CG3160_in3- Best orthologs

CG3160_in3	chrX:5582203-5582254 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 5582230-5582254
   star strand at position 5582204-5582225
   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:5582188-5582269 -		1	TTGTCTACCTTTGTGGTAAGTTGCAT--TGTATTCTAA---------------------------GCACTAGT--AAAT------------------ACAAATG--A-------------------------TATACTTACAGAAGCCTCGAAGGCGT
droSim1	chrX:4333816-4333897 -	LASTZ	4	TTGTCCACCTTTGTGGTAGGTTGCAT--TGTATCCTAA---------------------------ACACTATT--AAAT------------------ACTAATG--A-------------------------TATACTTACAGAAGCCCCGAAGGCGT
droSec1	super_4:1176184-1176265 +	LASTZ	5	TTGTCCACCTTTGTGGTAGGTTGCAG--AATATTCAAA---------------------------GCACTATT--AAAT------------------TCTAATG--A-------------------------TATACTTACAGAAGCCCCGAAGGCGT
droYak2	chrX:2886884-2886965 +	LASTZ	5	TTGTCCACCTTTGTGGTAGGTTGCAT--TGTATTTAAA---------------------------ACACCATT--AAAT------------------GCTAAAT--A-------------------------TATAATTACAGAAGCCTCGAAGGCGT
droEre2	scaffold_4690:2935043-2935124 -	LASTZ	4	TTGTCAACCTTTGTGGTAGGTTGCAT--TGTATTTAAA---------------------------ACACTATG--AAGT------------------ACTAAAT--A-------------------------TGTACTTACAGAAGCCTCGAAGGCGT
droEug1	scf7180000409095:622922-623003 -	LASTZ	5	TTATCCACATTTGTAGTAGGTTCCTA--CGGATTTCCA---------------------------TATCAATC--AAAT------------------ACTTAAG--A-------------------------TATATCCACAGAAACCACGGAGACGA
droBia1	scf7180000302069:240686-240767 +	LASTZ	5	CTAGCCACCTTTGTCGTAGGTTCCTA--GAACTGCCAA---------------------------TCTCTGTC--CAAT------------------ACTAAAA--A-------------------------TATACCCACAGAAGCCAAGAAGACGA
droTak1	scf7180000415704:943029-943121 +	LASTZ	5	TTAGCCACCTTTGTCGTGGGTTCCTA--GCACTATTCT---ATAT-----------ATCT-TT-ATATATCTATAT--ATC--------------AT----G-TA-T-------------------------ATATATCACAGAAACCGCGGAGACGG
droEle1	scf7180000491001:865333-865422 +	LASTZ	5	CTGTCCACCTTTGTGGTAAGTTCTTC--CTGATTTCGA---------------------------TCTCTATT--CTAT------TATTAC------GCTCAAGAAA-------------------------TACCCACACAGAAGTCACGAAGGCGT
droRho1	scf7180000779976:691191-691274 +	LASTZ	5	TTGTCTACATTTGTGGTATGTTTTTTTTCGAATTTCGG---------------------------TCGCTATT--CCAC------------------ACTAAAT--A-------------------------TGTACCCACAGAAGCCGCGAAGCCGT
droFic1	scf7180000454072:2528858-2528939 +	LASTZ	5	CTGTCGACTTTTGTGGTAGGTTCCTG--CAATCTGAGG---------------------------TGTTTATA--CCAA------------------ACTTAAG--G-------------------------TTTATCCACAGAAGCCACGCAGGCGT
droKik1	scf7180000302344:685348-685434 -	LASTZ	5	CTCGCCCACTTTGTGGTGAGTTTCCC--CCAGGCCCAG---------------------------ACG--ATT--CCAT------GCCGCT------GATTACTA-A-------------------------TTAACCCCCAGAAACCACGAAGGCGT
droAna3	scaffold_13117:3260782-3260871 -	LASTZ	5	CTGCACACCTTTGTGGTGAGTATATA--ATACAATAAT---------------------------ATTATATA--ATAA------TATTCAC---A-TTTGAAC--A-------------------------CGATTTTGCAGAAACCACGAAGGCGC
droBip1	scf7180000396434:597307-597385 +	LASTZ	5	CTCCACAGCTTTGTGGTGAGTATATA--GGACCCT-CC---------------------------GCAAT-TC--ATAT------------------TCTAA-T--A-------------------------GGATTCTTCAGAAACCACGCAGGCGC
dp4	chrXL_group1e:588994-589086 -	LASTZ	5	CTGTCTCACTTTGTGGTAGATTCTAA--TGCTTATAATAACTTATAATTTCTTCATCA---------------TTT--ATC--------------GC----G-T--C-------------------------TGGTTTTTCAGAAGCGGCCAAGTCGC
droPer1	super_30:621799-621888 +	LASTZ	5	CTGTCTCACTTTGTGGTAGATTCTAA--TGCTTATAAC---TTATAATTTCTTCATCA---------------TTT--ATC--------------GC----G-T--C-------------------------TGGTTTTTCAGAAGCGGCCAAGTCGC
droWil1	scaffold_180702:827721-827807 -	LASTZ	5	ATGGCACATTTTATCGTAAGTTAATT--TCAAAA---G-----------------GTT--TTCTTGCCAACTT--AATG------------------ACAAATT--T-------------------------TTTGAATGCAGAAACCCAGGAGTCGC
droVir3	scaffold_12928:357066-357149 -	LASTZ	5	GTGGCGCATTTTGTGGTTGGCATTTG--TTT-----------------------TACA---------------CTT--GTCGCATGTTCTATAAT--ACTCTAC--A----------------------------TATTTTAGAAACCGAGGATACGG
droMoj3	scaffold_6328:487653-487744 +	LASTZ	5	TTGGGACACTTTGTGGTAAATGACAT--GCGAGGCTTC----------------TCAACT-TG-CTCAATCCATTT--A------------------ACTTATTC-T-------------------------GTATCTTGTAGAAATCGCCAACACGT
droGri2	scaffold_15203:6798783-6798893 -	LASTZ	5	CTGTCGCACTTTGTGGTAAGCAAACA--AGCA-----------------------ATA--TT---ATT-------------GTGTGATTAAAAAA--ACGAAAT--ATTGTTACTATCAAATCTTCGTTTTCTATCGATCTAGAAACAACGAACTCGC

