block998659- Best orthologs

block998659	chr2R:4838727-4838822 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 4838780-4838801
   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	chr2R:4838712-4838837 +		1	TTGAGCGTTAAA---AAGAAGTTT----------CCTTAC------------TTCAA-------------------------------------------------ATTCT---TGTTGCATTTCCAACGCTTTCAGAATTTGAAACTTT-----------------GGAAATGTAACATCTTTAAA-GTTGATGGGAGTA--------------------------------------------CACATGCAAAA------ATA--T-TGCGG
droSim1	chr2R:3508456-3508586 +	LASTZ	5	TTGAGCGTTAAA---ACGAAGTTT----------CCTTAC------------TTCAA-------------------------------------------------ATTTT---TATTGCATTTCCAACGCTTTCAGAATTTGAAAATTTTT------------AATGTAAATGTAACATCTTTAAA-ATTGATGGGAGTA--------------------------------------------CACATGCATAA------ATA--T-TGCGA
droSec1	super_1:2476919-2477049 +	LASTZ	3	TTGAGCGTTAAA---ACGAAGTTT----------CCTTAC------------TTCAA-------------------------------------------------ATTTT---TATTGCATTAACAACGCTTTCAGAATTTGAAAATTTTT------------AATGTAAATGTAACATCTTTAAA-ATTGATGGGAGTA--------------------------------------------CACATGAGTAA------ATA--T-TGCGA
droYak2	chr2L:17496772-17496913 +	LASTZ	0	ATGATCACTTAA---AATTTGTAT----------TTTATT------------TTCAA-----------------TGCTTCCTTTTTTTTCGAAAGGTTTCTTTAAA--------------------------TATGCAGGTTTTATTTTTTTAT----------ATTTATCATTTTATAATTTAACA-CTTGTCGAGTGGA--------------------------------------------CATCCTTGTCA------ATC--C-TATGG
droEre2	scaffold_4929:17811133-17811287 -	LASTZ	0	TTGAACGTTAAT---ACGATATGT----------AT-----GTATGATTA-TGTA----------------AAA--------------------------------ATTTCCAATTTAACATTTTCAACGCTTTCTGAATTAAAAGGCTT-----------------GTGAATGTGAAACCTGGGTG----------AATT-------------GAGAAGTAATCTCCTTTGGAACAAGAGTGTGCAAACGCAGAA------A------TGCAT
droEug1	scf7180000409183:491556-491654 +	LASTZ	0	TTAAAAATTAAA---AAAAAGTTC----------------------------TTCAAATCACTACAGTCTGTAAT---------------------------------------TATTGCAATCCCAA--------ATACTTAAAAATGTTT------------A--------------------------------TTTG--------------------------------------------TCTGTACAATT------ATA--T-TATAG
droBia1	scf7180000302292:1079271-1079412 +	LASTZ	0	TTGAAAACTAAT---GAGAGGATGTTAAAGAAAGCCGTAC------------AGTTA--------------ACAT---------------------------------TTT-------TCTGTTTCTACATCATTAGAAATTACCACGAA----AGGAATTTCTGATTT-------ACACCCGTTTA-CTGGTTGTTAATA-------------CCT-----------------------------AAATTTAAAT------ATA--T-GTTCG
droTak1	scf7180000415386:400102-400165 -	LASTZ	0	TTAAACACCATT---AGTATGTAT----------A--ATC------------TTCAA-----------------T---------------------------------TTC---AGCGGCATTACT------------------------------------------------------------------------------------------------------------------------ACATTAACAA------A-A--T-ATGAA
droEle1	scf7180000490483:14898-15025 -	LASTZ	0	TGTTAAAAGGC-----------------------CTGACC------------TTCCA-------------------------------------------------ATTTT---TGTTA--TTAAT---------AAAATTTAAAATTCGTT--GAATATATTTGATTTAAGTGATATAT-----------------TGAATTTATTCAAAAACCCT-------------AA--------------AATTTTAAATATTATATTA--A-ATCGA
droRho1	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droFic1	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droKik1	scf7180000302476:2590990-2591133 -	LASTZ	0	ATATGTTTTGCGAGGGCAAAGTTC----------TTACGCTGTAAAATTAATTTA----------------AAAT----------------------TTTTTTGGT-----------AATAAT-------TTAAAAAAATTTAAGCATTATA------------GGTTAAAAACATACATTTA-AAG-GATTCTGCATTTA--------------------------------------------TTTATGCAAGA------ATACTTCGACGA
droAna3	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000396427:2121504-2121618 -	LASTZ	0	GAGGAA--TAAT---ATTAAATCG----------ACTACA-ATAAAATTCATCTA----------------AAGT----------------------ATTTTTGAT--------------------------CACAAACTTTTAAAACTTTT------------AAGGCCGCCATGATATATTCAAATG-----------------------------------------------------------GTACTCCA------ATG--T-AGCCG
dp4	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181009:2189187-2189301 +	LASTZ	0	GCTAA------A---GAAAGGTT--------------TAT------------TTTAA-------------------------------------------------ATTTTGCTCTTTGCATTCTTAACTTAATTAGAATTGTAATGTTT-----------------GTT---------------------------AAAA-------------TCTATTTATTTTCCCTTTG------------TTTACGTGACT---A-TTTC--T-TGCAA
droVir3	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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	TTGAGCGTTAAAAAGAAGTTTCCTTACTTCAAATTCTTGTTGCATTTCCAACGCTTTCAGAATTTGAAACTTT-----GGAAATGTAACATCTTTAAAGTTGATGGGAGTACACATGCAAAAATATTGCGG
droSim1	TTGAGCGTTAAAACGAAGTTTCCTTACTTCAAATTTTTATTGCATTTCCAACGCTTTCAGAATTTGAAAATTTTTAATGTAAATGTAACATCTTTAAAATTGATGGGAGTACACATGCATAAATATTGCGA
droSec1	TTGAGCGTTAAAACGAAGTTTCCTTACTTCAAATTTTTATTGCATTAACAACGCTTTCAGAATTTGAAAATTTTTAATGTAAATGTAACATCTTTAAAATTGATGGGAGTACACATGAGTAAATATTGCGA

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	None		None		None	None		None	None	None
UNAFold Image										None	None		None		None	None		None	None	None

Small RNA-seq read pileup

Species

Alignment

droSim1

TTGAGCGTTAAA---ACGAAGTTT----------CCTTAC------------TTCAA-------------------------------------------------ATTTT---TATTGCATTTCCAACGCTTTCAGAATTTGAAAATTTTT------------AATGTAAATGTAACATCTTTAAA-ATTGATGGGAGTA--------------------------------------------CACATGCATAA------ATA--T-TGCGA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.......................................................................................................................................................................GTAAATGTAACxTCTTTAAT-......................................................................................	19	1	2.00	0.00	0.00	2.00	0.00
.....................................................................................................................................................................ATGTAAATGTAAAAACTT...........................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................CAACGCTTTAAGAATCTG...................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................TTT------------ACTGTAAATGAAACA...............................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................................TTTAT------------AATGTAATTGTAAC................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droSec1

TTGAGCGTTAAA---ACGAAGTTT----------CCTTAC------------TTCAA-------------------------------------------------ATTTT---TATTGCATTAACAACGCTTTCAGAATTTGAAAATTTTT------------AATGTAAATGTAACATCTTTAAA-ATTGATGGGAGTA--------------------------------------------CACATGAGTAA------ATA--T-TGCGA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.................................................................................................................................................AATTTAT------------AATGTAATTGTA..................................................................................................	19	1	2.00	0.00	1.00	1.00
................................................................................................................................................AAATTTAT------------AATGTAATTGT...................................................................................................	19	1	1.00	1.00	0.00	0.00

droYak2

ATGATCACTTAA---AATTTGTAT----------TTTATT------------TTCAA-----------------TGCTTCCTTTTTTTTCGAAAGGTTTCTTTAAA--------------------------TATGCAGGTTTTATTTTTTTAT----------ATTTATCATTTTATAATTTAACA-CTTGTCGAGTGGA--------------------------------------------CATCCTTGTCA------ATC--C-TATGG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.....................................................................................................................................ATACAGGxTTTATTTTTTTAT----------..............................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00

droEre2

TTGAACGTTAAT---ACGATATGT----------AT-----GTATGATTA-TGTA----------------AAA--------------------------------ATTTCCAATTTAACATTTTCAACGCTTTCTGAATTAAAAGGCTT-----------------GTGAATGTGAAACCTGGGTG----------AATT-------------GAGAAGTAATCTCCTTTGGAACAAGAGTGTGCAAACGCAGAA------A------TGCAT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
....................................................................................................................................................TT-----------------GTGAGTGTGAAAGCTG...........................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

TTAAAAATTAAA---AAAAAGTTC----------------------------TTCAAATCACTACAGTCTGTAAT---------------------------------------TATTGCAATCCCAA--------ATACTTAAAAATGTTT------------A--------------------------------TTTG--------------------------------------------TCTGTACAATT------ATA--T-TATAG

Size

Hit Count

Total Norm

droBia1

TTGAAAACTAAT---GAGAGGATGTTAAAGAAAGCCGTAC------------AGTTA--------------ACAT---------------------------------TTT-------TCTGTTTCTACATCATTAGAAATTACCACGAA----AGGAATTTCTGATTT-------ACACCCGTTTA-CTGGTTGTTAATA-------------CCT-----------------------------AAATTTAAAT------ATA--T-GTTCG

Size

Hit Count

Total Norm

droTak1

TTAAACACCATT---AGTATGTAT----------A--ATC------------TTCAA-----------------T---------------------------------TTC---AGCGGCATTACT------------------------------------------------------------------------------------------------------------------------ACATTAACAA------A-A--T-ATGAA

Size

Hit Count

Total Norm

droEle1

TGTTAAAAGGC-----------------------CTGACC------------TTCCA-------------------------------------------------ATTTT---TGTTA--TTAAT---------AAAATTTAAAATTCGTT--GAATATATTTGATTTAAGTGATATAT-----------------TGAATTTATTCAAAAACCCT-------------AA--------------AATTTTAAATATTATATTA--A-ATCGA

Size

Hit Count

Total Norm

droRho1

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

droFic1

Size

Hit Count

Total Norm

droKik1

ATATGTTTTGCGAGGGCAAAGTTC----------TTACGCTGTAAAATTAATTTA----------------AAAT----------------------TTTTTTGGT-----------AATAAT-------TTAAAAAAATTTAAGCATTATA------------GGTTAAAAACATACATTTA-AAG-GATTCTGCATTTA--------------------------------------------TTTATGCAAGA------ATACTTCGACGA

Size

Hit Count

Total Norm

droAna3

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

GAGGAA--TAAT---ATTAAATCG----------ACTACA-ATAAAATTCATCTA----------------AAGT----------------------ATTTTTGAT--------------------------CACAAACTTTTAAAACTTTT------------AAGGCCGCCATGATATATTCAAATG-----------------------------------------------------------GTACTCCA------ATG--T-AGCCG

Size

Hit Count

Total Norm

dp4

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

GCTAA------A---GAAAGGTT--------------TAT------------TTTAA-------------------------------------------------ATTTTGCTCTTTGCATTCTTAACTTAATTAGAATTGTAATGTTT-----------------GTT---------------------------AAAA-------------TCTATTTATTTTCCCTTTG------------TTTACGTGACT---A-TTTC--T-TGCAA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..................AGGTT--------------TAT------------TTAAA-------------------------------------------------ATATT...................................................................................................................................................................	18	2	4.00	0.00	0.00	4.00	0.00
......................................AT------------TTTAA-------------------------------------------------TTATTGCTCTT.............................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................AAAGGTT--------------TAT------------TTAAA-------------------------------------------------ATATT...................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
................AGAGGTT--------------TAT------------TTAAA-------------------------------------------------ATTTT...................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................................................................................TTTGTTTTCCATTTG------------TTT..........................	18	6	0.17	0.00	0.17	0.00	0.00
..................AGGTT--------------TAT------------TTGAA-------------------------------------------------ATATT...................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:12:22 EDT

block998659

chr2R:4838727-4838822 +

Candidate

intergenic

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