dme-mir-4918- Best orthologs

dme-mir-4918	chr3R:4134153-4134207 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 4134184-4134207
   star strand at position 4134153-4134173
   mutations
   read mismatches

Notes: droMoj and droVir has better lastz orthologs and hairpins

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3R:4134138-4134222 -		1	TCGCACATGTCTAAGGTGAGCAC-GA-----TGGCCAC--ATTTA-TTG--GGCA-A-----------------------------CCAATGAA----------TT---CC-CGCCTGCCCACAGGTTCACTCG--GTCTGC
droSim1	chr3R:17124439-17124521 +	LASTZ	5	TCGCACATGTCCAAGGTGAGCAC-GA-----TGGCCAC--ATTTA-TTG--GGCA-A-----------------------------CCCATGAA----------T-----C-CTCCTGCCCACAGGTTCACTCG--GTCTGC
droSec1	super_0:17695137-17695219 +	LASTZ	5	TCGCACATGTCCAAGGTGAGCAC-GA-----TGGCCAC--ATTTA-TTG--GGCA-A-----------------------------CCCATGAA----------T-----C-CTCCTGCCCACAGGTTCACTCG--GTCTGC
droYak2	chr3R:8209596-8209678 -	LASTZ	5	GCGCACATGTCCAAGGTGAGCAC-GG-----CGGCCCCAA--------------AATCAAAGT----------TCT----------CTGACCAA-------------AA----TCCCGCCCACAGGTTCACTCC--GTCTGC
droEre2	scaffold_4770:17439359-17439448 +	LASTZ	5	GCGCACATGTCCAAGGTGAGCAC-GA-----TGGCCCCGA--------------CATCGAAATTCTAAATCCCC----------AATCCA---A-------------AA----TCCCGCCCACAGGTTCACTCA--GTCTGC
droEug1	scf7180000409490:587161-587244 +	LASTZ	5	GCTCACATGTCCAAGGTGAGCAT-TG-----TTTCCCGTTAATTCT------------GAA------------TT--T--------CTCTA--A-------------AATC-CGTCTGTCCACAGGTTCACTCT--GTTTGC
droBia1	scf7180000302402:6823672-6823766 -	LASTZ	5	GCGCACATGTCCAAGGTGAGCGC-GA-----TTTCCCGCCAATCCT------------GGGGA----------CTCCTCTCTGAAATCCA-GAG----------T-----C-CTCCTGCCCACAGGTGCACTCG--GTTTGC
droTak1	scf7180000415750:47169-47269 -	LASTZ	5	GCGCACATGTCCAAGGTAAACAC-GA-----TTTCCCGCCAAT-TA------------AGAAG----------CATCTCTCTGCAATCCAAGAATCCCCC---------TT-TCCACATCCACAGGTTCACTCG--GTTTGC
droEle1	scf7180000491212:1694399-1694504 +	LASTZ	5	GCGCACATGTCCAAGGTGAGCTT-GA-----TGTTCCCAGAGGTTC------------AAAGA----------TTTCTTACTAAAAATTGAGACTTGTCTTCATTGAAA----TC--CTTTCCAGGTTCACTCC--GTCTGC
droRho1	scf7180000779995:99582-99685 -	LASTZ	5	GCGCACATGTCCAAGGTGAGCTT-GA-----TTTCCGTTCCAC-TT------------AAAGA----------TTCCTCTCTAAAACTTGTAACTCCCAT---TTGAAA----TGCTGTCCACAGGTGCACTCC--GTTTGC
droFic1	scf7180000454073:3313771-3313857 +	LASTZ	5	GCGCACATGTCCAAGGTGAGCTT-GG-----CTTCCCTGCAATCCTTTGGTGC--------------------C----------GATCTGTAAA----------------C-CTCCCTTTTATAGGTTCACTCT--GTCTGC
droKik1	scf7180000302810:169514-169599 +	LASTZ	5	GCGCACATTTCCAAGGTAGGAGT-GA-----ATTCTGTGGGCTCTAGCG--GA--------------------CTT----------GCCACTGA----------T-----T-CTCCTGGTTGCAGGTCCATTCG--GTGTTC
droAna3	scaffold_13340:13231716-13231803 -	LASTZ	5	GCCCATCTGAACAAGGTAATTTG-AA-----TTTGTGT--TTTTGGCCAGGAGCA-A-----------------------------TTGATGTA----------TT---TG-TTTATGTTCGAAGGTACACTCT--GTTTGC
droBip1	scf7180000396691:2102175-2102262 -	LASTZ	5	GCGCATCTGAACAAGGTAATTGG-AA-----TTGATGT--TTTTAGCCTGTCAAA-A-----------------------------TGTATGCA----------TT---TT-TTTATATTTGAAGGTACACTCG--GTTTGC
dp4	chr2:14657774-14657858 -	LASTZ	5	GCCCACACGTCCAAGGTAAGAAG--C-----TAGTCGAAA--------------AATTGAGGC----------ATT----------TTCACGAA----------ACAA--T--TGTCTGAGGCAGGTTCACTCC--GTCTGC
droPer1	super_0:5758126-5758210 +	LASTZ	5	GCCCACACGTCCAAGGTAAGAAG--C-----TGGTCGAAA--------------AATTGAGGC----------ATT----------TTCACGAA----------ACAAA----TGTCTGAGGCAGGTTCACTCC--GTCTGC
droWil1	scaffold_181089:2794443-2794538 +	LASTZ	5	GCACATATGTCCAAGGTAATCAA-AT-----TTAATGT--AATTTACCA--GACAAGCGTTCC----------CTT----------TTTACAAA----------TT---TT-CTTTCCCTGGCAGGTTCACTCG--GTTTGC
droVir3	scaffold_12822:435887-435972 +	LASTZ	5	CCACACATGTCAAAGGTGGGTAT-AA-----AACCATT-TAGTCTGTCGGTGG--------------------CAT----------TTAATTGG----------------T-TTTCTTTTCGTAGGTGCATTCG--GTGTGC
droMoj3	scaffold_6540:27855886-27855971 -	LASTZ	0	CAGCAATAG-CAACAGCAACAGC-AA-----TAGCAAC--AGCAA-CAG-CAGCA-A-----------------------------CACCTGCA----------AG---CCGCGGCAGCCCAAAGTCTCGTTCG--CACCGC
droGri2	scaffold_15245:11304334-11304423 -	LASTZ	0	ATGCACAGCTCCTTAAGCAATATGAACAGCAGAGCCTGGG--------------TAGTGATGT------------------------ACCTGGA----------TC---CC-GGCCCATCTACACGTTCAGTGGACATCAGC

