sblock192886- Best orthologs

sblock192886	chrX:453811-453911 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 453872-453892
   star strand at position 453830-453851
   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:453796-453926 +		1	CATCTC------------------------------------------------AA---------------AGGAAAAGACTAGGTCTG------------AGAA-ACGTTCATTGTTGTCTGTTCATAATTAGAGA----------GGGA-AAATCTC-----------------------TCGCGTTGAGTGCAATTAGCGTGGGCATTGTCTGCAAACTC-GCTG---CAGGACACCACTTA
droSim1	chrX:339791-339921 +	LASTZ	4	TATCTC------------------------------------------------AA---------------AGGAAAAGCCCAGGTCTG------------AGAA-AAGTTCATTGTTGTCTGTTTATAATTAGAGA----------GTGA-AAATCTC-----------------------TCTCGTTGAGTGCAATCGGCGTCGGCATTGTCGGCAAACTC-GCTG---CAGGACACCATTTA
droSec1	super_10:302522-302652 +	LASTZ	4	TATCTC------------------------------------------------AG---------------AGGAAAAGCCCAGGTCTG------------AGAA-ACGTTCATTGTTGTCTGTTCATAATTAGAGA----------GTGA-AAATCTC-----------------------TCTCGTTGAGTGCAATCGGCGTCGGCATTGTCTGCAAACTC-GCTG---CAGGACACCATTTA
droYak2	chrX:374570-374700 +	LASTZ	5	CATCTC------------------------------------------------AA---------------AGGAAAAGTCCAGATCTA------------AGAA-ACTTCCATTGTTGCCTGCTCGTAATTAGAGA----------GGGA-AAATCTC-----------------------TCGCGTTGAGTGCAATCAGCGCAGGCATTGTCTGCAAACTC-GCTG---CAGGACCCCATTCA
droEre2	scaffold_4644:400337-400446 +	LASTZ	5	CATCT-----------------------------------------------------------------------------------G------------GGAA-ACTTTCATTGTGC-CTGTTCATAATTAGAGA----------GTGA-AAATCCG-----------------------TTGCGCTGAGTGCAATCAGCAGCGGCATTGTCTGCCAACTC-GCTG---CAGGACCCCATTCA
droEug1	scf7180000409277:837087-837231 +	LASTZ	5	TAGCCG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGAA-ACTCCCATTGTTG-CCGGTCATAATTGGAGA----------GTGG-AAATCTC-GGG-------CCGGCATGCAACTCGCTTTGATTGCAATCAGCGCCGGCATTGTCTCCCAATTC-TGCT---CCGAATCCCGCTCC
droBia1	scf7180000301760:1504308-1504434 +	LASTZ	5	TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------AAAA-ACTACCATTGTTG-CCGGTCATAATTGGAGA----------GTGA-AAAGCTG-GGG-------CCGGCGAGCAACTCGCTTTGATTGCAATCAGCGCCGGCATTGTCTCAAAACTC----------------------
droTak1	scf7180000415281:267243-267386 -	LASTZ	5	TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGAA-ACTCCCATTGTTG-CTGGTCATAATTGGAGA----------GTGG-AAATCTCGGGG-------CCGGCGAGCAACTCGCTTTGATTGCAATCAGCACCGGCATTGTCTCGCAATTCTGCTC---GAA-AT--CTCCAC
droEle1	scf7180000491023:732380-732525 +	LASTZ	5	TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGGA-GCACCCATTGTTG-CTGGTCATAATTGGAGA----------GTGG-AAATCTA-GGG-------CCGGCGAGCAACTCGCTTTGATTGCAATCAGCGCCGGCATTGTCTTCCAATTCTGCCC---CAAAATCCCTCGCC
droRho1	scf7180000779514:227802-227944 +	LASTZ	5	TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGAA-ACTCCCATTGTTG-CTGGTCATAATTGGAGA----------GTGG-AAATCTC-GGG-------CTGGCGAGCAACTCGCTTTGATTGCAATCAGTGTCGGCATTGTCTTTCAATTC-TCCC---CGAAACCCCCCT--
droFic1	scf7180000453927:933548-933674 +	LASTZ	5	TAGCTG------------------------------------------------AA---------------AGGAAAAGGACAGATCAG------------GGAA-ACTCCCATTGTTG-CTGGTCATAATTGGAGA----------ATGG-AAATCTC-GGG-------CCGCCGAGCAACTCGCTTTGATTGCAATCAGCGCCGCCATTGTTTCACAATTC----------------------
droKik1	scf7180000302469:1872056-1872218 -	LASTZ	5	CAGGAG-----------------------------A------------------AAATGAAAGA-------AAGTAAAGCGCGGATCGGCCGGTAAGGCTGGAGA-TTTGCCATTGTTG-CTGGCCATAATTGGAGAGAAGAGAGAGTGGGAAAATCTC-TG---------CAGC-AGCAACTCGCTTTGATTGCAATCAGAGGTGGCATTGTCTCTCAATTCAGCTG---CA------------
droAna3	scaffold_12929:346312-346432 +	LASTZ	5	GATTGA-----------------------------A-------AGAGATGGCTAGAATGGAAAAAAATGGCAAA-------------AA------------AAGG-ACTCCCTTTTT-ATCTCATC--------------------------------------------CTGGCAAACAACTCGCTTTGATTGC--------CCATCATTGTCTTTCGATTC---------GGGAGGCAATTCA
droBip1	scf7180000395176:43762-43879 -	LASTZ	5	CGAATC------------------------------------------------GC---------------AAAAAGAACTC--------------------------GGCCATTGTTG-CAGCTCATAATTGGTAA----------ATCA-GAGCATG-AGAGTGAGGGCT--AGAGGGAGTCCTTTTTTT-----------------TTGTCT--TATCGC-ATCC---TGGCAAACAACTAA
dp4	chrXL_group1e:183509-183683 +	LASTZ	4	CAAATAGAACAGAGCGGGAGGTGGCACGGAGGTGGAAATTGAAGCTGTGAATT-AA---------------AAGCAAAGCGCAGATCGC------------AAAATACGTTTATTGTTC-CCGGTCATAATTGAGAG----------CTGG-AAA-----------------------------GCTTTGATTGCAATCAGCGTTGGCATTGTCTCCGATCTC-TCCCAGGCCGTATTACCCTTA
droPer1	super_60:145517-145640 -	LASTZ	4	TT----------------------------------------------------AA---------------AAGCAAAGCGCAGATCGC------------AAAATACGTTTATTGTTC-CCGGTCATAATTGAGAG----------CTGG-AAA-----------------------------GCTTTGATTGCAATCAGCGTTGGCATTGTCTCCGATCTC-TCCCAGGCCGTATTACCCTTA
droWil1	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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	CATCTC------------------------------------------------AA---------------AGGAAAAGACTAGGTCTG------------AGAA-ACGTTCATTGTTGTCTGTTCATAATTAGAGA----------GGGA-AAATCTC-----------------------TCGCGTTGAGTGCAATTAGCGTGGGCATTGTCTGCAAACTC-GCTG---CAGGACACCACTTA
droSim1	TATCTC------------------------------------------------AA---------------AGGAAAAGCCCAGGTCTG------------AGAA-AAGTTCATTGTTGTCTGTTTATAATTAGAGA----------GTGA-AAATCTC-----------------------TCTCGTTGAGTGCAATCGGCGTCGGCATTGTCGGCAAACTC-GCTG---CAGGACACCATTTA
droSec1	TATCTC------------------------------------------------AG---------------AGGAAAAGCCCAGGTCTG------------AGAA-ACGTTCATTGTTGTCTGTTCATAATTAGAGA----------GTGA-AAATCTC-----------------------TCTCGTTGAGTGCAATCGGCGTCGGCATTGTCTGCAAACTC-GCTG---CAGGACACCATTTA
droYak2	CATCTC------------------------------------------------AA---------------AGGAAAAGTCCAGATCTA------------AGAA-ACTTCCATTGTTGCCTGCTCGTAATTAGAGA----------GGGA-AAATCTC-----------------------TCGCGTTGAGTGCAATCAGCGCAGGCATTGTCTGCAAACTC-GCTG---CAGGACCCCATTCA
droEre2	CATCT-----------------------------------------------------------------------------------G------------GGAA-ACTTTCATTGTGC-CTGTTCATAATTAGAGA----------GTGA-AAATCCG-----------------------TTGCGCTGAGTGCAATCAGCAGCGGCATTGTCTGCCAACTC-GCTG---CAGGACCCCATTCA
droEug1	TAGCCG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGAA-ACTCCCATTGTTG-CCGGTCATAATTGGAGA----------GTGG-AAATCTC-GGG-------CCGGCATGCAACTCGCTTTGATTGCAATCAGCGCCGGCATTGTCTCCCAATTC-TGCT---CCGAATCCCGCTCC
droBia1	TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------AAAA-ACTACCATTGTTG-CCGGTCATAATTGGAGA----------GTGA-AAAGCTG-GGG-------CCGGCGAGCAACTCGCTTTGATTGCAATCAGCGCCGGCATTGTCTCAAAACTC----------------------
droTak1	TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGAA-ACTCCCATTGTTG-CTGGTCATAATTGGAGA----------GTGG-AAATCTCGGGG-------CCGGCGAGCAACTCGCTTTGATTGCAATCAGCACCGGCATTGTCTCGCAATTCTGCTC---GAA-AT--CTCCAC
droEle1	TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGGA-GCACCCATTGTTG-CTGGTCATAATTGGAGA----------GTGG-AAATCTA-GGG-------CCGGCGAGCAACTCGCTTTGATTGCAATCAGCGCCGGCATTGTCTTCCAATTCTGCCC---CAAAATCCCTCGCC
droRho1	TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGAA-ACTCCCATTGTTG-CTGGTCATAATTGGAGA----------GTGG-AAATCTC-GGG-------CTGGCGAGCAACTCGCTTTGATTGCAATCAGTGTCGGCATTGTCTTTCAATTC-TCCC---CGAAACCCCCCT--
droFic1	TAGCTG------------------------------------------------AA---------------AGGAAAAGGACAGATCAG------------GGAA-ACTCCCATTGTTG-CTGGTCATAATTGGAGA----------ATGG-AAATCTC-GGG-------CCGCCGAGCAACTCGCTTTGATTGCAATCAGCGCCGCCATTGTTTCACAATTC----------------------
droKik1	CAGGAG-----------------------------A------------------AAATGAAAGA-------AAGTAAAGCGCGGATCGGCCGGTAAGGCTGGAGA-TTTGCCATTGTTG-CTGGCCATAATTGGAGAGAAGAGAGAGTGGGAAAATCTC-TG---------CAGC-AGCAACTCGCTTTGATTGCAATCAGAGGTGGCATTGTCTCTCAATTCAGCTG---CA------------
droAna3	GATTGA-----------------------------A-------AGAGATGGCTAGAATGGAAAAAAATGGCAAA-------------AA------------AAGG-ACTCCCTTTTT-ATCTCATC--------------------------------------------CTGGCAAACAACTCGCTTTGATTGC--------CCATCATTGTCTTTCGATTC---------GGGAGGCAATTCA
droBip1	CGAATC------------------------------------------------GC---------------AAAAAGAACTC--------------------------GGCCATTGTTG-CAGCTCATAATTGGTAA----------ATCA-GAGCATG-AGAGTGAGGGCT--AGAGGGAGTCCTTTTTTT-----------------TTGTCT--TATCGC-ATCC---TGGCAAACAACTAA
dp4	CAAATAGAACAGAGCGGGAGGTGGCACGGAGGTGGAAATTGAAGCTGTGAATT-AA---------------AAGCAAAGCGCAGATCGC------------AAAATACGTTTATTGTTC-CCGGTCATAATTGAGAG----------CTGG-AAA-----------------------------GCTTTGATTGCAATCAGCGTTGGCATTGTCTCCGATCTC-TCCCAGGCCGTATTACCCTTA
droPer1	TT----------------------------------------------------AA---------------AAGCAAAGCGCAGATCGC------------AAAATACGTTTATTGTTC-CCGGTCATAATTGAGAG----------CTGG-AAA-----------------------------GCTTTGATTGCAATCAGCGTTGGCATTGTCTCCGATCTC-TCCCAGGCCGTATTACCCTTA

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
UNAFold Image																	None	None	None	None

Small RNA-seq read pileup

Species

Alignment

droSim1

TATCTC------------------------------------------------AA---------------AGGAAAAGCCCAGGTCTG------------AGAA-AAGTTCATTGTTGTCTGTTTATAATTAGAGA----------GTGA-AAATCTC-----------------------TCTCGTTGAGTGCAATCGGCGTCGGCATTGTCGGCAAACTC-GCTG---CAGGACACCATTTA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......................................................................................................................................................................................................................GGCxAACTC-GGTG---CAGGAC........	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

TATCTC------------------------------------------------AG---------------AGGAAAAGCCCAGGTCTG------------AGAA-ACGTTCATTGTTGTCTGTTCATAATTAGAGA----------GTGA-AAATCTC-----------------------TCTCGTTGAGTGCAATCGGCGTCGGCATTGTCTGCAAACTC-GCTG---CAGGACACCATTTA

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

CATCTC------------------------------------------------AA---------------AGGAAAAGTCCAGATCTA------------AGAA-ACTTCCATTGTTGCCTGCTCGTAATTAGAGA----------GGGA-AAATCTC-----------------------TCGCGTTGAGTGCAATCAGCGCAGGCATTGTCTGCAAACTC-GCTG---CAGGACCCCATTCA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
............................................................................................................................................................................................................................CTC-GCTG---CAxGACCTCATTC.	19	1	1.00	0.00	0.00	0.00	0.00	1.00

droEre2

CATCT-----------------------------------------------------------------------------------G------------GGAA-ACTTTCATTGTGC-CTGTTCATAATTAGAGA----------GTGA-AAATCCG-----------------------TTGCGCTGAGTGCAATCAGCAGCGGCATTGTCTGCCAACTC-GCTG---CAGGACCCCATTCA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..............................................................................................................................................................................................AGTGCAATCTGCAGCAGC.....................................	18	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................ATAATTAGCGA----------GxGA-AAAT.........................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droEug1

TAGCCG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGAA-ACTCCCATTGTTG-CCGGTCATAATTGGAGA----------GTGG-AAATCTC-GGG-------CCGGCATGCAACTCGCTTTGATTGCAATCAGCGCCGGCATTGTCTCCCAATTC-TGCT---CCGAATCCCGCTCC

Size

Hit Count

Total Norm

droBia1

TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------AAAA-ACTACCATTGTTG-CCGGTCATAATTGGAGA----------GTGA-AAAGCTG-GGG-------CCGGCGAGCAACTCGCTTTGATTGCAATCAGCGCCGGCATTGTCTCAAAACTC----------------------

Size

Hit Count

Total Norm

droTak1

TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGAA-ACTCCCATTGTTG-CTGGTCATAATTGGAGA----------GTGG-AAATCTCGGGG-------CCGGCGAGCAACTCGCTTTGATTGCAATCAGCACCGGCATTGTCTCGCAATTCTGCTC---GAA-AT--CTCCAC

Size

Hit Count

Total Norm

droEle1

TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGGA-GCACCCATTGTTG-CTGGTCATAATTGGAGA----------GTGG-AAATCTA-GGG-------CCGGCGAGCAACTCGCTTTGATTGCAATCAGCGCCGGCATTGTCTTCCAATTCTGCCC---CAAAATCCCTCGCC

Size

Hit Count

Total Norm

droRho1

TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGAA-ACTCCCATTGTTG-CTGGTCATAATTGGAGA----------GTGG-AAATCTC-GGG-------CTGGCGAGCAACTCGCTTTGATTGCAATCAGTGTCGGCATTGTCTTTCAATTC-TCCC---CGAAACCCCCCT--

Size

Hit Count

Total Norm

droFic1

TAGCTG------------------------------------------------AA---------------AGGAAAAGGACAGATCAG------------GGAA-ACTCCCATTGTTG-CTGGTCATAATTGGAGA----------ATGG-AAATCTC-GGG-------CCGCCGAGCAACTCGCTTTGATTGCAATCAGCGCCGCCATTGTTTCACAATTC----------------------

Size

Hit Count

Total Norm

droKik1

CAGGAG-----------------------------A------------------AAATGAAAGA-------AAGTAAAGCGCGGATCGGCCGGTAAGGCTGGAGA-TTTGCCATTGTTG-CTGGCCATAATTGGAGAGAAGAGAGAGTGGGAAAATCTC-TG---------CAGC-AGCAACTCGCTTTGATTGCAATCAGAGGTGGCATTGTCTCTCAATTCAGCTG---CA------------

Size

Hit Count

Total Norm

droAna3

GATTGA-----------------------------A-------AGAGATGGCTAGAATGGAAAAAAATGGCAAA-------------AA------------AAGG-ACTCCCTTTTT-ATCTCATC--------------------------------------------CTGGCAAACAACTCGCTTTGATTGC--------CCATCATTGTCTTTCGATTC---------GGGAGGCAATTCA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
........................................................ATGGAAAAAAAGGGTAAA-------------AA------------................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............................................................AAAAGGACAAA-------------AA------------AAGG-A..........................................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33
...........................................................GAAAAAAACGCCAAA-------------AA------------AA..............................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
............................................................AAAAAAACAGCAAA-------------AA------------AA..............................................................................................................................................	18	15	0.07	0.00	0.00	0.00	0.07
..........................................................AGAAAAAAACGGCAAA-------------AA------------A...............................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
..............................................................AAAAATGTCGAA-------------AA------------AAGG-A..........................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...............................................ATGGxTAGAATGGAAAAGA...................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
............................................................AAAAAAAAGGCAGA-------------AA------------AA..............................................................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25

droBip1

CGAATC------------------------------------------------GC---------------AAAAAGAACTC--------------------------GGCCATTGTTG-CAGCTCATAATTGGTAA----------ATCA-GAGCATG-AGAGTGAGGGCT--AGAGGGAGTCCTTTTTTT-----------------TTGTCT--TATCGC-ATCC---TGGCAAACAACTAA

Size

Hit Count

Total Norm

dp4

CAAATAGAACAGAGCGGGAGGTGGCACGGAGGTGGAAATTGAAGCTGTGAATT-AA---------------AAGCAAAGCGCAGATCGC------------AAAATACGTTTATTGTTC-CCGGTCATAATTGAGAG----------CTGG-AAA-----------------------------GCTTTGATTGCAATCAGCGTTGGCATTGTCTCCGATCTC-TCCCAGGCCGTATTACCCTTA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TT----------------------------------------------------AA---------------AAGCAAAGCGCAGATCGC------------AAAATACGTTTATTGTTC-CCGGTCATAATTGAGAG----------CTGG-AAA-----------------------------GCTTTGATTGCAATCAGCGTTGGCATTGTCTCCGATCTC-TCCCAGGCCGTATTACCCTTA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........................................................................................................................................................................................GTTTTGATTGCAGTCAGC...........................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................................................TTAATTGAAAG----------CTGG-AAA-----------------------------.............................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

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

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

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 05:23:35 EDT

sblock192886

chrX:453811-453911 +

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