dme-mir-2494- Best orthologs

dme-mir-2494	chr3R:12444488-12444604 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 12444559-12444581
   star strand at position 12444510-12444530
   mutations
   read mismatches

Notes: droSec1 has insertion in the miR* and substitution in the miR that causes it to lose expression. droKik has a tRNA like structure. Many potential paralogs found for pseudoobscura miRNAs

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3R:12444473-12444619 +		1	GGC--AACCTGCCACTGTCCATCTTCCGACCGGCGATCAGTAAGTGCACC-----AGATTGGGAA------TAAC------------C-TTCAAAAGCTGCAACT-TAAATA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC-
droSim1	chr3R:9022585-9022731 -	LASTZ	1	GGC--AACCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACC-----AGATTGGGAA------TAAC------------C-TTCAAAAGCTGCAACT-TAAATA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC-
droSec1	super_12:1702814-1702963 -	LASTZ	4	GGC--ATCCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACCATA-GTAAA-TGGAA------TAAC------------C-TTCAAAATCTGCAACT-TAAATA--------TTC---CCAGTAATGTCCGCTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC-
droYak2	chr3R:11948210-11948356 -	LASTZ	1	GGC--GACCTGCCACTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCACC-----AGATTGGGAT------TAAC------------C-TTCAAAAGCTGCAGCT-TAACTA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGATGGCTGGGTGGACAA--CCTATTCGGACC-
droEre2	scaffold_4770:9192977-9193123 -	LASTZ	1	GGC--AACCTGCCCCTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCAAC-----AGATTGGGAG------TAAC------------C-GTCAAAAGCTACAACT-TCAATA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGCTGGATAGACAA--CCTATTCGGACC-
droEug1	scf7180000409557:86539-86685 -	LASTZ	5	GGC--AACCTGCCCGTGAGCATCTTTCGACCAGCGATCAGTAAGTCCACC-----AGATTGGGAT------TAAT------------C-TTCAAAAGTTGCAACT-TAAATA--------TTC---CCAGTAATGTCCACCTACAAGGAGCCTCTGAATGGGTGGGTGGACAA--TCTATTTGGACC-
droBia1	scf7180000299102:379899-380045 +	LASTZ	5	GGC--AACCTGCCCCTGTGTGTCTACCGGCCGGCGATCAGTAAGTGCATC-----AGATTGGAGT------TAAT------------C-TTGAACAGCTGCAACT-TAAATA--------TTC---CCAGTTATGTCCACCTACAAGGAGCCCGTAAGCGGGTGGGTGGACAA--TCTGTTTGGACC-
droTak1	scf7180000415580:230298-230451 -	LASTZ	5	GGC--AACCTGCCCCTGTCCATCTTCCGGCCGGCGATCAGTAAGTGCTTTACC-CCGCATGGGAT------TAAC------------C-TTCAAAAGCTGCAACT-TGAATA--------TTCCATCCAGTAATGTCCACCTACAAGGAGCCACTGAATGGGTGGGTGGACAA--TCTGTACGGACC-
droEle1	scf7180000490967:720355-720501 +	LASTZ	5	GAC--GCCCTGCCCTTGTGCATCTTCCGACCGGCGATCAGTAAGTGCTCC-----CGATTGGAAT------TGAC------------A-TTCA-AAGCTACAACCACAAATA--------TTC---CCAGTAATGTCCACCTACAAGGAGCCACTGCGTGGGTGGGTGGACAA--CCTATTCGGACC-
