sblock2216- Best orthologs

sblock2216	chr2L:2765182-2765267 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 2765229-2765251
   star strand at position 2765199-2765220
   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	chr2L:2765167-2765282 -		1	TTTGTGTAACCATTATCTCACAC--------------TCGCAAAATATGTAGGTA-------CAG-----------------------------------------------------------------------------------------TGGATAATCTCTAAGGCGAATAT-TGTCTGT-ATC---------------------TTCTTAGGTGTCTGGGAGCGAGCCACA---AGTGCTGA---GTAT
droSim1	chr2L:2727612-2727727 -	LASTZ	5	TTTGTGTAACCATTACCTCACAC--------------TCGCCAAATATGAAGGTA-------CAG-----------------------------------------------------------------------------------------TGGAAAATCTCTAAGGCGAATAT-TGTCTGT-ATC---------------------TTCCTAGGTGTCTGGGAGCGAGCCACA---AGTGCGGA---GTAT
droSec1	super_5:931138-931253 -	LASTZ	3	TTTGTGTAACCATTTTCTCACAC--------------TCGCCAAATATGAAGGTA-------CAG-----------------------------------------------------------------------------------------TGGAAAATCTATAAGGCGAATAT-TGTCTGT-ATC---------------------TTCGTAGGTGTCTGGGAACGAGACACA---AGTGCGGA---ATAT
droYak2	chr2L:2760749-2760863 -	LASTZ	5	TTTGTATAATCATTATCTTACAT--------------TCAAATAATATGTAGGTA-------CAG-----------------------------------------------------------------------------------------TGGAAACTCTCTAAGCTGAACAT-TTTCTA-TA-T---------------------CTTCCAGGTGTCTGGGAGCGACCCACT---ACTGCGGA---GTAT
droEre2	scaffold_4929:2817993-2818131 -	LASTZ	4	TAAAACC----ATAATCTCACAT--------------TTGCATAATATGTAGGTA-------CA-----------------------------------------TGGA------------AAAACGATCATCA---------GTAGGTCACAGTGGAAACTCTCTAAGACGAATGT-GGTCTAT-ATC---------------------TTCCTAGGTGTCTGGGAGCGACCCGCT---AGTGCTGA---ATAC
droEug1	scf7180000409554:3346024-3346246 +	LASTZ	4	TTTGTATAATCATAATTTCCCATGACTATATTTCAATGCCCCTATTGTGGGGCTT-------CAG----TACA-CATCTTCA---AGAATCATTTAATATTCACATTGGGATGCAGATTATCATATAATCATCACCTTAGTGTGTAAAGGACAATGAAAGCTT-CCAAAAAAAATTT---TTTA-TT-T--------AAGTTTTTCCATCTTTTTAGGTGTCTGGGAGCGGCCAACAATGAGTTCCGA---GTAC
droBia1	scf7180000302188:1767970-1768092 -	LASTZ	5	TTTGTATAAG-GTCTA-----------------------------------AGGACATTGGCCGTTAT-TAA--C--CATAT---AAA--------------------------------------------------------------ACTATAAAAATTACATAACTTAAATAT-ACTTATT-TCC---------------------TGTTTAGGTTTCTGGGAGCGACCCACAACCAGTGCCGA---GTAC
droTak1	scf7180000415705:514059-514162 -	LASTZ	5	ATTCATTGAAT------------------------------------------CCATTCATGCAGTGCTCTA--A--TATGTATAG--------------------------------------------------------------------CAAATAAT-----------ATATATTTTTG-TA-C---------------------CTTTTAGGTTTCTGGGAGCGACCAACGTCTAGCGCCGA---GTAC
droEle1	scf7180000491273:412313-412354 +	LASTZ	5	TTTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGGTGTCTGGGAGCGACCCACGTCTAATGCCGA---CTTC
droRho1	scf7180000766156:59158-59229 +	LASTZ	5	CTAAAGCAACATTTATTA----T---------------------------------------------------------------------------------------------------------------------------------------------------------T-TGTTTCAAA-A---------------------CTTGTAGATGTCTGGGCGCGACCCACAACAAATGCCGA---GTAC
droFic1	scf7180000453924:716599-716727 -	LASTZ	4	TATGTACATATGGA-------------------------------------T-----GAGTATA----------C--TTTTT---AAAATTAAAAAATATATAAATTGG------------TTTA-----------------------------TGAATATCATCTCA-ATAAATAC-TTTTTG-AA-C---------------------TTTTTAGGTGTCTGGGAGCGACCCACAACGAATTCCGA---GTAT
droKik1	scf7180000302271:228107-228177 -	LASTZ	5	TTTCTAAAACC---------------------------------------------------------------------------------------------------------------------------------------------------------------TCAACAA-ATTATG-T--A---------------------TTTATAGGAGTCTGGGAGCGACCCTCATCGAGTACCGAAACCTTT
droAna3	scaffold_12984:244381-244458 -	LASTZ	5	TAC------------------------------------------------------------AGTGGGAACG--------------------------------------------------------------------------------------AGTCTTAAAAATGAAAAA-T---------A---------------------TTTTCAGGCATCTGGGAGCGACCAGCACAGACGGCCACTTCTTAT
droBip1	scf7180000396574:369645-369692 -	LASTZ	5	AT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A---------------------CTTTCAGGTATCTGGGAGCGACCAGCACAGACGGCCGCTTCTTAT
dp4	chr4_group4:2108184-2108280 -	LASTZ	4	TTTGACGCTA-ATTGG-----------------------------------TGCACACTAAGCAGTGGGTCCGG-------TCTGA------------------------------------------------------------------------------------CAAA-----TGAAG-TT-T---------------------TCCGCAGGTTTCTGGGAGCGCCCCACATCGTCCACCAC---GTAT
droPer1	super_10:1114845-1114941 -	LASTZ	4	TTTGACGCTA-ATTGG-----------------------------------TGCACACTAAGCAGTGGGTCCGG-------TCTGA------------------------------------------------------------------------------------CAAA-----TGAAG-TT-T---------------------TCCGCAGGTTTCTGGGAGCGCCCCACATCGTCCACCAC---GTAT
droWil1	scaffold_180772:1542185-1542212 -	LASTZ	0	CT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTGGGAACGACCAGC------CACAAA---ATAT
droVir3	scaffold_12963:11387645-11387742 -	LASTZ	0	TGCGTATGCTAGATA------------------------------------------CC-AGAAGCAGATCAAG-------TTTG-------------------------------------------------------------------------------CTCA-CTTTACAT-TTTATG-TC-C---------------------GCAACAGCTTTCTGGGAGAGTTTTAATCCAGTTAAAAG---ATTT
droMoj3	scaffold_6500:20137581-20137687 -	LASTZ	0	TGAGCTA----ATTGG-----------------------------------AATCCAAAGTGCAGTTTTTTA--T--ATTATATAT--------------------------------------------------------------------ACAT---------A-CAT-ATATATATATG-TA-T---------------------ATTTAAGCGTTCTGGGAGAGCTACAATTCAGCTAAAAA---GTTT
droGri2	scaffold_15126:5047932-5047984 -	LASTZ	0	AATATTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAA-TT-CCCAATAGC-------------TTGCTGGA---AGAAGAGCTTTCCACA--------TAG---GTTT

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	TTTGTGTAACCATTATCTCACAC--------------TCGCAAAATATGTAGGTA-------CAG-------------------------------------------------------------------------------------TGGATAATCTC-TAAGGCGAATA----------TTGTC-TGTATCTTCTTAGGTGTCTGGGAGCGAGCCACA---AGTGCTGA---GTAT
droSim1	TTTGTGTAACCATTACCTCACAC--------------TCGCCAAATATGAAGGTA-------CAG-------------------------------------------------------------------------------------TGGAAAATCTC-TAAGGCGAATA----------TTGTC-TGTATCTTCCTAGGTGTCTGGGAGCGAGCCACA---AGTGCGGA---GTAT
droSec1	TTTGTGTAACCATTTTCTCACAC--------------TCGCCAAATATGAAGGTA-------CAG-------------------------------------------------------------------------------------TGGAAAATCTA-TAAGGCGAATA----------TTGTC-TGTATCTTCGTAGGTGTCTGGGAACGAGACACA---AGTGCGGA---ATAT
droYak2	TTTGTATAATCATTATCTTACAT--------------TCAAATAATATGTAGGTA-------CAG-------------------------------------------------------------------------------------TGGAAACTCTC-TAAGCTGAACA----------TTTTC-TATATC-TTCCAGGTGTCTGGGAGCGACCCACT---ACTGCGGA---GTAT
droEre2	TAA----AACCATAATCTCACAT--------------TTGCATAATATGTAGGTA-------CA-------------------------------------TGGA------------AAAACGATCATCA---------GTAGGTCACAGTGGAAACTCTC-TAAGACGAATG----------TGGTC-TATATCTTCCTAGGTGTCTGGGAGCGACCCGCT---AGTGCTGA---ATAC
droEug1	TTTGTATAATCATAATTTCCCATGACTATATTTCAATGCCCCTATTGTGGGGCTT-------CAG--TACA--CATCTTCAAGAATCATTTAATATTCACATTGGGATGCAGATTATCATATAATCATCACCTTAGTGTGTAAAGGACAATGAAAGCTT-C-CAAAAAAAATTTTTTATTTAAGTTTT-TCCATCTTTTTAGGTGTCTGGGAGCGGCCAACAATGAGTTCCGA---GTAC
droBia1	TTTGTATAAG-GTCTA-----------------------------------AGGACATTGGCCGTTATTAA--C--CATATAA--------------------------------------------------------------AACTATAAAAATTACA-TAACTTAAATA----------TACTT-ATTTCCTGTTTAGGTTTCTGGGAGCGACCCACAACCAGTGCCGA---GTAC
droTak1	ATTCATTGAATCCATTCATGCAG--------------TGCTCTAATAT------------------------------------------------------------------------------------------------------------GTATAGCAAATAATATA----------TATTTTTGTA-CCTTTTAGGTTTCTGGGAGCGACCAACGTCTAGCGCCGA---GTAC
droEle1	TTTG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGGTGTCTGGGAGCGACCCACGTCTAATGCCGA---CTTC
droRho1	CTAAAGCAACATTTATTA----T----------------------------------------------------------------------------------------------------------------------------------------------------------------TTGTT-TCAAAACTTGTAGATGTCTGGGCGCGACCCACAACAAATGCCGA---GTAC
droFic1	TATGTACATA-------------------------------------TGGATG----------AG--TATA--C--TTTTTAAAATTAAAAAATATATAAATTGG------------TTTA-----------------------------TGAATATCATC-TCA-ATAAATA----------CTTTT-TG-AACTTTTTAGGTGTCTGGGAGCGACCCACAACGAATTCCGA---GTAT
droKik1	TTTCTAAAACCTCA--------------------------------------------------------------------------------------------------------------------------------------------------------ACAAATT----------AT-------GTATTTATAGGAGTCTGGGAGCGACCCTCATCGAGTACCGAAACCTTT
droAna3	TA------------------------------------------------------------CAGTGGGAACG----------------------------------------------------------------------------------AGTCTT-AAAAATGAAAA-------------------ATATTTTCAGGCATCTGGGAGCGACCAGCACAGACGGCCACTTCTTAT
droBip1	AT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTTTCAGGTATCTGGGAGCGACCAGCACAGACGGCCGCTTCTTAT
dp4	TTTGACGCTA-ATTGG-----------------------------------TGCACACTAAGCAGTGGGTCCG-----------------------------------------------------------------------------------GTCTG-----ACAAATG----------AAGT------TTTCCGCAGGTTTCTGGGAGCGCCCCACATCGTCCACCAC---GTAT
droPer1	TTTGACGCTA-ATTGG-----------------------------------TGCACACTAAGCAGTGGGTCCG-----------------------------------------------------------------------------------GTCTG-----ACAAATG----------AAGT------TTTCCGCAGGTTTCTGGGAGCGCCCCACATCGTCCACCAC---GTAT

