dme-mir-4965- Best orthologs

dme-mir-4965	chrX:16500140-16500227 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 16500158-16500178
   star strand at position 16500195-16500215
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:16500125-16500242 +		1	GTATTCGCAGTACAA---GCA-C--AAGGTGATCGA----TGG--GAG----ATGAG-----CG------CCTGATG--TGATGATGAA---GTAGATCGATCACACCACACAC-----------------------T------------CACTCA-CCCAGG-TTTCATCCATACA--AATG--TGTTTG
droSim1	chrX_random:4339044-4339160 +	LASTZ	4	GTATTCGCAATACAA---GCA-C--AAGGTGATCGA----TGG--GAG----CTGAG-----CG------CCTGATG--TGATGATGAA---GTAGATCGATCACACCACACAC-----------------------T------------CACTCA-CCCA-G-TTTCATCCATGCA--AATG--TGTTTG
droSec1	super_17:323461-323577 +	LASTZ	4	GTATTCGCAATACAA---GCA-C--AAGGTGATCGA----TGG--GAG----CTGAG-----CG------CCTGATG--TGATGATGAA---GTAGATCGATCACACCACACAC-----------------------T------------CACTCA-CCCA-G-TTTCATCCATGCA--AATG--TGTTTG
droYak2	chrX:10606276-10606397 +	LASTZ	4	GAATTTAGAATAAAA---ACA-A--AAGGTGATCGA----TGG--GAG----CTGAC-----CTTGAGCCTGAGCTG--AGATGATGAA---GTAGATCGATCACAC-ACTCAC-----------------------T------------CACTCA-CTCA-G-TTTCATCCATGCA--AATT--TGTTTG
droEre2	scaffold_4690:6858711-6858812 +	LASTZ	4	CC-----CAATAAAA---CCA-A--AAGGTGATCGA----TGG--GAG----CTGAG-----CC--------TGAAG--TGATGATGAA---GTAAATCGATCACA-----CAC---------------------------------TCA-------CTCA-G-ATTCATCCATGCA--AATT--TGTTTG
droEug1	scf7180000409110:53770-53870 -	LASTZ	5	GAAATCC-AATTAAT-GCCCA-AAAGATATGATCGA----TGG--GAG----CAAAG-----CT------CCAACTGAATGATGATGAA---A------------------------------------------AAT------T--TCT-------CTCA-T-TTTCATCCATGCA--AATT--TGTTTG
droBia1	scf7180000302421:1779397-1779498 -	LASTZ	5	GTAAC-CCAGTGAAA---CCA-A--GAGATGATCGA----TGG--GAG----CAGAGCAGAGCT------CGCGATG--TGATGATATAAAC-------------------------------------------AAT------C--TCT-------CTCA-C-TTTCATCCATGCA--AATT--TGTTTG
droTak1	scf7180000415351:273301-273376 +	LASTZ	5	GTATT-GCAGTAAAA---CCA-A--GAGGTGATCGA----TGT--GTG----ATAAG----------------------------------C-------------------------------------------AA----------TCT-------CTCA-C-CTTCATCCATGCAGCAATT--TGTTTG
droEle1	scf7180000491023:1394532-1394635 -	LASTZ	5	CTATTAA-ACTATCAAA-CTATC--CCGATGATCGAAGGTGGG--GAG----CTAAGCTGAGCT--------CGATG--TGATGA---A--C-------------------------------------------AAT------CCCTCT-------CTCA-C-TTTCATCCATGCA--AATT--TGTGTG
droRho1	scf7180000779841:628688-628776 -	LASTZ	5	ACTATCCCTAAAAAT---CCA-A--GAGGTGATCGA----TGG--GAG----CAGAG-----CT--------CGATG--TGATGAA-----C-------------------------------------------AA----------TCT-------CTCA-C-TATCATCCATGCA--AATT--TGTTTG
droFic1	scf7180000454045:1297042-1297121 +	LASTZ	5	A------------------------GAGGTGATCGA----TGG--GAG----CCTAG-----CT------CCCGATG--TGATGATGAA--C-------------------------------------------AAT------CAGTCT-------CTCA-C-CTTCATCCATGCA--AATT--TGTTTG
droKik1	scf7180000302724:273010-273099 -	LASTZ	5	AATTC-CCAA------------A--GAGGTGATCGA----TAG--GAG----CAAAG-----CACG-----ACGATG--TGATGCAACG-------------------------------------------AAACAC---------CTT-------CATA-A-TTCCATCCATGCA--AATC--TGTTAA
droAna3	scaffold_13337:17013621-17013746 +	LASTZ	0	GAAATCTCAGCAGCAAGCTCA-G-----CGGATCGGGTGTTGG--AGG------------------------TGGTC--TGCCATTGAC---GAAGAGCAACAGCACCAATTCC-TTCC---------AGGAGCAT--------A--GCGCTCCCAA--GC-G-TCGTCCCAGTATG--GGTG--CCTTGG
droBip1	scf7180000396425:405817-405907 -	LASTZ	0	A------------------------------ATCGA----TGGAAGAG----CAGAG-----CA--------CGATGCGCGATGC---G--C-------GATCA-------------GTATCAGTATC------A-GTATCCGTA--CCT-------CTCA-CTTCTCATCCATGCA--AAGT--T----G
dp4	chrXL_group1a:8134511-8134553 -	LASTZ	0	ACTCC-------------------------------------------------------------------------------------------------------ACACAC-----------------------A------------CACA---CACA-C-AGACAGACATATA--AAGG--A-CATG
droPer1	super_5:779941-779973 +	LASTZ	0	ACACTCGCACTCC------CA-C--AAGAAGAGCAG----CAG--TAG-----------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_180698:6476640-6476654 +	LASTZ	0	ATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG--AATG--TGTGTG
droVir3	scaffold_13042:4246856-4246902 -	LASTZ	0	CACACAC-AC----------------------------------------------------------------------------------------------------ACAC-----------------------A------------CACATGTACAG-C-TTTCACTCATGCA--TATT--TGTT--
droMoj3	scaffold_6500:26586811-26586907 +	LASTZ	0	GCATTTGCACTGC------TC-G--AAAATGAGCAA----TTG--CAAAGATCATTG-----CA--------C---------------A---ATACATTGC---------------------------AGAGAAAT--------A--CTG-------CACA-A-AATAATTTAGTTA--ATTTTAAGTTGA
droGri2	scaffold_15245:5234538-5234618 -	LASTZ	0	GCAAAATGAA----C---ACA-A--AAACTGTTG--------------------------------------------------------------------CATACCACACACTAACTGTAAATATC------ACAT---------------------TT-T-TATTATTCTTATA--ATTA--TTAATA

