dme-mir-973- Best orthologs

dme-mir-973	chrX:19445561-19445661 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 19445579-19445599
   star strand at position 19445623-19445644
   mutations
   read mismatches

Notes: "chrX:11,892,000-11,893,400 yakuba gap was resequenced; found the 973 and 974 ortholog. Did not find the 972 ortholog."

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:19445546-19445676 +		1	AATAT-ACTT----CACT-----T---------TACCGTCGTCGACTTTTCGTGGTTGGTGGTTGAACTTCGATTTTAA--GTATTT----------AAATAAAATGAAATCTGTTCATTCTCCGACACAAGAAGTTCAC-GCAAAGGA------GCTGC------------------AGCTGCGAA
droSim1	chrX:15011303-15011407 +	LASTZ	1	C---------------------------------------GTATACTTTTCCGGGTTGGTGGTTGAACTTCGATTTTAA--GCATTT----------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCAC-GTGAAGAA------GCAGC------------------GAA------
droSec1	super_8:1727974-1728085 +	LASTZ	1	ACT--------------------------------TCAACGTATACTTTTCGGGGTTGGTGGTTGAACTTCGATTTTAG--GTATTT----------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCAC-GTGAAGAA------GCAGC------------------GAG------
droYak2	Unknown	MAF	1	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEre2	scaffold_4690:9682299-9682417 +	LASTZ	1	ACTAT-A--C----CATT-----T------------TAACGTCGACTTTTCGTGGTTGGTGGCTGAACTTAGATTTTGA--GTATTC----------AAATAAAA-TAAATCTGTTCATTCCTCGACACAAGAAGTTGAC-GTGCAGGA------GCGGC------------------AAA------
droEug1	scf7180000409109:6855-6998 -	LASTZ	4	AAGTC-A----AACTTTTATAAATCATTAAAGATTCCAACGACGACTTCTCGTGTTTGGTGACTGAACTTGGATTTTGA--ATATTT----------AAATAAAA-TAAATCTGTTCAATCCTCAACACGAGAAGTCGAC-GTAAATGA------CCAGC------------------AAACATAAA
droBia1	scf7180000302069:1157467-1157589 -	LASTZ	4	AATGA-ATTT----GATG-----T------------TAACGCCGACTTTAGGTGTTTGGTGGCTGAACTTGGATTTTTA--ACAGTT----------GAATGTAT-TAAATCTGTTCATTCCTCAACACAAAAAGTTGAC-GTTAAGGC------CCAGC------------------ATA----AA
droTak1	scf7180000415169:850730-850846 -	LASTZ	4	AGTTT-A--------ATT-----T------------TAACGTCGACTTTTCGTGTTTGGGGGCTGAACTCTGATTTTTA--ATAATT----------GAATTAAG-TAAATCTGTTCATTCCTCGACACAAGAAGTTGGC-GTAAAGTA------ACAGC------------------GCA------
droEle1	scf7180000490751:1106831-1106973 +	LASTZ	4	AAAAC-GGTTATACAACTTAGAATTATTTAATAGTATGACATCGACTTTTTGTGTTTGGCGGATGAACTTAGATTTTTC--TTATTT----------GTA-AAAA-CAAATCTGTTCATTCCTCGACGCAAAAAGTTGATTGTTAAAAA------CCAGC------------------ACAC-----
droRho1	scf7180000761121:198723-198828 -	LASTZ	4	A-------------------------------------ACATCGACTTCTCGTGTTTGGCGTCTGAACTCAGATTCTTA--ACAGTT----------GTGTTAAATAAAATCTGTTCATTCCTCGACACAAGAAGTTGAC-GTTAAG-A------CCAGC------------------ATA------
droFic1	scf7180000454073:1723943-1724040 +	LASTZ	4	G-------------------------------------ACATTGACATCTCGTGTTTGGCGAATGAGCTCGGATTTTTGTAGTATTT----------GAATAAGA-TAAATCTGTTCATTCCTCGACACAAGAAGTTGAA-GTTGAT----------------------------------------
droKik1	scf7180000302517:1176199-1176317 +	LASTZ	4	AAAAACACAC----AATA-------------------TAAATTGACTTTTCGTGCTTGGCGATTGAAGGTGGATTTGTG--ATTTTT----------AAGC-AAT-TAAATCTGTTCAATCGTCAACACTAAAAGTTGAT-GTTATTTA------GCTTC------------------GAA------
droAna3	scaffold_13417:2478622-2478750 -	LASTZ	1	G-------------------------------------ACACCGACTCCTCGTGTTTGGCGATTGAACCTGGATTTTTA--ATTTTC----------GAGTACGA-GAAATCTGTTCATTCCTCGACACTAGTAGTTGGC-GCGACA-C------TCAGCGCACCAAACATGAACCGCGGCTCAAAT
droBip1	scf7180000395874:49685-49789 -	LASTZ	4	------------------------------------------CGACTTCTCGTGTTAGGCGATTGAACCTGGATTT-AA--ATTTTC----------GAGTACGA-GAAATCTGTTCAATCCTCGACACTAGCAGTTGGC-GCGACCG-------ACTGC------------------GCATAAAAA
dp4	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181096:7946449-7946592 +	LASTZ	1	AAAAT-ATAT----C----------GGGAATATTGTCGACATGGCCTTTTCGTGTTTGGTGATTGAACTTGGATTTTGT-TCTATATACATATATAAAAAT-ATG-TAAATCTGTTCATTCCTCGACACTAGAAGTTCAT-GTCAATAACTTCATTTCCTGC----------------A--------
droVir3	scaffold_13042:918337-918453 -	LASTZ	1	AGAAC-AGTT----AAAA-----TCAT--------CGGACATTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTT--TTATAT---------------ACA-CAAATCTGTTCATTCCTCGACACTAGAAGTTTGC-GTCAATAA------GCTGC---------------------------
droMoj3	scaffold_6328:2909116-2909204 -	LASTZ	1	------------------------------------CGGCTTTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTA--AAATAT----------GA---AAA-GAAATCTGTTCATTCCTCGACACTAAGAGTTTAG-G---------------------------------------------
droGri2	scaffold_15081:2051526-2051596 -	LASTZ	3	G-------------------------------------ACATTTACTTTTTGTGTTGGGTGATTC----------------------------------------------TGATTCACTTTTCGACACATCAAGTTCAC-CTCAATAA------ACTGC------------------A--------

