dme-mir-4974- Best orthologs

dme-mir-4974	chr2L:21263932-21264034 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 21263992-21264013
   star strand at position 21263955-21263976
   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	chr2L:21263917-21264049 +		1	GCATTGACTT---CTTTTGTTCT---T--TGTTTTTATTCCCTGTCAG--AGAGTATATTGATTTTAGGTG-----------------------GACAT-TTGC-GACCATATAAAATAT-ATATATTCCTGATAAAGAATATTTAATATATCTTCTTTTTCG----------------------------------GTATAC
droSim1	chr2L:20861453-20861585 +	LASTZ	5	GCACTGACTT---CTTTTGTTCT---T--TGTTTTTATTCCCTAGCAG--AGAGTATATTGATTTTAGGCG-----------------------GTCAT-TTGC-GACCATATAAAGTAT-ACATATTCCTGATCAGAACTATTTAATATATCTTTTTTTTCG----------------------------------GTACAC
droSec1	super_18:1195266-1195398 +	LASTZ	5	GCACTGACTT---CTTTTGTTCT---T--TGTTTTTATTCCCTAGCAG--AGAGTATATTGATTTTAGGCG-----------------------GTCAT-TTGC-GACCATATAAAGTAT-ACATATTCCTGATCAGAACTATTTAATATATCTTTTTTTTCG----------------------------------GTATAC
droYak2	chrU:19793626-19793766 +	LASTZ	5	GAACTTAATT---ATATCGTTCT---C---TCTCTTACACCCTTAAAG--AGGGTGTATTGATTTTAACCGGAAA-----AACGCAAAAAAGGAGACAT-TTGC-GGCCATATAAAGTAA-ATATATTCTTAATCAGTATCAAC------------------------------GTCAGTT-------------TTAAGATCC
droEre2	scaffold_4784:24793627-24793751 +	LASTZ	5	TAATTGAATT---TCTTTGGTTT---T---TTTACCATTTACTTTTAG--AGAATATACTAGAATTTCTGAGAAGTGTGTAACAGGCAGAAGGAAACGT-TTTC-GACCATATAAATTAT-ATATATTCTTGATCAGGA----------------------------------------------------------------
droEug1	scf7180000409122:862766-862897 -	LASTZ	5	-------------------------------TTTTTATACCCTTGCAA--AGTTTGTAACGCAG-----------------------TGAAGGAGACGT-TTCC-GAACCCATAAAGTAT-ATATATTCTTGATCAGGATCAATAGGGGAGTATATATAG-CC---------ATGTCCGTCTGTTTCATCTCTGT--CTATAT
droBia1	scf7180000301268:374-502 -	LASTZ	5	TTAT----------------------C--CCTTTTTATACCCTTGCAG--AGGTTATAATGATTTGAAG------------------TGAAGGAGACGT-TTCC-GACCCCATAAAGTAT-ATATATTCTTGATCAGCGTCACTAGACGATTCCACCTAG-CC---------ATGTTCGTC-----------------TGTCC
droTak1	scf7180000411086:12009-12140 +	LASTZ	5	ACGTAAAAGT---CAGTTCTTGT---C--TATTTTTATAACCTTGCAG--AGGGTATTATGATTTTAGTAAGA-----------------------AGT-TTGC-AACCCTATAAAGTAT-AAATGTTCTTGATCAGCATCACTAGACGAGTCGATCTAA-CC----------------------------------ATGTCC
droEle1	scf7180000490489:41546-41679 -	LASTZ	5	ATTAC---TT---CCT---ATTT---A--TTTTTTTATATTATTGCAG--AGGGTATTATGATTTCAGTCAGA-----------------------AGT-TTGC-GACCCTGTAAAGTAT-ATATATTCTTGATCAGCATCACTAGGAGAGTCGATCTAG-CC---------ATGTCCGTC-----------------TGTCC
droRho1	scf7180000780205:9144-9271 -	LASTZ	5	TTG---AGGT---ATTTTATT-T---T--TGTTTTTATACCCTTGCAG--AGGGTATTATAATTTTGGTCAAAAGTGTGCAACGCAGTGAAGGAGACAT-CTCC-GACCATATAAAGTAT-ATATATTCTTGATCAGGATCACCT----------------------------------------------------------
