dme-mir-4955- 12- and 20-way alignments

dme-mir-4955	chrX:2438772-2438941 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 2438797-2438818
   star strand at position 2438893-2438914
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:2438757-2438956 -	T-T-GCTGATGTCAAATCACCG---ATTTGCTT-----------------CCCCT-------TTT------------------------------------------------TCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATCT----------------------------------------------CTGTCTCTG------TCTAACGCTT-----AATTGTTGCTCAATTGCGAATTAATGTCTGGGGCTTTTTT---TCTCCGTGCAGTGCCATAGCCGTAA-CCACAACCT----GCCAGCCGTT-------------T---------------------AAAG--------C
droSim1	chrX:1743323-1743546 -	T-TTGCTGATGTCAAATCACCG---ATTTGTTT-----------------CCCCC-------TTT------------------------------------------------TCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATATCTATCTCAGTCTGGGCCCAAGTG----------------------TCTGTCCCTG------TCTGACGCTT-----AATTGTTGCCCAATTGCGAATTAATGTC-GGGGCTTTTTT---TCTCCGTGCAGTGCCATAGCCGTAA-CCACAACCT----GCCAGCCGTT-------------T---------------------AAAG--------C
droSec1	super_10:2212704-2212927 -	T-TTGCTGATGTCAAATCACCG---ATTTGTTT-----------------CCCCT-------TTT------------------------------------------------TCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATATCTATCTCAGTCTGGGCCCAACTG----------------------TCTGTCCCTG------TCTGACGCTT-----AATTGTTGCTCAATTGCGAATTAATGTC-GGGGCTTTTTT---TCTCCGTGCAGTGCCATAGCCGTAA-CCACAACCT----GCCAGCCGTT-------------T---------------------AAAG--------C
droYak2	chrX:5905985-5906183 +	T-T-GCTGATGTG--TTCACCG---ATTTGTTT-----------------CCCCT-------TTT------------------------------------------------TCCGTGCGCCGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCT--------------------------------------------------CCCTGTCTCTG------TCTTACGCTTAATTTAATTGTCGCTCAATTGCGAATTAATGTCGGGGGCTTTTTT---TCTCCGTGCAGTGCCATAGCCGTAA-CCAAAACCT----GCCAGCCGTT-------------C---------------------AAAG--------C
droEre2	scaffold_4644:2389120-2389319 -	T-TTGCTGATGTG--TTCACCG---ATTTGTTT-----------------CCCCT-------TTT------------------------------------------------TCCGTGCGCTGAGAAAAAAATCCCCAGAAACCTAATATCAGGATGCTCTCTGTCTC--------------------------------------------CCTGTCTCTG------TCTCACGGCA-----AATTGTTGCTTAATTGCGAATTAATGTC-GGGGCTTTTTT---TCTCCGTGCAGTGCCATAGCCGTAA-CCACAACCT----GCCGACCGTT-------------T---------------------AAAG--------C
droAna3	scaffold_12929:2354505-2354776 -	T-C-GCTGATGTT---TGAAAA---AAAAGCTTCTCTTTTTTGTGTTTCTTCCAAATCTTCAgTTgTgTTgTgTTTTgTTTTgTTTggTTgTTgTGTTTTTTTTTTTTGTTGGTCCCTGCACGGAGAAGAAGT-TGTTAGGA-CA-----TT-----------------------AGAGTGGACCTTAGTGTGGTTAATAGATCATATGACTCATTGTCCTTG-----------CAATTATTTCACAACTCGCTCCA---------------------CTTTTC---TCTCTGTGCAGTGCCATAACCGTAA-CCACAACCT----GCCAGCCGTT-------------C---------------------AAAAAAAAAACCC
dp4	chrXL_group3a:2134676-2134848 -	T-TCGCTGATTC-------GGGAATATATTCTCCACCCCCCCAC-CCTCTACCAT-------TTC------------------------------------------------CTCTTCTGCTGACCTA----------------------CACGATTTTCC--------------------------------------------------CCCTCTCTCTTAACGATCTTAACGC----------------TCCAC----------TCTTTCT---GTCTCTCTCGATTTTTGCAGTGCCATAGCCGTAAAACACTGTCT----TCCTACCGTT-------------T---------------------ACCG--------T
droPer1	super_11:2542328-2542497 +	T-TCGCTGATTC-------GGGAATATATTCTCCACCCCCC----CCTCTACCAT-------TTC------------------------------------------------CTCTTCTGCTGAGCTACAC----------------------GATTTTCC--------------------------------------------------CCCTCTATGTTAACGATTATAATGC----------------TCCTC----------TCTATCT---GTCTCTCTCGATTTTTGCAGTGCCATAGCCGTAAAACACTGTCT----TCCTACCGTT-------------T---------------------ACCG--------T
droWil1	Unknown	T-TgGgTGtTTT-------TGG---ttttgtTT-----------------TgTTt-------TTT------------------------------------------------GgTgTggT------------------------------------TTttT--------------------------------------------------TTtTGTTTTTG------TtTt------------------------T----------TTTTTtT---GTTTtT---TTTGTTTGCAGTGCCATAA-CATAATA-ATA-GTTAATACTTATTGTGTTCACACAAAAATTTTGGGCCGCCGAATCGAAAACGAATA--------T
droVir3	scaffold_12928:1476017-1476072 -	T-TTGT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---TTTACTTGCAGTGCCATAAACATCG-TAACCTTTT----TCTTTCTTTA-------------T---------------------CACG--------T
droMoj3	scaffold_6473:13536163-13536217 +	C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTTTT---CTCTCTTGCAGTGCCATAAACATCGTA-ATT-TTT----TTCATTTATT-------------T----------------------ACG--------T
droGri2	scaffold_15203:8273975-8274050 +	AATAGCTGAAAT---------------TT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTTTCCTCATTTCTTGCAGTGCCATAAACATCGTAACCTTTTT--TCTTTTTTTTTC-------------T---------------------TACG--------T

