dme-mir-4961- Best orthologs

dme-mir-4961	chrX:1267655-1267788 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 1267719-1267741
   star strand at position 1267685-1267706
   mutations
   read mismatches

Notes: Alignment is very dirty

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:1267640-1267803 +		1	AGATAT-TA----CCCAGA----AGCGA---------TATCCAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCT------------ATG----------------------------------------TGTATGTATGTAT--CTTGC----------------------------TATCCAT--ATATGTATATCCATA---TCAGAGAGCCAGGATT-----------------GGTTGAGACCATACGAT------A----T-AACCCGAAAC---C-------------------------------AC--A----CTGGCC-AGGA----A----TAGCAAATCCA
droSim1	chr3L:16407222-16407379 -	LASTZ	1	AGC----------------------------------------------------GA----------------------------A-ATTTTTCGACATTTCT----------ATTTAAAG---------------TACATATAGACATTACTATATACATACATATAT--ACTAT----------------------------ACCTTAT--------------------------ATACATGAAT-----------------ATTTATATACATATTT---------------------------AATATACGACGTTTACAAGCTAAGTTGGGTATTC--A----TTTTAT-ACGA----A----GCGTGAATCGA
droSec1	super_10:1091085-1091248 +	LASTZ	1	AGATAT-TA----CCCAGA----AGCAA---------TATCCAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCT------------ATG----------------------------------------TGAATGTATGTAT--CTTGC----------------------------TATCCAT--TTATGTATATCCATA---TCAGAGAGCCAGGATT-----------------GGTTGAGACCATACGAT------A----T-AACCCGAAAC---C-------------------------------AT--A----CTGGCC-AGGA----A----TAGCAAATCCA
droYak2	chrX:1175521-1175702 +	LASTZ	3	AGATAT-AA----CCGAGA----AGCAA---------TACCCAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCTCTGCGTCTCTCTATG----------------------------------------TGTATGTATGTAT--TTCGC----------------------------TATCCAT--ATATGTATATCCATG---TCAGAGAGCCAGGATC-----------------GGTTGAGACCATACTATATCTATA----T-AACCCGAAAC---C-------------------------------AT--A----CTGGCC-AGGA----A----TAGCAAATCCA
droEre2	scaffold_4644:1251466-1251631 +	LASTZ	3	AGATAT-AA----CCCAAA----AGAAA---------TACCGAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCTCT----------ATG----------------------------------------TGTATGTATGTAT--TTCGT----------------------------TATCCAT--ATATGTATATCCATG---TCAGAGAGCCAGGATC-----------------GGTTGAGACCATACTAT------A----T-AACCCAAAAC---C-------------------------------AT--A----CTGGCC-AGGA----A----TAGCAAGTCCA
droEug1	scf7180000409008:208095-208232 -	LASTZ	0	CT---------------------------------------------------------------------------------------CTCTC--TCTCT------------ATC-------TCTC---------TCTCTCTGTCTGTTCTTATATATATATATATAC--ATTCT-----------------------A-TATATACCAT---------------------------------ATT-----------------TAT--------------------ATATTT-AATT---------ACCAAAAACAAAATACAAAATC---CAAAA------ACAAATGCAAA-ATGA----A----AACAAAATCAA
droBia1	scf7180000302075:3548008-3548156 -	LASTZ	0	TATATAGATACAATGCA------------------------AAAG----TGTTGCCAATTACTTCATTAATGTATGAGGTAGAGAT-GT--------------------------------------------------------------------------------------------------------------------CTGCAT--ATGTGTGGGTGAGTA---TGTGTGAGC------T-----------------TATTAATAACATTTTACTCGTT-C----G-TATTCGTAAC---C-------------------------------GT--A----A--TCC-GTGA----T----ACGTAATTTAT
droTak1	scf7180000415289:447785-447964 +	LASTZ	0	AGATAT-AT----GCCAAAAAAAAGCTT----AAA--AATTGAAC----AATATCAA--------------------------TAT-ATCTCTCGCTCTCT------------ATG----------------------------------------TGAATGTATGTAT--GTTGTAAT-------------------------TGAATAT--ATATGTATATCCATC---TCAGAGAGCCAGGATCGAT---------CGATCGGTTGAGACTATACTAT------A----T-AAACTATA-----T-------------------------------TT--A----CTGGCC-AGGA----A----TAGCGAATC--
droEle1	scf7180000490996:88170-88351 +	LASTZ	0	AAATAG-TCCACATCCAG--------------------ATCCAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCTCT----------ATG----------------------------------------TGTATGTATGTAT--GTTGT----------------------------AACCCGT--ATATGTATATCCATG---TCAGAGACCCAGGATT-----------------GGTTAAGACCATACTATATATATA--TAT-AATCCAAAAC---T--------------------AAAATAAAAACAT--A----CTGGCC-AGGA----A----TAGCAAATCCA
droRho1	scf7180000778087:78186-78354 +	LASTZ	0	AGATAT-AA----TCCAA--------------------ATCCAAT----AACAGCCA----------------------------A-CTCTCTCGCTCTCTCTGCGTCTCTCTATG----------------------------------------TGTATGTATGTAT--GTTGT----------------------------AACCCGT--ATATGTATATCCATG---TCAGAGAGCCAGGAAA-----------------GGTTGAGTCCAAACTAT------A----A-AACCCAAAGC---T-------------------------------AC--A----CTGGCC-AGGA----A----CAGCAAATCCA