droFic1	scf7180000451789:400159-400291 -	LASTZ	5	AATTCAACTTAAGAACTCGTTTC---A--TGTTTTTATACCCTTGCAG--AGCATATATTATTTTTAGTTGGAAGTTTGAAACTCAGTAAAGGAGACTTACTCC-GAAAACTGTAAAAAT-ATATATTCTTAAGAAAGGTA-------------------------------------------------------------A
droKik1	scf7180000302373:155872-155996 +	LASTZ	5	T-------------------------------TTTTATACCCTTGCAG----GGTATTATAAGT---------------------------GGAGACGT-TTCC-GACCCTATAAAGTAT-ATATATTCTTGATCATATAAAATTATAACTTGGCTGTTTTTCAATATTTTTGCATCTTTT-------------TTGAGATAT
droAna3	scaffold_13499:388035-388162 -	LASTZ	5	TTAT----TT---CCTTTGTTCT---T--CGTTTTTATACCCTTGCAG--AGGGTATTATAATTTTGGTCAAAAGTGTGCAACGCAGAGAAGGAGACAT-CTCC-GACCCTATAAAGTAT-ATATATTCTTGATCAGGATCACCT----------------------------------------------------------
droBip1	scf7180000392227:732-861 +	LASTZ	5	A--TTTAGTT---TTGTTGTTCT---T--GTTTTTTATACCCTTGCAG--AGGGTATTATAATTTTGGTCAGAAGTGTGCAACGCAGTAAAGGAGACAT-CTCC-GACCCTATAAAGTAT-ATATATTCTTGATCAGGATCACCT----------------------------------------------------------
dp4	chr2:13223937-13224089 -	LASTZ	0	CCGTTCGCCT---TTTTGGTTCTTTAT--TGTTTTTATACCCTTCTAG--AGAGTATTACGATTTTGGGCTAATGTCTGCAAGACTGGA-ACCTGCAAC-ATAG-AATCCCATAGGGTATTATATAT-----ATGAGGATCGGTAGCCATCTCTCTT-TTTCT----------------------------------ATACAC
droPer1	super_0:7229185-7229317 +	LASTZ	0	CCGTTCGCCT---TTTTGGTTCTTTAT--TGTTTTTATACCCTTCTAG--AGAGTATTATGATTTTGGGCTGCTGTCTGCAAGGCTGAAATCTA-TTGC-ATAG-AATCCTATAGGGTATTATATAT-----GTCAGGATCGG-------------------------------------------------------TAGCC
droWil1	scaffold_181150:776667-776791 -	LASTZ	0	TTT-----------TTTTGATTT---T--CTTTTTTATAACCTTGCAAAAAGGGTATATTCATTTTGGTCAAAGGAA-----------------TGCAT-CTCC-GACCATGTAAATTAT-ATATATTCTTGATTAGCACGACGAGACGAGTTCATATAG------------------------------------------C
droVir3	scaffold_12963:16876342-16876466 -	LASTZ	0	GAACTCGTTT---CTGGTGTACG---TCGTGTTTTTATACCCTTGTAG--AGAGTATTTTAATTTTGTCGTGGAATGTGCAACGCATGGATGGAGACAT-TTGG-GACCCCATAAAGTAT-ATGTATTCTAGATAA-------------------------------------------------------------------
droMoj3	Unknown	MAF	0	GGTTTCAGTT---CTTTTGTTTT---T--T--TTTGATATCCC---AA--A-TGTGAAGT-------GCTAAAGAGTTGAAATTCG-GAATGTAGATTGGCATTGAGTTCAATAAGATAT---------------------------GGCGGATATATTGT------------------------------------AT-ACA
droGri2	scaffold_3049:4191-4318 -	LASTZ	0	ATTGACAA------ATTTATTTT---T--AATTCTTCTTTTGTTCGAG--TGGGTATAACAGGTA-----------------------GAAGGAAGCAT-CTCC-GACGCCATAAAGTAT-ATATGTTTCTGAGAAGGATCAATTGAGGAGTCGATGTAGTTC-------------------------------------GTC