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	GTATTCG-CAGTACAA--GCA--CAAGGTGATCGAT----GGGAGATGAG-----CG------CCTGATG--TGATGA--TGAAGTAGATCGATCACACCACACACTCACTCACCCAGGTTTCATCCATACA--AATGTGTTTG
droSim1	GTATTCG-CAATACAA--GCA--CAAGGTGATCGAT----GGGAGCTGAG-----CG------CCTGATG--TGATGA--TGAAGTAGATCGATCACACCACACACTCACTCACCCA-GTTTCATCCATGCA--AATGTGTTTG
droSec1	GTATTCG-CAATACAA--GCA--CAAGGTGATCGAT----GGGAGCTGAG-----CG------CCTGATG--TGATGA--TGAAGTAGATCGATCACACCACACACTCACTCACCCA-GTTTCATCCATGCA--AATGTGTTTG
droYak2	GAATTTA-GAATAAAA--ACA--AAAGGTGATCGAT----GGGAGCTGAC-----CTTGAGCCTGAGCTG--AGATGA--TGAAGTAGATCGATCACAC-ACTCACTCACTCACTCA-GTTTCATCCATGCA--AATTTGTTTG
droEre2	-----CC-CAATAAAA--CCA--AAAGGTGATCGAT----GGGAGCTGAG-----C--------CTGAAG--TGATGA--TGAAGTAAATCGATCACA-----CA----CTCACTCA-GATTCATCCATGCA--AATTTGTTTG
droEug1	GAAATC--CAATTAATGCCCAAAAGATATGATCGAT----GGGAGCAAAG-----CT------CCAACTGAATGATGA--TGAAAAATT---------------------TCTCTCA-TTTTCATCCATGCA--AATTTGTTTG
droBia1	GTAA-CC-CAGTGAAA--CCA--AGAGATGATCGAT----GGGAGCAGAGCAGAGCT------CGCGATG--TGATGA--TATAAA-----------------CAAT--CTCTCTCA-CTTTCATCCATGCA--AATTTGTTTG
droTak1	GTATT-G-CAGTAAAA--CCA--AGAGGTGATCGAT----GTGTGATAAG-----------------------------------------------------CAA----TCTCTCA-CCTTCATCCATGCAGCAATTTGTTTG
droEle1	CTATTAAACTATCAAA--CTA-TCCCGATGATCGAAGGTGGGGAGCTAAGCTGAGC--------TCGATG--TGATGA-----A-------------------CAATCCCTCTCTCA-CTTTCATCCATGCA--AATTTGTGTG
droRho1	ACTATCC-CTAAAAAT--CCA--AGAGGTGATCGAT----GGGAGCAGAG-----CT--------CGATG--TGATGA--A----------------------CAA----TCTCTCA-CTATCATCCATGCA--AATTTGTTTG
droFic1	-----------------------AGAGGTGATCGAT----GGGAGCCTAG-----CT------CCCGATG--TGATGA--TGAA-------------------CAATCAGTCTCTCA-CCTTCATCCATGCA--AATTTGTTTG
droKik1	AATT-CC-CAA------------AGAGGTGATCGAT----AGGAGCAAAG-----CACG-----ACGATG--TGATGCAACGAAACA----------------------CCTTCATA-ATTCCATCCATGCA--AATCTGTTAA

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
UNAFold Image															None		None

Small RNA-seq read pileup

Species

Alignment

droSim1

GTATTCGCAATACAA---GCA-C--AAGGTGATCGA----TGG--GAG----CTGAG-----CG------CCTGATG--TGATGATGAA---GTAGATCGATCACACCACACAC-----------------------T------------CACTCA-CCCA-G-TTTCATCCATGCA--AATG--TGTTTG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..................GCA-C--AAGGTGGTCGA----TGC--..................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00

droSec1

GTATTCGCAATACAA---GCA-C--AAGGTGATCGA----TGG--GAG----CTGAG-----CG------CCTGATG--TGATGATGAA---GTAGATCGATCACACCACACAC-----------------------T------------CACTCA-CCCA-G-TTTCATCCATGCA--AATG--TGTTTG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..................................GA----TGG--GAG----CTGAG-----CG------CCTGATG--TG..............................................................................................................	24	2	0.50	0.00	0.50	0.00
............CAA---Gxx-C--AAGGTGATCGA----TGG--..................................................................................................................................................	19	2	0.50	0.50	0.00	0.00
...................................................................................GATGAA---GAAGATCGGTCAC......................................................................................	19	2	0.50	0.50	0.00	0.00

droYak2

GAATTTAGAATAAAA---ACA-A--AAGGTGATCGA----TGG--GAG----CTGAC-----CTTGAGCCTGAGCTG--AGATGATGAA---GTAGATCGATCACAC-ACTCAC-----------------------T------------CACTCA-CTCA-G-TTTCATCCATGCA--AATT--TGTTTG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.............AA---ACA-A--AAGGTGATCGA----TGG--GA................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

CC-----CAATAAAA---CCA-A--AAGGTGATCGA----TGG--GAG----CTGAG-----CC--------TGAAG--TGATGATGAA---GTAAATCGATCACA-----CAC---------------------------------TCA-------CTCA-G-ATTCATCCATGCA--AATT--TGTTTG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.........................................................................GAAG--TxATGATCAA---GTAAA..............................................................................................	18	1	19.00	0.00	0.00	0.00	19.00
.........................................................................GAAG--TTATGATCAA---GTAAA..............................................................................................	19	1	4.00	0.00	0.00	0.00	4.00
.........................................................................GAAG--TGATGATCAA---GTAA...............................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.........................................................................GAAG--TAATGATCAA---GTAA...............................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..........................................................................AAT--TGATGATGAA---GTAAG..............................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
........................................................................TGAAC--TGATGATGAA---GTCA...............................................................................................	19	1	1.00	0.00	0.00	0.00	1.00

droEug1

GAAATCC-AATTAAT-GCCCA-AAAGATATGATCGA----TGG--GAG----CAAAG-----CT------CCAACTGAATGATGATGAA---A------------------------------------------AAT------T--TCT-------CTCA-T-TTTCATCCATGCA--AATT--TGTTTG

Size

Hit Count

Total Norm

droBia1

GTAAC-CCAGTGAAA---CCA-A--GAGATGATCGA----TGG--GAG----CAGAGCAGAGCT------CGCGATG--TGATGATATAAAC-------------------------------------------AAT------C--TCT-------CTCA-C-TTTCATCCATGCA--AATT--TGTTTG

Size

Hit Count

Total Norm

droTak1

GTATT-GCAGTAAAA---CCA-A--GAGGTGATCGA----TGT--GTG----ATAAG----------------------------------C-------------------------------------------AA----------TCT-------CTCA-C-CTTCATCCATGCAGCAATT--TGTTTG

Size

Hit Count

Total Norm

droEle1

CTATTAA-ACTATCAAA-CTATC--CCGATGATCGAAGGTGGG--GAG----CTAAGCTGAGCT--------CGATG--TGATGA---A--C-------------------------------------------AAT------CCCTCT-------CTCA-C-TTTCATCCATGCA--AATT--TGTGTG

Size

Hit Count

Total Norm

droRho1

ACTATCCCTAAAAAT---CCA-A--GAGGTGATCGA----TGG--GAG----CAGAG-----CT--------CGATG--TGATGAA-----C-------------------------------------------AA----------TCT-------CTCA-C-TATCATCCATGCA--AATT--TGTTTG

Size

Hit Count

Total Norm

droFic1

A------------------------GAGGTGATCGA----TGG--GAG----CCTAG-----CT------CCCGATG--TGATGATGAA--C-------------------------------------------AAT------CAGTCT-------CTCA-C-CTTCATCCATGCA--AATT--TGTTTG

Size

Hit Count

Total Norm

droKik1

AATTC-CCAA------------A--GAGGTGATCGA----TAG--GAG----CAAAG-----CACG-----ACGATG--TGATGCAACG-------------------------------------------AAACAC---------CTT-------CATA-A-TTCCATCCATGCA--AATC--TGTTAA

Size

Hit Count

Total Norm

droAna3

GAAATCTCAGCAGCAAGCTCA-G-----CGGATCGGGTGTTGG--AGG------------------------TGGTC--TGCCATTGAC---GAAGAGCAACAGCACCAATTCC-TTCC---------AGGAGCAT--------A--GCGCTCCCAA--GC-G-TCGTCCCAGTATG--GGTG--CCTTGG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
........................................................................................C---AAAGAACAACAGCACCA..................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..............................GATCGGGTCTTGG--TGG------------------------TGGT...................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.........GCAGCCAGCTCT-G-----CGGATCG............................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
......................................................................................GAC---CAAGAGCAACAGGAC....................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...................CC-G-----CGGATAGGGTGTTGG--..................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droBip1

A------------------------------ATCGA----TGGAAGAG----CAGAG-----CA--------CGATGCGCGATGC---G--C-------GATCA-------------GTATCAGTATC------A-GTATCCGTA--CCT-------CTCA-CTTCTCATCCATGCA--AAGT--T----G

Size

Hit Count

Total Norm

dp4

ACTCC-------------------------------------------------------------------------------------------------------ACACAC-----------------------A------------CACA---CACA-C-AGACAGACATATA--AAGG--A-CATG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.............................................................................................................CACAC-----------------------A------------CACA---CACA-G-AGAGAG.....................	21	6	0.17	0.17	0.00	0.00	0.00
...............................................................................................................CAC-----------------------A------------CACA---CACA-C-AGAAACACATA................	24	3	0.33	0.00	0.33	0.00	0.00
......................................................................................................................................................TACA---CACA-G-AGACAGACAT.................	19	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................CACAC-----------------------A------------TACA---CACA-C-AGACAG.....................	21	6	0.17	0.00	0.00	0.00	0.17
...............................................................................................................CAC-----------------------A------------CACA---CACA-C-AGAGAGAG...................	21	6	0.17	0.17	0.00	0.00	0.00
.............................................................................................................CACAC-----------------------A------------TACA---CACA-C-AGACGG.....................	21	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................ACACAC-----------------------x------------CACA---CACA-C-GGA........................	18	6	0.17	0.00	0.17	0.00	0.00

droPer1

ACACTCGCACTCC------CA-C--AAGAAGAGCAG----CAG--TAG-----------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...........CC------AA-C--AAGAATAGCAG----CA.....................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00	0.00

droWil1

ATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG--AATG--TGTGTG

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

CACACAC-AC----------------------------------------------------------------------------------------------------ACAC-----------------------A------------CACATGTACAG-C-TTTCACTCATGCA--TATT--TGTT--	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...ACAC-AC----------------------------------------------------------------------------------------------------ACAA-----------------------A------------CTCATG...................................	17	14	0.07	0.00	0.07	0.00	0.00	0.00
...ACAC-AC----------------------------------------------------------------------------------------------------ACGC-----------------------A------------CGCATGT..................................	18	4	0.25	0.00	0.00	0.25	0.00	0.00
CACACAC-AC----------------------------------------------------------------------------------------------------ACAC-----------------------A------------CACACGT..................................	21	28	0.04	0.04	0.00	0.00	0.00	0.00
CATACAC-AC----------------------------------------------------------------------------------------------------ACAC-----------------------A------------CACGTG...................................	20	11	0.09	0.00	0.09	0.00	0.00	0.00
CACACAC-AC----------------------------------------------------------------------------------------------------ACAC-----------------------A------------CACAGCT..................................	21	48	0.02	0.02	0.00	0.00	0.00	0.00

droMoj3

GCATTTGCACTGC------TC-G--AAAATGAGCAA----TTG--CAAAGATCATTG-----CA--------C---------------A---ATACATTGC---------------------------AGAGAAAT--------A--CTG-------CACA-A-AATAATTTAGTTA--ATTTTAAGTTGA

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

GCAAAATGAA----C---ACA-A--AAACTGTTG--------------------------------------------------------------------CATACCACACACTAACTGTAAATATC------ACAT---------------------TT-T-TATTATTCTTATA--ATTA--TTAATA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:17:46 EDT

dme-mir-4965

chrX:16500140-16500227 +

Known_mirbase

intron

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup