Secondary structure and small RNA-seq evidence for dme-mir-957

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:22511281-22511406 -	TTATATCCG---TAGTGT------------TGTCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT--CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGCGCGAGCATCTA----TCCAAA
droSim1	chr3L:21812307-21812432 -	TTGTATCCG---TAGTGT------------TGTCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT--CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGCGTGAGCATCTA----TCCAAA
droSec1	super_11:2446955-2447080 -	TTGTATCCG---TAGTGT------------TGTCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT--CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGCGTGAGCATCTA----TCCAAA
droYak2	chr3L:22973852-22973977 -	TCATATCCG---TAGTGT------------TGTCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT--ATATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGCGTGAGCAACTA----TCCAAA
droEre2	scaffold_4784:22180738-22180863 -	CCATATCCG---TAGTGT------------TGTCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT--CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGCGTGAGCATCTA----TCCAAA
droAna3	scaffold_13337:22247678-22247807 -	TAAGATTCG---TAATATAGTAATATATACTGCCTACAATGGCCCTTAGTTTTCGACGTGTTTTGGTGTGCAGGGG-AGTT--CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGCGTGAGCATC------------
dp4	chrXR_group8:186470-186597 -	ACCCACCAG---TAA-----------ATACTGTCCACAATGGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT-GATATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GCGGCATGAGCATCTA----ACCAAA
droPer1	super_80:80367-80497 +	ACAACCCACCAGAAT-----------ATACTGTCCACAATGGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT-GATATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GCGGCATGAGCATCTA----ACCAAA
droWil1	scaffold_180698:7262478-7262610 +	TCTCTCGCA---TCATA-------------TATCCGCAATGGACCTTAGTTTTCGACGTGTTTTGGTGTGCTTAGGAAGTTTTCTATTCCGATTGAAACCGTCCAAAACTGAGGCCAATTGTTGTGATAGAAGCAACCATGAAAACAAA
droVir3	scaffold_13049:17242400-17242523 +	TTATTTCCTAACTAG-----------ATAATGCCCACAATGGTTCTTAGTTTTAGACGTGTTTTGGTGTGCTTG-A-AGTT--TTGTTCCGATTGAAACCGTCCAAAACTGAGGCCGATTGT-GAGGTAAAAGCGTCCA---------A
droMoj3	scaffold_6680:22273688-22273794 +	------------------------------TGCCCACAATGGATCTTAGTTTTAGACGTGTTTTGGTGTGCTTGGG-AGTT--TTGTTCCGATTGAAACCGTCCAAAACTGAGGCCAATTGT-GAGGCGAAAGCATCCA----G-----
droGri2	scaffold_15110:14942014-14942124 -	T------------------------------ACCCACAATGGATCTTAGTTTTAGACGTGTTTTGGTGTGCTTGGG-AGTT--TTGTTCCGATTGAAACCGTCCAAAACTGAGGCCAATTGT-GTGGTAAAAGCATCCA----AATATC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:22511281-22511406 -	TTATATCCG---TAGTGT------------TGTCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT--CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGCGCGAGCATCTA----TCCAAA
droSim1	chr3L:21812307-21812432 -	TTGTATCCG---TAGTGT------------TGTCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT--CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGCGTGAGCATCTA----TCCAAA
droSec1	super_11:2446955-2447080 -	TTGTATCCG---TAGTGT------------TGTCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT--CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGCGTGAGCATCTA----TCCAAA
droYak2	chr3L:22973852-22973977 -	TCATATCCG---TAGTGT------------TGTCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT--ATATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGCGTGAGCAACTA----TCCAAA
droEre2	scaffold_4784:22180738-22180863 -	CCATATCCG---TAGTGT------------TGTCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT--CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGCGTGAGCATCTA----TCCAAA
droAna3	scaffold_13337:22247678-22247807 -	TAAGATTCG---TAATATAGTAATATATACTGCCTACAATGGCCCTTAGTTTTCGACGTGTTTTGGTGTGCAGGGG-AGTT--CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGCGTGAGCATC------------
dp4	chrXR_group8:186470-186597 -	ACCCACCAG---TAA-----------ATACTGTCCACAATGGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT-GATATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GCGGCATGAGCATCTA----ACCAAA
droPer1	super_80:80367-80497 +	ACAACCCACCAGAAT-----------ATACTGTCCACAATGGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGG-AGTT-GATATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GCGGCATGAGCATCTA----ACCAAA
droWil1	scaffold_180698:7262478-7262610 +	TCTCTCGCA---TCATA-------------TATCCGCAATGGACCTTAGTTTTCGACGTGTTTTGGTGTGCTTAGGAAGTTTTCTATTCCGATTGAAACCGTCCAAAACTGAGGCCAATTGTTGTGATAGAAGCAACCATGAAAACAAA
droVir3	scaffold_13049:17242400-17242523 +	TTATTTCCTAACTAG-----------ATAATGCCCACAATGGTTCTTAGTTTTAGACGTGTTTTGGTGTGCTTG-A-AGTT--TTGTTCCGATTGAAACCGTCCAAAACTGAGGCCGATTGT-GAGGTAAAAGCGTCCA---------A
droMoj3	scaffold_6680:22273688-22273794 +	------------------------------TGCCCACAATGGATCTTAGTTTTAGACGTGTTTTGGTGTGCTTGGG-AGTT--TTGTTCCGATTGAAACCGTCCAAAACTGAGGCCAATTGT-GAGGCGAAAGCATCCA----G-----
droGri2	scaffold_15110:14942014-14942124 -	T------------------------------ACCCACAATGGATCTTAGTTTTAGACGTGTTTTGGTGTGCTTGGG-AGTT--TTGTTCCGATTGAAACCGTCCAAAACTGAGGCCAATTGT-GTGGTAAAAGCATCCA----AATATC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TTGTATCCGTA-GTGTTGTCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGGAGTT-CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGTGAGGCGTGAGCATCTATCCAAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.............................................................................TGAAACCGTCCAAAACTGAGGC.............................	22	1	120.00	120	120
.............................................................................TGAAACCGTCCAAAACTGAGG..............................	21	1	9.00	9	9
..............................CTTAGTTTTCGACGTGTTTTGGT...........................................................................	23	1	3.00	3	3

dp4

ACCCACCAGTAAATACTGTCCACAATGGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGGAGTTGATATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGTGCGGCATGAGCATCTAACCAAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.............................................................................TGAAACCGTCCAAAACTGAGGC.............................	22	1	7751.00	7751	96	7655
.............................................................................TGAAACCGTCCAAAACTGAGG..............................	21	1	7288.00	7288	11	7277
.............................................................................TGAAACCGTCCAAAACTGAG...............................	20	1	488.00	488	0	488
.............................................................................TGAAACCGTCCAAAACTGAGGCC............................	23	1	29.00	29	0	29
.............................................................................TGAAACCGTCCAAAACTGA................................	19	1	25.00	25	0	25
..............................CTTAGTTTTCGACGTGTTTTGGT...........................................................................	23	1	16.00	16	6	10
..............................................................................GAAACCGTCCAAAACTGAGG..............................	20	1	13.00	13	0	13
..............................................................................GAAACCGTCCAAAACTGAGGC.............................	21	1	11.00	11	0	11
...............................................................................AAACCGTCCAAAACTGAGGC.............................	20	1	6.00	6	0	6
...............................................................................AAACCGTCCAAAACTGAGG..............................	19	1	5.00	5	0	5

Secondary Structure

dm3

-30.8	-30.8	-30.7	-30.7	-30.6	-30.5

droSim1

-30.8	-30.8	-30.7	-30.7	-30.6	-30.5

droSec1

-30.8	-30.8	-30.7	-30.7	-30.6	-30.5

droYak2

-30.8	-30.7	-30.6	-30.5	-30.5	-30.4

droEre2

-30.8	-30.8	-30.7	-30.7	-30.6	-30.5

droAna3

-36.0	-36.0	-36.0	-35.9	-35.9	-35.9

dp4

-36.8	-36.2	-36.2	-36.2

droPer1

-36.8	-36.2	-36.2	-36.2

droWil1

-35.6	-35.6	-35.5	-35.5

droVir3

-35.4	-35.4	-35.0	-35.0	-35.0	-35.0

droMoj3

-39.8	-39.8	-39.7	-39.7	-39.3	-39.3

droGri2

-37.3	-37.3	-37.2	-37.2	-36.3	-36.3

Generated: 01/05/2013 at 05:31 PM