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	GCATTGACTTCT---TTTGTTCTTTGTTTTTATTCCCTGTCAGAGAGTATATT--GATTTTAGGTG-----------------------GACAT-TTGCGACCATATAAAATATATATATTCCTGATAAAGAATATTTAATATATCT----------------------------------TCTTTTTCGGTATAC
droSim1	GCACTGACTTCT---TTTGTTCTTTGTTTTTATTCCCTAGCAGAGAGTATATT--GATTTTAGGCG-----------------------GTCAT-TTGCGACCATATAAAGTATACATATTCCTGATCAGAACTATTTAATATATCT----------------------------------TTTTTTTCGGTACAC
droSec1	GCACTGACTTCT---TTTGTTCTTTGTTTTTATTCCCTAGCAGAGAGTATATT--GATTTTAGGCG-----------------------GTCAT-TTGCGACCATATAAAGTATACATATTCCTGATCAGAACTATTTAATATATCT----------------------------------TTTTTTTCGGTATAC
droYak2	GAACTTAATTAT---ATCGTTCTCT-CTCTTACACCCTTAAAGAGGGTGTATT--GATTTTAACCGGAAA-----AACGCAAAAAAGGAGACAT-TTGCGGCCATATAAAGTAAATATATTCTTAATCAGTATCAAC---------G----------------------------------TCAGTTTTAAGATCC
droEre2	TAATTGAATTTC---TTTGGTTTTT-TTACCATTTACTTTTAGAGAATATACTAGAATTTC--TGAGAAGTGTGTAACAGGCAGAAGGAAACGT-TTTCGACCATATAAATTATATATATTCTTGATCAGGA----------------------------------------------------------------
droEug1	--------------------------TTTTTATACCCTTGCAAAGTTTGTAA-------------------------CGCAGTGAAGGAGACGT-TTCCGAACCCATAAAGTATATATATTCTTGATCAGGATCAATAGGGGAGTATATA-TAGCCATGTCCGTCT---------GTTTCATCTCTGT--CTATAT
droBia1	TTA-------------------TCCCTTTTTATACCCTTGCAGAGGTTATAAT--GATTTGA------------------AGTGAAGGAGACGT-TTCCGACCCCATAAAGTATATATATTCTTGATCAGCGTCACTAGACGATTCCACC-TAGCCATGTTCGTCT--------------------------GTCC
droTak1	ACGTAAAAGTCA---GTTCTTGTCTATTTTTATAACCTTGCAGAGGGTATTAT--GATTTTAGTAA-----------------------GAAGT-TTGCAACCCTATAAAGTATAAATGTTCTTGATCAGCATCACTAGACGAGTCGATC-TAACC----------------------------------ATGTCC
droEle1	A---TTACTTCC---T---ATTTATTTTTTTATATTATTGCAGAGGGTATTAT--GATTTCAGTCA-----------------------GAAGT-TTGCGACCCTGTAAAGTATATATATTCTTGATCAGCATCACTAGGAGAGTCGATC-TAGCCATGTCCGTCT--------------------------GTCC
droRho1	T---TGAGGTAT---TTTAT-TTTTGTTTTTATACCCTTGCAGAGGGTATTAT--AATTTTGGTCAAAAGTGTGCAACGCAGTGAAGGAGACAT-CTCCGACCATATAAAGTATATATATTCTTGATCAGGATCACCT----------------------------------------------------------
droFic1	AATTCAACTTAAGAACTCGTTTCATGTTTTTATACCCTTGCAGAGCATATATT--ATTTTTAGTTGGAAGTTTGAAACTCAGTAAAGGAGACTTACTCCGAAAACTGTAAAAATATATATTCTTAAGAAAGGT-------------------------------------------------------------AA
droKik1	--------------------------TTTTTATACCCTTGCAGG--GTATTAT--AAGT---------------------------GGAGACGT-TTCCGACCCTATAAAGTATATATATTCTTGATCATAT-------AAAATTATAACTTGGC------TGTTTTTCAATATTTTTGCATCTTTTTTGAGATAT
droAna3	TTA----TTTCC---TTTGTTCTTCGTTTTTATACCCTTGCAGAGGGTATTAT--AATTTTGGTCAAAAGTGTGCAACGCAGAGAAGGAGACAT-CTCCGACCCTATAAAGTATATATATTCTTGATCAGGATCACCT----------------------------------------------------------
droBip1	A--TTTAGTTTT---GTTGTTCTTGTTTTTTATACCCTTGCAGAGGGTATTAT--AATTTTGGTCAGAAGTGTGCAACGCAGTAAAGGAGACAT-CTCCGACCCTATAAAGTATATATATTCTTGATCAGGATCACCT----------------------------------------------------------

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

GCACTGACTT---CTTTTGTTCT---T--TGTTTTTATTCCCTAGCAG--AGAGTATATTGATTTTAGGCG-----------------------GTCAT-TTGC-GACCATATAAAGTAT-ACATATTCCTGATCAGAACTATTTAATATATCTTTTTTTTCG----------------------------------GTACAC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.................................................................................................GT-TTGC-GACCATATAAAGT.....................................................................................	19	8	0.13	0.13	0.00	0.00	0.00
....................................................................................................TTCG-GACCATATAAAGTA....................................................................................	18	7	0.14	0.00	0.00	0.00	0.14
.....................................................GTATATTGATTTTAGGCG-----------------------GT...........................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................GTAT-ATATATTCTTGATCAGAA................................................................	22	5	0.20	0.00	0.00	0.00	0.20
..............................................................................................................TATAAAGTAT-ACATATTCTTGATCAGGA................................................................	28	4	0.25	0.00	0.00	0.00	0.25
.....................................................GTATATTGATTTTAGGCG-----------------------GTCT.........................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................AAATGAT-ACATATTCCTG.......................................................................	18	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................................TTATATCTTTTTGTTCG----------------------------------GT....	19	1	1.00	0.00	0.00	1.00	0.00
.....................................................GTATATTGATTTTAGGCG-----------------------GTC..........................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00

droSec1

GCACTGACTT---CTTTTGTTCT---T--TGTTTTTATTCCCTAGCAG--AGAGTATATTGATTTTAGGCG-----------------------GTCAT-TTGC-GACCATATAAAGTAT-ACATATTCCTGATCAGAACTATTTAATATATCTTTTTTTTCG----------------------------------GTATAC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...........................................TGCAG--AGAxTATATTGATT...........................................................................................................................................	18	3	0.33	0.00	0.33	0.00

droYak2

GAACTTAATT---ATATCGTTCT---C---TCTCTTACACCCTTAAAG--AGGGTGTATTGATTTTAACCGGAAA-----AACGCAAAAAAGGAGACAT-TTGC-GGCCATATAAAGTAA-ATATATTCTTAATCAGTATCAAC------------------------------GTCAGTT-------------TTAAGATCC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..........................................................................................................................TATATTCTTGATCAGTATCAGC------------------------------.............................	22	9	0.11	0.00	0.11	0.00	0.00	0.00

