Secondary structure and small RNA-seq evidence for dme-mir-309

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:15549196-15549294 -	AA-------GTTT---GGAATAG-CAATTATACGACAAACCTTGTTCGGTTTTGCCA----------------ATTTCCA------AG-CCAGCACTGGGTAAAGTTTGTCCTATAATCCCGAAACGA--------------C-GACC
droSim1	chr2R:14254629-14254727 -	AA-------GTTT---GGAACAG-CAATTATACGACAAACCTTGTTCGGTTTTGCCA----------------ATTTCCA------AG-CCAGCACTGGGTAAAGTTTGTCCTATAATCCCGAAACGA--------------C-GACC
droSec1	super_1:13063923-13064021 -	AA-------GTTT---GGAACAG-CAATTATACGACAAACCTTGTTCGGTTTTGCCA----------------ATTTCCA------AG-CCAGCACTGGGTAAAGTTTGTCCTATAATCCCGAAACGA--------------C-GACC
droYak2	chr2R:13623487-13623590 +	AA--GCAAAGTTT---GGAACAG-CAATTATACGACAAACCTTGTTCTGTTTTGCCA----------------ATTTCCT------AG-CCAGCACTGGGTAAAGTTTGTCCTATAATCCCGAAACGA--------------C-GACC
droEre2	scaffold_4845:9749440-9749538 -	GA-------GTTT---GGAACAG-CAATTATACGACAAACCTTGTTCGGTTTTGCCA----------------ATTTCCT------AG-CCAGCACTGGGTAAAGTTTGTCCTATAATCCCGAAACGA--------------C-GACC
droAna3	scaffold_13266:9731105-9731197 +	GA-----------------AGAT-C-ATTATACGACAAACCTTGTTCGGTTTTGCCA----------------ATTTCCT------A--GCAGCACTGGGTAAAGTTTGTCCTATAATCTATAAAAAA--------G-----CCGTCC
dp4	chr3:12677873-12677971 -	AA-------CTAT---CTCGGAA-CTATTATACGATAAACTTTGTTCAGTTTTGCCA----------------ACTTGCT------T--GCAGCACTGGGTGAAGTTTGTCTTATAATCCCACAGTAA--------G-----C-GATC
droPer1	super_2:8905688-8905793 +	AAAAACGAACTATCTCGGA---A-CTATTATACGATAAACTTTGTTCAGTTTTGCCA----------------ACTTGCT------T--GCAGCACTGGGTGAAGTTTGTCTTATAATCCCACAGTAA--------G-----C-GATC
droWil1	scaffold_180701:1652063-1652174 -	A---------TTT---CATATAA-T-ATTATATGATAAACTTTGTTCAGTTTTGCAATCAAAAAATCAAGAAAA-TTCCT------TA-GCATCACTGGGTGAAGTTTGTCTTATAATCTTTAAACTA--------------C-AATC
droVir3	scaffold_12875:4111798-4111897 +	TA---------------TAACAA-ATATTATATGGTAAACTTTGTTCAGTTTTGCCA----------------GGCTCTT-TTTGTGC-GCATCACTGGGTGAAGTTTGTCGTATAATCGCAAAAAGA--------------A-CAGC
droMoj3	scaffold_6496:20937092-20937209 -	TA-------TACA---AGAACAGAATATTATAAGGTAAACTTTGTTCAGTTTTGCCG----------------GGTTCTATGTTGTGC-GCATCACTGGGTGAAGTTTGTCGTATAATCG--AAACGAAACAGCAAGGAAAAA-GTCC
droGri2	scaffold_15112:2109131-2109231 -	AA-------ATAT---ATAATTA-C-ATTATATGGCAAACCTTGTTCAGTTTTGACA----------------ACTTTGTTTCTGTGCATCATCACTGGGTGAAGTTTGTCGTATAATC--GAAATG-----------------GATC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:15549196-15549294 -	AA-------GTTT---GGAATAG-CAATTATACGACAAACCTTGTTCGGTTTTGCCA----------------ATTTCCA------AG-CCAGCACTGGGTAAAGTTTGTCCTATAATCCCGAAACGA--------------C-GACC
droSim1	chr2R:14254629-14254727 -	AA-------GTTT---GGAACAG-CAATTATACGACAAACCTTGTTCGGTTTTGCCA----------------ATTTCCA------AG-CCAGCACTGGGTAAAGTTTGTCCTATAATCCCGAAACGA--------------C-GACC
droSec1	super_1:13063923-13064021 -	AA-------GTTT---GGAACAG-CAATTATACGACAAACCTTGTTCGGTTTTGCCA----------------ATTTCCA------AG-CCAGCACTGGGTAAAGTTTGTCCTATAATCCCGAAACGA--------------C-GACC
droYak2	chr2R:13623487-13623590 +	AA--GCAAAGTTT---GGAACAG-CAATTATACGACAAACCTTGTTCTGTTTTGCCA----------------ATTTCCT------AG-CCAGCACTGGGTAAAGTTTGTCCTATAATCCCGAAACGA--------------C-GACC
droEre2	scaffold_4845:9749440-9749538 -	GA-------GTTT---GGAACAG-CAATTATACGACAAACCTTGTTCGGTTTTGCCA----------------ATTTCCT------AG-CCAGCACTGGGTAAAGTTTGTCCTATAATCCCGAAACGA--------------C-GACC
droAna3	scaffold_13266:9731105-9731197 +	GA-----------------AGAT-C-ATTATACGACAAACCTTGTTCGGTTTTGCCA----------------ATTTCCT------A--GCAGCACTGGGTAAAGTTTGTCCTATAATCTATAAAAAA--------G-----CCGTCC
dp4	chr3:12677873-12677971 -	AA-------CTAT---CTCGGAA-CTATTATACGATAAACTTTGTTCAGTTTTGCCA----------------ACTTGCT------T--GCAGCACTGGGTGAAGTTTGTCTTATAATCCCACAGTAA--------G-----C-GATC
droPer1	super_2:8905688-8905793 +	AAAAACGAACTATCTCGGA---A-CTATTATACGATAAACTTTGTTCAGTTTTGCCA----------------ACTTGCT------T--GCAGCACTGGGTGAAGTTTGTCTTATAATCCCACAGTAA--------G-----C-GATC
droWil1	scaffold_180701:1652063-1652174 -	A---------TTT---CATATAA-T-ATTATATGATAAACTTTGTTCAGTTTTGCAATCAAAAAATCAAGAAAA-TTCCT------TA-GCATCACTGGGTGAAGTTTGTCTTATAATCTTTAAACTA--------------C-AATC
droVir3	scaffold_12875:4111798-4111897 +	TA---------------TAACAA-ATATTATATGGTAAACTTTGTTCAGTTTTGCCA----------------GGCTCTT-TTTGTGC-GCATCACTGGGTGAAGTTTGTCGTATAATCGCAAAAAGA--------------A-CAGC
droMoj3	scaffold_6496:20937092-20937209 -	TA-------TACA---AGAACAGAATATTATAAGGTAAACTTTGTTCAGTTTTGCCG----------------GGTTCTATGTTGTGC-GCATCACTGGGTGAAGTTTGTCGTATAATCG--AAACGAAACAGCAAGGAAAAA-GTCC
droGri2	scaffold_15112:2109131-2109231 -	AA-------ATAT---ATAATTA-C-ATTATATGGCAAACCTTGTTCAGTTTTGACA----------------ACTTTGTTTCTGTGCATCATCACTGGGTGAAGTTTGTCGTATAATC--GAAATG-----------------GATC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AAGTTTGGAACAGCAATTATACGACAAACCTTGTTCGGTTTTGCCAATTTCCAAGCCAGCACTGGGTAAAGTTTGTCCTATAATCCCGAAACGA-CGACC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..........................................................GCACTGGGTAAAGTTTGTCCTA....................	22	1	974.00	974	974
..........................................................GCACTGGGTAAAGTTTGTCCT.....................	21	1	606.00	606	606
..........................................................GCACTGGGTAAAGTTTGTCC......................	20	1	26.00	26	26
.....................CGACAAACCTTGTTCGGTTTTG.........................................................	22	1	20.00	20	20
..........................................................GCACTGGGTAAAGTTTGTC.......................	19	1	10.00	10	10
.....................CGACAAACCTTGTTCGGTTTT..........................................................	21	1	5.00	5	5
..........................................................GCACTGGGTAAAGTTTGTCCTAT...................	23	1	2.00	2	2
............................................................ACTGGGTAAAGTTTGTCCTA....................	20	1	1.00	1	1
.........................................................AGCACTGGGTAAAGTTTGTCCT.....................	22	1	1.00	1	1
............................................................ACTGGGTAAAGTTTGTCCT.....................	19	1	1.00	1	1
...........................................................CACTGGGTAAAGTTTGTCCT.....................	20	1	1.00	1	1
........................................................CAGCACTGGGTAAAGTTTGTCCT.....................	23	1	1.00	1	1

dp4

AACTATCTCGGAACTATTATACGATAAACTTTGTTCAGTTTTGCCAACTTGCTTG-CAGCACTGGGTGAAGTTTGTCTTATAATCCCACAGTAAGCGATC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..........................................................GCACTGGGTGAAGTTTGTCTTA....................	22	1	1132.00	1132	1132	0
..........................................................GCACTGGGTGAAGTTTGTCTT.....................	21	1	159.00	159	159	0
.........................................................AGCACTGGGTGAAGTTTGTCTT.....................	22	1	8.00	8	8	0
.........................................................AGCACTGGGTGAAGTTTGTCTTA....................	23	1	7.00	7	7	0
..........................................................GCACTGGGTGAAGTTTGTCTTAT...................	23	1	5.00	5	5	0
.....................CGATAAACTTTGTTCAGTTTTG.........................................................	22	1	4.00	4	4	0
..........................................................GCACTGGGTGAAGTTTGTCT......................	20	1	4.00	4	4	0
.........................................................AGCACTGGGTGAAGTTTGTCT......................	21	1	3.00	3	3	0
.....................CGATAAACTTTGTTCAGTTTT..........................................................	21	1	2.00	2	2	0
...........................................................CACTGGGTGAAGTTTGTCTTAT...................	22	1	1.00	1	1	0
....................ACGATAAACTTTGTTCAGTTTT..........................................................	22	1	1.00	1	1	0

Secondary Structure

dm3

-16.7	-16.6	-16.5	-16.4	-16.3	-16.3

droSim1

-16.7	-16.6	-16.5	-16.4	-16.3	-16.3

droSec1

-16.7	-16.6	-16.5	-16.4	-16.3	-16.3

droYak2

-13.9	-13.7	-13.6	-13.6	-13.4	-13.3

droEre2

-16.7	-16.6	-16.5	-16.4	-16.3	-16.3

droAna3

-20.5	-20.2

dp4

-22.4	-22.1	-22.1	-21.8	-21.8	-21.8

droPer1

-22.4	-22.1	-22.1	-21.8	-21.8	-21.8

droWil1

-22.1	-21.8	-21.8	-21.5

droVir3

-24.2	-24.1	-24.0	-23.9	-23.9	-23.8

droMoj3

-19.4	-19.1	-19.1	-18.8	-18.4

droGri2

-22.8	-22.5	-22.5	-22.5	-22.2	-22.2

Generated: 01/05/2013 at 05:16 PM