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	AATAT-ACTT----CACT-----T---------TACCGTCGTCGACTTTTCGTGGTTGGTGGTTGAACTTCGATTTTAA--GTATTT----------AAATAAAATGAAATCTGTTCATTCTCCGACACAAGAAGTTCAC-GCAAAGGA------GCTGC------------------AGCTGCGAA
droSim1	C---------------------------------------GTATACTTTTCCGGGTTGGTGGTTGAACTTCGATTTTAA--GCATTT----------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCAC-GTGAAGAA------GCAGC------------------GAA------
droSec1	ACT--------------------------------TCAACGTATACTTTTCGGGGTTGGTGGTTGAACTTCGATTTTAG--GTATTT----------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCAC-GTGAAGAA------GCAGC------------------GAG------
droYak2	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEre2	ACTAT-A--C----CATT-----T------------TAACGTCGACTTTTCGTGGTTGGTGGCTGAACTTAGATTTTGA--GTATTC----------AAATAAAA-TAAATCTGTTCATTCCTCGACACAAGAAGTTGAC-GTGCAGGA------GCGGC------------------AAA------
droEug1	AAGTC-A----AACTTTTATAAATCATTAAAGATTCCAACGACGACTTCTCGTGTTTGGTGACTGAACTTGGATTTTGA--ATATTT----------AAATAAAA-TAAATCTGTTCAATCCTCAACACGAGAAGTCGAC-GTAAATGA------CCAGC------------------AAACATAAA
droBia1	AATGA-ATTT----GATG-----T------------TAACGCCGACTTTAGGTGTTTGGTGGCTGAACTTGGATTTTTA--ACAGTT----------GAATGTAT-TAAATCTGTTCATTCCTCAACACAAAAAGTTGAC-GTTAAGGC------CCAGC------------------ATA----AA
droTak1	AGTTT-A--------ATT-----T------------TAACGTCGACTTTTCGTGTTTGGGGGCTGAACTCTGATTTTTA--ATAATT----------GAATTAAG-TAAATCTGTTCATTCCTCGACACAAGAAGTTGGC-GTAAAGTA------ACAGC------------------GCA------
droEle1	AAAAC-GGTTATACAACTTAGAATTATTTAATAGTATGACATCGACTTTTTGTGTTTGGCGGATGAACTTAGATTTTTC--TTATTT----------GTA-AAAA-CAAATCTGTTCATTCCTCGACGCAAAAAGTTGATTGTTAAAAA------CCAGC------------------ACAC-----
droRho1	A-------------------------------------ACATCGACTTCTCGTGTTTGGCGTCTGAACTCAGATTCTTA--ACAGTT----------GTGTTAAATAAAATCTGTTCATTCCTCGACACAAGAAGTTGAC-GTTAAG-A------CCAGC------------------ATA------
droFic1	G-------------------------------------ACATTGACATCTCGTGTTTGGCGAATGAGCTCGGATTTTTGTAGTATTT----------GAATAAGA-TAAATCTGTTCATTCCTCGACACAAGAAGTTGAA-GTTGAT----------------------------------------
droKik1	AAAAACACAC----AATA-------------------TAAATTGACTTTTCGTGCTTGGCGATTGAAGGTGGATTTGTG--ATTTTT----------AAGC-AAT-TAAATCTGTTCAATCGTCAACACTAAAAGTTGAT-GTTATTTA------GCTTC------------------GAA------
droAna3	G-------------------------------------ACACCGACTCCTCGTGTTTGGCGATTGAACCTGGATTTTTA--ATTTTC----------GAGTACGA-GAAATCTGTTCATTCCTCGACACTAGTAGTTGGC-GCGACA-C------TCAGCGCACCAAACATGAACCGCGGCTCAAAT
droBip1	------------------------------------------CGACTTCTCGTGTTAGGCGATTGAACCTGGATTT-AA--ATTTTC----------GAGTACGA-GAAATCTGTTCAATCCTCGACACTAGCAGTTGGC-GCGACCG-------ACTGC------------------GCATAAAAA
droWil1	AAAAT-ATAT----C----------GGGAATATTGTCGACATGGCCTTTTCGTGTTTGGTGATTGAACTTGGATTTTGT-TCTATATACATATATAAAAAT-ATG-TAAATCTGTTCATTCCTCGACACTAGAAGTTCAT-GTCAATAACTTCATTTCCTGC----------------A--------
droVir3	AGAAC-AGTT----AAAA-----TCAT--------CGGACATTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTT--TTATAT---------------ACA-CAAATCTGTTCATTCCTCGACACTAGAAGTTTGC-GTCAATAA------GCTGC---------------------------
droMoj3	------------------------------------CGGCTTTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTA--AAATAT----------GA---AAA-GAAATCTGTTCATTCCTCGACACTAAGAGTTTAG-G---------------------------------------------
droGri2	G-------------------------------------ACATTTACTTTTTGTGTTGGGTGATTC----------------------------------------------TGATTCACTTTTCGACACATCAAGTTCAC-CTCAATAA------ACTGC------------------A--------

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				None											None	None
UNAFold Image				None											None	None

Small RNA-seq read pileup

Species

Alignment

droSim1

C---------------------------------------GTATACTTTTCCGGGTTGGTGGTTGAACTTCGATTTTAA--GCATTT----------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCAC-GTGAAGAA------GCAGC------------------GAA------	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..............................................................................................................TCTGTTCATTCTTCGACCCAAA.......................................................	22	1	276.00	0.00	3.00	272.00	1.00
..............................................................................................................TCTGTTCATTCTTCGACCCAA........................................................	21	1	207.00	0.00	7.00	200.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACCCA.........................................................	20	1	83.00	0.00	17.00	66.00	0.00
.............................................................................................................ATCTGTTCATTCTTCGACCCA.........................................................	21	1	15.00	0.00	0.00	15.00	0.00
............................................................................................................AATCTGTTCATTCTTCGACCC..........................................................	21	1	12.00	0.00	1.00	11.00	0.00
............................................................................................................AATCTGTTCATTCTTCGACCCA.........................................................	22	1	12.00	0.00	0.00	12.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACCCAAAA......................................................	23	1	12.00	0.00	0.00	12.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACCC..........................................................	19	1	10.00	0.00	1.00	9.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACC...........................................................	18	1	9.00	0.00	3.00	6.00	0.00
.............................................................................................................ATCTGTTCATTCTTCGACCCAA........................................................	22	1	7.00	0.00	0.00	7.00	0.00
.............................................................................................................ATCTGTTCATTCTTCGACCCAAA.......................................................	23	1	5.00	0.00	0.00	5.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACCCAG........................................................	21	1	4.00	0.00	0.00	4.00	0.00
............................................................................................................AATCTGTTCATTCTTCGACCCT.........................................................	22	1	4.00	0.00	0.00	2.00	2.00
..............................................................................................................TCTGTTCATTCTTCGACCCG.........................................................	20	1	3.00	0.00	0.00	3.00	0.00
.............................................................................................................ATCTGTTCATTCTTCGACCC..........................................................	20	1	3.00	0.00	0.00	3.00	0.00
.............................................................................................................ATCTGTTCATTCTTCGACC...........................................................	19	1	3.00	0.00	1.00	2.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACCCAAT.......................................................	22	1	2.00	0.00	0.00	2.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACCCT.........................................................	20	1	2.00	0.00	0.00	2.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACCCACC.......................................................	22	1	2.00	0.00	0.00	2.00	0.00
............................................................................................................AATCTGTTCATTCTTCGACCCAA........................................................	23	1	2.00	0.00	0.00	2.00	0.00
............................................................................................................AATCTGTTCATTCTTCGAC............................................................	19	1	2.00	0.00	0.00	2.00	0.00
.............................................................................................................ATCTGTTCATTCTTCAACCCA.........................................................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTATTCGACCC..........................................................	19	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACCCAAG.......................................................	22	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................ATCTGTTCATTCTTCGACCAAA........................................................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACCCCAA.......................................................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTGATTCTTCGACCCAAA.......................................................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCTTCTACCCAAA.......................................................	22	1	1.00	0.00	0.00	1.00	0.00
............................................................................................................AATCTGTTCATTCTTCGACTC..........................................................	21	1	1.00	0.00	0.00	1.00	0.00
............................................................................................................AGTCTGTTCATTCTTCGACCC..........................................................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCTTCCACCCAAA.......................................................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTTTTCATTCTTCGACCCAAA.......................................................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCGGTTCATTCTTCGACCCA.........................................................	20	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TTTGTTCATTCTTCGACCCAA........................................................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGATCATTCTTCGACCCAAA.......................................................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCTTCGGCCCAAA.......................................................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TATGTTCATTCTTCGACCCAAA.......................................................	22	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCCGTTCATTCTTCGACCCAAA.......................................................	22	1	1.00	0.00	0.00	1.00	0.00
............................................................................................................AATCTGTTCATTCTTCGACC...........................................................	20	1	1.00	0.00	0.00	1.00	0.00
..................................................TCGCGTTGGTGGTTGAACTTC....................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................CTGTTCATTCTTCGACCCAA........................................................	20	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................ATCTGTTCATTCTTCGACCCT.........................................................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCTTCCACCCA.........................................................	20	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................ATCCGTTCATTCTTCGACCCA.........................................................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACCCAC........................................................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACCCAAAGA.....................................................	24	1	1.00	0.00	0.00	1.00	0.00

droSec1

ACT--------------------------------TCAACGTATACTTTTCGGGGTTGGTGGTTGAACTTCGATTTTAG--GTATTT----------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCAC-GTGAAGAA------GCAGC------------------GAG------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.............................................................................................................ATCTGTTCATTCTTCGACCCAA........................................................	22	1	6.00	3.00	1.00	2.00
..............................................................................................................TCTGTTCATTCTTCGACCCAA........................................................	21	1	3.00	2.00	1.00	0.00
.............................................................................................................ATCTGTTCATTCTTCGACCCA.........................................................	21	1	2.00	1.00	1.00	0.00
..................................................CGGGGTTGGTGGTTGAACTTCGATT................................................................................................................	25	1	1.00	0.00	1.00	0.00
..................................................................................................................TTCATTCTTCGACCCAAAAAGT...................................................	22	1	1.00	1.00	0.00	0.00
.......................................................................................................................TATTCGACCCAATAAGTT..................................................	18	2	0.50	0.00	0.00	0.50
...................................................GGGGTTGGTGGTTGAACTTCGA..................................................................................................................	22	1	1.00	1.00	0.00	0.00
...................................................GGGGTTGGTGGTTGAACTTCG...................................................................................................................	21	1	1.00	1.00	0.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACCCAAA.......................................................	22	1	1.00	0.00	1.00	0.00
.............................................................................................................ATCTGTTCATTCTTCGACCCAAA.......................................................	23	1	1.00	1.00	0.00	0.00
................................................TTCGGGGTCGGTGGTTCAA........................................................................................................................	19	1	1.00	1.00	0.00	0.00

droYak2

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

ACTAT-A--C----CATT-----T------------TAACGTCGACTTTTCGTGGTTGGTGGCTGAACTTAGATTTTGA--GTATTC----------AAATAAAA-TAAATCTGTTCATTCCTCGACACAAGAAGTTGAC-GTGCAGGA------GCGGC------------------AAA------	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..............................................................................................................TCTGTTCATTCCTCGACACAAGT......................................................	23	1	6.00	0.00	1.00	0.00	5.00
..............................................................................................................TCTGTTCATTCCTCGACACAAG.......................................................	22	1	5.00	0.00	1.00	0.00	4.00
..............................................................................................................TCTGTTCATTCCTCGACACA.........................................................	20	1	2.00	0.00	1.00	0.00	1.00
..............................................................................................................TCTGTTCATTCCTCGACACAA........................................................	21	1	2.00	0.00	0.00	0.00	2.00
..............................................................................................................TCTGTTCATTCCTCGGCACAAGT......................................................	23	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................TCTGCTCATTCCTCGACACAAG.......................................................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................TCTGTCCATTCCTCGACACAAG.......................................................	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................CAGGGAGTTGAC-GTGCAGG.......................................	19	1	1.00	1.00	0.00	0.00	0.00
..................................................CGTGGTTGGTGGCTGAACTTAGA..................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00

droEug1

AAGTC-A----AACTTTTATAAATCATTAAAGATTCCAACGACGACTTCTCGTGTTTGGTGACTGAACTTGGATTTTGA--ATATTT----------AAATAAAA-TAAATCTGTTCAATCCTCAACACGAGAAGTCGAC-GTAAATGA------CCAGC------------------AAACATAAA

Size

Hit Count

Total Norm

droBia1

AATGA-ATTT----GATG-----T------------TAACGCCGACTTTAGGTGTTTGGTGGCTGAACTTGGATTTTTA--ACAGTT----------GAATGTAT-TAAATCTGTTCATTCCTCAACACAAAAAGTTGAC-GTTAAGGC------CCAGC------------------ATA----AA

Size

Hit Count

Total Norm

droTak1

AGTTT-A--------ATT-----T------------TAACGTCGACTTTTCGTGTTTGGGGGCTGAACTCTGATTTTTA--ATAATT----------GAATTAAG-TAAATCTGTTCATTCCTCGACACAAGAAGTTGGC-GTAAAGTA------ACAGC------------------GCA------

Size

Hit Count

Total Norm

droEle1

AAAAC-GGTTATACAACTTAGAATTATTTAATAGTATGACATCGACTTTTTGTGTTTGGCGGATGAACTTAGATTTTTC--TTATTT----------GTA-AAAA-CAAATCTGTTCATTCCTCGACGCAAAAAGTTGATTGTTAAAAA------CCAGC------------------ACAC-----

Size

Hit Count

Total Norm

droRho1

A-------------------------------------ACATCGACTTCTCGTGTTTGGCGTCTGAACTCAGATTCTTA--ACAGTT----------GTGTTAAATAAAATCTGTTCATTCCTCGACACAAGAAGTTGAC-GTTAAG-A------CCAGC------------------ATA------

Size

Hit Count

Total Norm

droFic1

G-------------------------------------ACATTGACATCTCGTGTTTGGCGAATGAGCTCGGATTTTTGTAGTATTT----------GAATAAGA-TAAATCTGTTCATTCCTCGACACAAGAAGTTGAA-GTTGAT----------------------------------------

Size

Hit Count

Total Norm

droKik1

AAAAACACAC----AATA-------------------TAAATTGACTTTTCGTGCTTGGCGATTGAAGGTGGATTTGTG--ATTTTT----------AAGC-AAT-TAAATCTGTTCAATCGTCAACACTAAAAGTTGAT-GTTATTTA------GCTTC------------------GAA------

