Secondary structure and small RNA-seq evidence for dme-mir-1004

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:3767606-3767703 +	GTGGCTGGACAAAAGGT-TGGGGG--ACATTGATCTCGGAGACG-------------G-------------------------CGGTTTAACT--------------------GATCCATTCTCTCACATCACTT---CCCTCACAGTGCACGGTGCTTGTA
droSim1	chr2L:3722744-3722841 +	GTGGCTGGACAAGAGGT-TGGGGG--ACATTGATCTCGGAGACG-------------G-------------------------CGGTTTAACT--------------------GATCCATTCTCTCACATCACTT---CCCTCACAGTGCGCGGTGCTTGTA
droSec1	super_5:1870685-1870782 +	GTGGCTGGACAAGAGGT-TGGGGG--ACATTGATCTCTGAGACG-------------G-------------------------CGGTTTAACT--------------------GATCCATTCTCTCACATCACTT---CCCTCACAGTGCGCGGTGCTTGTA
droYak2	chr2L:3769291-3769388 +	GTGGCTGGACAAGAGGT-TGGGGG--ACATTGATCTCGGAGACG-------------G-------------------------CGGTTTAACT--------------------GATCCATTCTCTCACATCACTT---CCCTCACAGTGCGCGATGTTTGTA
droEre2	scaffold_4929:3814030-3814127 +	GTGGCTGGACAAGAGGT-TGGGGG--ACATTGATCTCGGAGACG-------------G-------------------------CGGTTTAACT--------------------GATCCAATCTCTCACATCACTT---CCCTCACAGTGCGCGGTGCTTGTA
droAna3	scaffold_12916:5837615-5837739 +	GTGGCTGGACAAGAGGT-GAGATAACACGTT-----CTAACCAACTGATATGAAACTA------CGAATGTTTTTATCGCTGTCGATTCGAAC--------------------GA-----TCTCTCATATAACCGTACCTATTACAGTGCGCGGTGTCTGTA
dp4	chr4_group3:4962038-4962146 -	GTGGCTGGACAAGAGGTGTGTGGG--ATACTGATTTTAGAGAAAAAAAAA----------A----------------------CCAT-T--AACGTGAGG--------------CTTCG-TTTCTCACATCATTT-TCCCCTCACAGTGCCCGGTGCCTGTA
droPer1	super_1:6454682-6454788 -	GTGGCTGGACAAGAGGTGTGTGGG--ATACTGATTTTAGAGAAAA------------ATAA----------------------CCAT-T--AACGTGAGG--------------CTTCG-TTTCTCACATCATTT-TCCCCTCACAGTGCCCGGTGCCTGTA
droWil1	scaffold_180708:9298763-9298869 -	ATGGTTGGATAAAAGGT--GGGGT--ACAACAACAACAAAAAT--------------A-------------------------CGAATATAATGGT-AAACTCTC-------TCTCTCAT---CTCTTATCATTT-TCTCCTCACAGTGCGCGTTCACTTTA
droVir3	scaffold_12963:14941260-14941364 -	GTGGCTGGACAAAAGGT-TGGGGC--ACATTGATCTTCAAGAAACTCACAGCCA---G-------------------------CTCATT------------------------TACTCACTCTCTCTC-TCTTCT-CTCCCTCACAGTGCCCGCTGTCTGTA
droMoj3	scaffold_6500:17898451-17898546 -	GTGGCTGGACAAGAGGT-AATTGATCACTCCTATCTCTGTCT-----------------------------------------CTCTTTCTCT--------------------TTCTGACTCTCTCCCA-CTCTT---TATTTGTAGTGCTCGCTGCCTGTA
droGri2	scaffold_15126:4437367-4437497 +	GTGGCTGGACAAAAGGT-AGGAGAGCACATTGATCTTGAAGAAACTTGCAGAAA---A--CTCTCTAATACTCTCAC---------TCCATTT------------CTCTAACTCTCCCTCTCTCTTATTTAACTT---C-ATTTTAGTGCGCGCTGTTTATA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:3767606-3767703 +	GTGGCTGGACAAAAGGT-TGGGGGACATTGATCTCGGAGA------------------------------------------CGGCGGTTTAACTGATCCATTCTCTCACATCACTT---CCCTCACAGTGCACGGTGCTTGTA
droSim1	chr2L:3722744-3722841 +	GTGGCTGGACAAGAGGT-TGGGGGACATTGATCTCGGAGA------------------------------------------CGGCGGTTTAACTGATCCATTCTCTCACATCACTT---CCCTCACAGTGCGCGGTGCTTGTA
droSec1	super_5:1870685-1870782 +	GTGGCTGGACAAGAGGT-TGGGGGACATTGATCTCTGAGA------------------------------------------CGGCGGTTTAACTGATCCATTCTCTCACATCACTT---CCCTCACAGTGCGCGGTGCTTGTA
droYak2	chr2L:3769291-3769388 +	GTGGCTGGACAAGAGGT-TGGGGGACATTGATCTCGGAGA------------------------------------------CGGCGGTTTAACTGATCCATTCTCTCACATCACTT---CCCTCACAGTGCGCGATGTTTGTA
droEre2	scaffold_4929:3814030-3814127 +	GTGGCTGGACAAGAGGT-TGGGGGACATTGATCTCGGAGA------------------------------------------CGGCGGTTTAACTGATCCAATCTCTCACATCACTT---CCCTCACAGTGCGCGGTGCTTGTA
droAna3	scaffold_12916:5837615-5837739 +	GTGGCTGGACAAGAGGT-GAGATAACACG-TTCT------------AACCAACTGATATGAAACTACGAATGTTTTTATCGCTGTCGATTCGAACGAT-----CTCTCATATAACCGTACCTATTACAGTGCGCGGTGTCTGTA
dp4	chr4_group3:4962038-4962146 -	GTGGCTGGACAAGAGGTGTGTGGGATACTGATTTTAGAGAAAAAAAAAACCATTAACGTG-------------------------AGGCT--------TCG-TTTCTCACATCATTTT-CCCCTCACAGTGCCCGGTGCCTGTA
droPer1	super_1:6454682-6454788 -	GTGGCTGGACAAGAGGTGTGTGGGATACTGATTTTAGAGAAAA--ATAACCATTAACGTG-------------------------AGGC--------TTCG-TTTCTCACATCATTTT-CCCCTCACAGTGCCCGGTGCCTGTA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GTGGCTGGACAAGAGGT-TGGGGGACATTGATCTCGGAGA----------------CG-GCGGTTTAACTGATCCATTCTCTCACATCACTT--CCCTCACAGTGCGCGGTGCTTGTA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...............................................................................TCTCACATCACTT--CCCTCACAG...............	22	1	26.00	26	26
...............GT-TGGGGGACATTGATCTCGGAGA----------------..............................................................	24	1	16.00	16	16
...............GT-TGGGGGACATTGATCTCGGAG...............................................................................	23	1	3.00	3	3
................................................................................CTCACATCACTT--CCCTCACAGT..............	22	1	3.00	3	3
...............................................................................TCTCACATCACTT--CCCTCACA................	21	1	1.00	1	1