droFic1	scf7180000454072:1846816-1846999 -	LASTZ	0	AGAAAA-AGCCGATCCAAA----ACTTA---------TATCCAAT----AGTACCCG----------------------------A-CTCTCTCGCTCTCTTT----------ATG----------------------------------------TGTATGTATGTAT--GTTGT----------------------------ACCCCGT--ATATGTATATTCATG---TTAGAGAGCCAGGATC-----------------GGTCGATACCATACTATTTCTGTT----TAAACCAAAAACCAAT-------------------------------ACTGA----CTGGCC-AGGA--ACA----TAGCAAATCCA
droKik1	scf7180000302621:326473-326630 -	LASTZ	0	AAATAC-AA----AAAAGA----AATCC----AAAAATAAATCGC----AGTCTTGA----------------------------AACTTTGTCTA-CTTTCC----------GTT----------------TCTTTTTTTTCTT--------CCATTTTTATTTGT----ATTTT-----------------------AT---TTTTGGTGG-AACGCA-----------TCCTAGTGCCA------------------------------------------------------AAAGCAAC---C-------------------------------GC--A----CAGAAT-CGGAAAACG----CAGCAAGGATA
droAna3	scaffold_13117:1856374-1856503 -	LASTZ	0	CT---------------------------------------------------------------------------------------CTCTC--TCTCTCTGTGTCTCTCTAAA----------------------------T--------GCATGTATGTATGT----GTTGT-----------------------AT---TATCCGTATATATGTATATCCATG---TTAGAGAGCCAGGACG-----------------GGTTGAGATT---------------------GCCCAAGA----------------------------------------A----CTGGCCTAGGA----A----TAGCAAATC-A
droBip1	scf7180000396425:207025-207154 +	LASTZ	0	CT---------------------------------------------------------------------------------------CTCTC--TCTCTCTGTGCCTCTCTAAG----------------------------------------TGCATGTATGTATGTGTTGT-----------------------AT---TATCCGTATATATGTATATCCATG---TTAGAGAGCCAGGACG-----------------GGTTGAGATT---------------------GCCCAAGA----------------------------------------A----CTGGCCTAGGA----A----TAGCAAATC-A
dp4	chr2:10126391-10126530 +	LASTZ	0	GAATAA-TC----CATA-A----ACAAA---------TATCTA------TGTAGTCA----------------------------C-ATCTATCTCTCTCTCT----------ATA----------------------------------------TATCTCTCTCTCT--CTTTC----------------------------TTTATTT--GTACATGTATTTATT---TCATGGGTTTAGTTTT-----------------GC---AAATGGTATAAA------A----C-ATCTCCAAAA---T-------------------------------AC--A----TT-----------------------------
droPer1	super_2:4840479-4840636 -	LASTZ	0	TAATAT-AT----TGGAGT----AGCAA---------TATCTATT----TGTATTCA----------------------------G-ATTTGTATTTATTT------------ATG------------------------------TGTTTGTGGTGATACAGATAT-------------------------------------ATAGTAT--ATATAGAAAT--ATA---TTTTAAAATCA---TA-----------------GGTACATACAGTATATT------G----T-ATCCCTATCC---A-------------------------------AT--G----C----A-TATG----T----GAACGTACTTA
droWil1	scaffold_180700:3267577-3267741 +	LASTZ	0	AAATAT-CA----TACCCA-----AAAA---------TATATACT----ACTACACA----------------------------ACCTCTCTCTCTCTCT------------CTA----------------------------------------TCTATCTATCTAT--CTTTGAACATAAAATGTACCTATACTAAAACAAAAACTCT--ATATCTAAATCGTTG---TGC-TTACCATTCATT-----------------TTCTACTACTATACTAT------A----T-AGGGCGAAAC---------------------------------------------------------------------------
droVir3	scaffold_12855:2148540-2148695 +	LASTZ	0	ATA-----A----CCCAAA----AGATA---------CCTCAATT----TGCATA-----------------------------------------TATATCTATGTCTATATAGA----------------------------------------TATATACATACAT--ATATA----------------------------TATACAT--ATATATATATAAATA---TATGTGTGCGTGCATT---------------------ATCGTCTTGTGAC------T----A-GGTCCAGAAC---T-------------------------------TT--A----CAGGTG-CGCA----G----TGTCGAAATCA
droMoj3	scaffold_6496:26031347-26031515 +	LASTZ	0	TGATGC-CA----CCCAG--------------------CCCCCAC----CGCCTCCT----------------------------G-CTCCCTCCCTCTCTAT--GTTTATATGTG----------------------------------------TATATGTGTGTG------------------------------------TGTCTGT--GTGTTTGTGTCCCTTCGATTGGCGTGCCTGAATGGCTGTGAAAACACAGCCAGTTGCAGCT-------------------------GTATC---C-------------------------------AC--A----A--TCA-TTAT----CACAAAAGCAAACTAC
droGri2	scaffold_14853:6570585-6570746 +	LASTZ	0	AAAAAC-AA----AAAACA----AACGAAGTAACA--GCCCAAGCCGACAATGGCTG----------------------------A-ATATATA--------------------TGTTATGTATTTGTATTATTGTCGTGTATA--------TATATCTATATATGTAT--ATTAC-----------------------ACTATATACTAT----ATGTAT------------------------------------------------------------------A----T-ATATATAGAC---A-------------------------------AT--G----TCTGAT-GGCT----A----TGCCAAAGCCA

