dme-mir-4978- Best orthologs

dme-mir-4978	chr2R:9893364-9893511 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 9893465-9893486
   star strand at position 9893385-9893405
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2R:9893349-9893526 -		1	CGGAA-------AAGCCAA-GGCGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------TTTTC---GTTT-GGCTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATTG-CC--------TCTAT----G--G----CTCG--GC-AGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--TCGAA-----AAGC-CTGGCAAGCA-----CACAGCT-------CGCACAAATT---------------------TTC
droSim1	chr2R:8329883-8330063 -	LASTZ	5	CGGAA-------AATCCAA-GGCGC-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------CTTTCCACGTCT-GGCTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATTG-CC--------TCTAT----G--G----CTCG--GC-CGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--TCGAA-----AAGC-CTGGCAAGCG-----CACAGCT-------CGCACAAATT---------------------TTC
droSec1	super_1:7418494-7418674 -	LASTZ	5	CGGAA-------AAGCCAA-GGCGC-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------CTTTCCACGTCT-GGCTGGCCTGGAAAAGCTATC---------TT-TC--------TCTATTA-CC--------TCTAT----G--G----CTCG--GC-AGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTCCG---AGCCAAAAAC-----CA--TCGAA-----ATGC-CTGGCAAGCA-----CACAGCT-------CGCACAAATT---------------------TTC
droYak2	chr2R:7060227-7060403 +	LASTZ	5	CGGAA-------AAGCCAA-GGTGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------TTTTC---GTTT-GTCTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATTC--C--------TCTAT----G--G----CTCG--CC-AGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--TCGAA-----TAGC-CCGGCAAGCA-----CACAGCT-------CGCACAAATT---------------------TTC
droEre2	scaffold_4845:15928216-15928392 +	LASTZ	5	CTGAA-------AAGCCAA-GGCGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------TTTTC---GTCT-GGCTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATGC--C--------TCTAT----G--G----CTCG--GC-AGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--TCGAA-----TAGC-CGTGCAAGCA-----CACAGCT-------CGCACAAATT---------------------TTC
droEug1	scf7180000409462:2948624-2948813 +	LASTZ	5	CGAAGCCAAGCCAAGCCAA-GGTGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------TTTTTTTTTTCT-CGCTGGCCTGGAAAAGCTCTC---------TTTTC--------TCTATTT--C--------TCTAT----TC-G----CTCT--GCAGGCTCTGGGCGCCTAATCCAAAATGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--CCGAA-----AAGC-CAGGCAATGC-----GGCAGCT-------CGCACAAATT---------------------TTC
droBia1	scf7180000301592:46006-46174 -	LASTZ	5	GGGA--------AAGCCAA-GGTGG-------------------------------------------------------------------------------------------------------------ACTTTCCGC-----------------------------TTTTC---------GCTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATGC--C--------TCTAT----GCGG----CTCG--GA-GGCGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--CCGAA-----AAGC-CAGGCG----------GCAGCT-------CGCACAAATT---------------------TTC
droTak1	scf7180000415376:113688-113874 -	LASTZ	5	TGAAA-------AAGCCAA-GGTGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------TTTT-------T-CGCTGGCCTGGAAAAGCTCTCCTCTTCGCATT-TC--------TCTATTT--C--------TCTATCTATGCAG----CTCT--GC-AGCGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--CCGAA-----AAGC-CAGTCAGC-C-----AGCAGCT-------CGCACAAATT---------------------TTC
droEle1	scf7180000491214:56892-57055 +	LASTZ	5	AGGAA-------AAGCCAA--GCGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------TTTTT------T-CACTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATTT--C--------TCTAT----G--G----CTCT--GC-GGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--CCGAA-----AAGC-CA--------------ACAGCT-------CGCACAAAAT---------------------TTC
droRho1	scf7180000777200:215843-216013 -	LASTZ	5	AGGAA-------AAGCCAA--GCGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------TTTT-------T-CACTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATTC--CTATATTTCTCTAT----G--G----CTCT--GC-GGCGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--CCGAA-----AAGC-CA--------------ACAGCT-------CGCAAAAATT---------------------TTC
droFic1	scf7180000453948:518193-518357 +	LASTZ	5	GG--A-------AAGCCAT-TGCGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------ATTTT------G-CGCTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATTT--C--------TCAAT----G--G----CTCC--GC-TGCGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--CCGAA-----AAGC-CAGG-------------CAGCT-------CGCACAAAAT---------------------GCT
droKik1	scf7180000302385:7649-7806 -	LASTZ	5	G---------------------CTA-------------------------------------------------------------------------------------------------------------ACGTTCCAC-----------------------------TGCT-------T-TTCCTGCCTGGAAAAGCTCGC---------AT-T---------------------------TCCAT----G--G----CTTG--CC-CCAGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--TCGAAACGAAAAGC-CAA----G---------CAGCT-------CGCACAAAATCGCC------------TTGTTGTT
droAna3	scaffold_13266:6006643-6006792 +	LASTZ	0	--------------------------------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------T----------------CGCTGGAAAAAGCTTTC---------AT------------CCATTC--CGGTTG----CA---------ACTTGCCAC--TC-GACTCTGGGCTCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAACCGAGCCA--CCGAAAC---TGGT-CAA----G---------TAGTA-------CGCACAAATT---------------------CAA
droBip1	scf7180000395839:165965-166171 +	LASTZ	0	GGGGC-------AAGTGGG-AGTGGAGT-------------------------------------------------------------------------TTGGAAATGGCCGTGCAGCCGGCCGGGGCAAGCACTTTCC---------------------------------------------ACTCGCTGGAAAAAGCTTTC---------AT------------CCATTCCC-GGTTGTGCTGCCC----G--A----CTCG--AC-GACTCTGGGCTCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAACCAAGCTA--CCGAAAG---TGGCCCAA----G---------TAGTA-------CGCACAAATT---------------------CAG
dp4	chr3:11241780-11242024 +	LASTZ	0	CGAAT-------GAGAGAAAGGTGGAGATACAAAGAGAGAAACAATGTTGCCTGCCTTTTCCCCAGTTTCCCCAGTG------------------------------------------------------------------------------------------------TTTGTGTGTGTGGGGCGAACTGGAAAACCTCTG---------TT-T---------TCCATCCCC----------CT----------------TTTTGG-CGCGCTGAGCGCCTATTCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAG----CCA--CCAAA------AGCCCAA----GGAGTTGTCGCACTCCGGACTACGCATAAAATCCCCCAAAAGCAGAACT----CGC
droPer1	super_4:6644552-6644788 +	LASTZ	0	CGAAT-------GAGAGAAAGGTGGAGATACAAAGAGAGAAACAATGTTGCCTGCCTTTTCCCCAGTTTCCCCAGTGTTTGTGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--TGACGGACTGGAAAACCTCTG---------TT-T---------TCCATCCCC----------CT----------------TTTTGG-CGCGCTGAGCGCCTATTCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAG----CCA--CCAAA------AGCCCAA----GGAGTTGTCGCACTCCGGACTACGCATAAAAT------------------------
droWil1	scaffold_180745:1743803-1743968 +	LASTZ	0	CGGAA-------AAGCCAA-AGCAT-------------------------------------------------------------------------------------------------------------ATACT--------------------------------------------A-GATTGTACTGGAAAAGCTCTG---------CA-ACCAAAAAATTGCGTCGGT----------CA----------------TCTCTG-AGGTCTGTGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTTGGAGAGCCCA---C-----CACGTTGAA-----AG--------------------GAGTACGTACAATGAAAAAAATTG-------------------GCC
droVir3	scaffold_12875:2042187-2042370 +	LASTZ	0	CAGGA-------AAAGCAT--GCGGAAA---------------------------------------------AGT--------------GCGTGTATGGAAAAGCAGCA------------------------ATC--GCAAACGCCTGGAAAAGCGACCGACTG----------------------------------CCGCCG---------TT-T---------GCCA--------CA-----GCAC-------G----CTTTTTCG-ATATCTGTGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTAG---AGCTAG-------------TTCAA------GGCACACGCAG----TT--CGCAGCT------------CCACT---------------------GTG
droMoj3	scaffold_6496:23220919-23221095 -	LASTZ	0	TGGAA-------AAGCGCG-TGTGGAGA-------------------------------------------------------------------------CAAGCAGCG------------------------ACCGTACGCCCGCCTGGAAAGCCGACTGCCCGCCAGCA-TTTGTAG-----------------------------------------------------CT--CTGTAG----CA---------G----CTTGTTGG-ATAGCTGAGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTAG---AGCTAG-------------TTCAA-----GGCA-CACGCAGCTC-----CACAGCG-------GGCACAA---------------------------
droGri2	scaffold_15112:4157535-4157620 +	LASTZ	0	CGGAA-------AAGC-----GCAA-------------------------------------------------------------------------------------------------------------AATTTGCGA-----------------------------CACTC---------------------------------------------------------------------------------G----CTCAACTG-GCAGCTGGGCGCCTAATCCAAACTGCGAGAAAGATCCGCTTTTAG---AGCTA--------------------------------------------------------------------------------------------

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	CGGAA-------AAGCCAAGGCGGACTTTCCACTTTT----CGTTTGGCTGGCCTGGAAAAGCTCTC---------TT-TCTCTATTGCC--------TCTAT----G--GCTCGGC-AGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGA-----AAAGCCTGGCAAGCACACAGCTCGCACAAATT---------TTC
droSim1	CGGAA-------AATCCAAGGCGCACTTTCCACCTTT-CCACGTCTGGCTGGCCTGGAAAAGCTCTC---------TT-TCTCTATTGCC--------TCTAT----G--GCTCGGC-CGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGA-----AAAGCCTGGCAAGCGCACAGCTCGCACAAATT---------TTC
droSec1	CGGAA-------AAGCCAAGGCGCACTTTCCACCTTT-CCACGTCTGGCTGGCCTGGAAAAGCTATC---------TT-TCTCTATTACC--------TCTAT----G--GCTCGGC-AGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTCCGAGCCAAAAACCATCGA-----AATGCCTGGCAAGCACACAGCTCGCACAAATT---------TTC
droYak2	CGGAA-------AAGCCAAGGTGGACTTTCCACTTTT----CGTTTGTCTGGCCTGGAAAAGCTCTC---------TT-TCTCTATT-CC--------TCTAT----G--GCTCGCC-AGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGA-----ATAGCCCGGCAAGCACACAGCTCGCACAAATT---------TTC
droEre2	CTGAA-------AAGCCAAGGCGGACTTTCCACTTTT----CGTCTGGCTGGCCTGGAAAAGCTCTC---------TT-TCTCTATG-CC--------TCTAT----G--GCTCGGC-AGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGA-----ATAGCCGTGCAAGCACACAGCTCGCACAAATT---------TTC
droEug1	CGAAGCCAAGCCAAGCCAAGGTGGACTTTCCACTTTT-TTTTTTCTCGCTGGCCTGGAAAAGCTCTC---------TTTTCTCTATT-TC--------TCTAT----TC-GCTCTGCAGGCTCTGGGCGCCTAATCCAAAATGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCACCGA-----AAAGCCAGGCAATGCGGCAGCTCGCACAAATT---------TTC
droBia1	GGG-A-------AAGCCAAGGTGGACTTTCCGCTTTT---------CGCTGGCCTGGAAAAGCTCTC---------TT-TCTCTATG-CC--------TCTAT----GCGGCTCGGA-GGCGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCACCGA-----AAAGCCAGGCG-----GCAGCTCGCACAAATT---------TTC
droTak1	TGAAA-------AAGCCAAGGTGGACTTTCCACTTTT-T-------CGCTGGCCTGGAAAAGCTCTCCTCTTCGCATT-TCTCTATT-TC--------TCTATCTATGCAGCTCTGC-AGCGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCACCGA-----AAAGCCAGTCAG-CCAGCAGCTCGCACAAATT---------TTC
droEle1	AGGAA-------AAGCCAA-GCGGACTTTCCACTTTTTT-------CACTGGCCTGGAAAAGCTCTC---------TT-TCTCTATT-TC--------TCTAT----G--GCTCTGC-GGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCACCGA-----AAAGCCA---------ACAGCTCGCACAAAAT---------TTC
droRho1	AGGAA-------AAGCCAA-GCGGACTTTCCACTTTT-T-------CACTGGCCTGGAAAAGCTCTC---------TT-TCTCTATT-CCTATATTTCTCTAT----G--GCTCTGC-GGCGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCACCGA-----AAAGCCA---------ACAGCTCGCAAAAATT---------TTC
droFic1	GG--A-------AAGCCATTGCGGACTTTCCACATTTTG-------CGCTGGCCTGGAAAAGCTCTC---------TT-TCTCTATT-TC--------TCAAT----G--GCTCCGC-TGCGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCACCGA-----AAAGCCAGG--------CAGCTCGCACAAAAT---------GCT
droKik1	--------------------GCTAACGTTCCACTGCT-T-------TTCCTGCCTGGAAAAGCTCGC---------AT-T------------------TCCAT----G--GCTTGCC-CCAGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGAAACGAAAAGCCAAG--------CAGCTCGCACAAAATCGCCTTGTTGTT

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

CGGAA-------AATCCAA-GGCGC-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------CTTTCCACGTCT-GGCTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATTG-CC--------TCTAT----G--G----CTCG--GC-CGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--TCGAA-----AAGC-CTGGCAAGCG-----CACAGCT-------CGCACAAATT---------------------TTC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
................................................................................................................................................................................................................................................................................CGAGCTGGGCGCCxAATCCGA............................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................AATTGCGAGAAAGAGACG...........................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00

droSec1

CGGAA-------AAGCCAA-GGCGC-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------CTTTCCACGTCT-GGCTGGCCTGGAAAAGCTATC---------TT-TC--------TCTATTA-CC--------TCTAT----G--G----CTCG--GC-AGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTCCG---AGCCAAAAAC-----CA--TCGAA-----ATGC-CTGGCAAGCA-----CACAGCT-------CGCACAAATT---------------------TTC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................................................................................................................................................................................................................................................................................................................................................AGCA-----CACAGCT-------CGGAGAA...........................	18	2	0.50	0.00	0.50	0.00

droYak2

CGGAA-------AAGCCAA-GGTGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------TTTTC---GTTT-GTCTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATTC--C--------TCTAT----G--G----CTCG--CC-AGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--TCGAA-----TAGC-CCGGCAAGCA-----CACAGCT-------CGCACAAATT---------------------TTC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.........................................................................................................................................................................................GTCTGGCCTGGTAATGCT......................................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
...................................................................................................................................................................................................................................................................................................GAATTGCGAGAGAGATCGG...........................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................AGCCAAAAAC-----GA--TCGAA-----GA..................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

CTGAA-------AAGCCAA-GGCGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------TTTTC---GTCT-GGCTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATGC--C--------TCTAT----G--G----CTCG--GC-AGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--TCGAA-----TAGC-CGTGCAAGCA-----CACAGCT-------CGCACAAATT---------------------TTC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..............................................................................................................................................................................................GCCTGGAAAAGCTCTC---------TT-TC--------T............................................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00

droEug1

CGAAGCCAAGCCAAGCCAA-GGTGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------TTTTTTTTTTCT-CGCTGGCCTGGAAAAGCTCTC---------TTTTC--------TCTATTT--C--------TCTAT----TC-G----CTCT--GCAGGCTCTGGGCGCCTAATCCAAAATGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--CCGAA-----AAGC-CAGGCAATGC-----GGCAGCT-------CGCACAAATT---------------------TTC

Size

Hit Count

Total Norm

droBia1

GGGA--------AAGCCAA-GGTGG-------------------------------------------------------------------------------------------------------------ACTTTCCGC-----------------------------TTTTC---------GCTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATGC--C--------TCTAT----GCGG----CTCG--GA-GGCGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--CCGAA-----AAGC-CAGGCG----------GCAGCT-------CGCACAAATT---------------------TTC

Size

Hit Count

Total Norm

droTak1

TGAAA-------AAGCCAA-GGTGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------TTTT-------T-CGCTGGCCTGGAAAAGCTCTCCTCTTCGCATT-TC--------TCTATTT--C--------TCTATCTATGCAG----CTCT--GC-AGCGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--CCGAA-----AAGC-CAGTCAGC-C-----AGCAGCT-------CGCACAAATT---------------------TTC

Size

Hit Count

Total Norm

droEle1

AGGAA-------AAGCCAA--GCGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------TTTTT------T-CACTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATTT--C--------TCTAT----G--G----CTCT--GC-GGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--CCGAA-----AAGC-CA--------------ACAGCT-------CGCACAAAAT---------------------TTC

Size

Hit Count

Total Norm

droRho1

AGGAA-------AAGCCAA--GCGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------TTTT-------T-CACTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATTC--CTATATTTCTCTAT----G--G----CTCT--GC-GGCGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--CCGAA-----AAGC-CA--------------ACAGCT-------CGCAAAAATT---------------------TTC

Size

Hit Count

Total Norm

droFic1

GG--A-------AAGCCAT-TGCGG-------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------ATTTT------G-CGCTGGCCTGGAAAAGCTCTC---------TT-TC--------TCTATTT--C--------TCAAT----G--G----CTCC--GC-TGCGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--CCGAA-----AAGC-CAGG-------------CAGCT-------CGCACAAAAT---------------------GCT

Size

Hit Count

Total Norm

droKik1

G---------------------CTA-------------------------------------------------------------------------------------------------------------ACGTTCCAC-----------------------------TGCT-------T-TTCCTGCCTGGAAAAGCTCGC---------AT-T---------------------------TCCAT----G--G----CTTG--CC-CCAGCTGGGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC-----CA--TCGAAACGAAAAGC-CAA----G---------CAGCT-------CGCACAAAATCGCC------------TTGTTGTT

Size

Hit Count

Total Norm

droAna3

--------------------------------------------------------------------------------------------------------------------------------------ACTTTCCAC-----------------------------T----------------CGCTGGAAAAAGCTTTC---------AT------------CCATTC--CGGTTG----CA---------ACTTGCCAC--TC-GACTCTGGGCTCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAACCGAGCCA--CCGAAAC---TGGT-CAA----G---------TAGTA-------CGCACAAATT---------------------CAA

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

GGGGC-------AAGTGGG-AGTGGAGT-------------------------------------------------------------------------TTGGAAATGGCCGTGCAGCCGGCCGGGGCAAGCACTTTCC---------------------------------------------ACTCGCTGGAAAAAGCTTTC---------AT------------CCATTCCC-GGTTGTGCTGCCC----G--A----CTCG--AC-GACTCTGGGCTCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAACCAAGCTA--CCGAAAG---TGGCCCAA----G---------TAGTA-------CGCACAAATT---------------------CAG

Size

Hit Count

Total Norm

dp4

CGAAT-------GAGAGAAAGGTGGAGATACAAAGAGAGAAACAATGTTGCCTGCCTTTTCCCCAGTTTCCCCAGTG------------------------------------------------------------------------------------------------TTTGTGTGTGTGGGGCGAACTGGAAAACCTCTG---------TT-T---------TCCATCCCC----------CT----------------TTTTGG-CGCGCTGAGCGCCTATTCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAG----CCA--CCAAA------AGCCCAA----GGAGTTGTCGCACTCCGGACTACGCATAAAATCCCCCAAAAGCAGAACT----CGC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
........................................................................CAGTG------------------------------------------------------------------------------------------------TTTGTGTGGGGGGG......................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.........................................................................AGTG------------------------------------------------------------------------------------------------TGCGTGTGTGTGGG......................................................................................................................................................................................................................................	18	7	0.14	0.00	0.00	0.14	0.00
.........................................................................AGTG------------------------------------------------------------------------------------------------TGTGxGTGTGTGGGG.....................................................................................................................................................................................................................................	18	2	0.50	0.50	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................................................................TGTTGTCGTACTCCGGAC....................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

CGAAT-------GAGAGAAAGGTGGAGATACAAAGAGAGAAACAATGTTGCCTGCCTTTTCCCCAGTTTCCCCAGTGTTTGTGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--TGACGGACTGGAAAACCTCTG---------TT-T---------TCCATCCCC----------CT----------------TTTTGG-CGCGCTGAGCGCCTATTCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAG----CCA--CCAAA------AGCCCAA----GGAGTTGTCGCACTCCGGACTACGCATAAAAT------------------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...........................................................................TGTTTGTTTGTGTGTGTGTGT.................................................................................................................................................................................................................................................................................................................................	21	29	0.55	0.55	0.00	0.00	0.00	0.00
...............................................................................TGTTTGTTTGTGTGTGTGT----------------------------------------------------------------------------------GT...........................................................................................................................................................................................................................................	21	29	0.55	0.55	0.00	0.00	0.00	0.00
.................................................................................TGTTTGTTTGTGTGTGT----------------------------------------------------------------------------------GTG--T.......................................................................................................................................................................................................................................	21	29	0.55	0.55	0.00	0.00	0.00	0.00
..................................................................................GTGCGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--C.......................................................................................................................................................................................................................................	20	50	0.24	0.06	0.18	0.00	0.00	0.00
................................................................................GTGCGTGTGTGTGTGTGT----------------------------------------------------------------------------------GC...........................................................................................................................................................................................................................................	20	50	0.24	0.06	0.18	0.00	0.00	0.00
....................................................................................GTGCGTGTGTGTGT----------------------------------------------------------------------------------GTG--TGC.....................................................................................................................................................................................................................................	20	50	0.24	0.06	0.18	0.00	0.00	0.00
................................................................................GTGCGTGTGTGTGTGTGT----------------------------------------------------------------------------------G............................................................................................................................................................................................................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
....................................................................................GTGCGTGTGTGTGT----------------------------------------------------------------------------------GTG--T.......................................................................................................................................................................................................................................	18	47	0.17	0.02	0.15	0.00	0.00	0.00
....................................................................................GTGCGTGTGTGTGT----------------------------------------------------------------------------------GTG--TG......................................................................................................................................................................................................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
..................................................................................GTGCGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--........................................................................................................................................................................................................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
..................................................................................GTGCGTGTGTGTGTGT----------------------------------------------------------------------------------GT...........................................................................................................................................................................................................................................	18	47	0.17	0.02	0.15	0.00	0.00	0.00
................................................................................GTGCGTGTGTGTGTGTGT----------------------------------------------------------------------------------.............................................................................................................................................................................................................................................	18	47	0.17	0.02	0.15	0.00	0.00	0.00
...................................................................................TGTGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--........................................................................................................................................................................................................................................	18	41	0.17	0.07	0.00	0.07	0.02	0.00
...................................................................................TGTTTGTTTGTGTGT----------------------------------------------------------------------------------GTG--TG......................................................................................................................................................................................................................................	20	40	0.18	0.10	0.03	0.00	0.05	0.00
.................................................................................TGTTTGTTTGTGTGTGT----------------------------------------------------------------------------------GTG--........................................................................................................................................................................................................................................	20	40	0.18	0.10	0.03	0.00	0.05	0.00
...........................................................................TGTTTGTTTGTGTGTGTGTG..................................................................................................................................................................................................................................................................................................................................	20	40	0.18	0.10	0.03	0.00	0.05	0.00
...............................................................................TGTGTGTGTGTGTGTGTG................................................................................................................................................................................................................................................................................................................................	18	41	0.17	0.07	0.00	0.07	0.02	0.00
.................................................................................TGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------G............................................................................................................................................................................................................................................	18	41	0.17	0.07	0.00	0.07	0.02	0.00
.....................................................................................TGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--TG......................................................................................................................................................................................................................................	18	41	0.17	0.07	0.00	0.07	0.02	0.00
...............................................................................TGTTTGTTTGTGTGTGTGT----------------------------------------------------------------------------------G............................................................................................................................................................................................................................................	20	40	0.18	0.10	0.03	0.00	0.05	0.00
...............................................................................TGTGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------.............................................................................................................................................................................................................................................	19	32	0.16	0.16	0.00	0.00	0.00	0.00
...........................................................................TGTGTGTGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------G............................................................................................................................................................................................................................................	24	29	0.17	0.10	0.00	0.03	0.03	0.00
................................................................................GTGCGTGTGTGTGTGTGT----------------------------------------------------------------------------------GCG--........................................................................................................................................................................................................................................	21	41	0.12	0.10	0.02	0.00	0.00	0.00
..................................................................................GTGCGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--CG......................................................................................................................................................................................................................................	21	41	0.12	0.10	0.02	0.00	0.00	0.00
...............................................................................TGTGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--TG......................................................................................................................................................................................................................................	24	29	0.17	0.10	0.00	0.03	0.03	0.00
.............................................................................TGTGTGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--........................................................................................................................................................................................................................................	24	29	0.17	0.10	0.00	0.03	0.03	0.00
.................................................................................TGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------GT...........................................................................................................................................................................................................................................	19	32	0.16	0.16	0.00	0.00	0.00	0.00
...................................................................................TGTGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--T.......................................................................................................................................................................................................................................	19	32	0.16	0.16	0.00	0.00	0.00	0.00
.................................................................................TGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--TG......................................................................................................................................................................................................................................	22	50	0.08	0.08	0.00	0.00	0.00	0.00
.............................................................................TGTGTGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------G............................................................................................................................................................................................................................................	22	50	0.08	0.08	0.00	0.00	0.00	0.00
...............................................................................TGTGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--........................................................................................................................................................................................................................................	22	50	0.08	0.08	0.00	0.00	0.00	0.00
...........................................................................TGTGTGTGTGTGTGTGTGTGTG................................................................................................................................................................................................................................................................................................................................	22	50	0.08	0.08	0.00	0.00	0.00	0.00
................................................................................GTGTGTGTGTGTGxGTGT----------------------------------------------------------------------------------GTG--TC......................................................................................................................................................................................................................................	22	49	0.08	0.08	0.00	0.00	0.00	0.00
...............................................................................CGTGCGTGTGTGTGTGTGT----------------------------------------------------------------------------------G............................................................................................................................................................................................................................................	20	48	0.06	0.06	0.00	0.00	0.00	0.00
..................................................................................GTGTGTGTGTTTGTGT----------------------------------------------------------------------------------GTA--........................................................................................................................................................................................................................................	19	49	0.06	0.06	0.00	0.00	0.00	0.00
................................................................................GTGTGTGTGTTTGTGTGT----------------------------------------------------------------------------------A............................................................................................................................................................................................................................................	19	49	0.06	0.06	0.00	0.00	0.00	0.00
...................................................................................CGTGCGTGTGTGTGT----------------------------------------------------------------------------------GTG--TG......................................................................................................................................................................................................................................	20	48	0.06	0.06	0.00	0.00	0.00	0.00
..................................................................................GTGTGTGTGCGTGTGT----------------------------------------------------------------------------------GAG--TG......................................................................................................................................................................................................................................	21	30	0.10	0.10	0.00	0.00	0.00	0.00
................................................................................GTGTGTGTGCGTGTGTGA----------------------------------------------------------------------------------GTG--........................................................................................................................................................................................................................................	21	30	0.10	0.10	0.00	0.00	0.00	0.00
............................................................................GTTTGTTTGTGTGTGTGTGT.................................................................................................................................................................................................................................................................................................................................	20	35	0.09	0.09	0.00	0.00	0.00	0.00
.................................................................................GGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------GT...........................................................................................................................................................................................................................................	19	40	0.08	0.08	0.00	0.00	0.00	0.00
....................................................................................GTGTGTGTGTTTGT----------------------------------------------------------------------------------GTG--TA......................................................................................................................................................................................................................................	19	49	0.06	0.06	0.00	0.00	0.00	0.00
...........................................................................TGTGTGTGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--........................................................................................................................................................................................................................................	26	18	0.17	0.17	0.00	0.00	0.00	0.00
.................................................................................CGTGCGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--........................................................................................................................................................................................................................................	20	48	0.06	0.06	0.00	0.00	0.00	0.00
................................................................................GTGTTTGTGTGTGTGTTT----------------------------------------------------------------------------------GTG--........................................................................................................................................................................................................................................	21	32	0.09	0.09	0.00	0.00	0.00	0.00
...............................................................................GGTGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------.............................................................................................................................................................................................................................................	19	40	0.08	0.08	0.00	0.00	0.00	0.00
..................................................................................GTGTTTGTGTGTGTGT----------------------------------------------------------------------------------TTG--TG......................................................................................................................................................................................................................................	21	32	0.09	0.09	0.00	0.00	0.00	0.00
..................................................................................GTTTGTTTGTGTGTGT----------------------------------------------------------------------------------GTG--T.......................................................................................................................................................................................................................................	20	35	0.09	0.09	0.00	0.00	0.00	0.00
................................................................................GTGTGTGTGTGTGTATGT----------------------------------------------------------------------------------GT...........................................................................................................................................................................................................................................	20	73	0.04	0.04	0.00	0.00	0.00	0.00
.............................................................................TGTGTGTGTGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--TG......................................................................................................................................................................................................................................	26	18	0.17	0.17	0.00	0.00	0.00	0.00
................................................................................GTTTGTTTGTGTGTGTGT----------------------------------------------------------------------------------GT...........................................................................................................................................................................................................................................	20	35	0.09	0.09	0.00	0.00	0.00	0.00
...................................................................................GGTGTGTGTGTGTGT----------------------------------------------------------------------------------GTG--T.......................................................................................................................................................................................................................................	19	40	0.08	0.08	0.00	0.00	0.00	0.00
..........................................................................GTGTTTGTGTGTGTGTTTGTG..................................................................................................................................................................................................................................................................................................................................	21	32	0.09	0.09	0.00	0.00	0.00	0.00

droWil1

CGGAA-------AAGCCAA-AGCAT-------------------------------------------------------------------------------------------------------------ATACT--------------------------------------------A-GATTGTACTGGAAAAGCTCTG---------CA-ACCAAAAAATTGCGTCGGT----------CA----------------TCTCTG-AGGTCTGTGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTTGGAGAGCCCA---C-----CACGTTGAA-----AG--------------------GAGTACGTACAATGAAAAAAATTG-------------------GCC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......................................................................................................................................TAGT--------------------------------------------A-GAxTGTACTGGAAA..........................................................................................................................................................................................................................	18	1	17.00	0.00	13.00	1.00	3.00
........................................................................................................................................AGT--------------------------------------------A-GAxTGTACTGGAAAA.........................................................................................................................................................................................................................	18	1	11.00	0.00	9.00	0.00	2.00
.......................................................................................................................................TAGT--------------------------------------------A-GAxTGTACTGGAAAA.........................................................................................................................................................................................................................	19	1	10.00	2.00	6.00	0.00	2.00
......................................................................................................................................ATAGT--------------------------------------------A-GAxTGTACTGGAAA..........................................................................................................................................................................................................................	19	1	9.00	0.00	9.00	0.00	0.00
......................................................................................................................................ATAGT--------------------------------------------A-GAxTGTACTGGAA...........................................................................................................................................................................................................................	18	1	6.00	0.00	5.00	0.00	1.00
......................................................................................................................................ATAGT--------------------------------------------A-GAxTGTACTGGAAAA.........................................................................................................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
........................T-------------------------------------------------------------------------------------------------------------ATAGT--------------------------------------------A-GAxTGTACTGGAA...........................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................................................G---------CA-GCCAAAGAATTGCGTCGGT----------..........................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.......................AC-------------------------------------------------------------------------------------------------------------ATACT--------------------------------------------A-GAxTGTACTGGA............................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00

droVir3

CAGGA-------AAAGCAT--GCGGAAA---------------------------------------------AGT--------------GCGTGTATGGAAAAGCAGCA------------------------ATC--GCAAACGCCTGGAAAAGCGACCGACTG----------------------------------CCGCCG---------TT-T---------GCCA--------CA-----GCAC-------G----CTTTTTCG-ATATCTGTGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTAG---AGCTAG-------------TTCAA------GGCACACGCAG----TT--CGCAGCT------------CCACT---------------------GTG	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
................................................................................................................................................................CGACTG----------------------------------TCGCTG---------TT-T---------GCC..........................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	1.00	1.00
..........................................................................................................................................................................................................................................................C-------G----CTTTATCG-ATATTTGTGC.......................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

TGGAA-------AAGCGCG-TGTGGAGA-------------------------------------------------------------------------CAAGCAGCG------------------------ACCGTACGCCCGCCTGGAAAGCCGACTGCCCGCCAGCA-TTTGTAG-----------------------------------------------------CT--CTGTAG----CA---------G----CTTGTTGG-ATAGCTGAGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTAG---AGCTAG-------------TTCAA-----GGCA-CACGCAGCTC-----CACAGCG-------GGCACAA---------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
................................................................................................................................................................................................................................................................................................................................................................A-CACGGAGCTC-----CACAGTG-------..................................	18	1	1.00	0.00	1.00	0.00	0.00

droGri2

CGGAA-------AAGC-----GCAA-------------------------------------------------------------------------------------------------------------AATTTGCGA-----------------------------CACTC---------------------------------------------------------------------------------G----CTCAACTG-GCAGCTGGGCGCCTAATCCAAACTGCGAGAAAGATCCGCTTTTAG---AGCTA--------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:18:46 EDT

dme-mir-4978

chr2R:9893364-9893511 -

Known_mirbase

intergenic

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