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:2438757-2438956 -	NA	TT--GCTGATGTCAAA---------------------------TCA---CCGATTTGCTTCCCCT---------TT-T---------TCCGTGCGCGGAGAAAAAAATCCCC---------------AGAAA-CATAAT------------------------ATCAGGATGCTCTCTATCT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCTAACGCTTA-----ATTGTTGC-TCAATTGCGAAT----------------------------------------TAA-------TGTCTGGGGCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-TAAAGC
droSim1	chrX:1743323-1743545 -	1	TT--GCTGATGTCAAA---------------------------TCA---CCGATTTGTTTCCCCC---------TT-T---------TCCGTGCGCGGAGAAAAAAATCCCC---------------AGAAA-CATAAT------------------------ATCAGGATGCTCTCTATATCTATCTCAGTCT-------------GGG-------------------------------------C-CCAAGTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCCCTG------TCTGACGCTTA-----ATTGTTGC-CCAATTGCGAAT----------------------------------------TAA-------TGTCGGG-GCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-TAAAGC
droSec1	super_10:2212704-2212927 -	1	TT-TGCTGATGTCAAA---------------------------TCA---CCGATTTGTTTCCCCT---------TT-T---------TCCGTGCGCGGAGAAAAAAATCCCC---------------AGAAA-CATAAT------------------------ATCAGGATGCTCTCTATATCTATCTCAGTCT-------------GGG-------------------------------------C-CCAACTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCCCTG------TCTGACGCTTA-----ATTGTTGC-TCAATTGCGAAT----------------------------------------TAA-------TGTCGGG-GCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-TAAAGC
droYak2	chrX:5905985-5906183 +	1	TT--GCTGATGT-----------------------------GTTCA---CCGATTTGTTTCCCCT---------TT-T---------TCCGTGCGCCGAGAAAAAAATCCCC---------------AGAAA-CATAAT------------------------ATCAGGATGCTCTC-------------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCTTACGCTTAATTTAATTGTCGC-TCAATTGCGAAT----------------------------------------TAA-------TGTCGGGGGCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCAAA-ACCTGCC--------------------------AGCCGTT-CAAAGC
droEre2	scaffold_4644:2389120-2389318 -	3	TT--GCTGATGT-----------------------------GTTCA---CCGATTTGTTTCCCCT---------TT-T---------TCCGTGCGCTGAGAAAAAAATCCCC---------------AGAAA-CCTAAT------------------------ATCAGGATGCTCTCTGTCTC-------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCTCACGGCAA-----ATTGTTGC-TTAATTGCGAAT----------------------------------------TAA-------TGTCGGG-GCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------GACCGTT-TAAAGC
droEug1	scf7180000409277:126495-126773 -	2	TT--GCTGAAATCGGG------AAACGCGTCCCGTTTCTGTGTTCT---CCGATTTGTTTCCCCC---------TTTATT-TTTTTATTAGTGCACCGAGAAAAAATCGACC---------------ATAG-----AATTCA----------------------------------------------GATTT----------------------------------------------------------------------------------TAAAGTATTTTATAGATTAATTAATGTTAGGAG---------------TTTTTATGCCTAA----------------AGCAGGGGACACATTGT---------------------------------------------------------------------------------------------------------------------------------------------------TTTCTATAGTT--------------TCTATAGTTTTTCAATTAACGTATTAATAAATTATTTCGGG-GCT--TTTTTTCTCTGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CAACA-ACCTGCC--------------------------AGCCGTG-AAAAAC
droBia1	scf7180000301760:4721669-4721893 +	1	TT--GCTGATATCGGG------AAACGTGTCCCGTTTCTGTGCTCT---CCGATTTGTTTACCCT---------TTCC---------TAAGTGCACCGAGAAAAAACGCCCC---------------TAAG-----AATGCTAAA-------------------------------------------------------------------------------------------------AAA----------------------------------------------------AAAGCTAGGAG---------------AAAATATCCTTCAAAGAGAATTTAAATCA-AAA--TG---AAT----------------------------------------------------------------------------------------------------------------------TGCCT----------------------------TTAAT------------------------A-----------------------ACCCATTTCGGG-GAC--TTTTTTCTCTGTGCAGTGCCATAGCCGCA------------------------------------------------------------A----CA-ACCTGCC--------------------------AACCTTT-TGAAAC