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

TTTGTGTAACCATTACCTCACAC--------------TCGCCAAATATGAAGGTA-------CAG-----------------------------------------------------------------------------------------TGGAAAATCTCTAAGGCGAATAT-TGTCTGT-ATC---------------------TTCCTAGGTGTCTGGGAGCGAGCCACA---AGTGCGGA---GTAT

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

TTTGTGTAACCATTTTCTCACAC--------------TCGCCAAATATGAAGGTA-------CAG-----------------------------------------------------------------------------------------TGGAAAATCTATAAGGCGAATAT-TGTCTGT-ATC---------------------TTCGTAGGTGTCTGGGAACGAGACACA---AGTGCGGA---ATAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.............................................................................................................................................................................................................................CTGGGAACGAGACACA---AGTGC..........	21	1	1.00	0.00	0.00	1.00
.....................................................................................................................................................................................................................AAAGGTGTCTGGGAACGAGA......................	20	1	1.00	1.00	0.00	0.00
.......................................................................................................................................................................................................................AGGTGTCTGGGAACGAGA......................	18	1	1.00	0.00	1.00	0.00
............................................................................................................................................................................................................................TCTGGGAACGAGACACA---AGTGC..........	22	1	1.00	1.00	0.00	0.00
...........................................AGTATGAAGGTA-------CAA-----------------------------------------------------------------------------------------TGG..................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

TTTGTATAATCATTATCTTACAT--------------TCAAATAATATGTAGGTA-------CAG-----------------------------------------------------------------------------------------TGGAAACTCTCTAAGCTGAACAT-TTTCTA-TA-T---------------------CTTCCAGGTGTCTGGGAGCGACCCACT---ACTGCGGA---GTAT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..........................................................................................................................................................................................................................TGTCTGGGxGCGGCCCA....................	16	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

TAAAACC----ATAATCTCACAT--------------TTGCATAATATGTAGGTA-------CA-----------------------------------------TGGA------------AAAACGATCATCA---------GTAGGTCACAGTGGAAACTCTCTAAGACGAATGT-GGTCTAT-ATC---------------------TTCCTAGGTGTCTGGGAGCGACCCGCT---AGTGCTGA---ATAC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......C----ATTATCTCACAT--------------TTGGAT....................................................................................................................................................................................................................	19	1	5.00	4.00	0.00	0.00	1.00
...........ATTATCTCACAT--------------TTGGAT....................................................................................................................................................................................................................	18	1	4.00	0.00	0.00	0.00	4.00
......C----ATTATCTCACAT--------------TTGGA.....................................................................................................................................................................................................................	18	1	3.00	3.00	0.00	0.00	0.00
..AAAAC----ATTATCTCACAT--------------TTG.......................................................................................................................................................................................................................	20	1	2.00	2.00	0.00	0.00	0.00
...AAAC----ATTATCTCACAT--------------TTG.......................................................................................................................................................................................................................	19	1	2.00	2.00	0.00	0.00	0.00
......C----ATTATCTCACAT--------------TTGCATT...................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
............................................................................................................................................................GAAGCTCTCGAAGACGAA.................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......C----ATTATCTCACAT--------------TTGTAT....................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droEug1

TTTGTATAATCATAATTTCCCATGACTATATTTCAATGCCCCTATTGTGGGGCTT-------CAG----TACA-CATCTTCA---AGAATCATTTAATATTCACATTGGGATGCAGATTATCATATAATCATCACCTTAGTGTGTAAAGGACAATGAAAGCTT-CCAAAAAAAATTT---TTTA-TT-T--------AAGTTTTTCCATCTTTTTAGGTGTCTGGGAGCGGCCAACAATGAGTTCCGA---GTAC

Size

Hit Count

Total Norm

droBia1

TTTGTATAAG-GTCTA-----------------------------------AGGACATTGGCCGTTAT-TAA--C--CATAT---AAA--------------------------------------------------------------ACTATAAAAATTACATAACTTAAATAT-ACTTATT-TCC---------------------TGTTTAGGTTTCTGGGAGCGACCCACAACCAGTGCCGA---GTAC

