dme-mir-4912- Best orthologs

dme-mir-4912	chr2L:4829980-4830039 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 4830017-4830039
   star strand at position 4829980-4830001
   mutations
   read mismatches

Notes: droEle slice acceptor appears incorrect but there are other GT's downstream

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:4829965-4830054 -		1	CATTCGCAGCTTTAAGTGAGTAGTCGT---ATGTTTATTAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT-TTACTTTCTATAAAT----------------------------------------------------T-AATGT--CC-----ACTACTTTTAGTCTCTATGACGATGA
droSim1	chr2L:4699797-4699886 -	LASTZ	5	CATTCGCAGCTTTAAGTGAGTAATCGT---ATGTTTATTAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT-TCACTTTCTATAAAC----------------------------------------------------T-AATTT--GC-----ACTACTTGTAGTCTCTATGACGACGA
droSec1	super_5:2925673-2925762 -	LASTZ	5	CATTCGCAGCTTTAAGTGAGTAATCGT---ATGTTTATTAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT-TCACTTTCTATAAAC----------------------------------------------------T-AATTT--GC-----ACTACTTGTAGTCTCTATGACGACGA
droYak2	chr2L:4839794-4839887 -	LASTZ	5	CATTCGCAGCTTTAAGTGAGTAAAACT---ATGTCTATTA--------------------------------------------GGT---------------------------------------------------------------------------------------------------------------------GA----AAT-TAACTTTCTATAAAT----------------------------------------------------T-ACTTT--TC-----TTTATTTTTAGTCTATATGACGACGA
droEre2	scaffold_4929:4910720-4910828 -	LASTZ	5	CATTCGCAGTTTTAAGTGAGTAAAATT---AGGTTTAATTT--------------------------------GG-TTTATTA-GGAGAA--------------------------------------------T-TTTAA------------------------------------------------------------AATT----------A-C-TTTTTTAAAT----------------------------------------------------T-GCTTT--TC-----ATTATTTGCAGTCTCTATGACGACGA
droEug1	scf7180000409005:708020-708177 -	LASTZ	5	AATTCGCAGCTTCAAGTAAGTATATGT---ATATATGTATATATTATTC-------------------------------------------------------AAATCGA------------------------------TGA--------------------------------------------TTAAATATAGATTAG----GTCAATTC--------------C-------TATTTGAATCCATTTATTCATAAAGGTTCCTTTTTATTCAAAA-TA--TTCCTAT-----TTTATTTTCAGACTCTACGACGACGA
droBia1	scf7180000302188:1402569-1402698 -	LASTZ	5	CATACGCAGTTTCAAGTGAGTGGGGAT---TT----------------------TGGGGAG-------------------------------------------------------------------------TCATTAAAGC-CTTTAAAGATGTCGAACTTTATGGTA-----------------TTAAG--------C------------AAGCAT--------------------------TTAATGGA-------------------------TT-T-ATG----AACGTATATACTTCCAGACTCTACGACGACGA
droTak1	scf7180000415705:123599-123784 -	LASTZ	5	CATAAAAAGCTTCAAGTGAGTGGGGATAGCAAGTTTATA---------------------------GCACATAGGTTCTATTA---------------------CAA---------------------------CAGATCTACATATCTAAAGTCATTGAAATTT--GGCCTAAAATTGCTTTTATATTAGTTATTTTATTA----------------------------------------------------ACATAAATGATAAAGCTTTAATAAAT-TC--TCCCCAT-----TGTAATTCCAGACTCTACGACGACGA
droEle1	scf7180000491046:2483308-2483395 -	LASTZ	5	GATTTACAT--TCAATCAAGTTTTTGT---TC------------------------------------------------------------------------------------------------------------AAGT--------------------------------------------TTAAGTACTTATTGA----CTCAATTT--------------CACT-----------------------------------------------------TT--TT-----TAAATTTATAGACTCTATGACGACGA
droRho1	scf7180000768274:29807-29997 +	LASTZ	5	CATTCGTACCTTCAAGTGAGTGGGGAT---TTGGGAA-----------------------TTCATTCCAAATAGATTTTATAAAGGG-GACATTTATAATGTTCAAATTCAAGACCCCCAGACAATTTTGTTCCTTTTTAAAGTTATTTATTTC------------------------------AAGTTCGTTAATTTACTAA----TTTAATTT--------------TGCC-------------------------------------------------TTACT----A----ATGTTTTTCCAGGCTCTTCGACGATGA
droFic1	scf7180000453842:1425509-1425600 +	LASTZ	5	TATTCGCACCTTCAAGTAAGTGGTTGT---ACATT----------ATAC-------------------------------------------------------A--------------------------------------------------------------------------------------AATATCGA--AATGAGTTCAATAC--------------------------------------------------------------------CATTC--CT-----ATTATCTCCAGGCTTTATGACGACGA
droKik1	scf7180000302472:3508957-3509047 -	LASTZ	5	CATACGCACCTTCAAGTGAGTCTAATTATTA-------------------------------------------------------------------------------------------------------------AC--------------------------------------------------------------C------------------------TCTTTTTTTGTAT----GTTTTA-------------------------AATT-CAGTCT--CT-----GATCCTTGCAGCCTCTATGATGATGA
droAna3	scaffold_12916:9399289-9399374 -	LASTZ	5	CATTCGAAGCTTCAAGTATGTTAAGAA---AT----------------------CCA-----------------------------------------------------------------------------C------------------------------------------------------------------GATTT----TTTTA------------------------TAT----T------TTCATACA---------------AA---------------ATTCA-TTTTTTCAGCTTGTACGACGACGA
droBip1	scf7180000396535:1966691-1966779 -	LASTZ	5	CATTAGGAGTTTCAAGTGGGTTAAGAA---AT------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCATAGCTTT----ACTTA------------------------TAT----T------TTCATTAA-----------------------GA-------ATTCG-TTATTTCAGCCTGTACGATGACGA
dp4	chr4_group3:3587822-3587933 -	LASTZ	5	CATACGCACATTTAAGTGAGTAGGAAA---AA----------------------TCG-----------------------------------------------------------------------------TTGTTTAAGCTGTTTACTGC--------------------------------------------------------GATTG--------------TACTTTACTGTAT----TTACTGTA-------------------------TT-TGGTA----C-----ATGCCTTGCAGCCTCTATGATTCCGA
droPer1	super_1:5067398-5067508 -	LASTZ	5	CATACGCACATTTAAGTGAGTAGGAAA---AT-----------------------CG-----------------------------------------------------------------------------CTGTTTAAGCTGTTTACTGC--------------------------------------------------------GATTG--------------TACTTTACTGTAT----TTACTGTA-------------------------TT-TGGTA----C-----ATGCCTTGCAGCCTCTATGATTCCGA
droWil1	scaffold_180772:1562219-1562313 -	LASTZ	5	CATTAAAACGTTTAAGTGAGTAGTAAA---TC-------------TTGGTTAACCCA-----------------------------------------------------------------------------A------------------------------------------------------------------TAC------GATT--------------------------------TCATTGGCGTTT--------------------------ATA----AATTCCT-CCACCTTAGCCTTTACGACGACGA
droVir3	scaffold_12963:8507047-8507138 +	LASTZ	5	CATACGCACATTCAAGTATGTCAACTA---T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT------------AAAATGCTTTGCAGTAC----TCTTTAAA-------------------------TA-TTGTAT--TC-----TCATTCGATAGCCTCTATGACGACGA
droMoj3	scaffold_6500:1118880-1118971 +	LASTZ	5	CATACGTACATTCAAGTAAGCCCAATTCGCCG------------------------------------------------------------------------------------------------------------AC--------------------------------------------------------------GT----TAT------------------------GGTAT----T------CATATACA---------------AATGCT-AATCA--TT-----TATCCCTTTAGCCTCTATGACGACGA
droGri2	scaffold_15252:11699277-11699378 +	LASTZ	5	CATACGCACCTTCAAGTATGTGCAATGGGTAA--------------------ACCAT-----------------------------------------------------------------------------ATGTGAGAGATTTAAACCTT--------------------------------------------------------AATTT--------------TACTTTCCTATAT-----------------------------------------------------CTG-CCCAAACAGTCTGTACGATGACGA