droTak1	scf7180000415151:362895-363093 +	1	TT--GCTGGTATCGGG------AAACGTGTCCCGTTTCTGTGCTCTCCACCAAACTGTTTCCCCC---------TTTT---------TTAGTGCACCGAGAAAAAACACCTCCTT------------AGGAA-TAGAAT--------------------------------------------------------------------CCAACTTATTATTGAG---------TAA----------------------------------------------------GAT--------------------------------------------------------------C---------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAT------------------------A-----------------------TCCAATCTTGGGGGCT--TTTTTTCTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CAACA-ACCTGCC--------------------------AACCGCT-TAAAAC
droEle1	scf7180000491011:764569-764826 -	2	TT--GCCAAATTCAAA-----------------------------A---CCAAA-AATATCCATT---------TT-T---------TAAATATACAAT--------------------------------------------------------------------------------------------AAT-------------TAACTTTAAAGA-AAAAATCTTCGTTAATGTTTTAAAAAA----------------------------------------------------------------------------------------------------------TAA--TAATTTATTATCCTTTGAATAATTTCACCATTATCATGCTATGTTAATTTT---TTAA--------------ACATTTGCCAATGAGCGTTTTACTGAAATACAGAACTAATTGA---------------------------------------------------------------------------------------------------ATTTTTCGTGGGATA-TTTTTTCTCTGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-TAAGAC
droRho1	scf7180000779506:556816-557127 -	2	CT--GCTGATGATGGG------AAACGCGTCCCGTTTCTGTGCTCT---CCGATTTGTTGTCTCT---------TTTT---------T--TTAG-ACGAGAAAAAAACAGTT---AAAGAATTTCCAAGAAAGCAT-------------TGAAATCAAACAAAAA---------------CCATATATTATTCTAAAAATAGTCCGTTTACCATAGTGA-AAT---------TAAGGTTTTAAAACC-------------------------------------------------------------------------------------------------------------------TAATTATCCTTTAAGTAATCTCACCA------TGCTATAT-CATTTT---GAAA--------------GCATTTCTTTTTGGGCGTTTTTCTAAAATACCAAAG---------------------------------------------------------------------------------------------------------------------TAT--ATTTTTCTCTGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCTTT-TAAAAC
droFic1	scf7180000453927:241567-241837 -	3	TT--GCTGATGTCGGG------AAACGCGTCCCGTTTCTGTGTTCT---CCGATTTGCTTCCCCC---------TTTCTT-TT----ATAGTGCACAGAGAAAAAATGCATC---------------AAAAA-CT-----------------------------------------------------AATAAT-------------AAA-------------------------------------T-CCTT----------T-T---------------------TAGAACAAAAAA--AAAAGAA---------------TA--------------------------------------------------------TTCACAATTACTAAG----------------TGAAACATCTTTTCGTAAT-------CAACGATCTTTTTGTT---------------------------------------------------------------------------TTAAGTAATAAGTTTTCA-----------------------ATCTATCTCGGGTGCTA-TTTTTTCTCTGTGCAGTGCCATAACCGTA------------------------------------------------------------A-CCACA-TCCTGCC--------------------------AGCCGTT-TAATAC
droKik1	scf7180000302258:595697-595976 -	2	TT--GTTTACT--------------------------------------TTAATTTTTTTTTTTT---------T--T---------TTGTTGCACAGAGACAAAAATAGTT---T-------TC--T---------TTGCTAAAATATAAAAAATATACGAGAGCAGAAT-TTATATATATATATATTTTTCT-------------A---------------------------------------CTTAAAATGTATGGAATAATGCTTCTGATAAGTAACTTCAGAGATTCC-------------A---------------------------------------------------------------TTAGATAAGAATATTA------TATTAT---------AAA-----------------------------------------------------------------------------------------------------------------GCCGTAAACTAATTTGTCGACA-------------------------TTTTTTCGGTTGATATTTTTATCTCTGTGCAGTGCCATAGCCTTA------------------------------------------------------------A-CCACAAACCTGCC--------------------------AGCCGTT-TAA-AC