droRho1	scf7180000778413:42160-42305 -	LASTZ	5	GGC--AACCTGCCCTTGTGCATCTTCCGACCGGCAATCAGTAAGTGCACC-----AGATTGGGGT------GGAC------------C-TT-AAACGCTGCAACT-TAAATA--------TTC---ACAGTAATGTCCACCTACAAGGAGCCTTTCGACGGGTGGGTGGACAA--CATGTTCGGACC-
droFic1	scf7180000453796:140197-140344 -	LASTZ	5	GGC--GACCTGCCGCTCTGCATCTTCCGACCGGCGATCAGTAAGTGCACC-----AAACTTATAT------TGTC-----------TC-TTCAAAGGCTGCCACT-TGAATC--------TTT---ACAGTAATGTCCACCTACAAGGAACCCCTGCATGGCTGGGTGGACAA--CCTGTTTGGACC-
droKik1	scf7180000302475:105618-105766 -	LASTZ	5	GGT--GACCTGCCCCTGTGCGTCTTCCGACCGGCGATCAGTAAGTTA-AT-----AAATTAGGATACCCCAG---------------A-ATCTGGCGCTGCAACT-AACTTA--------TCC---TTAGTTATGCCTACCTACAAGGACCCCGTCGTTGGATGGACGGAGAA--TTTATATGGACC-
droAna3	scaffold_13340:7435217-7435360 -	LASTZ	5	GGC--AGCCTGCCAGTCAGCATTTATCGGCCTTCCATAAGTAAGTACTAT-----ATACGTCCTG------CTGT------------C-TTATAAAATTGTTATT-T---TT--------TTT---CTAGTAATTGCCACATATAAGGAGCCATTAGTTGGATGGGTGGATAA--CCTTTATGGACC-
droBip1	scf7180000396708:1418496-1418640 +	LASTZ	5	GGT--AGCCTACCGGTCAGCATTTATCGACCTGCCATAAGTAAGTGCTGT-----A--TTAATATTT----CTGT------------G-TTCTGAAACTGTTATT----GTT--------TCT---CTAGTAATTGGCACTTACAAGGAGCCATTAGTTGGGTGGATAGATAA--CCTCTATGGACCG
dp4	chr2:5294042-5294203 -	MAF	5	GGC--GACCTGCCCGTGTGCATTTTTCGGCCGGCCATTAGTAAGTTTTTCCTTAGATG--ATGCA------AGGCCTTGGATGGAA-CTGAAACATTGTGTAACA-TGACTC--------TCC---ACAGTCGTGCCCACCTACCAGGAGCCCGTCGTTGGTTGGACTGACAA--TCTGTACGGGCC-
droPer1	super_19:1006170-1006331 -	MAF	5	GGC--GACCTGCCCGTGTGCATTTTTCGGCCGGCCATTAGTAAGTTTTTCCTTAGATG--ATGCA------AGGCCTTGGATGGAA-CTGAAACATTGTGTAACA-TGACTC--------TCC---ACAGTCGTGCCCACCTACAAGGAGCCCGTCGTTGGTTGGACTGACAA--TCTGTACGGGCC-
droWil1	scaffold_181108:4575766-4575914 -	LASTZ	5	GGC--AATCTACCAATCTGTATTTTTCGCCCTGGTGTCAGTAAGTCCTCA-----AAATTCAACT------TGTA-----------AC-TAT---AGCT----GT-TAAATTTTCTCCTTATT---ATAGTTATTGCCACCGCCAAGGAGCCAGTTTCGGGTTGGATTGACAA--TTTATATGGACC-
droVir3	scaffold_13047:18500357-18500519 -	MAF	5	ACAAAAAGCTGCCCATTATCGTCACAAGGCCTTCCATCGGTATGTAGGTCCCG-CTAA--CTGGT------TGGGCTTGACAAGTA-ACCATATTTATTTTTTTT-TTTGTT--------CGC---CCAGTGACGGCGGCCATACACGAGCCCATGCCCGGATGGATTGAGGG--CGTGAACGGACC-
droMoj3	scaffold_6496:22335084-22335230 -	MAF	5	GCC--GGTCTGCCGGCAGCCATAGTTAGGCCATCCATAGGTGAGTCG---------AAGTATAAA------TCTA-----------AT-TGAGAAGGCCCTAACT-GA-CTG------CTATT---ACAGTATACGGTACACTGGAGCACCCCATGAAGGGCTGGGTGGGCAATGCCAACTCGGGTC-
droGri2	scaffold_15074:333824-333971 -	LASTZ	5	AGC--GGTTTGCCCATAAGCATCTTTCGCCCGGGTGTCAGTAAGTTCGTC-----GAATCATTAA------GATC-----------AG-TAAGAAGATGTTCTC----AGTC-----TCCATT---TCAGTTATTGGCAGCTACAAGGACCCCCTCCCGGGCTGGGTTGACAA--TCTATATGGTCC-