Size

Hit Count

Total Norm

droTak1

ATTCATTGAAT------------------------------------------CCATTCATGCAGTGCTCTA--A--TATGTATAG--------------------------------------------------------------------CAAATAAT-----------ATATATTTTTG-TA-C---------------------CTTTTAGGTTTCTGGGAGCGACCAACGTCTAGCGCCGA---GTAC

Size

Hit Count

Total Norm

droEle1

TTTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGGTGTCTGGGAGCGACCCACGTCTAATGCCGA---CTTC

Size

Hit Count

Total Norm

droRho1

CTAAAGCAACATTTATTA----T---------------------------------------------------------------------------------------------------------------------------------------------------------T-TGTTTCAAA-A---------------------CTTGTAGATGTCTGGGCGCGACCCACAACAAATGCCGA---GTAC

Size

Hit Count

Total Norm

droFic1

TATGTACATATGGA-------------------------------------T-----GAGTATA----------C--TTTTT---AAAATTAAAAAATATATAAATTGG------------TTTA-----------------------------TGAATATCATCTCA-ATAAATAC-TTTTTG-AA-C---------------------TTTTTAGGTGTCTGGGAGCGACCCACAACGAATTCCGA---GTAT

Size

Hit Count

Total Norm

droKik1

TTTCTAAAACC---------------------------------------------------------------------------------------------------------------------------------------------------------------TCAACAA-ATTATG-T--A---------------------TTTATAGGAGTCTGGGAGCGACCCTCATCGAGTACCGAAACCTTT

Size

Hit Count

Total Norm

droAna3

TAC------------------------------------------------------------AGTGGGAACG--------------------------------------------------------------------------------------AGTCTTAAAAATGAAAAA-T---------A---------------------TTTTCAGGCATCTGGGAGCGACCAGCACAGACGGCCACTTCTTAT

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

AT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A---------------------CTTTCAGGTATCTGGGAGCGACCAGCACAGACGGCCGCTTCTTAT

Size

Hit Count

Total Norm

dp4

TTTGACGCTA-ATTGG-----------------------------------TGCACACTAAGCAGTGGGTCCGG-------TCTGA------------------------------------------------------------------------------------CAAA-----TGAAG-TT-T---------------------TCCGCAGGTTTCTGGGAGCGCCCCACATCGTCCACCAC---GTAT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
......................................................ACACTAAGCGGTGGATCC.......................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.....................................................CACTCTAAGCGGTGGGTC........................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................................................................................................AAGGTTTCTGGGAGCGCC.......................	18	1	1.00	0.00	0.00	1.00	0.00

droPer1

TTTGACGCTA-ATTGG-----------------------------------TGCACACTAAGCAGTGGGTCCGG-------TCTGA------------------------------------------------------------------------------------CAAA-----TGAAG-TT-T---------------------TCCGCAGGTTTCTGGGAGCGCCCCACATCGTCCACCAC---GTAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.............................................................GCAGTGGGTCCGG-------GCAGA------------------------------------------------------------------------------------.....................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

CT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTGGGAACGACCAGC------CACAAA---ATAT

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

TGCGTATGCTAGATA------------------------------------------CC-AGAAGCAGATCAAG-------TTTG-------------------------------------------------------------------------------CTCA-CTTTACAT-TTTATG-TC-C---------------------GCAACAGCTTTCTGGGAGAGTTTTAATCCAGTTAAAAG---ATTT

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TGAGCTA----ATTGG-----------------------------------AATCCAAAGTGCAGTTTTTTA--T--ATTATATAT--------------------------------------------------------------------ACAT---------A-CAT-ATATATATATG-TA-T---------------------ATTTAAGCGTTCTGGGAGAGCTACAATTCAGCTAAAAA---GTTT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...................................................................................TAT--------------------------------------------------------------------ACAT---------A-CAT-ATATACATGT........................................................................	21	32	0.03	0.03	0.00	0.00	0.00

droGri2

AATATTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAA-TT-CCCAATAGC-------------TTGCTGGA---AGAAGAGCTTTCCACA--------TAG---GTTT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:18:55 EDT

sblock2216

chr2L:2765182-2765267 -

Candidate

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