dp4

GTGGCTGGACAAGAGGTGTGTGGGATACTGATTTTAGAGAAAAAAAAAACCATTAACGTGAGGCTT--------CG-TTTCTCACATCATTTTCCCCTCACAGTGCCCGGTGCCTGTA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.................................................................................TCACATCATTTTCCCCTCACAGT..............	23	1	38.00	38	2	36
.................................................................................TCACATCATTTTCCCCTCACAG...............	22	1	16.00	16	2	14
.................................................................................TCACATCATTTTCCCCTCACA................	21	1	2.00	2	0	2
...................................................................................ACATCATTTTCCCCTCACAGT..............	21	1	2.00	2	0	2
...............GTGTGTGGGATACTGATTTTAGAGA..............................................................................	25	1	1.00	1	1	0
..................................................................................CACATCATTTTCCCCTCACAGT..............	22	1	1.00	1	0	1

Secondary Structure

dm3

-19.3	-19.0	-18.7	-18.4	-18.4

droSim1

-19.3	-19.0	-18.7	-18.4	-18.4

droSec1

-18.3	-18.2	-18.2	-18.0	-17.9	-17.9

droYak2

-19.3	-19.0	-18.7	-18.4	-18.4

droEre2

-19.3	-19.0	-18.7	-18.4	-18.4

droAna3

-14.3	-14.0	-13.9	-13.8	-13.6	-13.4

dp4

-17.3	-16.7	-16.6	-16.4	-16.4	-16.3

droPer1

-18.1	-17.8	-17.3

droWil1

-8.7	-7.7	-7.7

droVir3

-6.2	-5.5

droMoj3

-0.5	0.0

droGri2

-10.4	-10.3	-10.0	-9.9	-9.9	-9.8

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