Size

Hit Count

Total Norm

droAna3

G-------------------------------------ACACCGACTCCTCGTGTTTGGCGATTGAACCTGGATTTTTA--ATTTTC----------GAGTACGA-GAAATCTGTTCATTCCTCGACACTAGTAGTTGGC-GCGACA-C------TCAGCGCACCAAACATGAACCGCGGCTCAAAT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..............................................................................................................TCTGTTCATTCCTCGACACTAG.......................................................	22	1	13.00	9.00	2.00	2.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTAGT......................................................	23	1	6.00	4.00	2.00	0.00	0.00
..................................................CGTGTTTGGCGATTGAACCTGG...................................................................................................................	22	1	5.00	5.00	0.00	0.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTA........................................................	21	1	4.00	4.00	0.00	0.00	0.00
..................................................CGTGTTTGGCGATTGAACCTGGAT.................................................................................................................	24	1	2.00	2.00	0.00	0.00	0.00
..................................................CGTGTTTGGCGATTGAACCTGGATT................................................................................................................	25	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................ATGTTCATTCCTCGACACTAG.......................................................	21	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................CTCTGTTCATTCCTCGACACTAG.......................................................	23	1	1.00	1.00	0.00	0.00	0.00
..................................................CGTGTTTGGCGATTGAACCTGGAA.................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................TCTGTTCAATCCTCGACACTAG.......................................................	22	1	1.00	1.00	0.00	0.00	0.00
.....................................................GTTTGGCTATGGAACCTGGATT................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................CTGTTCAGTCCTCGACACTAGT......................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................TGTTTGGCGATTGAACCTGGA..................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................TCTGTCCATTCCTCCACACTAG.......................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................................TGTTTGGCGATTGAACCTGGATT................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
..................................................CGTGTTTGGCGATTGAACCTGGT..................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
....................................................TGTTTGGCGCTTGAACCTGGTTT................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................CTGTTCATTCCTCGACACTAG.......................................................	21	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................CCTGTTCATTCCTCGACACTAGT......................................................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACT.........................................................	20	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................AAA-A------TCAGCGCACCAAACA.................	19	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................CTGTTCATTCCTCGACACTAGT......................................................	22	1	1.00	1.00	0.00	0.00	0.00

droBip1

------------------------------------------CGACTTCTCGTGTTAGGCGATTGAACCTGGATTT-AA--ATTTTC----------GAGTACGA-GAAATCTGTTCAATCCTCGACACTAGCAGTTGGC-GCGACCG-------ACTGC------------------GCATAAAAA

Size

Hit Count

Total Norm

dp4

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

AAAAT-ATAT----C----------GGGAATATTGTCGACATGGCCTTTTCGTGTTTGGTGATTGAACTTGGATTTTGT-TCTATATACATATATAAAAAT-ATG-TAAATCTGTTCATTCCTCGACACTAGAAGTTCAT-GTCAATAACTTCATTTCCTGC----------------A--------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..............................................TTTTCGTGTTTGGTGATTGAACT......................................................................................................................	23	1	64.00	30.00	0.00	1.00	33.00
..............................................TTTTCGTGTTTGGTGATTGAAC.......................................................................................................................	22	1	30.00	29.00	0.00	0.00	1.00
..............................................................................................................TCTGTTCATTCCTCGACACTAG.......................................................	22	1	23.00	0.00	0.00	0.00	23.00
..................................................................................................................TTCATTCCTCGACACTAGAAGT...................................................	22	1	20.00	20.00	0.00	0.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTAGA......................................................	23	1	13.00	0.00	0.00	0.00	13.00
..............................................TTTTCGTGTTTGGTGATTGAA........................................................................................................................	21	1	9.00	6.00	0.00	0.00	3.00
..............................................TTTTCGTGTTTGGTGATTGA.........................................................................................................................	20	1	5.00	5.00	0.00	0.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACT.........................................................	20	1	5.00	0.00	0.00	0.00	5.00
..................................................CGTGTTTGGTGATTGAACTTGGATT................................................................................................................	25	1	2.00	0.00	1.00	1.00	0.00
..............................................TTTTCGTGTTTGGTGATTGAACTT.....................................................................................................................	24	1	2.00	0.00	0.00	0.00	2.00
..............................................................................................................TCTGTTCATTCCTCGACACTA........................................................	21	1	2.00	1.00	0.00	0.00	1.00
...............................................TTTCGTGTTTGGTGATTGAACT......................................................................................................................	22	1	2.00	1.00	0.00	0.00	1.00
..............................................TTTTCGTGTTTGTTGATTGAACT......................................................................................................................	23	1	2.00	0.00	0.00	0.00	2.00
..............................................................................................................TCTGTTCATTCCTCGACACTAGG......................................................	23	1	2.00	0.00	0.00	0.00	2.00
..................................................................................................................TTCATTCCTCGACACTAGAAG....................................................	21	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................TCTGTTCATTCCTCGACACTAGC......................................................	23	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................TCTGTTCATTCCTCGGCACTAG.......................................................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................TCTGTTCATTCCTCGACAC..........................................................	19	1	1.00	0.00	0.00	0.00	1.00
..............................................TTTTCGTGTTTGTTGATTGAA........................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............................................TTTTCGTGTTTGCTGATTGAAC.......................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
..................................................CGTGTTTGGTGATTGAACTTGGATC................................................................................................................	25	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................TCTxTTCATTCCTCGACACTAG.......................................................	21	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................TCTGTTCATTCCTCTACACTAG.......................................................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................TCTGTTCATTCCTCGACACTAGT......................................................	23	1	1.00	0.00	0.00	0.00	1.00
..................................................CGTGTTTGGCGATTGAACTTGGATT................................................................................................................	25	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................TCCGTTCATTCCTCGACACTAG.......................................................	22	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................................TTCATTCCTCGACACTAGAAGTT..................................................	23	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................ATACATATATAAAACT-GTG-T................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
..............................................TTTTCGTGTTTGGTTATTGAACT......................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00