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	TTGTCTACCTTTGTGGTAAGTTGCAT--TGTATTCTAA---------------------------GCACTAGT--AAAT------------------ACAAATG--A-------------------------TATACTTACAGAAGCCTCGAAGGCGT
droSim1	TTGTCCACCTTTGTGGTAGGTTGCAT--TGTATCCTAA---------------------------ACACTATT--AAAT------------------ACTAATG--A-------------------------TATACTTACAGAAGCCCCGAAGGCGT
droSec1	TTGTCCACCTTTGTGGTAGGTTGCAG--AATATTCAAA---------------------------GCACTATT--AAAT------------------TCTAATG--A-------------------------TATACTTACAGAAGCCCCGAAGGCGT
droYak2	TTGTCCACCTTTGTGGTAGGTTGCAT--TGTATTTAAA---------------------------ACACCATT--AAAT------------------GCTAAAT--A-------------------------TATAATTACAGAAGCCTCGAAGGCGT
droEre2	TTGTCAACCTTTGTGGTAGGTTGCAT--TGTATTTAAA---------------------------ACACTATG--AAGT------------------ACTAAAT--A-------------------------TGTACTTACAGAAGCCTCGAAGGCGT
droEug1	TTATCCACATTTGTAGTAGGTTCCTA--CGGATTTCCA---------------------------TATCAATC--AAAT------------------ACTTAAG--A-------------------------TATATCCACAGAAACCACGGAGACGA
droBia1	CTAGCCACCTTTGTCGTAGGTTCCTA--GAACTGCCAA---------------------------TCTCTGTC--CAAT------------------ACTAAAA--A-------------------------TATACCCACAGAAGCCAAGAAGACGA
droTak1	TTAGCCACCTTTGTCGTGGGTTCCTA--GCACTATTCT---ATAT-----------ATCT-TT-ATATATCTATAT--ATC--------------AT----G-TA-T-------------------------ATATATCACAGAAACCGCGGAGACGG
droEle1	CTGTCCACCTTTGTGGTAAGTTCTTC--CTGATTTCGA---------------------------TCTCTATT--CTAT------TATTAC------GCTCAAGAAA-------------------------TACCCACACAGAAGTCACGAAGGCGT
droRho1	TTGTCTACATTTGTGGTATGTTTTTTTTCGAATTTCGG---------------------------TCGCTATT--CCAC------------------ACTAAAT--A-------------------------TGTACCCACAGAAGCCGCGAAGCCGT
droFic1	CTGTCGACTTTTGTGGTAGGTTCCTG--CAATCTGAGG---------------------------TGTTTATA--CCAA------------------ACTTAAG--G-------------------------TTTATCCACAGAAGCCACGCAGGCGT
droKik1	CTCGCCCACTTTGTGGTGAGTTTCCC--CCAGGCCCAG---------------------------ACG--ATT--CCAT------GCCGCT------GATTACTA-A-------------------------TTAACCCCCAGAAACCACGAAGGCGT
droAna3	CTGCACACCTTTGTGGTGAGTATATA--ATACAATAAT---------------------------ATTATATA--ATAA------TATTCAC---A-TTTGAAC--A-------------------------CGATTTTGCAGAAACCACGAAGGCGC
droBip1	CTCCACAGCTTTGTGGTGAGTATATA--GGACCCT-CC---------------------------GCAAT-TC--ATAT------------------TCTAA-T--A-------------------------GGATTCTTCAGAAACCACGCAGGCGC
dp4	CTGTCTCACTTTGTGGTAGATTCTAA--TGCTTATAATAACTTATAATTTCTTCATCA---------------TTT--ATC--------------GC----G-T--C-------------------------TGGTTTTTCAGAAGCGGCCAAGTCGC
droPer1	CTGTCTCACTTTGTGGTAGATTCTAA--TGCTTATAAC---TTATAATTTCTTCATCA---------------TTT--ATC--------------GC----G-T--C-------------------------TGGTTTTTCAGAAGCGGCCAAGTCGC
droWil1	ATGGCACATTTTATCGTAAGTTAATT--TCAAAA---G-----------------GTT--TTCTTGCCAACTT--AATG------------------ACAAATT--T-------------------------TTTGAATGCAGAAACCCAGGAGTCGC
droVir3	GTGGCGCATTTTGTGGTTGGCATTTG--TTT-----------------------TACA---------------CTT--GTCGCATGTTCTATAAT--ACTCTAC--A----------------------------TATTTTAGAAACCGAGGATACGG
droMoj3	TTGGGACACTTTGTGGTAAATGACAT--GCGAGGCTTC----------------TCAACT-TG-CTCAATCCATTT--A------------------ACTTATTC-T-------------------------GTATCTTGTAGAAATCGCCAACACGT
droGri2	CTGTCGCACTTTGTGGTAAGCAAACA--AGCA-----------------------ATA--TT---ATT-------------GTGTGATTAAAAAA--ACGAAAT--ATTGTTACTATCAAATCTTCGTTTTCTATCGATCTAGAAACAACGAACTCGC