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	CATTCGCAGCTTTAAGTGAGTAGTCGT---ATGTTTATTAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT-TTACTTTCTATAAAT----------------------------------------------------T-AATGT--CC-----ACTACTTTTAGTCTCTATGACGATGA
droSim1	CATTCGCAGCTTTAAGTGAGTAATCGT---ATGTTTATTAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT-TCACTTTCTATAAAC----------------------------------------------------T-AATTT--GC-----ACTACTTGTAGTCTCTATGACGACGA
droSec1	CATTCGCAGCTTTAAGTGAGTAATCGT---ATGTTTATTAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT-TCACTTTCTATAAAC----------------------------------------------------T-AATTT--GC-----ACTACTTGTAGTCTCTATGACGACGA
droYak2	CATTCGCAGCTTTAAGTGAGTAAAACT---ATGTCTATTA--------------------------------------------GGT---------------------------------------------------------------------------------------------------------------------GA----AAT-TAACTTTCTATAAAT----------------------------------------------------T-ACTTT--TC-----TTTATTTTTAGTCTATATGACGACGA
droEre2	CATTCGCAGTTTTAAGTGAGTAAAATT---AGGTTTAATTT--------------------------------GG-TTTATTA-GGAGAA--------------------------------------------T-TTTAA------------------------------------------------------------AATT----------A-C-TTTTTTAAAT----------------------------------------------------T-GCTTT--TC-----ATTATTTGCAGTCTCTATGACGACGA
droEug1	AATTCGCAGCTTCAAGTAAGTATATGT---ATATATGTATATATTATTC-------------------------------------------------------AAATCGA------------------------------TGA--------------------------------------------TTAAATATAGATTAG----GTCAATTC--------------C-------TATTTGAATCCATTTATTCATAAAGGTTCCTTTTTATTCAAAA-TA--TTCCTAT-----TTTATTTTCAGACTCTACGACGACGA
droBia1	CATACGCAGTTTCAAGTGAGTGGGGAT---TT----------------------TGGGGAG-------------------------------------------------------------------------TCATTAAAGC-CTTTAAAGATGTCGAACTTTATGGTA-----------------TTAAG--------C------------AAGCAT--------------------------TTAATGGA-------------------------TT-T-ATG----AACGTATATACTTCCAGACTCTACGACGACGA
droTak1	CATAAAAAGCTTCAAGTGAGTGGGGATAGCAAGTTTATA---------------------------GCACATAGGTTCTATTA---------------------CAA---------------------------CAGATCTACATATCTAAAGTCATTGAAATTT--GGCCTAAAATTGCTTTTATATTAGTTATTTTATTA----------------------------------------------------ACATAAATGATAAAGCTTTAATAAAT-TC--TCCCCAT-----TGTAATTCCAGACTCTACGACGACGA
droEle1	GATTTACAT--TCAATCAAGTTTTTGT---TC------------------------------------------------------------------------------------------------------------AAGT--------------------------------------------TTAAGTACTTATTGA----CTCAATTT--------------CACT-----------------------------------------------------TT--TT-----TAAATTTATAGACTCTATGACGACGA
droRho1	CATTCGTACCTTCAAGTGAGTGGGGAT---TTGGGAA-----------------------TTCATTCCAAATAGATTTTATAAAGGG-GACATTTATAATGTTCAAATTCAAGACCCCCAGACAATTTTGTTCCTTTTTAAAGTTATTTATTTC------------------------------AAGTTCGTTAATTTACTAA----TTTAATTT--------------TGCC-------------------------------------------------TTACT----A----ATGTTTTTCCAGGCTCTTCGACGATGA
droFic1	TATTCGCACCTTCAAGTAAGTGGTTGT---ACATT----------ATAC-------------------------------------------------------A--------------------------------------------------------------------------------------AATATCGA--AATGAGTTCAATAC--------------------------------------------------------------------CATTC--CT-----ATTATCTCCAGGCTTTATGACGACGA
droKik1	CATACGCACCTTCAAGTGAGTCTAATTATTA-------------------------------------------------------------------------------------------------------------AC--------------------------------------------------------------C------------------------TCTTTTTTTGTAT----GTTTTA-------------------------AATT-CAGTCT--CT-----GATCCTTGCAGCCTCTATGATGATGA
droAna3	CATTCGAAGCTTCAAGTATGTTAAGAA---AT----------------------CCA-----------------------------------------------------------------------------C------------------------------------------------------------------GATTT----TTTTA------------------------TAT----T------TTCATACA---------------AA---------------ATTCA-TTTTTTCAGCTTGTACGACGACGA
droBip1	CATTAGGAGTTTCAAGTGGGTTAAGAA---AT------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCATAGCTTT----ACTTA------------------------TAT----T------TTCATTAA-----------------------GA-------ATTCG-TTATTTCAGCCTGTACGATGACGA
dp4	CATACGCACATTTAAGTGAGTAGGAAA---AA----------------------TCG-----------------------------------------------------------------------------TTGTTTAAGCTGTTTACTGC--------------------------------------------------------GATTG--------------TACTTTACTGTAT----TTACTGTA-------------------------TT-TGGTA----C-----ATGCCTTGCAGCCTCTATGATTCCGA
droPer1	CATACGCACATTTAAGTGAGTAGGAAA---AT-----------------------CG-----------------------------------------------------------------------------CTGTTTAAGCTGTTTACTGC--------------------------------------------------------GATTG--------------TACTTTACTGTAT----TTACTGTA-------------------------TT-TGGTA----C-----ATGCCTTGCAGCCTCTATGATTCCGA
droWil1	CATTAAAACGTTTAAGTGAGTAGTAAA---TC-------------TTGGTTAACCCA-----------------------------------------------------------------------------A------------------------------------------------------------------TAC------GATT--------------------------------TCATTGGCGTTT--------------------------ATA----AATTCCT-CCACCTTAGCCTTTACGACGACGA
droVir3	CATACGCACATTCAAGTATGTCAACTA---T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT------------AAAATGCTTTGCAGTAC----TCTTTAAA-------------------------TA-TTGTAT--TC-----TCATTCGATAGCCTCTATGACGACGA
droMoj3	CATACGTACATTCAAGTAAGCCCAATTCGCCG------------------------------------------------------------------------------------------------------------AC--------------------------------------------------------------GT----TAT------------------------GGTAT----T------CATATACA---------------AATGCT-AATCA--TT-----TATCCCTTTAGCCTCTATGACGACGA
droGri2	CATACGCACCTTCAAGTATGTGCAATGGGTAA--------------------ACCAT-----------------------------------------------------------------------------ATGTGAGAGATTTAAACCTT--------------------------------------------------------AATTT--------------TACTTTCCTATAT-----------------------------------------------------CTG-CCCAAACAGTCTGTACGATGACGA