droEre2

TAATTGAATT---TCTTTGGTTT---T---TTTACCATTTACTTTTAG--AGAATATACTAGAATTTCTGAGAAGTGTGTAACAGGCAGAAGGAAACGT-TTTC-GACCATATAAATTAT-ATATATTCTTGATCAGGA----------------------------------------------------------------	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.............................................................................................AAACGT-TTCC-GACCATAT..........................................................................................	18	10	0.10	0.00	0.00	0.00	0.10
.................................................................................ACAGGCAGAAGGAAGCGT-.......................................................................................................	18	7	0.14	0.00	0.00	0.00	0.14
........................................................................................GAAGGAAACGT-TTCC-GACC..............................................................................................	19	7	0.14	0.00	0.00	0.00	0.14
..............................................................................TTAACAGGCAGAAGGAAG...........................................................................................................	18	5	0.20	0.00	0.00	0.00	0.20
................................................................................AACAGGCAGAAGGAAACGT-TT.....................................................................................................	21	4	0.25	0.00	0.00	0.00	0.25
...............................................................................TAAATGGCAGAAGGAAACGT-TT.....................................................................................................	22	4	0.25	0.00	0.00	0.00	0.25
................................................................................AACAGGCAGAAGGAAACGT-.......................................................................................................	19	4	0.25	0.00	0.00	0.00	0.25
.............................................................................TGTAACAGGCAGAAGGGA............................................................................................................	18	7	0.14	0.00	0.00	0.00	0.14
................................................................................AACAGGCAGAAGAAAGCG.........................................................................................................	18	6	0.17	0.00	0.00	0.00	0.17
.....................................................................................................................TAT-ATATATGCATGATCAG..................................................................	19	11	0.09	0.00	0.00	0.00	0.09
...............................................................................TAACAGGCAGAAGGAAACGT-TTCC-..................................................................................................	24	4	0.25	0.00	0.00	0.00	0.25
.....................................................................................GCAGAAGGAAGCGT-TTCC-GACCAT............................................................................................	24	5	0.20	0.20	0.00	0.00	0.00
................................................................................AACAGGCAGAAGGAAGTGT-.......................................................................................................	19	5	0.20	0.00	0.00	0.00	0.20
................................................................................AACAGGCAGAAGGAAGCGT-TT.....................................................................................................	21	7	0.14	0.00	0.00	0.00	0.14
..............................................................................GTAACAGGTAGAAGGAACCGT-.......................................................................................................	21	6	0.17	0.17	0.00	0.00	0.00
......................................................................................................................AT-TTAAATTCTTGATCAG..................................................................	18	11	0.09	0.00	0.00	0.00	0.09
............................................................................ATGTAACAGGCAGAAGGA.............................................................................................................	18	7	0.14	0.14	0.00	0.00	0.00
...........................................................................................................................ATATTCTTGATCAGGA----------------------------------------------------------------	18	18	0.06	0.00	0.00	0.00	0.06
......................................................................................CAGAAGGAATCGT-TTTC-GACC..............................................................................................	21	4	0.25	0.00	0.00	0.00	0.25
................................................................................AACAGGCAGAAGGAAGCGT-TTCC-G.................................................................................................	24	5	0.20	0.00	0.00	0.00	0.20
....................................................................................GGCAGAAGGAAACGT-TTCC-GAC...............................................................................................	22	4	0.25	0.00	0.00	0.00	0.25
.................................................................................ACAGGCAGAAGGAAGTGT-T......................................................................................................	19	5	0.20	0.20	0.00	0.00	0.00
......................................................................................................................TT-ATATATTCTTGATCAGAA----------------------------------------------------------------	20	10	0.10	0.10	0.00	0.00	0.00

droEug1

-------------------------------TTTTTATACCCTTGCAA--AGTTTGTAACGCAG-----------------------TGAAGGAGACGT-TTCC-GAACCCATAAAGTAT-ATATATTCTTGATCAGGATCAATAGGGGAGTATATATAG-CC---------ATGTCCGTCTGTTTCATCTCTGT--CTATAT

Size

Hit Count

Total Norm

droBia1

TTAT----------------------C--CCTTTTTATACCCTTGCAG--AGGTTATAATGATTTGAAG------------------TGAAGGAGACGT-TTCC-GACCCCATAAAGTAT-ATATATTCTTGATCAGCGTCACTAGACGATTCCACCTAG-CC---------ATGTTCGTC-----------------TGTCC

Size

Hit Count

Total Norm

droTak1

ACGTAAAAGT---CAGTTCTTGT---C--TATTTTTATAACCTTGCAG--AGGGTATTATGATTTTAGTAAGA-----------------------AGT-TTGC-AACCCTATAAAGTAT-AAATGTTCTTGATCAGCATCACTAGACGAGTCGATCTAA-CC----------------------------------ATGTCC

Size

Hit Count

Total Norm

droEle1

ATTAC---TT---CCT---ATTT---A--TTTTTTTATATTATTGCAG--AGGGTATTATGATTTCAGTCAGA-----------------------AGT-TTGC-GACCCTGTAAAGTAT-ATATATTCTTGATCAGCATCACTAGGAGAGTCGATCTAG-CC---------ATGTCCGTC-----------------TGTCC

Size

Hit Count

Total Norm

droRho1

TTG---AGGT---ATTTTATT-T---T--TGTTTTTATACCCTTGCAG--AGGGTATTATAATTTTGGTCAAAAGTGTGCAACGCAGTGAAGGAGACAT-CTCC-GACCATATAAAGTAT-ATATATTCTTGATCAGGATCACCT----------------------------------------------------------

Size

Hit Count

Total Norm

droFic1

AATTCAACTTAAGAACTCGTTTC---A--TGTTTTTATACCCTTGCAG--AGCATATATTATTTTTAGTTGGAAGTTTGAAACTCAGTAAAGGAGACTTACTCC-GAAAACTGTAAAAAT-ATATATTCTTAAGAAAGGTA-------------------------------------------------------------A

Size

Hit Count

Total Norm

droKik1

T-------------------------------TTTTATACCCTTGCAG----GGTATTATAAGT---------------------------GGAGACGT-TTCC-GACCCTATAAAGTAT-ATATATTCTTGATCATATAAAATTATAACTTGGCTGTTTTTCAATATTTTTGCATCTTTT-------------TTGAGATAT

Size

Hit Count

Total Norm

droAna3

TTAT----TT---CCTTTGTTCT---T--CGTTTTTATACCCTTGCAG--AGGGTATTATAATTTTGGTCAAAAGTGTGCAACGCAGAGAAGGAGACAT-CTCC-GACCCTATAAAGTAT-ATATATTCTTGATCAGGATCACCT----------------------------------------------------------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
............................................................AATTTTGGTCAAAAGTGTGCAACGCA.....................................................................................................................	26	820	0.00	0.00	0.00	0.00	0.00
....................................................................................CAGAGAAGGAGCCAT-CTCC-GT................................................................................................	21	8	0.13	0.00	0.00	0.13	0.00
.....................................................................................AGAGAAGGAGGCAA-CTC....................................................................................................	17	11	0.09	0.00	0.00	0.09	0.00
............................................................................GTGCAACGCACAGCAGGAGACAT-C......................................................................................................	24	11	0.09	0.00	0.00	0.00	0.09
............................................................................GTGCAGCGCAxAGAAGGA.............................................................................................................	17	15	0.07	0.00	0.00	0.07	0.00
......................................................................AAAAGTGGGCAACGCAGAGAAGA..............................................................................................................	23	27	0.04	0.00	0.00	0.04	0.00
......................................................................AAAAGTGTGCAACGCAGAGAAGGA.............................................................................................................	24	796	0.00	0.00	0.00	0.00	0.00
............................................................................GTGCAGCGCAxAGAAGGAG............................................................................................................	18	15	0.07	0.00	0.00	0.07	0.00
.......................................................................AAAGTGTGCAACGCAGAAG.................................................................................................................	19	45	0.02	0.00	0.02	0.00	0.00
...........................................................................TGTGCAACGCAGAAAAGGAGACAT-.......................................................................................................	24	32	0.03	0.03	0.00	0.00	0.00

droBip1

A--TTTAGTT---TTGTTGTTCT---T--GTTTTTTATACCCTTGCAG--AGGGTATTATAATTTTGGTCAGAAGTGTGCAACGCAGTAAAGGAGACAT-CTCC-GACCCTATAAAGTAT-ATATATTCTTGATCAGGATCACCT----------------------------------------------------------

Size

Hit Count

Total Norm

dp4

CCGTTCGCCT---TTTTGGTTCTTTAT--TGTTTTTATACCCTTCTAG--AGAGTATTACGATTTTGGGCTAATGTCTGCAAGACTGGA-ACCTGCAAC-ATAG-AATCCCATAGGGTATTATATAT-----ATGAGGATCGGTAGCCATCTCTCTT-TTTCT----------------------------------ATACAC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
....................TCTTTAT--TGTTTTCTTAC...................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

CCGTTCGCCT---TTTTGGTTCTTTAT--TGTTTTTATACCCTTCTAG--AGAGTATTATGATTTTGGGCTGCTGTCTGCAAGGCTGAAATCTA-TTGC-ATAG-AATCCTATAGGGTATTATATAT-----GTCAGGATCGG-------------------------------------------------------TAGCC

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TTT-----------TTTTGATTT---T--CTTTTTTATAACCTTGCAAAAAGGGTATATTCATTTTGGTCAAAGGAA-----------------TGCAT-CTCC-GACCATGTAAATTAT-ATATATTCTTGATTAGCACGACGAGACGAGTTCATATAG------------------------------------------C	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.....................................................................................................................TAT-ATATATTCTTGATCAGCACGACG...........................................................	26	41	0.37	0.00	0.34	0.00	0.02
...........................................................................................................................ATATTCTTGATCAGCACGACG...........................................................	21	45	0.29	0.02	0.18	0.02	0.07
............................................................................................................................TATTCTTGATCAGCACGACGA..........................................................	21	45	0.29	0.02	0.02	0.02	0.22
.................................................................................................................................TTGATCAGCACGACGAGACGAGT...................................................	23	35	0.26	0.03	0.20	0.03	0.00
.................................................................................................................................TTGATCAGCACGACGAGACGAG....................................................	22	35	0.26	0.06	0.17	0.03	0.00
.....................................................................................................................................TCAGCACGACGAGACGAGTTC.................................................	21	33	0.24	0.09	0.03	0.12	0.00
.................................................................................................................................TTGATCAGCACGACGAGACGAGTTC.................................................	25	33	0.24	0.00	0.21	0.03	0.00
..................................................................................................................................TGATCAGCACGACGAGACGAG....................................................	21	35	0.20	0.11	0.06	0.03	0.00
.................................................................................................................................TTGATCAGCACGACGAGACGAGTT..................................................	24	35	0.17	0.03	0.14	0.00	0.00
.................................................................................................................................TTGATCAGCACGACGAGACGA.....................................................	21	36	0.17	0.03	0.08	0.06	0.00
.............................................................................................................................ATTCTTGATCAGCACGACGA..........................................................	20	45	0.11	0.07	0.00	0.00	0.04
..................................................................................................................................TGATCAGCACGAAGAGACGAG....................................................	21	36	0.14	0.08	0.00	0.06	0.00
.....................................................................................................................TAT-ATATATTCTTGATCAGCACGACGA..........................................................	27	40	0.13	0.00	0.13	0.00	0.00
.................................................................................................................................TTGATCAGCACGACGAGACG......................................................	20	39	0.13	0.05	0.03	0.03	0.03
..........................................................................................................................TATATTCTTGATCAGCACGAC............................................................	21	47	0.11	0.02	0.06	0.00	0.02
.................................................................................................................................TTGATCAGCACGACGAGACGAGTTCA................................................	26	33	0.15	0.06	0.09	0.00	0.00
..............................................................................................................................TTCTTGATCAGCACGAGGAGA........................................................	21	42	0.10	0.00	0.00	0.00	0.10
...............................................................................................................................TCTTGATCAGCACGACGAGACGAGTT..................................................	26	34	0.12	0.00	0.12	0.00	0.00
.................................................................................................................................TTGATCAGCACGACGAGACGAGTTG.................................................	25	35	0.11	0.00	0.11	0.00	0.00
...................................................................................................................................GATCAGCACGACGAGACGA.....................................................	19	36	0.11	0.08	0.03	0.00	0.00
..................................................................................................................................TGATCAGCACGACGAGACGAGT...................................................	22	35	0.09	0.00	0.03	0.06	0.00
.......................................................................................................................T-ATATATTCTTGATCAGCACGACGA..........................................................	25	42	0.07	0.00	0.07	0.00	0.00
...................................................................................................................................GATCAGCACGACGAGACGAGT...................................................	21	35	0.09	0.00	0.09	0.00	0.00
............................................................................................................................TATTCTTGATCAGCACGACG...........................................................	20	45	0.07	0.00	0.02	0.00	0.04
...............................................................................................................................TCTTGATCAGCACGACGAGACGAGT...................................................	25	34	0.09	0.00	0.09	0.00	0.00
..................................................................................................................................TGATCAGCACGACGAGACGAGTTCA................................................	25	33	0.09	0.00	0.09	0.00	0.00
......................................................................................................................AT-ATATATTCTTGATCAGCACGACG...........................................................	25	41	0.07	0.00	0.07	0.00	0.00
.......................................................................................................................................AGCATGACGAGACGAGTTCATATAG------------------------------------------C	26	32	0.09	0.00	0.09	0.00	0.00
...............................................................................................................................TCTTGATCAGCACGACGAGACGAG....................................................	24	34	0.09	0.00	0.09	0.00	0.00
..........................................................................................................................TATATTCTTGATCAGCACGACG...........................................................	22	44	0.07	0.00	0.05	0.00	0.02

droVir3

GAACTCGTTT---CTGGTGTACG---TCGTGTTTTTATACCCTTGTAG--AGAGTATTTTAATTTTGTCGTGGAATGTGCAACGCATGGATGGAGACAT-TTGG-GACCCCATAAAGTAT-ATGTATTCTAGATAA-------------------------------------------------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.........................................................TTTAATTTTGTCGTxGAATGTG............................................................................................................................	21	8	1.13	1.13	0.00	0.00	0.00	0.00
..........................................................TTAATTTTGTCGTxGAATGTGT...........................................................................................................................	21	7	0.71	0.57	0.14	0.00	0.00	0.00
.......................................................................................................................................A-------------------------------------------------------------------	18	2	1.50	0.00	0.00	0.00	0.00	1.50
...................................TATACCCTTGCAG--AGAGTATTA................................................................................................................................................	22	16	0.06	0.06	0.00	0.00	0.00	0.00
...........................................................TAATTTTGTCGTGGAAGT..............................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00	0.00
.......TTT---GTGGTGTACG---TTGTGT...........................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................................................................................................................................A-------------------------------------------------------------------	18	2	0.50	0.00	0.00	0.50	0.00	0.00

droMoj3

GGTTTCAGTT---CTTTTGTTTT---T--T--TTTGATATCCC---AA--A-TGTGAAGT-------GCTAAAGAGTTGAAATTCG-GAATGTAGATTGGCATTGAGTTCAATAAGATAT---------------------------GGCGGATATATTGT------------------------------------AT-ACA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.........................................................................AAGTTGAAATTCG-GTATGTAG............................................................................................................	21	1	2.00	2.00	0.00	0.00	0.00
...........................................................................GTTGAAATTCG-GTATGTAGGT..........................................................................................................	21	1	2.00	2.00	0.00	0.00	0.00
..........................................................................AGTTGAAATTCG-GTATGTAGG...........................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
............................................................................CTGAAATTTG-GAATGTAGA...........................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droGri2

ATTGACAA------ATTTATTTT---T--AATTCTTCTTTTGTTCGAG--TGGGTATAACAGGTA-----------------------GAAGGAAGCAT-CTCC-GACGCCATAAAGTAT-ATATGTTTCTGAGAAGGATCAATTGAGGAGTCGATGTAGTTC-------------------------------------GTC	Size	Hit Count	Total Norm	V109 Male body
..........................................................ACAGGCA-----------------------GAAGGAAGCAT-.......................................................................................................	18	1	1.00	1.00

Generated: 04/20/2012 at 05:18:35 EDT

dme-mir-4974

chr2L:21263932-21264034 +

Known_mirbase

intron

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