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	TCGCACATGTCTAAGGTGAGCACGATGGCC--ACATTT-----ATTGG--GCAA---------------------CC----------AATGAATT----------CCCGCCTG---CCCACAGGTTCACTCGGTCTGC
droSim1	TCGCACATGTCCAAGGTGAGCACGATGGCC--ACATTT-----ATTGG--GCAA---------------------CC----------CATGAAT------------CCTCCTG---CCCACAGGTTCACTCGGTCTGC
droSec1	TCGCACATGTCCAAGGTGAGCACGATGGCC--ACATTT-----ATTGG--GCAA---------------------CC----------CATGAAT------------CCTCCTG---CCCACAGGTTCACTCGGTCTGC
droYak2	GCGCACATGTCCAAGGTGAGCACGGCGGCCCCAAA----AT--------------CA-AAGT----------TCTCT----------GACCAA-------------AATCCCG---CCCACAGGTTCACTCCGTCTGC
droEre2	GCGCACATGTCCAAGGTGAGCACGATGGCCCCGAC----AT--------------CG-AAATTCTAAATCCCC---A-------ATCCA----------------AAATCCCG---CCCACAGGTTCACTCAGTCTGC
droEug1	GCTCACATGTCCAAGGTGAGCATTGTTTCCCGTTA----AT--------------TCTGA-------AT----TTCT----------CTAAAAT------------CCGTCTG---TCCACAGGTTCACTCTGTTTGC
droBia1	GCGCACATGTCCAAGGTGAGCGCGATTTCCCGCCA----ATCC-------------TGGGG------AC----TCCTCTCTGAAATCCA-GAGT------------CCTCCTG---CCCACAGGTGCACTCGGTTTGC
droTak1	GCGCACATGTCCAAGGTAAACACGATTTCCCGCCA----AT--------------TAAGAA------GC----ATCTCTCTGCAATCCAAGAATCCCCC------TTTCCACA---TCCACAGGTTCACTCGGTTTGC
droEle1	GCGCACATGTCCAAGGTGAGCTTGATGTTCCCAGA----GGT-------------TCAAAG------AT----TTCTTACTAAAAATTGAGACTTGTCTTCATTGAAATCC-----TTTCCAGGTTCACTCCGTCTGC
droRho1	GCGCACATGTCCAAGGTGAGCTTGATTTCCGTTCC----AC--------------TTAAAG------AT----TCCTCTCTAAAACTTGTAACTCCCAT---TTGAAATGCTG---TCCACAGGTGCACTCCGTTTGC
droFic1	GCGCACATGTCCAAGGTGAGCTTGGCTTCCCTGCA----ATCCTTTGG-----------TGC----------C---G-------ATCTGTAAA-------------CCTCCCT---TTTATAGGTTCACTCTGTCTGC
droKik1	GCGCACATTTCCAAGGTAGGAGTGAATTCTGTGGG----CTCTAGCGG--A-----------------C----TTGC----------CACTGAT------------TCTCCTG---GTTGCAGGTCCATTCGGTGTTC
droAna3	GCCCATCTGAACAAGGTAATTTGAATTTGT--GTTTTTG----GCCAGGAGCAA---------------------TT----------GATGTATT----------TGTTTATG---TTCGAAGGTACACTCTGTTTGC
droBip1	GCGCATCTGAACAAGGTAATTGGAATTGAT--GTTTTTA----GCCTGTCAAAA---------------------TG----------TATGCATT----------TTTTTATA---TTTGAAGGTACACTCGGTTTGC
dp4	GCCCACACGTCCAAGGTAAGAAG-CTAGTCGAAAA----AT--------------TG-AGGC----------ATTTT----------CACGAAAC----------AA---TTGTCTGAGGCAGGTTCACTCCGTCTGC
droPer1	GCCCACACGTCCAAGGTAAGAAG-CTGGTCGAAAA----AT--------------TG-AGGC----------ATTTT----------CACGAAAC----------AAAT---GTCTGAGGCAGGTTCACTCCGTCTGC
droWil1	GCACATATGTCCAAGGTAATCAAATTTAAT--GTAATTT----ACCAG--ACAAGCG-TTCC----------CTTTT----------TACAAATT----------TTCT---TTCCCTGGCAGGTTCACTCGGTTTGC
droVir3	CCACACATGTCAAAGGTGGGTATAAAACCAT-TTA----GTCTGTCGG-----------TGG----------CATTT----------AATTGG-------------TTTTCTT---TTCGTAGGTGCATTCGGTGTGC