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	AGATATTACCCAGAAGCGATATCCAATAGTAGCCAACTCTCTCGCTC------------TCTATGTGTATGTATGTATCTTGCTATCCATATATGTATAT-CCATATCAGAGAGCCAGGATTGGTTGAGACCATACG------------------A------TATAACCCGAAACCACACTGGCCAGGAATAGCAAATCCA
droSim1	A------------------------------GCGAAATTTTTCGACATTTCTATTTA-------AAGTACATATAGACATTACTATATACATACATATATACTATACCTTATATACATGAATATTTATATACATATTTAATATACGACGTTTACAA------GCTAAGTTGGGTATTCATTTTATACGAAGCGTGAATCGA
droSec1	AGATATTACCCAGAAGCAATATCCAATAGTAGCCAACTCTCTCGCTC------------TCTATGTGAATGTATGTATCTTGCTATCCATTTATGTATAT-CCATATCAGAGAGCCAGGATTGGTTGAGACCATACG------------------A------TATAACCCGAAACCATACTGGCCAGGAATAGCAAATCCA
droYak2	AGATATAACCGAGAAGCAATACCCAATAGTAGCCAACTCTCTCGCTCTCTCTGCGTCTCTCTATGTGTATGTATGTATTTCGCTATCCATATATGTATAT-CCATGTCAGAGAGCCAGGATCGGTTGAGACCATACT------------------ATATCTATATAACCCGAAACCATACTGGCCAGGAATAGCAAATCCA
droEre2	AGATATAACCCAAAAGAAATACCGAATAGTAGCCAACTCTCTCGCTCTC----------TCTATGTGTATGTATGTATTTCGTTATCCATATATGTATAT-CCATGTCAGAGAGCCAGGATCGGTTGAGACCATACT------------------A------TATAACCCAAAACCATACTGGCCAGGAATAGCAAGTCCA

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

Small RNA-seq read pileup

Species

Alignment

droSim1

AGC----------------------------------------------------GA----------------------------A-ATTTTTCGACATTTCT----------ATTTAAAG---------------TACATATAGACATTACTATATACATACATATAT--ACTAT----------------------------ACCTTAT--------------------------ATACATGAAT-----------------ATTTATATACATATTT---------------------------AATATACGACGTTTACAAGCTAAGTTGGGTATTC--A----TTTTAT-ACGA----A----GCGTGAATCGA

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

AGATAT-TA----CCCAGA----AGCAA---------TATCCAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCT------------ATG----------------------------------------TGAATGTATGTAT--CTTGC----------------------------TATCCAT--TTATGTATATCCATA---TCAGAGAGCCAGGATT-----------------GGTTGAGACCATACGAT------A----T-AACCCGAAAC---C-------------------------------AT--A----CTGGCC-AGGA----A----TAGCAAATCCA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
......................................................................................................................................................................................................................TATGTATATCCATA---TCAGAGAGC...........................................................................................................................................	23	3	5.00	2.67	0.67	1.67
.................................................................................................................................................................................................................................ATA---TCAGAGAGCCAGGATT-----------------G..................................................................................................................	20	3	0.33	0.00	0.33	0.00
......................................................................................................................................................................................................................TATGTATATCCATA---TCAGAGAG............................................................................................................................................	22	3	0.33	0.00	0.00	0.33
................................................................................................TCTCT------------ATG----------------------------------------TGAATGTATGTAT--................................................................................................................................................................................................................	21	3	0.33	0.33	0.00	0.00
..............................................................................................................................................................................................................................................GCCAGGATT-----------------GGTTGAGACCATACGAT------............................................................................................	26	3	0.33	0.00	0.33	0.00
....................................................................................................................................................................................................................................................................................................................................................T--A----CTGGCC-AGGA----A----TAGCA......	18	2	0.50	0.00	0.50	0.00
..................................................................................................................................................................................................................................TA---TCAGAGAGCCAGGATT-----------------GGTTGA.............................................................................................................	24	3	0.33	0.33	0.00	0.00
.............................................................................................................................................................................................................................ATCCATA---TCAGAGAGCCAGGAT.....................................................................................................................................	22	3	0.33	0.00	0.33	0.00
......................................................................................................................................................................................................................TATGTTTATCCATA---TCAGAGAGC...........................................................................................................................................	23	3	0.33	0.00	0.33	0.00
............................................................................................................................................................................................................................................GAGCCAGGATT-----------------GGTTGAGACCATA......................................................................................................	24	3	0.33	0.33	0.00	0.00
............................................................................................................................................................................................................................................GATCCAGGATT-----------------GGTTGAGACCATA......................................................................................................	24	3	0.33	0.33	0.00	0.00
.................................................................................................................................................................................................................................ATA---TCAGAGACACAGGATT-----------------...................................................................................................................	19	3	0.33	0.00	0.33	0.00

droYak2

AGATAT-AA----CCGAGA----AGCAA---------TACCCAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCTCTGCGTCTCTCTATG----------------------------------------TGTATGTATGTAT--TTCGC----------------------------TATCCAT--ATATGTATATCCATG---TCAGAGAGCCAGGATC-----------------GGTTGAGACCATACTATATCTATA----T-AACCCGAAAC---C-------------------------------AT--A----CTGGCC-AGGA----A----TAGCAAATCCA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..........................................................................................................................................................................................................................................GAGAGCCAGGATC-----------------GGTTGAGACCA........................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
....AT-AA----CCGAGA----AGCAA---------TACCCAAT----A.........................................................................................................................................................................................................................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................................................................................G---TCAGAGAGCCAGGATC-----------------GGTTGA.............................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

AGATAT-AA----CCCAAA----AGAAA---------TACCGAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCTCT----------ATG----------------------------------------TGTATGTATGTAT--TTCGT----------------------------TATCCAT--ATATGTATATCCATG---TCAGAGAGCCAGGATC-----------------GGTTGAGACCATACTAT------A----T-AACCCAAAAC---C-------------------------------AT--A----CTGGCC-AGGA----A----TAGCAAGTCCA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
....AT-AA----CACAAA----AGAAA---------TACCGA................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................................GCCAGGATC-----------------GGTTGAGACCAT.......................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................ATG----------------------------------------TGTATGTATGTAT--GG..............................................................................................................................................................................................................	18	9	0.11	0.00	0.00	0.00	0.11
............................................................................................................................................................................................................................................GAGCCAGGATC-----------------GGTTGATACCAT.......................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00

droEug1

CT---------------------------------------------------------------------------------------CTCTC--TCTCT------------ATC-------TCTC---------TCTCTCTGTCTGTTCTTATATATATATATATAC--ATTCT-----------------------A-TATATACCAT---------------------------------ATT-----------------TAT--------------------ATATTT-AATT---------ACCAAAAACAAAATACAAAATC---CAAAA------ACAAATGCAAA-ATGA----A----AACAAAATCAA

