Secondary structure and small RNA-seq evidence for dme-mir-4949

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:27044980-27045109 -	TGCGAAACG----------------TGTTTGA-T------AATGCGCCGCCATCTTGCGGCACACTCGCACA-C------ACACA-CGTGTGCC-----------ATTCTGG-------TTTTGC--AGTGGTGTGCGTGTGTGCCTC-------GAGTCGTTGCGTCACTGGAAAAGTT-----------AGAAAATC
droSim1	chr3R:26688146-26688275 -	TGCGAAACG----------------TGTTTGA-T------AATGCGCCGCCATCTTGCGGCACACTCGCACA-C------ACACA-CGTGTGCC-----------AGGCTGG-------TTTTGC--AGTGGTGTGCGTGTGTGCCTC-------GAGTCGTTGCGTCACTGGAAAAGTT-----------AGAAAATC
droSec1	super_4:5862973-5863106 -	TGCGAAACG----------------TGTTTGA-T------AATGCGCCGCCATCTTGCGGCACACTCGC---ACACACACACACA-CGTGTGCC-----------AGGCTGG-------TTTTGC--AGTGGTTTGCGTGTGTGCCTC-------AAGTCGTTGCGTCACTGAAAAAGTT-----------AGAAAATC
droYak2	chr3R:27981306-27981430 -	TGCGAAACG----------------TGTTTGA-A------AATCCGTCGCCATCTTGCGGCACACTCAC---AC------ACACA-CGTGTGCC-----------AATATGG-------T-TTGC--AGTGGTGTGCGTGT--GCCTC-------GAGTCGTTGCGTCACTGGAAAAGTC-----------AGAAAATC
droEre2	scaffold_4820:935924-936048 +	TGCAAAACG----------------TGTTGGA-A------AATTCGCCGCCATCTTGCGGCACACACA-----C------ACACA-CGTGTGCC-----------AGTCTGG-------T-TTGC--AGTGGTGTGCGTGTGGGCCTC-------GAGTCGTTGCGTCACTGGAAAAGTC-----------CGAAAATC
droAna3	scaffold_13340:14436299-14436405 -	CTCAAAACG----------------TGTTCAA-TGG----A----ATCGCCATCTTGCGGCTCACAC---------------ACA-CATGTGAC---------------------------------AGTTGTTCGTGCGTGTGTCTGG------GAGTCGTTGCGTCACTGAGAAAGTC-----------GGAAAAT-
dp4	chr2:85298-85449 +	TAC-------ATTTTCTCGAAAACGTGTCGAA------------TGTCGCCATCTTGCGGCACACACAC---AGACACACACACA-CATGTGAC-----------GAGAGGAATTGCCAGT--GCTCAATAGTGTGCCTGTGTG--TC-------GAGACGTTGCGTCACTGAAAAAGTCGAACAGC--AAAGTAAATT
droPer1	super_7:2877006-2877157 +	TAC-------ATTTTCTCGAAAACGTGTCGAA------------TGTCGCCATCTTGCGGCACACACAC---AGACACACACACA-CATGTGAC-----------GAGAGGAATTGCCAGT--GCTCAATAGTGTGCCTGTGTG--TC-------GAGACGTTGCGTCACTGAAAAAGTCGAACAGC--AAAGTAAATT
droWil1	scaffold_181108:712012-712143 -	TGAAAAATGTATTTTATC--TA--------GA-G------ATATTGTCGCCATTTTGCGGCACTCAC-------------ACACA-CGTGTCAC-----------AAGA-GAACTGTCAAATTGT--AGCTGTATGCGTGAG----AC-------CAGTCGTTGCGTCACAGCAAAAGTT-----------TTCAAATT
droVir3	scaffold_12855:1227223-1227391 +	TAA------TATTTTTTC--AAACGTGTTCAG------------TGTCGCCATCTTGCGGCACATACAC---ACACATTCAGACAAGATGTCACACGGACGTACGAAGA-GAACTGTCAGT--GTGTT-TTGTGTGCCGTAGTG--TGGAGTGTAAATTTGTTGCGTCACTAGAAAAGTTCAACTGT-TGAAGGAAATC
droMoj3	scaffold_6540:26974787-26974936 +	TAA------CATTTTTTC--AAACGTGTTCAA------------TGTCGCCATCTTGCGGCTCACGCAC---ACACTCA--TGCAAGATGTCACACGGGCGTATGAAGA-GAACTGTCAGT--GTT--AC------------TGTGTG-------AAGTCGTTGCGTCACTAGAAAAGTTCAACGATTTGAAGAAAATT
droGri2	scaffold_15245:5068344-5068468 +	G-CGACAAG----------------TGGTTGACTGCACCTGCACCCTCC-CAA---CAGACACACTCACACA-C------ACACA-CACAACCC-----------TCTGTGT-------GTGTGC--AAGTGTGTGTGTGTGTGTGTC-------AAA-CGCAGCA--ACTGCTGAAGTT-----------T----AAC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:27044980-27045109 -	TGCGAAACGTGTTTGATAATGCGCCGCCATCTTGCGGCACACTCGC----ACACACACACGTGTGCCATTCTGGTTTTGCAGTGGTGTGCGTGTGTGCCTCGAGTCGTTGCGTCACTGGAAAAGTTAGAAAATC
droSim1	chr3R:26688146-26688275 -	TGCGAAACGTGTTTGATAATGCGCCGCCATCTTGCGGCACACTCGC----ACACACACACGTGTGCCAGGCTGGTTTTGCAGTGGTGTGCGTGTGTGCCTCGAGTCGTTGCGTCACTGGAAAAGTTAGAAAATC
droSec1	super_4:5862973-5863106 -	TGCGAAACGTGTTTGATAATGCGCCGCCATCTTGCGGCACACTCGCACACACACACACACGTGTGCCAGGCTGGTTTTGCAGTGGTTTGCGTGTGTGCCTCAAGTCGTTGCGTCACTGAAAAAGTTAGAAAATC
droYak2	chr3R:27981306-27981430 -	TGCGAAACGTGTTTGAAAATCCGTCGCCATCTTGCGGCACACTC------ACACACACACGTGTGCCAATATGGT-TTGCAGTGGTGTGCGTG--TGCCTCGAGTCGTTGCGTCACTGGAAAAGTCAGAAAATC
droEre2	scaffold_4820:935924-936048 +	TGCAAAACGTGTTGGAAAATTCGCCGCCATCTTGCGGCACAC--------ACACACACACGTGTGCCAGTCTGGT-TTGCAGTGGTGTGCGTGTGGGCCTCGAGTCGTTGCGTCACTGGAAAAGTCCGAAAATC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGC---------GAAACGTGTTTGATAATGCGCCGCCATCTTGCGGCACACTCGC----ACACACACACGTGTGCCAGGCTGGTTTTGC-------AGTGGTGTGCGTGTGTGCCTCGAGTCGTTGCGTCACTGGAAAAGTT---------AGAAAATC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
................................................................................................AGTGGTGTGCGTGTGTGCCTCG.........................................	22	1	8.00	8	8
................................................................................................AGTGGTGTGCGTGTGTGCCT...........................................	20	1	1.00	1	1
...........................................................................CAGGCTGGTTTTGC-------AGTGGTGTGC.....................................................	24	1	1.00	1	1
.......................................................................................................TGCGTGTGTGCCTCGAGTCGT...................................	21	1	1.00	1	1
........................................................................................C-------AGTGGTGTGCGTGTGTGCCTCG.........................................	23	1	1.00	1	1

dp4

TACATTTTCTCGAAAACGTGTCGAAT-----GTCGCCATCTTGCGGCACACACACAGACACACACACACATGTGACGAGAGGAATTGCCAGTGCTCAATAGTGTGCCTGTGTG--TCGAGACGTTGCGTCACTGAAAAAGTCGAACAGCAAAGTAAATT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...................................................................................................AGTGTGCCTGTGTG--TCGAGACG....................................	22	1	1.00	1	0	1
.................................................................................................ATAGTGTGCCTGTGTG--TCGAGACG....................................	24	1	1.00	1	0	1
....................................................................CATGTGACGAGAGGAATTGCCA.....................................................................	22	1	1.00	1	0	1
......................................................................................................GTGCCTGTGTG--TCGAGACGTTGC................................	23	1	1.00	1	0	1
......................................................................................................GTGCCTGTGTG--TCGAGACGTT..................................	21	1	1.00	1	0	1
.................................................................................................ATAGTGTGCCTGTGTG--TCGAGAC.....................................	23	1	1.00	1	0	1

Secondary Structure

dm3

-45.2	-44.9	-44.8	-44.7	-44.5	-44.5

droSim1

-45.2	-44.9	-44.8	-44.7	-44.5	-44.5

droSec1

-41.1	-40.7	-40.6	-40.5	-40.3	-40.3

droYak2

-36.9	-36.8	-36.7	-36.5	-36.5	-36.4

droEre2

-36.5	-36.3	-36.3	-36.2	-36.2	-36.1

droAna3

-24.7	-24.6	-24.4	-23.9	-23.8	-23.7

dp4

-30.9	-30.5	-30.5	-30.2	-30.2	-30.1

droPer1

-30.9	-30.5	-30.5	-30.2	-30.2	-30.1

droWil1

-22.6	-22.2	-21.9	-21.8	-21.8	-21.7

droVir3

-37.3	-37.2	-37.0	-37.0	-37.0	-36.9

droMoj3

-27.3	-27.2	-26.5	-26.4	-26.3

droGri2

-41.8	-41.5	-41.4	-41.4	-41.4	-41.3

Generated: 01/05/2013 at 05:23 PM