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

TCGCACATGTCCAAGGTGAGCAC-GA-----TGGCCAC--ATTTA-TTG--GGCA-A-----------------------------CCCATGAA----------T-----C-CTCCTGCCCACAGGTTCACTCG--GTCTGC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...............................TGTCCAG--ATTTA-TTG--GGC........................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

TCGCACATGTCCAAGGTGAGCAC-GA-----TGGCCAC--ATTTA-TTG--GGCA-A-----------------------------CCCATGAA----------T-----C-CTCCTGCCCACAGGTTCACTCG--GTCTGC

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

GCGCACATGTCCAAGGTGAGCAC-GG-----CGGCCCCAA--------------AATCAAAGT----------TCT----------CTGACCAA-------------AA----TCCCGCCCACAGGTTCACTCC--GTCTGC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........GTCCAAGGTGAACAC-GG-----TGG............................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
............ATGGTGAGCAT-GG-----CGGCC..........................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

GCGCACATGTCCAAGGTGAGCAC-GA-----TGGCCCCGA--------------CATCGAAATTCTAAATCCCC----------AATCCA---A-------------AA----TCCCGCCCACAGGTTCACTCA--GTCTGC

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

GCTCACATGTCCAAGGTGAGCAT-TG-----TTTCCCGTTAATTCT------------GAA------------TT--T--------CTCTA--A-------------AATC-CGTCTGTCCACAGGTTCACTCT--GTTTGC

Size

Hit Count

Total Norm

droBia1

GCGCACATGTCCAAGGTGAGCGC-GA-----TTTCCCGCCAATCCT------------GGGGA----------CTCCTCTCTGAAATCCA-GAG----------T-----C-CTCCTGCCCACAGGTGCACTCG--GTTTGC

Size

Hit Count

Total Norm

droTak1

GCGCACATGTCCAAGGTAAACAC-GA-----TTTCCCGCCAAT-TA------------AGAAG----------CATCTCTCTGCAATCCAAGAATCCCCC---------TT-TCCACATCCACAGGTTCACTCG--GTTTGC

Size

Hit Count

Total Norm

droEle1

GCGCACATGTCCAAGGTGAGCTT-GA-----TGTTCCCAGAGGTTC------------AAAGA----------TTTCTTACTAAAAATTGAGACTTGTCTTCATTGAAA----TC--CTTTCCAGGTTCACTCC--GTCTGC

Size

Hit Count

Total Norm

droRho1

GCGCACATGTCCAAGGTGAGCTT-GA-----TTTCCGTTCCAC-TT------------AAAGA----------TTCCTCTCTAAAACTTGTAACTCCCAT---TTGAAA----TGCTGTCCACAGGTGCACTCC--GTTTGC

Size

Hit Count

Total Norm

droFic1

GCGCACATGTCCAAGGTGAGCTT-GG-----CTTCCCTGCAATCCTTTGGTGC--------------------C----------GATCTGTAAA----------------C-CTCCCTTTTATAGGTTCACTCT--GTCTGC

Size

Hit Count

Total Norm

droKik1

GCGCACATTTCCAAGGTAGGAGT-GA-----ATTCTGTGGGCTCTAGCG--GA--------------------CTT----------GCCACTGA----------T-----T-CTCCTGGTTGCAGGTCCATTCG--GTGTTC

Size

Hit Count

Total Norm

droAna3

GCCCATCTGAACAAGGTAATTTG-AA-----TTTGTGT--TTTTGGCCAGGAGCA-A-----------------------------TTGATGTA----------TT---TG-TTTATGTTCGAAGGTACACTCT--GTTTGC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...............................TTTGCGT--TTTCGGCCAGGAGC........................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...............................TTTGTGT--TTTTGGGCCGGAG.........................................................................................	20	1	1.00	1.00	0.00	0.00	0.00

droBip1

GCGCATCTGAACAAGGTAATTGG-AA-----TTGATGT--TTTTAGCCTGTCAAA-A-----------------------------TGTATGCA----------TT---TT-TTTATATTTGAAGGTACACTCG--GTTTGC

Size

Hit Count

Total Norm

dp4

GCCCACACGTCCAAGGTAAGAAG--C-----TAGTCGAAA--------------AATTGAGGC----------ATT----------TTCACGAA----------ACAA--T--TGTCTGAGGCAGGTTCACTCC--GTCTGC

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

GCCCACACGTCCAAGGTAAGAAG--C-----TGGTCGAAA--------------AATTGAGGC----------ATT----------TTCACGAA----------ACAAA----TGTCTGAGGCAGGTTCACTCC--GTCTGC

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

GCACATATGTCCAAGGTAATCAA-AT-----TTAATGT--AATTTACCA--GACAAGCGTTCC----------CTT----------TTTACAAA----------TT---TT-CTTTCCCTGGCAGGTTCACTCG--GTTTGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
................................................A--GACAAGAGTTCC----------CTT----------CT......................................................	18	1	11.00	0.00	11.00	0.00	0.00
.......................................................AGCGTTCA----------TTT----------TTTACAAA----------......................................	19	1	1.00	0.00	1.00	0.00	0.00

droVir3

CCACACATGTCAAAGGTGGGTAT-AA-----AACCATT-TAGTCTGTCGGTGG--------------------CAT----------TTAATTGG----------------T-TTTCTTTTCGTAGGTGCATTCG--GTGTGC

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

CAGCAATAG-CAACAGCAACAGC-AA-----TAGCAAC--AGCAA-CAG-CAGCA-A-----------------------------CACCTGCA----------AG---CCGCGGCAGCCCAAAGTCTCGTTCG--CACCGC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.........................A-----TATCAAG--AGCAA-CAG-CAGC........................................................................................	20	14	0.14	0.14	0.00	0.00	0.00
.AGCAATAG-CAAGAGCAAGAGC-A.....................................................................................................................	22	20	0.05	0.00	0.00	0.05	0.00
................CAACAGC-AA-----TCGCAAG--AGC...................................................................................................	19	19	0.05	0.05	0.00	0.00	0.00
..GCAATAG-CAAGAGCAAGAG........................................................................................................................	19	32	0.03	0.03	0.00	0.00	0.00
.....................CC-AA-----GAGCAAC--AGCAA-CAG-CAGCA-A-----------------------------CA......................................................	27	23	0.04	0.04	0.00	0.00	0.00
.....................GC-AA-----TAGCAAG--AGCAA-GAG-............................................................................................	19	32	0.03	0.03	0.00	0.00	0.00
..................ACAGC-AT-----TGGCAAC--AGCAA-CA..............................................................................................	21	27	0.04	0.04	0.00	0.00	0.00
....AATAG-CCACTGCAACAGC-AA-----TAG............................................................................................................	23	2	0.50	0.50	0.00	0.00	0.00
............ACAACAACAGC-AA-----TAGCAAC--......................................................................................................	20	36	0.03	0.00	0.00	0.03	0.00
....................AGC-AA-----TAGCAAG--AGCAA-GAG-CA..........................................................................................	22	20	0.05	0.00	0.00	0.05	0.00
.........................A-----TAGCCAT--AGCAA-CAG-CAGCA-......................................................................................	21	15	0.07	0.07	0.00	0.00	0.00

droGri2

ATGCACAGCTCCTTAAGCAATATGAACAGCAGAGCCTGGG--------------TAGTGATGT------------------------ACCTGGA----------TC---CC-GGCCCATCTACACGTTCAGTGGACATCAGC

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:33:59 EDT

dme-mir-4918

chr3R:4134153-4134207 -

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