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

TTGTCCACCTTTGTGGTAGGTTGCAT--TGTATCCTAA---------------------------ACACTATT--AAAT------------------ACTAATG--A-------------------------TATACTTACAGAAGCCCCGAAGGCGT

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

TTGTCCACCTTTGTGGTAGGTTGCAG--AATATTCAAA---------------------------GCACTATT--AAAT------------------TCTAATG--A-------------------------TATACTTACAGAAGCCCCGAAGGCGT

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

TTGTCCACCTTTGTGGTAGGTTGCAT--TGTATTTAAA---------------------------ACACCATT--AAAT------------------GCTAAAT--A-------------------------TATAATTACAGAAGCCTCGAAGGCGT

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

TTGTCAACCTTTGTGGTAGGTTGCAT--TGTATTTAAA---------------------------ACACTATG--AAGT------------------ACTAAAT--A-------------------------TGTACTTACAGAAGCCTCGAAGGCGT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...........TGTGGTAGGTTGTAT--AGT...............................................................................................................................	18	2	1.00	0.00	0.00	0.00	1.00
...........TGAGGTAGGTTGCAT--AGT...............................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...........TGTGGTAGGTTGTAT--AGTA..............................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50

droEug1

TTATCCACATTTGTAGTAGGTTCCTA--CGGATTTCCA---------------------------TATCAATC--AAAT------------------ACTTAAG--A-------------------------TATATCCACAGAAACCACGGAGACGA

Size

Hit Count

Total Norm

droBia1

CTAGCCACCTTTGTCGTAGGTTCCTA--GAACTGCCAA---------------------------TCTCTGTC--CAAT------------------ACTAAAA--A-------------------------TATACCCACAGAAGCCAAGAAGACGA

Size

Hit Count

Total Norm

droTak1

TTAGCCACCTTTGTCGTGGGTTCCTA--GCACTATTCT---ATAT-----------ATCT-TT-ATATATCTATAT--ATC--------------AT----G-TA-T-------------------------ATATATCACAGAAACCGCGGAGACGG

Size

Hit Count

Total Norm

droEle1

CTGTCCACCTTTGTGGTAAGTTCTTC--CTGATTTCGA---------------------------TCTCTATT--CTAT------TATTAC------GCTCAAGAAA-------------------------TACCCACACAGAAGTCACGAAGGCGT

Size

Hit Count

Total Norm

droRho1

TTGTCTACATTTGTGGTATGTTTTTTTTCGAATTTCGG---------------------------TCGCTATT--CCAC------------------ACTAAAT--A-------------------------TGTACCCACAGAAGCCGCGAAGCCGT

Size

Hit Count

Total Norm

droFic1

CTGTCGACTTTTGTGGTAGGTTCCTG--CAATCTGAGG---------------------------TGTTTATA--CCAA------------------ACTTAAG--G-------------------------TTTATCCACAGAAGCCACGCAGGCGT

Size

Hit Count

Total Norm

droKik1

CTCGCCCACTTTGTGGTGAGTTTCCC--CCAGGCCCAG---------------------------ACG--ATT--CCAT------GCCGCT------GATTACTA-A-------------------------TTAACCCCCAGAAACCACGAAGGCGT

Size

Hit Count

Total Norm

droAna3

CTGCACACCTTTGTGGTGAGTATATA--ATACAATAAT---------------------------ATTATATA--ATAA------TATTCAC---A-TTTGAAC--A-------------------------CGATTTTGCAGAAACCACGAAGGCGC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..........................................................................................................................................TGCAGAAACCACGAAAGG..	18	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................TGCAGAAACCATGAAGGC..	18	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................TGCAGAAACCATGAAGGCC.	19	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................GCAGATACCATGAAGGC..	17	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................GATTTTGCTGAAACCACCA......	19	1	1.00	0.00	0.00	0.00	1.00

droBip1

CTCCACAGCTTTGTGGTGAGTATATA--GGACCCT-CC---------------------------GCAAT-TC--ATAT------------------TCTAA-T--A-------------------------GGATTCTTCAGAAACCACGCAGGCGC

Size

Hit Count

Total Norm

dp4

CTGTCTCACTTTGTGGTAGATTCTAA--TGCTTATAATAACTTATAATTTCTTCATCA---------------TTT--ATC--------------GC----G-T--C-------------------------TGGTTTTTCAGAAGCGGCCAAGTCGC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
................................................................................C--------------GT----G-T--C-------------------------TGGTTTTTCAGT..............	18	1	1.00	0.00	1.00	0.00	0.00
...........TGTGGTAxATTCTAG--TGCT..............................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

CTGTCTCACTTTGTGGTAGATTCTAA--TGCTTATAAC---TTATAATTTCTTCATCA---------------TTT--ATC--------------GC----G-T--C-------------------------TGGTTTTTCAGAAGCGGCCAAGTCGC

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

ATGGCACATTTTATCGTAAGTTAATT--TCAAAA---G-----------------GTT--TTCTTGCCAACTT--AATG------------------ACAAATT--T-------------------------TTTGAATGCAGAAACCCAGGAGTCGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.............................................................................TG------------------AGAAATT--T-------------------------TTTGAATT..................	18	2	0.50	0.00	0.50	0.00	0.00
...............GTAAGTGAATT--TCAAAC---G-----------------GTT--..................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00

droVir3

GTGGCGCATTTTGTGGTTGGCATTTG--TTT-----------------------TACA---------------CTT--GTCGCATGTTCTATAAT--ACTCTAC--A----------------------------TATTTTAGAAACCGAGGATACGG

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TTGGGACACTTTGTGGTAAATGACAT--GCGAGGCTTC----------------TCAACT-TG-CTCAATCCATTT--A------------------ACTTATTC-T-------------------------GTATCTTGTAGAAATCGCCAACACGT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
TTGGGCCACTTTxTGGTAA...........................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droGri2

CTGTCGCACTTTGTGGTAAGCAAACA--AGCA-----------------------ATA--TT---ATT-------------GTGTGATTAAAAAA--ACGAAAT--ATTGTTACTATCAAATCTTCGTTTTCTATCGATCTAGAAACAACGAACTCGC	Size	Hit Count	Total Norm	V109 Male body
......CACTTTxTGGTAAGCAGAC.....................................................................................................................................	18	1	1.00	1.00

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

CG3160_in3

chrX:5582203-5582254 -

Candidate

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