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	GGC--AACCTGCCACTGTCCATCTTCCGACCGGCGATCAGTAAGTGCACC-----AGATTGGGAA------TAAC------------C-TTCAAAAGCTGCAACT-TAAATA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC-
droSim1	GGC--AACCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACC-----AGATTGGGAA------TAAC------------C-TTCAAAAGCTGCAACT-TAAATA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC-
droSec1	GGC--ATCCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACCATA-GTAAA-TGGAA------TAAC------------C-TTCAAAATCTGCAACT-TAAATA--------TTC---CCAGTAATGTCCGCTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC-
droYak2	GGC--GACCTGCCACTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCACC-----AGATTGGGAT------TAAC------------C-TTCAAAAGCTGCAGCT-TAACTA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGATGGCTGGGTGGACAA--CCTATTCGGACC-
droEre2	GGC--AACCTGCCCCTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCAAC-----AGATTGGGAG------TAAC------------C-GTCAAAAGCTACAACT-TCAATA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGCTGGATAGACAA--CCTATTCGGACC-
droEug1	GGC--AACCTGCCCGTGAGCATCTTTCGACCAGCGATCAGTAAGTCCACC-----AGATTGGGAT------TAAT------------C-TTCAAAAGTTGCAACT-TAAATA--------TTC---CCAGTAATGTCCACCTACAAGGAGCCTCTGAATGGGTGGGTGGACAA--TCTATTTGGACC-
droBia1	GGC--AACCTGCCCCTGTGTGTCTACCGGCCGGCGATCAGTAAGTGCATC-----AGATTGGAGT------TAAT------------C-TTGAACAGCTGCAACT-TAAATA--------TTC---CCAGTTATGTCCACCTACAAGGAGCCCGTAAGCGGGTGGGTGGACAA--TCTGTTTGGACC-
droTak1	GGC--AACCTGCCCCTGTCCATCTTCCGGCCGGCGATCAGTAAGTGCTTTACC-CCGCATGGGAT------TAAC------------C-TTCAAAAGCTGCAACT-TGAATA--------TTCCATCCAGTAATGTCCACCTACAAGGAGCCACTGAATGGGTGGGTGGACAA--TCTGTACGGACC-
droEle1	GAC--GCCCTGCCCTTGTGCATCTTCCGACCGGCGATCAGTAAGTGCTCC-----CGATTGGAAT------TGAC------------A-TTCA-AAGCTACAACCACAAATA--------TTC---CCAGTAATGTCCACCTACAAGGAGCCACTGCGTGGGTGGGTGGACAA--CCTATTCGGACC-
droRho1	GGC--AACCTGCCCTTGTGCATCTTCCGACCGGCAATCAGTAAGTGCACC-----AGATTGGGGT------GGAC------------C-TT-AAACGCTGCAACT-TAAATA--------TTC---ACAGTAATGTCCACCTACAAGGAGCCTTTCGACGGGTGGGTGGACAA--CATGTTCGGACC-
droFic1	GGC--GACCTGCCGCTCTGCATCTTCCGACCGGCGATCAGTAAGTGCACC-----AAACTTATAT------TGTC-----------TC-TTCAAAGGCTGCCACT-TGAATC--------TTT---ACAGTAATGTCCACCTACAAGGAACCCCTGCATGGCTGGGTGGACAA--CCTGTTTGGACC-
droKik1	GGT--GACCTGCCCCTGTGCGTCTTCCGACCGGCGATCAGTAAGTTA-AT-----AAATTAGGATACCCCAG---------------A-ATCTGGCGCTGCAACT-AACTTA--------TCC---TTAGTTATGCCTACCTACAAGGACCCCGTCGTTGGATGGACGGAGAA--TTTATATGGACC-
droAna3	GGC--AGCCTGCCAGTCAGCATTTATCGGCCTTCCATAAGTAAGTACTAT-----ATACGTCCTG------CTGT------------C-TTATAAAATTGTTATT-T---TT--------TTT---CTAGTAATTGCCACATATAAGGAGCCATTAGTTGGATGGGTGGATAA--CCTTTATGGACC-
droBip1	GGT--AGCCTACCGGTCAGCATTTATCGACCTGCCATAAGTAAGTGCTGT-----A--TTAATATTT----CTGT------------G-TTCTGAAACTGTTATT----GTT--------TCT---CTAGTAATTGGCACTTACAAGGAGCCATTAGTTGGGTGGATAGATAA--CCTCTATGGACCG
dp4	GGC--GACCTGCCCGTGTGCATTTTTCGGCCGGCCATTAGTAAGTTTTTCCTTAGATG--ATGCA------AGGCCTTGGATGGAA-CTGAAACATTGTGTAACA-TGACTC--------TCC---ACAGTCGTGCCCACCTACCAGGAGCCCGTCGTTGGTTGGACTGACAA--TCTGTACGGGCC-
droPer1	GGC--GACCTGCCCGTGTGCATTTTTCGGCCGGCCATTAGTAAGTTTTTCCTTAGATG--ATGCA------AGGCCTTGGATGGAA-CTGAAACATTGTGTAACA-TGACTC--------TCC---ACAGTCGTGCCCACCTACAAGGAGCCCGTCGTTGGTTGGACTGACAA--TCTGTACGGGCC-
droWil1	GGC--AATCTACCAATCTGTATTTTTCGCCCTGGTGTCAGTAAGTCCTCA-----AAATTCAACT------TGTA-----------AC-TAT---AGCT----GT-TAAATTTTCTCCTTATT---ATAGTTATTGCCACCGCCAAGGAGCCAGTTTCGGGTTGGATTGACAA--TTTATATGGACC-
droVir3	ACAAAAAGCTGCCCATTATCGTCACAAGGCCTTCCATCGGTATGTAGGTCCCG-CTAA--CTGGT------TGGGCTTGACAAGTA-ACCATATTTATTTTTTTT-TTTGTT--------CGC---CCAGTGACGGCGGCCATACACGAGCCCATGCCCGGATGGATTGAGGG--CGTGAACGGACC-
droMoj3	GCC--GGTCTGCCGGCAGCCATAGTTAGGCCATCCATAGGTGAGTCG---------AAGTATAAA------TCTA-----------AT-TGAGAAGGCCCTAACT-GA-CTG------CTATT---ACAGTATACGGTACACTGGAGCACCCCATGAAGGGCTGGGTGGGCAATGCCAACTCGGGTC-
droGri2	AGC--GGTTTGCCCATAAGCATCTTTCGCCCGGGTGTCAGTAAGTTCGTC-----GAATCATTAA------GATC-----------AG-TAAGAAGATGTTCTC----AGTC-----TCCATT---TCAGTTATTGGCAGCTACAAGGACCCCCTCCCGGGCTGGGTTGACAA--TCTATATGGTCC-

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

GGC--AACCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACC-----AGATTGGGAA------TAAC------------C-TTCAAAAGCTGCAACT-TAAATA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC-	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.........................................................................................................................TC---CCAGTAATGTCCACTTACAAG.........................................	23	1	2.00	2.00	0.00	0.00	0.00
.......................................GTAAGTGCACC-----AGATTGGGAA------T....................................................................................................................	22	1	2.00	1.00	0.00	1.00	0.00
.......................................GTAAGTGCACC-----AGATTGGGAC------.....................................................................................................................	21	1	2.00	1.00	0.00	1.00	0.00
.......................................GTAAGTGCACC-----AGATTGGGAA------.....................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.......................................GTAAGTGCACC-----AGATTGGG.............................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................................................................................................GTGAACAA--CCTAGTCGGA...	18	1	1.00	0.00	0.00	1.00	0.00
.......................................GTAAGTGCACC-----AGATTGGGAA------A....................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................AAGTGCAAC-----TGATTGGGA............................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.........................................AAGTGCAAC-----TGATTGGGAA------.....................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................TC---CCAGGAATGTCCACTTACAAG.........................................	23	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................AAAGCTGCAACT-TAAATG--------....................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................TC---CCAGTAATGTCCACTTACCAG.........................................	23	1	1.00	1.00	0.00	0.00	0.00

droSec1

GGC--ATCCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACCATA-GTAAA-TGGAA------TAAC------------C-TTCAAAATCTGCAACT-TAAATA--------TTC---CCAGTAATGTCCGCTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC-	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
................................................................................................................................................AAGGAGCCCTTCGTTGGA..........................	18	1	2.00	0.00	2.00	0.00
........................................................................................................................................................CCTGGCTGGxTGGGTGGAC.................	18	1	1.00	1.00	0.00	0.00