droAna3	scaffold_12929:2354513-2354742 -	2	GT--GTTTCTTCCAAATCTTCACTTCTCTTCTCTTTTCTTTTCTTT---CCTT-------CTTCTGTTTTTTTTTTTT----GTTGGTCCCTGCACGGAGAAGAAGTTG-TT---------------AGGAC-AT-----------------------------------------------------TAGAGT-------------GGACCTTAGTGT-GGT---------TAA----------------------------------------------------TAG--------------------------------------------------------------ATCATATGACTCATTGTCCTTGCAATTATTTCAC----------------------------------------------------------------------------------------------------------------------------------------------------------------A-----------------------ACTCG---CTCC--AC--TTTTCTCTCTGTGCAGTGCCATAACCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-CAAAAA
droBip1	scf7180000396434:346903-347133 -	1	TT--TTA--------------------TTTTTTATTTCCTCTT--------------CTTCCCTC---------TTGTTTTTTTTGGTTCCTGCACAGAGAAAAAGTTC--T---------------AGGAC-CT-----------------------------------------------------TAGAGT-------------GGA-------------------------------------C-CATA----------T-TTGTTGCCTATAAAGTGTTCTATAGATTCT-------------AAGATCCTTGAGGGATTTGTATGA-------------------------------------------------------------------C---------TAA-----------------------------------------------------------------------------------------------------------------TTTTTAGAATAATTATTTTACA-----------------------ACTTG---CTTG-AAT--TTTTCTCTCTGTGCAGTGCCATAACCGTA------------------------------------------------------------A-CCACA-ACCTGCC--------------------------AGCCGTT-CAA---
dp4	chrXL_group3a:2134676-2134849 -	6	TTTCGCTGATTCGGGA------ATATATTCTCCACCCCCCCACCCT---CT---------ACCAT---------TT-C---------CTCTTCTGCTGACC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACACGATTTTCCCCCTCTCTCTTAACGATCTTAACGCTCC-----ACT---------------------------------------------------------------------CTTTCTGTCT--CTCTCGATTTTTGCAGTGCCATAGCCGTA------------------------------------------------------------AAACACT-GTCTTCC--------------------------TACCGTT-TACCGT
droPer1	super_13:248212-248305 -	9	TC--TCTGGCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTCTCTG------TCTCAGGCGTA-----ACAGGTGCGTTGAGTGCATTT----------------------------------------CAA-------TTGTATG-GA--------TAATTGTGCTGTATTGTAATTGAA------------------------------------------------------------ATCCACA-A----------------------------------------------
droWil1	scaffold_181096:12164007-12164188 -	11	TC--GCTGATTTTGGA------AAACATTTCTTATTTGCTCTC-CT---TTAATTTATGTTTTTT---------TTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTTGT-TCTTTTGTATAT----------------------------------------T----------TTTTAT-G----TTTATTTTGTTTGCAGTGCCATAAC-ATAATAATAGTTAATACTTATTGTGTTCACACAAAAATTTTGGGCCGCCGAATCGAAAACGAAT---------------------------------------------AT-CAAAAC
droVir3	scaffold_12928:1476007-1476072 -	12	TT--T---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTTTTACTTGCAGTGCCATAAACATCGTA---------------------------------------------------------A-CC----TTTTTCT--TTCTTTATCACGTCTAAACG---------------CAT
droMoj3	scaffold_6473:13536163-13536218 +	5	CG--T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTCTCTCTTGCAGTGCCATAAACATC------------------------------------------------------------G-TAATT--TTTTTC--------------------------ATTTATT-TACGTC
droGri2	scaffold_15203:8273975-8274075 +	22	AATAGCTGAA------------------------------------------ATTTGTTTTCCTC---------A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTCTTGCAGTGCCATAAACATCGTA---------------------------------------------------------A-CC--T-TTTTTCTTTTTTTTTCTTACGTCAAAACGCATCGATCGCATCAGAGG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