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

CATTCGCAGCTTTAAGTGAGTAATCGT---ATGTTTATTAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT-TCACTTTCTATAAAC----------------------------------------------------T-AATTT--GC-----ACTACTTGTAGTCTCTATGACGACGA

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

CATTCGCAGCTTTAAGTGAGTAAAACT---ATGTCTATTA--------------------------------------------GGT---------------------------------------------------------------------------------------------------------------------GA----AAT-TAACTTTCTATAAAT----------------------------------------------------T-ACTTT--TC-----TTTATTTTTAGTCTATATGACGACGA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........GCTTTAAGTGACTAAAAG.........................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GTGAGTAAAACT---ATGACTAAT............................................................................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................................................................................................................................................................................TTCTAGACAT----------------------------------------------------T-ACTTT--TC-----T.........................	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

CATTCGCAGTTTTAAGTGAGTAAAATT---AGGTTTAATTT--------------------------------GG-TTTATTA-GGAGAA--------------------------------------------T-TTTAA------------------------------------------------------------AATT----------A-C-TTTTTTAAAT----------------------------------------------------T-GCTTT--TC-----ATTATTTGCAGTCTCTATGACGACGA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.........TTTTGAATGAGTAAAATT---.....................................................................................................................................................................................................................................................................................................	18	1	4.00	0.00	0.00	0.00	4.00
.......ATTTTTAAGxGAGTAAAATT---.....................................................................................................................................................................................................................................................................................................	19	1	3.00	0.00	0.00	0.00	3.00
.....................AAAGCT---AGGTTTAATTT--------------------------------GG-T......................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
....................TAAAGCT---AGGTTTAATTT--------------------------------GG-T......................................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...................GTAAGATT---AGCTTTAATT...........................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

AATTCGCAGCTTCAAGTAAGTATATGT---ATATATGTATATATTATTC-------------------------------------------------------AAATCGA------------------------------TGA--------------------------------------------TTAAATATAGATTAG----GTCAATTC--------------C-------TATTTGAATCCATTTATTCATAAAGGTTCCTTTTTATTCAAAA-TA--TTCCTAT-----TTTATTTTCAGACTCTACGACGACGA

Size

Hit Count

Total Norm

droBia1

CATACGCAGTTTCAAGTGAGTGGGGAT---TT----------------------TGGGGAG-------------------------------------------------------------------------TCATTAAAGC-CTTTAAAGATGTCGAACTTTATGGTA-----------------TTAAG--------C------------AAGCAT--------------------------TTAATGGA-------------------------TT-T-ATG----AACGTATATACTTCCAGACTCTACGACGACGA

Size

Hit Count

Total Norm

droTak1

CATAAAAAGCTTCAAGTGAGTGGGGATAGCAAGTTTATA---------------------------GCACATAGGTTCTATTA---------------------CAA---------------------------CAGATCTACATATCTAAAGTCATTGAAATTT--GGCCTAAAATTGCTTTTATATTAGTTATTTTATTA----------------------------------------------------ACATAAATGATAAAGCTTTAATAAAT-TC--TCCCCAT-----TGTAATTCCAGACTCTACGACGACGA

Size

Hit Count

Total Norm

droEle1

GATTTACAT--TCAATCAAGTTTTTGT---TC------------------------------------------------------------------------------------------------------------AAGT--------------------------------------------TTAAGTACTTATTGA----CTCAATTT--------------CACT-----------------------------------------------------TT--TT-----TAAATTTATAGACTCTATGACGACGA

Size

Hit Count

Total Norm

droRho1

CATTCGTACCTTCAAGTGAGTGGGGAT---TTGGGAA-----------------------TTCATTCCAAATAGATTTTATAAAGGG-GACATTTATAATGTTCAAATTCAAGACCCCCAGACAATTTTGTTCCTTTTTAAAGTTATTTATTTC------------------------------AAGTTCGTTAATTTACTAA----TTTAATTT--------------TGCC-------------------------------------------------TTACT----A----ATGTTTTTCCAGGCTCTTCGACGATGA

Size

Hit Count

Total Norm

droFic1

TATTCGCACCTTCAAGTAAGTGGTTGT---ACATT----------ATAC-------------------------------------------------------A--------------------------------------------------------------------------------------AATATCGA--AATGAGTTCAATAC--------------------------------------------------------------------CATTC--CT-----ATTATCTCCAGGCTTTATGACGACGA

Size

Hit Count

Total Norm

droKik1

CATACGCACCTTCAAGTGAGTCTAATTATTA-------------------------------------------------------------------------------------------------------------AC--------------------------------------------------------------C------------------------TCTTTTTTTGTAT----GTTTTA-------------------------AATT-CAGTCT--CT-----GATCCTTGCAGCCTCTATGATGATGA

Size

Hit Count

Total Norm

droAna3

CATTCGAAGCTTCAAGTATGTTAAGAA---AT----------------------CCA-----------------------------------------------------------------------------C------------------------------------------------------------------GATTT----TTTTA------------------------TAT----T------TTCATACA---------------AA---------------ATTCA-TTTTTTCAGCTTGTACGACGACGA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................................................................................................................................................................................TTT----TTTTA------------------------TAT----A------TTCTTA................................................................	18	5	0.20	0.00	0.00	0.20	0.00
......................................................CCA-----------------------------------------------------------------------------C------------------------------------------------------------------GAATT----TGTTA------------------------TAT----T------......................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......................................................TCA-----------------------------------------------------------------------------C------------------------------------------------------------------GATTT----TGTTA------------------------TAT----T------......................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................................................................................................................TAT----A------TTCATACA---------------AA---------------ATCCA-........................	19	1	1.00	0.00	0.00	0.00	1.00
......................................................CCA-----------------------------------------------------------------------------C------------------------------------------------------------------GATTT----TGTTA------------------------TAT----A------......................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droBip1

CATTAGGAGTTTCAAGTGGGTTAAGAA---AT------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCATAGCTTT----ACTTA------------------------TAT----T------TTCATTAA-----------------------GA-------ATTCG-TTATTTCAGCCTGTACGATGACGA

Size

Hit Count

Total Norm

dp4

CATACGCACATTTAAGTGAGTAGGAAA---AA----------------------TCG-----------------------------------------------------------------------------TTGTTTAAGCTGTTTACTGC--------------------------------------------------------GATTG--------------TACTTTACTGTAT----TTACTGTA-------------------------TT-TGGTA----C-----ATGCCTTGCAGCCTCTATGATTCCGA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

CATACGCACATTTAAGTGAGTAGGAAA---AT-----------------------CG-----------------------------------------------------------------------------CTGTTTAAGCTGTTTACTGC--------------------------------------------------------GATTG--------------TACTTTACTGTAT----TTACTGTA-------------------------TT-TGGTA----C-----ATGCCTTGCAGCCTCTATGATTCCGA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..............................................................................................................................................................................................................................................GTAT----TTACTGTA-------------------------TT-AAGTA----................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

CATTAAAACGTTTAAGTGAGTAGTAAA---TC-------------TTGGTTAACCCA-----------------------------------------------------------------------------A------------------------------------------------------------------TAC------GATT--------------------------------TCATTGGCGTTT--------------------------ATA----AATTCCT-CCACCTTAGCCTTTACGACGACGA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.....................................................................................................................................................................................................................T--------------------------------ACATTGGCGTTT--------------------------ATA----TATT............................	20	1	1.00	0.00	1.00	0.00	0.00

droVir3

CATACGCACATTCAAGTATGTCAACTA---T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT------------AAAATGCTTTGCAGTAC----TCTTTAAA-------------------------TA-TTGTAT--TC-----TCATTCGATAGCCTCTATGACGACGA

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

CATACGTACATTCAAGTAAGCCCAATTCGCCG------------------------------------------------------------------------------------------------------------AC--------------------------------------------------------------GT----TAT------------------------GGTAT----T------CATATACA---------------AATGCT-AATCA--TT-----TATCCCTTTAGCCTCTATGACGACGA

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CATACGCACCTTCAAGTATGTGCAATGGGTAA--------------------ACCAT-----------------------------------------------------------------------------ATGTGAGAGATTTAAACCTT--------------------------------------------------------AATTT--------------TACTTTCCTATAT-----------------------------------------------------CTG-CCCAAACAGTCTGTACGATGACGA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:20:52 EDT

dme-mir-4912

chr2L:4829980-4830039 -

Known_mirbase

mirtron

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