droYak2

GGC--GACCTGCCACTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCACC-----AGATTGGGAT------TAAC------------C-TTCAAAAGCTGCAGCT-TAACTA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGATGGCTGGGTGGACAA--CCTATTCGGACC-	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.......................................GTAAGTGCACC-----AGATTGGGAT------T....................................................................................................................	22	1	18.00	0.00	0.00	18.00	0.00	0.00
.......................................GTAAGTGCACC-----AGATTGGGAT------.....................................................................................................................	21	1	4.00	0.00	0.00	4.00	0.00	0.00
.......................................GTAAGTGCACC-----AGATTGGGA............................................................................................................................	20	1	2.00	0.00	0.00	2.00	0.00	0.00
...........................................................................................................................................CTTACAAGGAGCCCCTGGATGGCTGGGT.....................	28	1	2.00	0.00	0.00	2.00	0.00	0.00
.........................................................................................................................TC---CCAGTAATGTCCACTTACA...........................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................CTGAATGGCTTGGTGGAC.................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................................................................................................................AAGGAGCCAGTGGATGGCTGGG......................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................................................................................................TTC---CCAGTAATGTCCACTTACA...........................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................AGGATGGCTGGGTGGTC.................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................GTAACTGCACC-----AGATTGGGAT------T....................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................................................................TC---CCAGTAATGTCCACTTACAAG.........................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................................................................TC---CCAGTAATGTCCACTTACAAGT........................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

GGC--AACCTGCCCCTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCAAC-----AGATTGGGAG------TAAC------------C-GTCAAAAGCTACAACT-TCAATA--------TTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGCTGGATAGACAA--CCTATTCGGACC-	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.......................................GTAAGTGCAAC-----AGATTGGGAG------T....................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00

droEug1

GGC--AACCTGCCCGTGAGCATCTTTCGACCAGCGATCAGTAAGTCCACC-----AGATTGGGAT------TAAT------------C-TTCAAAAGTTGCAACT-TAAATA--------TTC---CCAGTAATGTCCACCTACAAGGAGCCTCTGAATGGGTGGGTGGACAA--TCTATTTGGACC-

Size

Hit Count

Total Norm

droBia1

GGC--AACCTGCCCCTGTGTGTCTACCGGCCGGCGATCAGTAAGTGCATC-----AGATTGGAGT------TAAT------------C-TTGAACAGCTGCAACT-TAAATA--------TTC---CCAGTTATGTCCACCTACAAGGAGCCCGTAAGCGGGTGGGTGGACAA--TCTGTTTGGACC-

Size

Hit Count

Total Norm

droTak1

GGC--AACCTGCCCCTGTCCATCTTCCGGCCGGCGATCAGTAAGTGCTTTACC-CCGCATGGGAT------TAAC------------C-TTCAAAAGCTGCAACT-TGAATA--------TTCCATCCAGTAATGTCCACCTACAAGGAGCCACTGAATGGGTGGGTGGACAA--TCTGTACGGACC-

Size

Hit Count

Total Norm

droEle1

GAC--GCCCTGCCCTTGTGCATCTTCCGACCGGCGATCAGTAAGTGCTCC-----CGATTGGAAT------TGAC------------A-TTCA-AAGCTACAACCACAAATA--------TTC---CCAGTAATGTCCACCTACAAGGAGCCACTGCGTGGGTGGGTGGACAA--CCTATTCGGACC-

Size

Hit Count

Total Norm

droRho1

GGC--AACCTGCCCTTGTGCATCTTCCGACCGGCAATCAGTAAGTGCACC-----AGATTGGGGT------GGAC------------C-TT-AAACGCTGCAACT-TAAATA--------TTC---ACAGTAATGTCCACCTACAAGGAGCCTTTCGACGGGTGGGTGGACAA--CATGTTCGGACC-

Size

Hit Count

Total Norm

droFic1

GGC--GACCTGCCGCTCTGCATCTTCCGACCGGCGATCAGTAAGTGCACC-----AAACTTATAT------TGTC-----------TC-TTCAAAGGCTGCCACT-TGAATC--------TTT---ACAGTAATGTCCACCTACAAGGAACCCCTGCATGGCTGGGTGGACAA--CCTGTTTGGACC-