T-T-GCTGATGTCAAATCACCG---ATTTGCTT-----------------CCCCT-------TTT------------------------------------------------TCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATCT----------------------------------------------CTGTCTCTG------TCTAACGCTT-----AATTGTTGCTCAATTGCGAATTAATGTCTGGGGCTTTTTT---TCTCCGTGCAGTGCCATAGCCGTAA-CCACAACCT----GCCAGCCGTT-------------T---------------------AAAG--------C

Size

Hit Count

Total Norm

droSim1

T-TTGCTGATGTCAAATCACCG---ATTTGTTT-----------------CCCCC-------TTT------------------------------------------------TCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATATCTATCTCAGTCTGGGCCCAAGTG----------------------TCTGTCCCTG------TCTGACGCTT-----AATTGTTGCCCAATTGCGAATTAATGTC-GGGGCTTTTTT---TCTCCGTGCAGTGCCATAGCCGTAA-CCACAACCT----GCCAGCCGTT-------------T---------------------AAAG--------C	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
............................................................................................................................................AATCATAATCTCAGGATG..................................................................................................................................................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
......................................................................................................................................................................ATCTATCTCAGTCTGGGCCCAAGT..................................................................................................................................................................................................	24	1	2.00	0.00	2.00	0.00	0.00
.............................................................................................................................................................................................................................................................................GTC-GGGGCTTTTTT---TCTCCG...........................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................................................................................................................................................GTAA-CCACAACCT----GCCAGCC...................................................	20	1	1.00	0.00	0.00	0.00	1.00
..........................................................................................................................................................................................................................CCCTG------TCTGACGCTT-----AATTGTTGCCC.................................................................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................G------TCTGACGCTT-----AATTGTTGCCC.................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
......................................................................................................................................................................ATCTATCTCAGTCTGGGC........................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droSec1

T-TTGCTGATGTCAAATCACCG---ATTTGTTT-----------------CCCCT-------TTT------------------------------------------------TCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATATCTATCTCAGTCTGGGCCCAACTG----------------------TCTGTCCCTG------TCTGACGCTT-----AATTGTTGCTCAATTGCGAATTAATGTC-GGGGCTTTTTT---TCTCCGTGCAGTGCCATAGCCGTAA-CCACAACCT----GCCAGCCGTT-------------T---------------------AAAG--------C	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.................................................................................................................................................................................................................................................................................................................GCCGTAA-CCACAACCT----GCCAGC....................................................	22	1	1.00	0.00	1.00	0.00
......................................................................................................................................................................................................................................................................................................................AA-CCACAACCT----GCCAGCCGT.................................................	20	1	1.00	0.00	1.00	0.00
..........................................................................................................................................................................................................................................................................................................................CACAACCT----GCCAGCCGTT-------------T---------------------.............	19	1	1.00	0.00	1.00	0.00
......................................................................................................................................................................................................................................................................................................................AA-CCACAACCT----GCCAGCCG..................................................	19	1	1.00	0.00	1.00	0.00

droYak2

T-T-GCTGATGTG--TTCACCG---ATTTGTTT-----------------CCCCT-------TTT------------------------------------------------TCCGTGCGCCGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCT--------------------------------------------------CCCTGTCTCTG------TCTTACGCTTAATTTAATTGTCGCTCAATTGCGAATTAATGTCGGGGGCTTTTTT---TCTCCGTGCAGTGCCATAGCCGTAA-CCAAAACCT----GCCAGCCGTT-------------C---------------------AAAG--------C

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

T-TTGCTGATGTG--TTCACCG---ATTTGTTT-----------------CCCCT-------TTT------------------------------------------------TCCGTGCGCTGAGAAAAAAATCCCCAGAAACCTAATATCAGGATGCTCTCTGTCTC--------------------------------------------CCTGTCTCTG------TCTCACGGCA-----AATTGTTGCTTAATTGCGAATTAATGTC-GGGGCTTTTTT---TCTCCGTGCAGTGCCATAGCCGTAA-CCACAACCT----GCCGACCGTT-------------T---------------------AAAG--------C	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.....................................................................................................................................................................................................................................................................................................................TAA-CCACAACCT----GCCGACCGTT-------------...................................	22	1	1.00	1.00	0.00	0.00	0.00
......................................................................................................................................................................................................................................................................................................................AA-CCACAACCT----GCCGACCGTT-------------...................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................................................................................................................................TTT---TCTGCATGCAGTGCCA.................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................................................................................................................................GGCTTTTTT---TCTCCGTGCAGTT....................................................................................	22	1	1.00	0.00	0.00	0.00	1.00

