dme-mir-4958- Best orthologs

dme-mir-4958	chrX:15974955-15975089 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	CDS

Legend:

   mature strand at position 15975037-15975058
   star strand at position 15974984-15975005
   mutations
   read mismatches

Notes: The alignment is poor despite this miRNA's location in a CDS region. droSim1 ortholog lies in an ambigous genomic location (maybe genomic rearrangement?). There are two chains (chrX and chrU) flanking the ortholog location.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:15974940-15975104 -		1	GTCCGAACCGTACGATCTC---TGGCAGCTGCAGTTCCGT---TTCCGGAGCGGGATCT-----------GGAACGGGCTCT---GGTTCTAGATCAGG------------------ATC------------------CA----------ATCATGCACC-CGGTCCAGG-----------TACCGCT---------CCAGGTCCCGT---TCC------CGGAAAC---GGTGCCACCGCCAATG---CAGC------------TGCAGCGGCATTCA
droSim1	chr2R_random:396788-396935 -	LASTZ	4	-------------------------CGGCTGCGGCTCCGG---CTCCGGCTCCGGCTCT-----------G------GCTTT---GAATCTAGATCAGG------------------ATC------------------TG----------GCCATTTGCCATTACCCAGA-----------TGCCCCTTGCCGATTGCCGATTGCCGT---TTG------CCACATG---GCAGCCACGAGCTGTGGAGCCTT------------TGCAGCT--GTGCT
droSec1	super_47:33133-33297 -	LASTZ	4	GTCCGAACCGTACGATCTC---TGGCAGCTGCAGTTCCGT---TTCCGCAGCGGGATCT-----------GGCACGGGCTCT---GCTTCTAGATCAGG------------------ATC------------------CA----------ATCATGCACC-CGGTCCAGG-----------TGCCGCT---------CCATGTCCCGT---ACC------CGGAAAC---GGAGCCACCGCCAATG---CAGC------------TGCAGCGGCATTCA
droYak2	chrX:10123735-10123899 -	LASTZ	4	GTCCAAATCCCACGATCTC---TGGCAGCTGCAGTTCCGT---TTCCGCAGCGGGTTCT-----------GGAACGGGCTCT---GGTTCTGGATCCGG------------------ATC------------------CA----------ATATGGCATC-CGGTCCTGG-----------TACCGCT---------CCAGTTCCCGT---ACC------CGGAAAC---GGTGCCACCGCCAATG---CAGC------------TGCAGCGGCCTTCA
droEre2	scaffold_4690:11103030-11103194 +	LASTZ	4	GTCCAAATCCCACGATCTC---TGGCAGCTGCAGTTCTGT---TTCCGGAACGGGTTCT-----------GGAACGGGCTCT---GGTTCGGGATCCGG------------------ATC------------------CA----------ATCTGGCACC-CGGTCCTGG-----------TACTGCT---------CCAGTTCCCGT---ACC------CGGTAAC---GGTGGCACCGCCAATG---CAGC------------TGCAGCGGCATTCA
droEug1	scf7180000409092:162915-163073 +	LASTZ	5	GTCCGAATCCCACGATTTC---CGGCAGCTGTAGTTCCGG---CTCCGGAGCGGGATCC-----------GGATCGGGTTCC---G------GTTCCGG------------------ATC------------------GA----------ATCTGGGCCC-CGGTCCAGG-----------TACCGTC---------CCAGTTTCAGT---TGC------CGGAAAT---AATGCTACCGCCAATG---CCGC------------AGCAGCTGCCTTTA