droVir3

AGAAC-AGTT----AAAA-----TCAT--------CGGACATTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTT--TTATAT---------------ACA-CAAATCTGTTCATTCCTCGACACTAGAAGTTTGC-GTCAATAA------GCTGC---------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..............................................................................................................TCTGTTCATTCCTCGACACTAG.......................................................	22	1	293.00	12.00	1.00	1.00	276.00	3.00
..............................................................................................................TCTGTTCATTCCTCGACACT.........................................................	20	1	257.00	1.00	0.00	0.00	247.00	9.00
.............................................................................................................ATCTGTTCATTCCTCGACACT.........................................................	21	1	134.00	9.00	0.00	0.00	123.00	2.00
..............................................................................................................TCTGTTCATTCCTCGACACTAGTC.....................................................	24	1	58.00	10.00	0.00	0.00	48.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTAGA......................................................	23	1	53.00	0.00	0.00	0.00	52.00	1.00
..............................................................................................................TCTGTTCATTCCTCGACACC.........................................................	20	1	39.00	0.00	0.00	0.00	38.00	1.00
..............................................................................................................TCTGTTCATTCCTCGACACTA........................................................	21	1	27.00	2.00	0.00	0.00	24.00	1.00
.............................................................................................................ATCTGTTCATTCCTCGACACTAG.......................................................	23	1	20.00	7.00	0.00	0.00	13.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTAGG......................................................	23	1	11.00	0.00	0.00	0.00	11.00	0.00
.............................................................................................................ATCTGTTCATTCCTCGACACC.........................................................	21	1	10.00	0.00	0.00	0.00	10.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTGG.......................................................	22	1	10.00	0.00	0.00	0.00	10.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACG.........................................................	20	1	10.00	0.00	0.00	0.00	10.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACAC..........................................................	19	1	7.00	0.00	0.00	0.00	7.00	0.00
..............................................................................................................TCTTTTCATTCCTCGACACTAG.......................................................	22	1	6.00	0.00	0.00	0.00	5.00	1.00
.............................................................................................................ATCTGTTCATTCCTCGACACTAGTC.....................................................	25	1	5.00	5.00	0.00	0.00	0.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACA...........................................................	18	1	4.00	0.00	0.00	0.00	4.00	0.00
..............................................................................................................TCTxTTCATTCCTCGACACTAG.......................................................	21	1	4.00	0.00	0.00	0.00	4.00	0.00
..............................................................................................................TCTGTTCATTCCTCTACACTAG.......................................................	22	1	4.00	0.00	0.00	0.00	4.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTAGT......................................................	23	1	3.00	0.00	0.00	0.00	3.00	0.00
..............................................................................................................TCTGTTCATTCCTxxACACTAG.......................................................	20	1	3.00	0.00	0.00	0.00	3.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACC...........................................................	18	1	3.00	0.00	0.00	0.00	3.00	0.00
.............................................................................................................ATCTGTTCATTCCTCGACACTGG.......................................................	23	1	2.00	0.00	0.00	0.00	2.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTG........................................................	21	1	2.00	0.00	0.00	0.00	2.00	0.00
.............................................................TTTGAAAATGGATTTTTT--T.........................................................................................................	19	1	2.00	0.00	0.00	0.00	2.00	0.00
.............................................................................................................ATCTGTTCATTCCTCGACA...........................................................	19	1	2.00	0.00	0.00	0.00	2.00	0.00
.............................................................................................................ATCTGTTCATTCCTCGACACTA........................................................	22	1	2.00	1.00	0.00	0.00	1.00	0.00
.............................................................................................................ATCTGTTCATTCCTCGACACG.........................................................	21	1	2.00	0.00	0.00	0.00	2.00	0.00
.............................................................................................................ATCTGTTCATTCCTCGACAC..........................................................	20	1	2.00	0.00	0.00	0.00	2.00	0.00
..............................................................................................................TCTGTTCATTCCTCGGCACTAG.......................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................CGTGTTCGATGTTTGAACT......................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................CCTGTTCATTCCTCGACACT.........................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................ATCTGTTCCTTCCTCGACACC.........................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................TCTTCATTCCTCGACACTAGA......................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCCTCTACACTAGA......................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGGTCATTCCTCGACACT.........................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................................TGTTCATTCCTCGACACTA........................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................CGTGTTCGATGTTTGAACTTGGATTT...............................................................................................................	26	1	1.00	1.00	0.00	0.00	0.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTAGC......................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCCTTGACACTAG.......................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................GCTGTTCATTCCTCGACACTAG.......................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
.............................................................................................................ATCTxTTCATTCCTCGACACTAG.......................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTTTTCATTCCTCGACACT.........................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................ATCTGTTCCTTCCTCGACACTAGG......................................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................ATCTGTTTATTCCTCGACACTAG.......................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................CTGTTCATTCCTCGACACT.........................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCCTCxACACTAG.......................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................ATCTTTTCATTCCTCGACACT.........................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTAGCC.....................................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCACTCCTCGACAC..........................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................TTTTTGAAGTTGGATTTTTT--..........................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTCGA......................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTC........................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................ATCTGTTCATTCCTCGAC............................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................ATCTGTTCATTCCTCTACACTC........................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................ATCTGTTCCTTCCTCGACACT.........................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACCC..........................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................CGTGTTCGATGTTTGAACTTGGATTTCC.............................................................................................................	28	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................ATCTGTTCATTCCTCTACACT.........................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTGTTCATTCTTCGACACTAG.......................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................TCTTTTCATTCCTCGACACTA........................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................CTGTTCATTCCTCGACACTAGTC.....................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.............................................................................................................ATCTGTTCATTCCTCAACACTAG.......................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................ATCTGTTCCTTCCTCGACACTAG.......................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00