droAna3

T-C-GCTGATGTT---TGAAAA---AAAAGCTTCTCTTTTTTGTGTTTCTTCCAAATCTTCAgTTgTgTTgTgTTTTgTTTTgTTTggTTgTTgTGTTTTTTTTTTTTGTTGGTCCCTGCACGGAGAAGAAGT-TGTTAGGA-CA-----TT-----------------------AGAGTGGACCTTAGTGTGGTTAATAGATCATATGACTCATTGTCCTTG-----------CAATTATTTCACAACTCGCTCCA---------------------CTTTTC---TCTCTGTGCAGTGCCATAACCGTAA-CCACAACCT----GCCAGCCGTT-------------C---------------------AAAAAAAAAACCC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.......................................................................................................................................................................................................................................................................................................................................GTAGCCGTT-------------C---------------------AAAAAAAAA....	19	1	1.00	0.00	1.00	0.00	0.00
.....TTGAGGTT---TGAAAA---AAAA...................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.........................................................................GTTTGTTGTGTTTGGTTGT....................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................TTGTGTTTGTGTTTTTTGT..................................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.....................................................................TGTGTTTGGTTGTGTTTGG........................................................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..........................................................................................TTTGTGTTTTTTTTTTTTTTTG................................................................................................................................................................................................................................................................................	22	8	0.13	0.13	0.00	0.00	0.00
...................................................................................................................................GT-TGTTAGGA-CA-----TT-----------------------AGAGTG...........................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................................AAGT-TGTTAGGA-CA-----TT-----------------------AGAGTG...........................................................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.........................................................CTTCGGTCGTGTTGTGTTT....................................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00

dp4

T-TCGCTGATTC-------GGGAATATATTCTCCACCCCCCCAC-CCTCTACCAT-------TTC------------------------------------------------CTCTTCTGCTGACCTA----------------------CACGATTTTCC--------------------------------------------------CCCTCTCTCTTAACGATCTTAACGC----------------TCCAC----------TCTTTCT---GTCTCTCTCGATTTTTGCAGTGCCATAGCCGTAAAACACTGTCT----TCCTACCGTT-------------T---------------------ACCG--------T	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................................................................................................................................................................................................................................................................................CT---GTCTCTCTCGATTTTTGCAG......................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................................................................................................................................................................TGCCATAGCCGTAAAACA....................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

T-TCGCTGATTC-------GGGAATATATTCTCCACCCCCC----CCTCTACCAT-------TTC------------------------------------------------CTCTTCTGCTGAGCTACAC----------------------GATTTTCC--------------------------------------------------CCCTCTATGTTAACGATTATAATGC----------------TCCTC----------TCTATCT---GTCTCTCTCGATTTTTGCAGTGCCATAGCCGTAAAACACTGTCT----TCCTACCGTT-------------T---------------------ACCG--------T	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
....................................................................................................................................................................................................................................................................................................................GTAAAACACTGTCT----TCCTACCGTT-------------T---------------------ACC..........	28	1	2.00	0.00	0.00	0.00	0.00	2.00
....................................................................................................................................................................................................................................................................................................................GTAAAACACTGTCT----TCCTACC...................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................................................................................................................................................................AAACACTGTCA----TCCTACCATT-------------...................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................................................................................................................................................................................................CTC----------TCTCTCT---GTCACTCTC.................................................................................................	19	4	0.25	0.00	0.00	0.00	0.00	0.25

droWil1

T-TgGgTGtTTT-------TGG---ttttgtTT-----------------TgTTt-------TTT------------------------------------------------GgTgTggT------------------------------------TTttT--------------------------------------------------TTtTGTTTTTG------TtTt------------------------T----------TTTTTtT---GTTTtT---TTTGTTTGCAGTGCCATAA-CATAATA-ATA-GTTAATACTTATTGTGTTCACACAAAAATTTTGGGCCGCCGAATCGAAAACGAATA--------T

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

T-TTGT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---TTTACTTGCAGTGCCATAAACATCG-TAACCTTTT----TCTTTCTTTA-------------T---------------------CACG--------T

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTTTT---CTCTCTTGCAGTGCCATAAACATCGTA-ATT-TTT----TTCATTTATT-------------T----------------------ACG--------T	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..............................................................................................................................................................................................................................................................................................................ATxAACAGCGTA-ATT-TTT----TT........................................................	19	1	1.00	1.00	0.00	0.00	0.00

droGri2

AATAGCTGAAAT---------------TT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTTTCCTCATTTCTTGCAGTGCCATAAACATCGTAACCTTTTT--TCTTTTTTTTTC-------------T---------------------TACG--------T

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