droBia1	scf7180000302126:1064767-1064934 +	LASTZ	5	GCCCCAATCCGACGATCTC---CGGCAGCTGCAGCTCCGG---CTCCGGAGCGGGCTCC-----------GGAACGGGTTCC---GGTTCCGGATCGGG------------------ATC------------------GA----------ACCTGGGACC-CGGTCCGGG-----------TACCGCT---------CCTGTTGCCGT---CCC------CGGAAATCCAGGTGCCACCGCCAACG---CCGC------------TGCAGCGGCCTTCT
droTak1	scf7180000415289:31224-31403 -	LASTZ	5	GCCCGAATCCCACGATTTC---CGGCAGCTGCAGCTCTGGCGGCTCCGGAGTGGGTTCC-----------GGAACGGGTTCCGGCGGTTCTGGATCGGG------------------ATC------------------GA----------ACCTGGGACC-CGGTCCGAA-----------TACCGCT---------CCTGTTACCGTTTTACCCGGAGGAGGAAAT---GGTGCCACCGCCAATG---CCGC------------CGCAGCGGCATTCA
droEle1	scf7180000490709:11511-11657 -	LASTZ	5	GTCCGAACCCCACGATCTC---TGGCAGCTGCAGCTCGGG---CTCTGGAGCGGGCTCC-----------GGG---------------------------------------------TC------------------GAACCTGGGGCC----TGGACC-CGGTCCGGG-----------AACCGCT---------CCCGTTCCGGT---ACC------GGGAAAT---AGTGCCACCGCCAACG---CCTC------------CGGCGGGGCATTTA
droRho1	scf7180000779586:28620-28772 +	LASTZ	5	GCCCGAACCCCACGATCTC---CGGCAGCTGCAGCTCGGG---CTCCGGAGCGGGCTCT-----------G---------------------GGTCCGG------------------GTC------------------GAACCTGGGACC----CGGGCC-TGGGCCGGG-----------AGCCGCT---------CCCGTTCCAGT---GCC------GGGCAAC---AGTGCCACCGCCAACG---CGGC------------CGCCGGCGCCTTTA
droFic1	scf7180000453495:241811-241990 -	LASTZ	5	GTCCGAATCCGACGATCTC---CGGCAGCTGCAGTTCCGGAGCATCCGGAGCTGGTTCG-----------GGAACGGGCTCC---G------GCTCCGGCTCCGGATCTGGATCCGGATC------------------GA----------CATTGGGACC-TGGCCCAGG-----------TGCCGCT---------CCAGTGCCAGT---GAC------CGGCAAC---AGTGCGTCGGCCAATG---CAGC------------TGCCGCCGCATTTA
droKik1	scf7180000302344:272406-272546 -	LASTZ	5	GCCCCAATCCCACGATCTC---CGGCAGCTGCAGCTCTGG---CTCCGGCACCGGTTCC-----------G---------------------GTTCCGG------------------TTCGACCATGTGCTCGGTATCGG----------GCTCTG--------------------------------------------GTCCCAGT----AC------CGGCACC---ACTGCCGCGACCAGTA---CTGC------------AGCTGCGGCCTTCA
droAna3	scaffold_13165:312527-312640 -	LASTZ	0	GCATAAGCCACATGGACTC---TGG--------------------------------------------------------------------ATCAGG------------------CTCCG------TATCTGCGTCAA----------TTTTGGG------------------------CACCGGT---------CCAGGCCCTTT---ACA------TGGAAAT---AGTGCGACCTCGAATG---TCTC------------TTCTGCACCCTTTA
droBip1	scf7180000395731:3232-3333 -	LASTZ	0	GCCCAAGCCCTATGGACTG---CGG--------------------------------------------------------------------ATCTGC------------------GTC------------------AA----------TT-------------TTAGG-----------CGCCGGC---------CCAGTCGCTTT---ACC------TAGAAAT---ATTGCTACCTCTAATG---CTTC------------TTCTGCAGCCTTTA
dp4	chrXL_group1e:9575758-9575916 -	LASTZ	0	GCCCCAATCCCAATGCCAGCAACGGCAGCTGTGGCTCCGC---CTCTGCCTCCGGTTCGTCCAGTGGCTCGGCACCGGCTCC---G------GCTCAGG------------------GTC------------------AG----------ACTCAGGCCA-CGACTCAGG-----------CACCGA--------------------C---TCA------CGGCAAC---ACT---TCGGCCGGTG---GCAC------------AGCCTCGGCGTACT
droPer1	super_22:633193-633346 +	LASTZ	0	GCCCCAATCCCAATGCCAGCAACGGCAGCTGTGGCTCCGC---CTCCGGTTCGTCCAGT-----------GGCTCGGCACCG---GTTCCGGGCTCAGG------------------GTC------------------AG----------ACTCAGGCCA-CGACTCAGG-----------CACC--------------------AGC---TCA------CGGCAAC---ACT---TCGGCCGGTG---GCAC------------AACCTCGGCGTACT
droWil1	scaffold_181096:10624772-10624892 +	LASTZ	0	CTGCA----------TCAT---CGGCATCGCCAACTT------ATCAGAAGGGCAGTCC-----------GAATCCAAATCC---CAATCTGAATGCAA------------------ATG------------------CA----------AC--GGCTGG-T-----------------------------------------------------------GGCTCT---GGAGCCAGTTCATCTG---CTGC------------CACCGCTGCCTTTA
droVir3	scaffold_12472:523224-523310 +	LASTZ	0	GCCCGAATCCCAATGGCGG---TGGCTCCAGCGGTGCC------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTCTATC---TGG------CAGTAAC---AATGTGACTGCCACCG---CTAC------------AGCCGCCGCCTTTG
droMoj3	scaffold_6308:2944361-2944510 -	LASTZ	0	GCCCGAATCCCAATGGCGG---CGGCAGCGGCGCCGGTGG---CGGTGGCGGTGCCGCT-----------G---------------------CTGCTGG------------------CTC------------------CA----------AC---------GGTGGCGGAAGTCTCTCGGGCAGCAGC---------AGCAGCAATGC---AGC------C---------------ACAGCCAATG---CTACAGCCACCGCCGGTGGCGCGGGCTTTG
droGri2	scaffold_15203:4433131-4433217 -	LASTZ	0	GCCCGAATCCCAATGGCTG---TGT---------CTCCAG------------------------------------------------------------------------------------------------------------------------------------------------CGGT---------GCCAGTCTCTC---TGG------CAGCAAC---ACTGTGACTGCCACCG---CTAC------------TGCCGCCGCCTTTG

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	GTCCGAACCGTACGATCTCTGGCAGCTGCAGTTCCGT---TTCCGGAGCGGGATCTGGAACGGGCTC------------TGGTTCTAGATCAGGATCCA---------ATCATGCACC-CGGTCCAGGTACCGCT---------CCAGGTCCCGT---TCCC------GGAAAC---GGTGCCACCGCCAATGCAGCTGCAGCGGCA-TTCA
droSim1	----------------------CGGCTGCGGCTCCGG---CTCCGGCTCCGGCTCTG------GCTT------------TGAATCTAGATCAGGATCTG---------GCCATTTGCCATTACCCAGATGCCCCTTGCCGATTGCCGATTGCCGT---TTGC------CACATG---GCAGCCACGAGCTGTGGAGCCTTTGCAGCTGTGCT
droSec1	GTCCGAACCGTACGATCTCTGGCAGCTGCAGTTCCGT---TTCCGCAGCGGGATCTGGCACGGGCTC------------TGCTTCTAGATCAGGATCCA---------ATCATGCACC-CGGTCCAGGTGCCGCT---------CCATGTCCCGT---ACCC------GGAAAC---GGAGCCACCGCCAATGCAGCTGCAGCGGCA-TTCA
droYak2	GTCCAAATCCCACGATCTCTGGCAGCTGCAGTTCCGT---TTCCGCAGCGGGTTCTGGAACGGGCTC------------TGGTTCTGGATCCGGATCCA---------ATATGGCATC-CGGTCCTGGTACCGCT---------CCAGTTCCCGT---ACCC------GGAAAC---GGTGCCACCGCCAATGCAGCTGCAGCGGCC-TTCA
droEre2	GTCCAAATCCCACGATCTCTGGCAGCTGCAGTTCTGT---TTCCGGAACGGGTTCTGGAACGGGCTC------------TGGTTCGGGATCCGGATCCA---------ATCTGGCACC-CGGTCCTGGTACTGCT---------CCAGTTCCCGT---ACCC------GGTAAC---GGTGGCACCGCCAATGCAGCTGCAGCGGCA-TTCA
droEug1	GTCCGAATCCCACGATTTCCGGCAGCTGTAGTTCCGG---CTCCGGAGCGGGATCCGGATCGGGTTC------------CGG------TTCCGGATCGA---------ATCTGGGCCC-CGGTCCAGGTACCGTC---------CCAGTTTCAGT---TGCC------GGAAAT---AATGCTACCGCCAATGCCGCAGCAGCTGCC-TTTA
droBia1	GCCCCAATCCGACGATCTCCGGCAGCTGCAGCTCCGG---CTCCGGAGCGGGCTCCGGAACGGGTTC------------CGGTTCCGGATCGGGATCGA---------ACCTGGGACC-CGGTCCGGGTACCGCT---------CCTGTTGCCGT---CCCC------GGAAATCCAGGTGCCACCGCCAACGCCGCTGCAGCGGCC-TTCT
droTak1	GCCCGAATCCCACGATTTCCGGCAGCTGCAGCTCTGGCGGCTCCGGAGTGGGTTCCGGAACGGGTTCCGG---------CGGTTCTGGATCGGGATCGA---------ACCTGGGACC-CGGTCCGAATACCGCT---------CCTGTTACCGTTTTACCCGGAGGAGGAAAT---GGTGCCACCGCCAATGCCGCCGCAGCGGCA-TTCA
droEle1	GTCCGAACCCCACGATCTCTGGCAGCTGCAGCTCGGG---CTCTGGAGCGGGCTCCGG------------------------------------GTCGAACCTGGGGC---CTGGACC-CGGTCCGGGAACCGCT---------CCCGTTCCGGT---ACCG------GGAAAT---AGTGCCACCGCCAACGCCTCCGGCGGGGCA-TTTA
droRho1	GCCCGAACCCCACGATCTCCGGCAGCTGCAGCTCGGG---CTCCGGAGCGGGCTCTG------------------------------GGTCCGGGTCGAACCTGGGAC---CCGGGCC-TGGGCCGGGAGCCGCT---------CCCGTTCCAGT---GCCG------GGCAAC---AGTGCCACCGCCAACGCGGCCGCCGGCGCC-TTTA
droFic1	GTCCGAATCCGACGATCTCCGGCAGCTGCAGTTCCGGAGCATCCGGAGCTGGTTCGGGAACGGGCTCCGGCTCCGGCTCCGGATCTGGATCCGGATCGA---------CATTGGGACC-TGGCCCAGGTGCCGCT---------CCAGTGCCAGT---GACC------GGCAAC---AGTGCGTCGGCCAATGCAGCTGCCGCCGCA-TTTA
droKik1	GCCCCAATCCCACGATCTCCGGCAGCTGCAGCTCTGG---CTCCGGCACCGGTTCCG------------------------------GTTCCGGTTCGA---------CC-ATGTGCT-CGGTATCGG----GCT---------CTGGTCCCAGT----ACC------GGCACC---ACTGCCGCGACCAGTACTGCAGCTGCGGCC-TTCA

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

-------------------------CGGCTGCGGCTCCGG---CTCCGGCTCCGGCTCT-----------G------GCTTT---GAATCTAGATCAGG------------------ATC------------------TG----------GCCATTTGCCATTACCCAGA-----------TGCCCCTTGCCGATTGCCGATTGCCGT---TTG------CCACATG---GCAGCCACGAGCTGTGGAGCCTT------------TGCAGCT--GTGCT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.............................................CCGGCTGCGGCTCT-----------G------GCT.......................................................................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
....................................CCGG---CTGCGGCTCTGGCT..............................................................................................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00

droSec1

GTCCGAACCGTACGATCTC---TGGCAGCTGCAGTTCCGT---TTCCGCAGCGGGATCT-----------GGCACGGGCTCT---GCTTCTAGATCAGG------------------ATC------------------CA----------ATCATGCACC-CGGTCCAGG-----------TGCCGCT---------CCATGTCCCGT---ACC------CGGAAAC---GGAGCCACCGCCAATG---CAGC------------TGCAGCGGCATTCA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........GTACGATCTC---TGGCAGCTGC.......................................................................................................................................................................................................................................................	20	1	2.00	1.00	1.00	0.00
........................GCAGCTGCAGTTCCGT---TTCCGC......................................................................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00
.........GTACGATCTC---TGGCAGCTGCA......................................................................................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00
..............................................................................................................................................................................................................GT---ACC------CGGAAAC---GGAGCCACC........................................	21	1	1.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................AATG---CAGA------------TGCAGxGGCATT..	19	1	1.00	0.00	0.00	1.00
............................................................................................................................................................................................................................................ACCTCCAATx---CAGC------------TGCAGC........	19	1	1.00	0.00	1.00	0.00

droYak2

GTCCAAATCCCACGATCTC---TGGCAGCTGCAGTTCCGT---TTCCGCAGCGGGTTCT-----------GGAACGGGCTCT---GGTTCTGGATCCGG------------------ATC------------------CA----------ATATGGCATC-CGGTCCTGG-----------TACCGCT---------CCAGTTCCCGT---ACC------CGGAAAC---GGTGCCACCGCCAATG---CAGC------------TGCAGCGGCCTTCA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
................................................................................CT---GGTGCCGGATCCGG------------------ATC------------------.............................................................................................................................................	19	1	2.00	0.00	0.00	0.00	0.00	2.00
..........................................................................CGGGCTCT---GGTTCTGGATCCGG------------------..................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................................................GTCT-----------GGAGCGGGCTCT---GG................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00	0.00
..............................................................................................................................................................................................................................................CGACAATx---CAGC------------TGCAGCGGC.....	20	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................GT---ACC------CGGAAAC---GGTGCCCCCGCCAAT..................................	27	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................................................TCTGGATCCGG------------------ATC------------------CA----------ATATGGCA.........................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

GTCCAAATCCCACGATCTC---TGGCAGCTGCAGTTCTGT---TTCCGGAACGGGTTCT-----------GGAACGGGCTCT---GGTTCGGGATCCGG------------------ATC------------------CA----------ATCTGGCACC-CGGTCCTGG-----------TACTGCT---------CCAGTTCCCGT---ACC------CGGTAAC---GGTGGCACCGCCAATG---CAGC------------TGCAGCGGCATTCA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.....................................................................................................................................................................................................CCAGTTCCCCT---ACC------AGGT.......................................................	18	1	2.00	2.00	0.00	0.00	0.00
.................................GTTCxGT---TTCCGGAGCGGG................................................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droEug1

GTCCGAATCCCACGATTTC---CGGCAGCTGTAGTTCCGG---CTCCGGAGCGGGATCC-----------GGATCGGGTTCC---G------GTTCCGG------------------ATC------------------GA----------ATCTGGGCCC-CGGTCCAGG-----------TACCGTC---------CCAGTTTCAGT---TGC------CGGAAAT---AATGCTACCGCCAATG---CCGC------------AGCAGCTGCCTTTA

Size

Hit Count

Total Norm

droBia1

GCCCCAATCCGACGATCTC---CGGCAGCTGCAGCTCCGG---CTCCGGAGCGGGCTCC-----------GGAACGGGTTCC---GGTTCCGGATCGGG------------------ATC------------------GA----------ACCTGGGACC-CGGTCCGGG-----------TACCGCT---------CCTGTTGCCGT---CCC------CGGAAATCCAGGTGCCACCGCCAACG---CCGC------------TGCAGCGGCCTTCT

Size

Hit Count

Total Norm

droTak1

GCCCGAATCCCACGATTTC---CGGCAGCTGCAGCTCTGGCGGCTCCGGAGTGGGTTCC-----------GGAACGGGTTCCGGCGGTTCTGGATCGGG------------------ATC------------------GA----------ACCTGGGACC-CGGTCCGAA-----------TACCGCT---------CCTGTTACCGTTTTACCCGGAGGAGGAAAT---GGTGCCACCGCCAATG---CCGC------------CGCAGCGGCATTCA

Size

Hit Count

Total Norm

droEle1

GTCCGAACCCCACGATCTC---TGGCAGCTGCAGCTCGGG---CTCTGGAGCGGGCTCC-----------GGG---------------------------------------------TC------------------GAACCTGGGGCC----TGGACC-CGGTCCGGG-----------AACCGCT---------CCCGTTCCGGT---ACC------GGGAAAT---AGTGCCACCGCCAACG---CCTC------------CGGCGGGGCATTTA

Size

Hit Count

Total Norm

droRho1

GCCCGAACCCCACGATCTC---CGGCAGCTGCAGCTCGGG---CTCCGGAGCGGGCTCT-----------G---------------------GGTCCGG------------------GTC------------------GAACCTGGGACC----CGGGCC-TGGGCCGGG-----------AGCCGCT---------CCCGTTCCAGT---GCC------GGGCAAC---AGTGCCACCGCCAACG---CGGC------------CGCCGGCGCCTTTA

Size

Hit Count

Total Norm

droFic1

GTCCGAATCCGACGATCTC---CGGCAGCTGCAGTTCCGGAGCATCCGGAGCTGGTTCG-----------GGAACGGGCTCC---G------GCTCCGGCTCCGGATCTGGATCCGGATC------------------GA----------CATTGGGACC-TGGCCCAGG-----------TGCCGCT---------CCAGTGCCAGT---GAC------CGGCAAC---AGTGCGTCGGCCAATG---CAGC------------TGCCGCCGCATTTA

Size

Hit Count

Total Norm

droKik1

GCCCCAATCCCACGATCTC---CGGCAGCTGCAGCTCTGG---CTCCGGCACCGGTTCC-----------G---------------------GTTCCGG------------------TTCGACCATGTGCTCGGTATCGG----------GCTCTG--------------------------------------------GTCCCAGT----AC------CGGCACC---ACTGCCGCGACCAGTA---CTGC------------AGCTGCGGCCTTCA

Size

Hit Count

Total Norm

droAna3

GCATAAGCCACATGGACTC---TGG--------------------------------------------------------------------ATCAGG------------------CTCCG------TATCTGCGTCAA----------TTTTGGG------------------------CACCGGT---------CCAGGCCCTTT---ACA------TGGAAAT---AGTGCGACCTCGAATG---TCTC------------TTCTGCACCCTTTA

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

GCCCAAGCCCTATGGACTG---CGG--------------------------------------------------------------------ATCTGC------------------GTC------------------AA----------TT-------------TTAGG-----------CGCCGGC---------CCAGTCGCTTT---ACC------TAGAAAT---ATTGCTACCTCTAATG---CTTC------------TTCTGCAGCCTTTA

Size

Hit Count

Total Norm

dp4

GCCCCAATCCCAATGCCAGCAACGGCAGCTGTGGCTCCGC---CTCTGCCTCCGGTTCGTCCAGTGGCTCGGCACCGGCTCC---G------GCTCAGG------------------GTC------------------AG----------ACTCAGGCCA-CGACTCAGG-----------CACCGA--------------------C---TCA------CGGCAAC---ACT---TCGGCCGGTG---GCAC------------AGCCTCGGCGTACT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................................................CTCCGGTTTGTCAAGTGG....................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

GCCCCAATCCCAATGCCAGCAACGGCAGCTGTGGCTCCGC---CTCCGGTTCGTCCAGT-----------GGCTCGGCACCG---GTTCCGGGCTCAGG------------------GTC------------------AG----------ACTCAGGCCA-CGACTCAGG-----------CACC--------------------AGC---TCA------CGGCAAC---ACT---TCGGCCGGTG---GCAC------------AACCTCGGCGTACT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......................................................................................................................................................................................................................................CT---TCGGCCGGTG---GCAC------------AACCT.........	21	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................................................................................................................................................................................................ACT---TCGGCCGGTA---GCAC------------T.............	18	1	1.00	0.00	0.00	0.00	1.00	0.00
............................CTGTGGCTCCAC---CTCCAGTT....................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
..........................................................................CGGCACCG---GTTCCxGGCTCAGG------------------GTC------------------.............................................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................CACCG---GTTCCxGGCTCAGG------------------GTC------------------AG----------ACT..............................................................................................................................	26	1	1.00	0.00	0.00	0.00	0.00	1.00
.................AGCAACGGCAGCTGTGCCGCC.................................................................................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
...........................................CTCCGGTTCGTCCAGT-----------GGCTC............................................................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.....AATCCCAGTGCCAACAAC................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00

droWil1

CTGCA----------TCAT---CGGCATCGCCAACTT------ATCAGAAGGGCAGTCC-----------GAATCCAAATCC---CAATCTGAATGCAA------------------ATG------------------CA----------AC--GGCTGG-T-----------------------------------------------------------GGCTCT---GGAGCCAGTTCATCTG---CTGC------------CACCGCTGCCTTTA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........................................................................................................................................CA----------AC--GGCTGC-T-----------------------------------------------------------GCCTCT---G................................................	18	1	1.00	1.00	0.00	0.00	0.00
...CA----------TCAT---CGAAATCGCCAAC....................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................GCTGG-T-----------------------------------------------------------GGGACT---GGAGCCA..........................................	19	1	1.00	0.00	1.00	0.00	0.00
..............................................AGAAGGGCAGTCC-----------GAATCCA..........................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..........................................................................................................................................................GGCTGG-T-----------------------------------------------------------GGGTCT---GGAGAC...........................................	19	1	1.00	0.00	0.00	1.00	0.00
.............................................CAGAAGGGCAGTCC-----------GAATCCAAA........................................................................................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................A------------------ATG------------------GA----------AC--TGCTGG-T-----------------------------------------------------------GGCT......................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............................................GAAGGGCAGTCC-----------GAATCCA..........................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droVir3

GCCCGAATCCCAATGGCGG---TGGCTCCAGCGGTGCC------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTCTATC---TGG------CAGTAAC---AATGTGACTGCCACCG---CTAC------------AGCCGCCGCCTTTG

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

GCCCGAATCCCAATGGCGG---CGGCAGCGGCGCCGGTGG---CGGTGGCGGTGCCGCT-----------G---------------------CTGCTGG------------------CTC------------------CA----------AC---------GGTGGCGGAAGTCTCTCGGGCAGCAGC---------AGCAGCAATGC---AGC------C---------------ACAGCCAATG---CTACAGCCACCGCCGGTGGCGCGGGCTTTG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...........................GCGGTGGCGGTGG---CGGTGGCGGT..................................................................................................................................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
....................................GTGG---CAGTxGCGGTGCCGC.............................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...................................GGTGG---AGGTGGCGGCG.................................................................................................................................................................................................................................	16	9	0.11	0.00	0.11	0.00	0.00
........................GCAGCGGGGCCGGTCG---CG..........................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..................G---CGGCAGCGGCGGCGGTGT---C...........................................................................................................................................................................................................................................	20	3	0.33	0.33	0.00	0.00	0.00
...............................TGGCGGTGG---CGGTGGCGGT..................................................................................................................................................................................................................................	19	9	0.11	0.00	0.00	0.11	0.00
...................................GGTGG---AGGTGGCGGTGGC...............................................................................................................................................................................................................................	18	3	0.33	0.33	0.00	0.00	0.00
.....................................TGG---CGGTGGCGGTGGCGGT-----------.................................................................................................................................................................................................................	19	9	0.11	0.00	0.00	0.11	0.00
...................................GGTGG---CGGTGGCGGCGGC...............................................................................................................................................................................................................................	18	19	0.05	0.05	0.00	0.00	0.00

droGri2

GCCCGAATCCCAATGGCTG---TGT---------CTCCAG------------------------------------------------------------------------------------------------------------------------------------------------CGGT---------GCCAGTCTCTC---TGG------CAGCAAC---ACTGTGACTGCCACCG---CTAC------------TGCCGCCGCCTTTG

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:26:13 EDT

dme-mir-4958

chrX:15974955-15975089 -

Known_mirbase

CDS

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