Size

Hit Count

Total Norm

droBia1

TATATAGATACAATGCA------------------------AAAG----TGTTGCCAATTACTTCATTAATGTATGAGGTAGAGAT-GT--------------------------------------------------------------------------------------------------------------------CTGCAT--ATGTGTGGGTGAGTA---TGTGTGAGC------T-----------------TATTAATAACATTTTACTCGTT-C----G-TATTCGTAAC---C-------------------------------GT--A----A--TCC-GTGA----T----ACGTAATTTAT

Size

Hit Count

Total Norm

droTak1

AGATAT-AT----GCCAAAAAAAAGCTT----AAA--AATTGAAC----AATATCAA--------------------------TAT-ATCTCTCGCTCTCT------------ATG----------------------------------------TGAATGTATGTAT--GTTGTAAT-------------------------TGAATAT--ATATGTATATCCATC---TCAGAGAGCCAGGATCGAT---------CGATCGGTTGAGACTATACTAT------A----T-AAACTATA-----T-------------------------------TT--A----CTGGCC-AGGA----A----TAGCGAATC--

Size

Hit Count

Total Norm

droEle1

AAATAG-TCCACATCCAG--------------------ATCCAAT----AGTAGCCA----------------------------A-CTCTCTCGCTCTCTCT----------ATG----------------------------------------TGTATGTATGTAT--GTTGT----------------------------AACCCGT--ATATGTATATCCATG---TCAGAGACCCAGGATT-----------------GGTTAAGACCATACTATATATATA--TAT-AATCCAAAAC---T--------------------AAAATAAAAACAT--A----CTGGCC-AGGA----A----TAGCAAATCCA

Size

Hit Count

Total Norm

droRho1

AGATAT-AA----TCCAA--------------------ATCCAAT----AACAGCCA----------------------------A-CTCTCTCGCTCTCTCTGCGTCTCTCTATG----------------------------------------TGTATGTATGTAT--GTTGT----------------------------AACCCGT--ATATGTATATCCATG---TCAGAGAGCCAGGAAA-----------------GGTTGAGTCCAAACTAT------A----A-AACCCAAAGC---T-------------------------------AC--A----CTGGCC-AGGA----A----CAGCAAATCCA

Size

Hit Count

Total Norm

droFic1

AGAAAA-AGCCGATCCAAA----ACTTA---------TATCCAAT----AGTACCCG----------------------------A-CTCTCTCGCTCTCTTT----------ATG----------------------------------------TGTATGTATGTAT--GTTGT----------------------------ACCCCGT--ATATGTATATTCATG---TTAGAGAGCCAGGATC-----------------GGTCGATACCATACTATTTCTGTT----TAAACCAAAAACCAAT-------------------------------ACTGA----CTGGCC-AGGA--ACA----TAGCAAATCCA

Size

Hit Count

Total Norm

droKik1

AAATAC-AA----AAAAGA----AATCC----AAAAATAAATCGC----AGTCTTGA----------------------------AACTTTGTCTA-CTTTCC----------GTT----------------TCTTTTTTTTCTT--------CCATTTTTATTTGT----ATTTT-----------------------AT---TTTTGGTGG-AACGCA-----------TCCTAGTGCCA------------------------------------------------------AAAGCAAC---C-------------------------------GC--A----CAGAAT-CGGAAAACG----CAGCAAGGATA

Size

Hit Count

Total Norm

droAna3

CT---------------------------------------------------------------------------------------CTCTC--TCTCTCTGTGTCTCTCTAAA----------------------------T--------GCATGTATGTATGT----GTTGT-----------------------AT---TATCCGTATATATGTATATCCATG---TTAGAGAGCCAGGACG-----------------GGTTGAGATT---------------------GCCCAAGA----------------------------------------A----CTGGCCTAGGA----A----TAGCAAATC-A	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..........................................................................................................................................................................................................................................GAGAGCCAGGACG-----------------GGTTGA.............................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................CTCTC--TCTCTGTGTGTCGCTCT..........................................................................................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................................GATT---------------------GCGCAATA----------------------------------------A----CTGGCCT........................	20	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................................................................................................................................................GA----------------------------------------A----CTGGCCTAGGA----A----TAGCAAAT...	23	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................GCATGTATGTATGT----GTTGT-----------------------....................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..........................................................................................................................................................................................................................................GAGAGCCAGGACG-----------------GGTTGAGATT---------------------G...................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................CTCTC--TCTCTGTGTGTCGCT............................................................................................................................................................................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
...........................................................................................CTC--TCTCTCTGTGTGTCGCT..........................................................................................................................................................................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
.................................................................................................................................................................GTATGT----GTTCT-----------------------Ax---TATCCG.........................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..................................................................................................................GA----------------------------T--------GTATGTATGTATGT----GT..............................................................................................................................................................................................................	19	3	0.33	0.33	0.00	0.00	0.00
........................................................................................................................................................................................................................TGTATATCCATG---TTAGAGAGC...........................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00

droBip1

CT---------------------------------------------------------------------------------------CTCTC--TCTCTCTGTGCCTCTCTAAG----------------------------------------TGCATGTATGTATGTGTTGT-----------------------AT---TATCCGTATATATGTATATCCATG---TTAGAGAGCCAGGACG-----------------GGTTGAGATT---------------------GCCCAAGA----------------------------------------A----CTGGCCTAGGA----A----TAGCAAATC-A

Size

Hit Count

Total Norm

dp4

GAATAA-TC----CATA-A----ACAAA---------TATCTA------TGTAGTCA----------------------------C-ATCTATCTCTCTCTCT----------ATA----------------------------------------TATCTCTCTCTCT--CTTTC----------------------------TTTATTT--GTACATGTATTTATT---TCATGGGTTTAGTTTT-----------------GC---AAATGGTATAAA------A----C-ATCTCCAAAA---T-------------------------------AC--A----TT-----------------------------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.............................................................................................................................................................................................................................................................................................................................................................G-----------------------------	24	2	0.50	0.50	0.00	0.00	0.00

droPer1

TAATAT-AT----TGGAGT----AGCAA---------TATCTATT----TGTATTCA----------------------------G-ATTTGTATTTATTT------------ATG------------------------------TGTTTGTGGTGATACAGATAT-------------------------------------ATAGTAT--ATATAGAAAT--ATA---TTTTAAAATCA---TA-----------------GGTACATACAGTATATT------G----T-ATCCCTATCC---A-------------------------------AT--G----C----A-TATG----T----GAACGTACTTA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........................................................A----------------------------G-GTTTGTAGTTATTT------------AT........................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

AAATAT-CA----TACCCA-----AAAA---------TATATACT----ACTACACA----------------------------ACCTCTCTCTCTCTCT------------CTA----------------------------------------TCTATCTATCTAT--CTTTGAACATAAAATGTACCTATACTAAAACAAAAACTCT--ATATCTAAATCGTTG---TGC-TTACCATTCATT-----------------TTCTACTACTATACTAT------A----T-AGGGCGAAAC---------------------------------------------------------------------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......................................................................................CTCTCTATCTCTCT------------CGA----------------------------------------TCTATCT........................................................................................................................................................................................................................	24	1	2.00	0.00	0.00	2.00	0.00
........................................................................................TCTGTCTGTCTCT------------CTA----------------------------------------TCT............................................................................................................................................................................................................................	19	43	0.02	0.00	0.00	0.00	0.02
............................................................................................TCTCTCGAT------------CTA----------------------------------------TCTATC.........................................................................................................................................................................................................................	18	16	0.06	0.00	0.00	0.00	0.06
...............................................................................................CTCTAT------------CTA----------------------------------------TCTATCTATCTAT--CAT.............................................................................................................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
................................................................................................TCTCT------------CGA----------------------------------------TCTATCTATC.....................................................................................................................................................................................................................	18	16	0.06	0.00	0.00	0.00	0.06
....................................................................................................T------------CTC----------------------------------------TCGATCTATCTAT--C...............................................................................................................................................................................................................	18	16	0.06	0.00	0.00	0.00	0.06
.......................................................................................CGCTCTCTCTCTCT------------CTA----------------------------------------T..............................................................................................................................................................................................................................	18	36	0.03	0.00	0.03	0.00	0.00
.......................................................................................CTCTCTCTCTCTCA------------CTA----------------------------------------TAT............................................................................................................................................................................................................................	20	48	0.02	0.00	0.02	0.00	0.00

droVir3

ATA-----A----CCCAAA----AGATA---------CCTCAATT----TGCATA-----------------------------------------TATATCTATGTCTATATAGA----------------------------------------TATATACATACAT--ATATA----------------------------TATACAT--ATATATATATAAATA---TATGTGTGCGTGCATT---------------------ATCGTCTTGTGAC------T----A-GGTCCAGAAC---T-------------------------------TT--A----CAGGTG-CGCA----G----TGTCGAAATCA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.......................................................................................................................................................................................................................ATATATATGCATA---TATGTGTGCGT.........................................................................................................................................	24	4	0.25	0.00	0.00	0.25	0.00	0.00

droMoj3

TGATGC-CA----CCCAG--------------------CCCCCAC----CGCCTCCT----------------------------G-CTCCCTCCCTCTCTAT--GTTTATATGTG----------------------------------------TATATGTGTGTG------------------------------------TGTCTGT--GTGTTTGTGTCCCTTCGATTGGCGTGCCTGAATGGCTGTGAAAACACAGCCAGTTGCAGCT-------------------------GTATC---C-------------------------------AC--A----A--TCA-TTAT----CACAAAAGCAAACTAC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...............................................................................................................................................................ATGTGTTTG------------------------------------TGTATGT--GTG...................................................................................................................................................................	19	45	0.04	0.02	0.02	0.00	0.00
.............................................................................................................ATATGTG----------------------------------------TATCTGTGTGTG------------------------------------T..............................................................................................................................................................................	20	28	0.07	0.07	0.00	0.00	0.00
.................................................................................................................................................................GTGTGTG------------------------------------TGGCTGT--GTGG..................................................................................................................................................................	18	18	0.06	0.06	0.00	0.00	0.00
.................................................................................................................................................................ATGCGTG------------------------------------TGTCTGT--GTGT..................................................................................................................................................................	18	48	0.02	0.00	0.02	0.00	0.00
.............................................................................................................GTAGGTG----------------------------------------TATATGTGTGTG------------------------------------TG.............................................................................................................................................................................	21	7	0.14	0.14	0.00	0.00	0.00
...........................................................................................................TTGTAGGTG----------------------------------------TATATGTGTGTG------------------------------------...............................................................................................................................................................................	21	3	0.33	0.33	0.00	0.00	0.00
...............................................................................................................................................................ATGTGTGTG------------------------------------TGTATGT--GTGTTT................................................................................................................................................................	22	34	0.03	0.03	0.00	0.00	0.00
..............................................................................................................................................................TATGTGTGTG------------------------------------TGTCTGA--GTGT..................................................................................................................................................................	21	24	0.04	0.04	0.00	0.00	0.00
..............................................................................................................TATGTG----------------------------------------TATATGTGTGTG------------------------------------TAA............................................................................................................................................................................	21	4	0.25	0.25	0.00	0.00	0.00
................................................................................................................................................................TCTGTATG------------------------------------TGTCTGT--GTGT..................................................................................................................................................................	19	49	0.02	0.02	0.00	0.00	0.00
...............................................................................................................ATGTG----------------------------------------TATGTGGGTGTG------------------------------------TGT............................................................................................................................................................................	20	30	0.03	0.00	0.03	0.00	0.00
.............................................................................................................................................................ATATGTGTATG------------------------------------TGTATGT--GTG...................................................................................................................................................................	21	29	0.03	0.03	0.00	0.00	0.00
..............................................................................................................................................................TATGTGAGTG------------------------------------TGTTTGT--GT....................................................................................................................................................................	19	30	0.03	0.03	0.00	0.00	0.00
................................................................................................................TCTG----------------------------------------TATGTGTGTGTG------------------------------------TGTC...........................................................................................................................................................................	20	44	0.02	0.02	0.00	0.00	0.00
.................................................................................................................GTG----------------------------------------TATATGTGTGTG------------------------------------TGTGTA.........................................................................................................................................................................	21	38	0.03	0.03	0.00	0.00	0.00
...................................................................................................................................................................GTGxG------------------------------------TGTCTGT--GTGTTTGTGT............................................................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00
.............................................................................................................ATACGTG----------------------------------------TATGTGTGTGT....................................................................................................................................................................................................................	18	46	0.02	0.00	0.02	0.00	0.00
..............................................................................................................................................................TATGTGTGTC------------------------------------TGTGTGT--GTGTTT................................................................................................................................................................	23	23	0.04	0.04	0.00	0.00	0.00
.................................................................................................................................................................GTGAGTG------------------------------------TGTCTGT--GCGTTTG...............................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...................................................................................................................G----------------------------------------TATATGTGTGTG------------------------------------TGTATGC--......................................................................................................................................................................	20	12	0.08	0.00	0.08	0.00	0.00
................................................................................................................................................................TGTGTGTG------------------------------------TGTCTGT--GAGA..................................................................................................................................................................	19	15	0.07	0.00	0.07	0.00	0.00
................................................................................................................................................................TGTGTGTG------------------------------------TGTCTGT--TTC...................................................................................................................................................................	18	43	0.02	0.00	0.02	0.00	0.00
................................................................................................................................................................TGTGTGTG------------------------------------TGTATGT--GGGTTT................................................................................................................................................................	21	18	0.06	0.06	0.00	0.00	0.00
................................................................................................................TGTG----------------------------------------TCTATGTGTGTG------------------------------------TGT............................................................................................................................................................................	19	11	0.09	0.09	0.00	0.00	0.00
......................................................................................................................................................................TG------------------------------------TGTGTGT--GTGTTTGTGTTC..........................................................................................................................................................	21	30	0.03	0.03	0.00	0.00	0.00
............................................................................................................TATATATG----------------------------------------TATATGTGCGTG------------------------------------...............................................................................................................................................................................	20	33	0.03	0.03	0.00	0.00	0.00
...............................................................................................................ATGTG----------------------------------------TGTATGTGTGTG------------------------------------CGT............................................................................................................................................................................	20	34	0.03	0.00	0.00	0.03	0.00
...............................................................................................................................................................ATGAGTGCG------------------------------------TGTCTGT--GTGT..................................................................................................................................................................	20	3	0.33	0.33	0.00	0.00	0.00
...............................................................................................................................................................GAGTGTGxG------------------------------------TGTCTGT--GTGT..................................................................................................................................................................	19	14	0.07	0.00	0.07	0.00	0.00
..............................................................................................................TATATG----------------------------------------TATATGTGTGTG------------------------------------T..............................................................................................................................................................................	19	38	0.03	0.03	0.00	0.00	0.00
.............................................................................................................ATATGTG----------------------------------------TATGTGTATGTG------------------------------------TG.............................................................................................................................................................................	21	29	0.03	0.03	0.00	0.00	0.00
................................................................................................................TGTG----------------------------------------TATATGTGTGTG------------------------------------TGCA...........................................................................................................................................................................	20	9	0.11	0.11	0.00	0.00	0.00
............................................................................................................TGTATGTG----------------------------------------TATATTTGTGT....................................................................................................................................................................................................................	19	19	0.05	0.00	0.00	0.00	0.05
..............................................................................................................TATGTA----------------------------------------TTTATGTGTGTG------------------------------------T..............................................................................................................................................................................	19	50	0.02	0.02	0.00	0.00	0.00
.......................................................................................................................................................................................................................................................................CAGTTGCAGCT-------------------------GTAGC---C-------------------------------GC--A----...............................	20	2	0.50	0.00	0.00	0.00	0.50
...............................................................................................................ATGTG----------------------------------------TATGTGTGTGTG------------------------------------TG.............................................................................................................................................................................	19	33	0.03	0.00	0.00	0.00	0.03
..............................................................................................................................................................TGTGxGTGTA------------------------------------TGTCTGT--GTGT..................................................................................................................................................................	20	21	0.05	0.00	0.05	0.00	0.00
...............................................................................................................ATGTG----------------------------------------TATATGTGTGTG------------------------------------TGCGT..........................................................................................................................................................................	22	6	0.17	0.17	0.00	0.00	0.00
...............................................................................................................ATGTG----------------------------------------TATATGTGTGTG------------------------------------TGTGC..........................................................................................................................................................................	22	9	0.11	0.11	0.00	0.00	0.00

droGri2

AAAAAC-AA----AAAACA----AACGAAGTAACA--GCCCAAGCCGACAATGGCTG----------------------------A-ATATATA--------------------TGTTATGTATTTGTATTATTGTCGTGTATA--------TATATCTATATATGTAT--ATTAC-----------------------ACTATATACTAT----ATGTAT------------------------------------------------------------------A----T-ATATATAGAC---A-------------------------------AT--G----TCTGAT-GGCT----A----TGCCAAAGCCA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:19:26 EDT

dme-mir-4961

chrX:1267655-1267788 +

Known_mirbase

three_prime_UTR

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup