total Norm	V109 Male body
..................................................................TGTGTGTGTGTTTGTGTGT.........................................................................................................................................................................................................................................................................	19	41	0.07	0.07
.....................................................................GTGTGTxCGGGTGTCTGTG......................................................................................................................................................................................................................................................................	18	3	1.00	1.00
............................................................TGTGTGTGTGTGTGTGTGCGTG............................................................................................................................................................................................................................................................................	22	34	0.09	0.09
..................................................................TGTGTGTGTGTGTGTGTGCGTG......................................................................................................................................................................................................................................................................	22	34	0.09	0.09
................................................................................TGTGTGTGTGTGTGTGTGCGTG........................................................................................................................................................................................................................................................	22	34	0.09	0.09
....................................................................TGTGTGTGTGTTTGTGTGT.......................................................................................................................................................................................................................................................................	19	41	0.07	0.07
........................................................................TGTGTGTGTGTGTGTGTGCGTG................................................................................................................................................................................................................................................................	22	34	0.09	0.09
......................................................................TGTGTGTGTGTTTGTGTGT.....................................................................................................................................................................................................................................................................	19	41	0.07	0.07
....................................................................TGTGTGTGTGTGTGTGTGCGTG....................................................................................................................................................................................................................................................................	22	34	0.09	0.09
......................................................TGTGTGTGTGTTTGTGTGT.....................................................................................................................................................................................................................................................................................	19	41	0.07	0.07

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