Size

Hit Count

Total Norm

droKik1

GGT--GACCTGCCCCTGTGCGTCTTCCGACCGGCGATCAGTAAGTTA-AT-----AAATTAGGATACCCCAG---------------A-ATCTGGCGCTGCAACT-AACTTA--------TCC---TTAGTTATGCCTACCTACAAGGACCCCGTCGTTGGATGGACGGAGAA--TTTATATGGACC-

Size

Hit Count

Total Norm

droAna3

GGC--AGCCTGCCAGTCAGCATTTATCGGCCTTCCATAAGTAAGTACTAT-----ATACGTCCTG------CTGT------------C-TTATAAAATTGTTATT-T---TT--------TTT---CTAGTAATTGCCACATATAAGGAGCCATTAGTTGGATGGGTGGATAA--CCTTTATGGACC-	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
................................................................................................AATGTGATT-T---TT--------TTT---CTA...........................................................	18	1	1.00	0.00	0.00	0.00	1.00
.........TGCCAGxCACCATTTATCGG...............................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
...............................TTCCATAAGCGAGTACTA...........................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droBip1

GGT--AGCCTACCGGTCAGCATTTATCGACCTGCCATAAGTAAGTGCTGT-----A--TTAATATTT----CTGT------------G-TTCTGAAACTGTTATT----GTT--------TCT---CTAGTAATTGGCACTTACAAGGAGCCATTAGTTGGGTGGATAGATAA--CCTCTATGGACCG

Size

Hit Count

Total Norm

dp4

GGC--GACCTGCCCGTGTGCATTTTTCGGCCGGCCATTAGTAAGTTTTTCCTTAGATG--ATGCA------AGGCCTTGGATGGAA-CTGAAACATTGTGTAACA-TGACTC--------TCC---ACAGTCGTGCCCACCTACCAGGAGCCCGTCGTTGGTTGGACTGACAA--TCTGTACGGGCC-

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

GGC--GACCTGCCCGTGTGCATTTTTCGGCCGGCCATTAGTAAGTTTTTCCTTAGATG--ATGCA------AGGCCTTGGATGGAA-CTGAAACATTGTGTAACA-TGACTC--------TCC---ACAGTCGTGCCCACCTACAAGGAGCCCGTCGTTGGTTGGACTGACAA--TCTGTACGGGCC-

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

GGC--AATCTACCAATCTGTATTTTTCGCCCTGGTGTCAGTAAGTCCTCA-----AAATTCAACT------TGTA-----------AC-TAT---AGCT----GT-TAAATTTTCTCCTTATT---ATAGTTATTGCCACCGCCAAGGAGCCAGTTTCGGGTTGGATTGACAA--TTTATATGGACC-	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.....................................CAGTAAGTGCTCx-----AAATTC...............................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

ACAAAAAGCTGCCCATTATCGTCACAAGGCCTTCCATCGGTATGTAGGTCCCG-CTAA--CTGGT------TGGGCTTGACAAGTA-ACCATATTTATTTTTTTT-TTTGTT--------CGC---CCAGTGACGGCGGCCATACACGAGCCCATGCCCGGATGGATTGAGGG--CGTGAACGGACC-	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
............................................................................................................ATAT--------GTG---TGTGTGTGTGTGT.................................................	20	9	0.89	0.89	0.00	0.00	0.00	0.00
..............................................................................................................AT--------GTG---TGTGTGTGTGTGT.................................................	18	11	0.18	0.00	0.00	0.18	0.00	0.00
..............................................................................................................AT--------GTG---TGTGTGTGTGTGTGT...............................................	20	21	0.10	0.10	0.00	0.00	0.00	0.00
.............................................................................................................CAT--------ATG---TGTGTGTGTGTGT.................................................	19	3	0.67	0.67	0.00	0.00	0.00	0.00
.............................................................................................................TAT--------GTG---TGTGTGTGTGTGT.................................................	19	24	0.08	0.04	0.04	0.00	0.00	0.00
.............................................................................................................CAT--------GTA---TGTGTGTGTGTGT.................................................	19	3	0.33	0.33	0.00	0.00	0.00	0.00
..............................................................................................................AT--------GTG---TGTGTGTGTGCGT.................................................	18	14	0.07	0.00	0.07	0.00	0.00	0.00
............................................................................................................GCAT--------GTG---TGTGTGTGTGTGT.................................................	20	9	0.11	0.00	0.00	0.11	0.00	0.00
............................................................................................................GCAT--------GTG---TGTGTGTGTGTG..................................................	19	11	0.09	0.09	0.00	0.00	0.00	0.00
.............................................................................................................CGT--------GTG---TGTGTGTGTGTGT.................................................	19	25	0.04	0.04	0.00	0.00	0.00	0.00
..............................................................................................................GT--------GTG---TGTGTGTCTGTGTGTG..............................................	21	18	0.06	0.06	0.00	0.00	0.00	0.00
..............................................................................................................AT--------GTG---TGTGTGTGTGTTT.................................................	18	12	0.08	0.00	0.00	0.08	0.00	0.00
..............................................................................................................AT--------GTG---TGTGTGTGTGTGTG................................................	19	26	0.04	0.04	0.00	0.00	0.00	0.00
..............................................................................................................AT--------GTG---TGTGTATGTGTGT.................................................	18	11	0.09	0.09	0.00	0.00	0.00	0.00
............................................................................................................ACAT--------ATG---TGTGTGTGTGTGT.................................................	20	2	0.50	0.50	0.00	0.00	0.00	0.00
............................................................................................................ACAT--------ATG---TGTGTGTGTGT...................................................	18	4	0.25	0.25	0.00	0.00	0.00	0.00
..............................................................................................................GT--------GTC---TGTGTGTCTGTGT.................................................	18	10	0.10	0.00	0.10	0.00	0.00	0.00
..............................................................................................................AT--------GTG---TATGTGTATGTGT.................................................	18	2	0.50	0.00	0.00	0.50	0.00	0.00
......................................................AACA--TGTTT------ATTTTTTTT............................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................................................TTTTTTTTTTTGTT-GGCTC................................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................................AT--------GCG---TGTGTGTGTGTGT.................................................	18	12	0.08	0.00	0.00	0.08	0.00	0.00
..............................................................................................................AT--------GTG---TGTGTGCGTGTGT.................................................	18	14	0.07	0.07	0.00	0.00	0.00	0.00
.............................................................................................................TAT--------GTG---TGTGTGTGTGTGTCT...............................................	21	7	0.14	0.14	0.00	0.00	0.00	0.00
..............................................................................................................AT--------GTG---TGTGTGTGTGTGTC................................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00
............................................................................................................AAAT--------GTG---TGTGTGTGTGTGT.................................................	20	3	0.33	0.00	0.00	0.33	0.00	0.00
.............................................................................................................CAT--------GTG---TGTTTGTGTGTGT.................................................	19	3	0.33	0.33	0.00	0.00	0.00	0.00
..............................................................................................................AT--------GTG---TGTGTGTGTGTGTGTG..............................................	21	19	0.05	0.05	0.00	0.00	0.00	0.00
...........................................................................................................TGCAT--------GTG---TGTGTGTGTG....................................................	18	12	0.08	0.08	0.00	0.00	0.00	0.00
................................................................A------ATTTTTTTTTTTGGT-CG...................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................................AT--------GTG---TGTGTGTGTGTGTGTGT.............................................	22	16	0.06	0.06	0.00	0.00	0.00	0.00
..............................................................................................................AT--------GCG---TGTGTGTGTGTG..................................................	17	15	0.07	0.00	0.07	0.00	0.00	0.00
..........................................................................................................ATGCAT--------GTG---TGTGTGTGTG....................................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00
..................................................GTA-AxCA--TTTTT------ATTTTTT..............................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

GCC--GGTCTGCCGGCAGCCATAGTTAGGCCATCCATAGGTGAGTCG---------AAGTATAAA------TCTA-----------AT-TGAGAAGGCCCTAACT-GA-CTG------CTATT---ACAGTATACGGTACACTGGAGCACCCCATGAAGGGCTGGGTGGGCAATGCCAACTCGGGTC-

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

AGC--GGTTTGCCCATAAGCATCTTTCGCCCGGGTGTCAGTAAGTTCGTC-----GAATCATTAA------GATC-----------AG-TAAGAAGATGTTCTC----AGTC-----TCCATT---TCAGTTATTGGCAGCTACAAGGACCCCCTCCCGGGCTGGGTTGACAA--TCTATATGGTCC-

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:20:22 EDT

dme-mir-2494

chr3R:12444488-12444604 +

Known_mirbase

mirtron

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup