dme-mir-2283- Best orthologs

dme-mir-2283	chr3R:5343246-5343321 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 5343293-5343313
   star strand at position 5343255-5343275
   mutations
   read mismatches

Notes: droSim1 ortholog is affected by a large gap at positions chr3R:15989677-15990052. All confident orthologs missing a large chunk of the star region after droSec1.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3R:5343231-5343336 +		1	GAAAACTCAC--TCCTGAGCTGCTCCGAAAATATCATGAATACGAC----------AATTATGTGCACATCATTTAGTATACGTGATATTT-T-AGGAGCA-GCTAAATTATATT-TAAAGT---
droSim1	chr3R:15990055-15990074 -	LASTZ	5	GACAACTCAC--TCTTGAGCTG-------------------------------------------------------------------------------------------------------
droSec1	super_0:16553595-16553710 -	LASTZ	3	GACAACTCAC--TCTTGAGCTGCTCCTAAAATATCACGTATACGACATGATGTCCCAATTACATGCACATCCTGTCGTATACGTGATATTT-T-AGGAGCA-GCTCAATTATATT-TAAAGT---
droYak2	chr3R:9394463-9394539 +	LASTZ	5	GGCAACCCAC--TCT--------------------------AA-------------TGTAATTGACACATCATGTCGTATACGTGATATTT-T-GGGAGCA-ACGCAATTATATT-TAAAGT---
droEre2	scaffold_4770:16257712-16257788 -	LASTZ	5	GGCAACTCAC--TCT--------------------------AA-------------TATAATTGTCACATAATGTCGTATACGTGATATTT-G-AGGAGCA-AGTCAATTATATT-TAAAGT---
droEug1	scf7180000407136:350514-350595 -	LASTZ	5	GACAACTCAC--TGT--------------------------AA-------------TATAATTGGCACCTCATGTCGTATACTTGATTTTT-AAATGACGTACATTAATTATATT-TTAACTTAT
droBia1	scf7180000302075:5353334-5353389 +	LASTZ	5	GACAACACAC---------------------------------------------------------------GTCGTATACGTGATTTTT-TGATGAACC-GCTCAATTATATT-CCAACT---
droTak1	scf7180000415397:445049-445122 -	LASTZ	5	GACAACTCAC--T-----------------------------------------------AGTGGCACATCGTGTCGTATACGTGATTTTT-TGATGAACA-GCTCAATTGTATGGTAAACTTCT
droEle1	scf7180000491047:308675-308724 -	LASTZ	5	GAC-----------------------------------------------------------------ATCATTACGTATACGTGATTTTT-A-GAG---A-GCTCAATTATATT-AAAACT---
droRho1	scf7180000777865:110673-110751 +	LASTZ	5	TAGTGGTTATTCTCT--------------------------AC-------------TGTAACTATGACATCATGACGTATACGTGATTTTC-G-ATGAACT-GCTCAATTATATT-TAAACT---
droFic1	scf7180000453488:620214-620293 +	LASTZ	5	GGCAACTCAG--AAT--------------------------AA-------------CAAATTTGGCACATCTAGTCGTATACGTGATTTTGATGATGAAAT-GCTTATTTATATGTTTAAAA---
droKik1	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------
droAna3	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------
droBip1	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------
dp4	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------
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	GAAAACTCAC--TCCTGAGCTGCTCCGAAAATATCATGAATACGAC----------AATTATGTGCACATCATTTAGTATACGTGATATTT-T-AGGAGCA-GCTAAATTATATT-TAAAGT---
droSim1	GACAACTCAC--TCTTGAGCTG-------------------------------------------------------------------------------------------------------
droSec1	GACAACTCAC--TCTTGAGCTGCTCCTAAAATATCACGTATACGACATGATGTCCCAATTACATGCACATCCTGTCGTATACGTGATATTT-T-AGGAGCA-GCTCAATTATATT-TAAAGT---
droYak2	GGCAACCCAC--TCT--------------------------AA-------------TGTAATTGACACATCATGTCGTATACGTGATATTT-T-GGGAGCA-ACGCAATTATATT-TAAAGT---
droEre2	GGCAACTCAC--TCT--------------------------AA-------------TATAATTGTCACATAATGTCGTATACGTGATATTT-G-AGGAGCA-AGTCAATTATATT-TAAAGT---
droEug1	GACAACTCAC--TGT--------------------------AA-------------TATAATTGGCACCTCATGTCGTATACTTGATTTTT-AAATGACGTACATTAATTATATT-TTAACTTAT
droBia1	GACAACACAC---------------------------------------------------------------GTCGTATACGTGATTTTT-TGATGAACC-GCTCAATTATATT-CCAACT---
droTak1	GACAACTCAC--T-----------------------------------------------AGTGGCACATCGTGTCGTATACGTGATTTTT-TGATGAACA-GCTCAATTGTATGGTAAACTTCT
droEle1	GAC-----------------------------------------------------------------ATCATTACGTATACGTGATTTTT-A-GAG---A-GCTCAATTATATT-AAAACT---
droRho1	TAGTGGTTATTCTCT--------------------------AC-------------TGTAACTATGACATCATGACGTATACGTGATTTTC-G-ATGAACT-GCTCAATTATATT-TAAACT---
droFic1	GGCAACTCAG--AAT--------------------------AA-------------CAAATTTGGCACATCTAGTCGTATACGTGATTTTGATGATGAAAT-GCTTATTTATATGTTTAAAA---

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

Small RNA-seq read pileup

Species

Alignment

droSim1

GACAACTCAC--TCTTGAGCTG-------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

GACAACTCAC--TCTTGAGCTGCTCCTAAAATATCACGTATACGACATGATGTCCCAATTACATGCACATCCTGTCGTATACGTGATATTT-T-AGGAGCA-GCTCAATTATATT-TAAAGT---	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
......................................................................CCTGTCGTATACGTGATATTT-T-...............................	22	8	1.00	0.50	0.50	0.00
.............................AATATCACGTATACGACATGA...........................................................................	21	8	0.50	0.00	0.50	0.00
......................................................................CCTGTCGTATACGTGATATTT-.................................	21	8	0.38	0.25	0.00	0.13
.............................AATATCACGTATACGACAGGAT..........................................................................	22	8	0.25	0.00	0.25	0.00
..................................................................ACATCCTGTCGTATACGTGATA.....................................	22	8	0.25	0.13	0.13	0.00
................................................................GCACATCCTGTCGTATACGTGA.......................................	22	4	0.50	0.25	0.25	0.00
..........................TAGAATATCACGTATACGACAT.............................................................................	22	8	0.13	0.00	0.00	0.13
.....................................................................................ATATTT-T-AGGAGCA-GCTCAAT................	21	8	0.13	0.13	0.00	0.00
.................................TCACGTATACGACATGATGTCC......................................................................	22	4	0.25	0.00	0.00	0.25
.............................AATATCACGTATACGACATGAT..........................................................................	22	8	0.13	0.00	0.13	0.00
..................................................................................GTGATATTT-T-AGGAGCA-GCTC...................	21	8	0.13	0.13	0.00	0.00
..............TTGAGCTGCTCCTAAAATAT...........................................................................................	20	8	0.13	0.13	0.00	0.00
.........................................................ATGACATGCAGATCCTGT..................................................	18	4	0.25	0.00	0.25	0.00
.............................AATATCACGTATACGACAGGA...........................................................................	21	8	0.13	0.00	0.13	0.00
.............................AATATCACGTATACGACATG............................................................................	20	8	0.13	0.00	0.13	0.00
.......................................................................CTGTCGTATACGTGATATTT-T-...............................	21	8	0.13	0.00	0.00	0.13
...................................................................................TGATATTT-T-AGGAGCA-GCTC...................	20	8	0.13	0.00	0.00	0.13

droYak2

GGCAACCCAC--TCT--------------------------AA-------------TGTAATTGACACATCATGTCGTATACGTGATATTT-T-GGGAGCA-ACGCAATTATATT-TAAAGT---	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...........................................................................CGTATACGTGATATTT-T-GGGAGC.........................	23	2	0.50	0.00	0.00	0.50	0.00	0.00
..............................................................................ATACGTGATATTT-T-GAAAGC.........................	20	2	0.50	0.00	0.00	0.00	0.00	0.50

droEre2

GGCAACTCAC--TCT--------------------------AA-------------TATAATTGTCACATAATGTCGTATACGTGATATTT-G-AGGAGCA-AGTCAATTATATT-TAAAGT---

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

GACAACTCAC--TGT--------------------------AA-------------TATAATTGGCACCTCATGTCGTATACTTGATTTTT-AAATGACGTACATTAATTATATT-TTAACTTAT

Size

Hit Count

Total Norm

droBia1

GACAACACAC---------------------------------------------------------------GTCGTATACGTGATTTTT-TGATGAACC-GCTCAATTATATT-CCAACT---

Size

Hit Count

Total Norm

droTak1

GACAACTCAC--T-----------------------------------------------AGTGGCACATCGTGTCGTATACGTGATTTTT-TGATGAACA-GCTCAATTGTATGGTAAACTTCT

Size

Hit Count

Total Norm

droEle1

GAC-----------------------------------------------------------------ATCATTACGTATACGTGATTTTT-A-GAG---A-GCTCAATTATATT-AAAACT---

Size

Hit Count

Total Norm

droRho1

TAGTGGTTATTCTCT--------------------------AC-------------TGTAACTATGACATCATGACGTATACGTGATTTTC-G-ATGAACT-GCTCAATTATATT-TAAACT---

Size

Hit Count

Total Norm

droFic1

GGCAACTCAG--AAT--------------------------AA-------------CAAATTTGGCACATCTAGTCGTATACGTGATTTTGATGATGAAAT-GCTTATTTATATGTTTAAAA---

Size

Hit Count

Total Norm

droKik1

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

Size

Hit Count

Total Norm

droAna3

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

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

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

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

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

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 05:27:56 EDT

dme-mir-2283

chr3R:5343246-5343321 +

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