droMoj3

------------------------------------CGGCTTTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTA--AAATAT----------GA---AAA-GAAATCTGTTCATTCCTCGACACTAAGAGTTTAG-G---------------------------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..............................................................................................................TCTGTTCATTCCTCGACACTA........................................................	21	1	14.00	14.00	0.00	0.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACT.........................................................	20	1	6.00	5.00	0.00	1.00	0.00
..................................................CGTGTTCGATGTTTGAACTTGGATTT...............................................................................................................	26	1	4.00	4.00	0.00	0.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTAA.......................................................	22	1	4.00	4.00	0.00	0.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTAT.......................................................	22	1	3.00	3.00	0.00	0.00	0.00
..................................................CGTGTTCGATGTTTGAACTTGGATT................................................................................................................	25	1	3.00	3.00	0.00	0.00	0.00
..................................................CGTGTTCGATGTTTGAACTTGGATC................................................................................................................	25	1	2.00	2.00	0.00	0.00	0.00
.............................................................................................................ATCTGTTCATTCCTCGACACT.........................................................	21	1	2.00	2.00	0.00	0.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTAAT......................................................	23	1	2.00	1.00	0.00	1.00	0.00
..................................................CGTGTTCGATGTTTGAACTTGGATTTC..............................................................................................................	27	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................ATCTGTTCATTCCTCTACACT.........................................................	21	1	1.00	0.00	0.00	1.00	0.00
..................................................CGTGTTCGATGTTTGAACTTGGATTTTC.............................................................................................................	28	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................ATCTGTTCATTCCTCGACACTA........................................................	22	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................ATCTGTTCATTCCTCGACACTAA.......................................................	23	1	1.00	0.00	0.00	1.00	0.00
..................................................CGTGTTCGATGTTTGAACTTGGATTC...............................................................................................................	26	1	1.00	1.00	0.00	0.00	0.00
..................................................CGTGTTCGATGTTTTAACTTGGATTT...............................................................................................................	26	1	1.00	1.00	0.00	0.00	0.00
..................................................CGTGTTCGATGTTTGGACTTGGATT................................................................................................................	25	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................TCTGTTCATTCCTCGACACTACC......................................................	23	1	1.00	1.00	0.00	0.00	0.00
..................................................CGTGTTCGATGTTTGAACTTGGTTTT...............................................................................................................	26	1	1.00	0.00	1.00	0.00	0.00

droGri2

G-------------------------------------ACATTTACTTTTTGTGTTGGGTGATTC----------------------------------------------TGATTCACTTTTCGACACATCAAGTTCAC-CTCAATAA------ACTGC------------------A--------	Size	Hit Count	Total Norm	V109 Male body
.........................................TTTACTTTTTGTGTTAGGAGA.............................................................................................................................	21	1	1.00	1.00

Generated: 04/20/2012 at 05:16:24 EDT

dme-mir-973

chrX:19445561-19445661 +

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