Secondary structure and small RNA-seq evidence for dme-mir-13a

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:11243249-11243353 -	CCAAG----C------------------CAT--AATTCTTACGTAACTCCTCAAAG-GGTTGTGAAATGTCGAC-TATTA-TCTACTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-C--GCG----GCA----------------------GCG
droSim1	chr3R:10237822-10237926 +	CCAAG----C------------------CAT--AGTTCTTACGTAACTCCTCAAAG-GGTTGTGAAATGTCGAC-TATTA-TCTACTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-C--TCG----GCA----------------------GCG
droSec1	super_0:10705053-10705157 +	CCAAG----C------------------CAT--AGTTCTTACGTAACTCCTCAAAG-GGTTGTGAAATGTCGAC-TATTA-TCTACTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-C--TGG----TCA----------------------GCG
droYak2	chr3R:15188577-15188681 +	CCAAG----C------------------CAT--AATTCTTACGTAACTCCTCAAAG-GGTTGTGAAATGTCGCC-TATTA-TCTACTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-C--TCG----GCA----------------------ACT
droEre2	scaffold_4770:10769389-10769493 -	CCAAG----A------------------CAC--AATTCTTACGTAACTCCTCAAAG-GGTTGTGAAATGTCGAC-TATTA-TCTACTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-T--TAA----AAA----------------------GCG
droAna3	scaffold_13340:12827611-12827739 -	ACAAGAATCCCCTCAAAAAAGGACGATCCATCGAGTTCTTACGTAACTCCTCAAAG-GGCTGTGAAATGTTGCCA--TTA-TCTACTCATATCACAGCCATTTTGATGAGTTTCGTGGGA-AT-C-GTCA----GAA----------------------AAC
dp4	chr2:9824930-9825029 +	CC-------C------------------CA-----TACTTACGTAACCCATCAAAC-GGTTGTGAAATGTTGCAT--TTA-TCAAATCATATCACAGCCATTTTGATGAGTTTCGTGTGG-AA-TGGCCA----GCA----------------------ATC
droPer1	super_0:10660066-10660165 -	CC-------C------------------CA-----TACTTACGTAACCCATCAAAC-GGTTGTGAAATGTTGCAT--TTA-TCAAATCATATCACAGCCATTTTGATGAGTTTCGTGTGG-AA-TGGCCA----GCA----------------------ATC
droWil1	scaffold_181089:2143204-2143324 -	CCGTT----CCGGCAAAAGATG-------GA--ATTTCTTACGTAACTCTTCAAGGGGGTTGTGAAATGTTGCCATTTTATTCAACTCATATCACAGCCATTTTGATGAGTTTCGTGCGAGTATT--CCT----GCA----------------------ACA
droVir3	scaffold_13047:13335625-13335725 +	CCACT----C-----------------------AATTCTTGCGTAACTCTTCAAGG-GGTTGTGAAATGTTGCCG--TTA-TCAAGTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-T--GCT----TAA----------------------ATT
droMoj3	scaffold_6540:10568336-10568468 +	CTCCG----C-----------------CCATTCAATTCTTGCGTAACTCTTCAAGG-GGTTGTGAAATGTAGCCA--TTA-TCAAGTCATATCACAGCCATTTTGATGAGTTTCGTGTGA-AT-T--GCTTTCAGCATTGTCCCATCCGTTTTGTGTCACTG
droGri2	scaffold_14906:4357674-4357778 -	CCAAG----C-----------------CCACCCAATTCTTGCGTAACTCTTCAAGG-GGTTGTGAAATGTGGGTA--TTA-TCAAGTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-T--GCTT---T-------------------------CA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:11243249-11243353 -	CCAAG----C------------------CAT--AATTCTTACGTAACTCCTCAAAG-GGTTGTGAAATGTCGAC-TATTA-TCTACTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-C--GCG----GCA----------------------GCG
droSim1	chr3R:10237822-10237926 +	CCAAG----C------------------CAT--AGTTCTTACGTAACTCCTCAAAG-GGTTGTGAAATGTCGAC-TATTA-TCTACTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-C--TCG----GCA----------------------GCG
droSec1	super_0:10705053-10705157 +	CCAAG----C------------------CAT--AGTTCTTACGTAACTCCTCAAAG-GGTTGTGAAATGTCGAC-TATTA-TCTACTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-C--TGG----TCA----------------------GCG
droYak2	chr3R:15188577-15188681 +	CCAAG----C------------------CAT--AATTCTTACGTAACTCCTCAAAG-GGTTGTGAAATGTCGCC-TATTA-TCTACTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-C--TCG----GCA----------------------ACT
droEre2	scaffold_4770:10769389-10769493 -	CCAAG----A------------------CAC--AATTCTTACGTAACTCCTCAAAG-GGTTGTGAAATGTCGAC-TATTA-TCTACTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-T--TAA----AAA----------------------GCG
droAna3	scaffold_13340:12827611-12827739 -	ACAAGAATCCCCTCAAAAAAGGACGATCCATCGAGTTCTTACGTAACTCCTCAAAG-GGCTGTGAAATGTTGCCA--TTA-TCTACTCATATCACAGCCATTTTGATGAGTTTCGTGGGA-AT-C-GTCA----GAA----------------------AAC
dp4	chr2:9824930-9825029 +	CC-------C------------------CA-----TACTTACGTAACCCATCAAAC-GGTTGTGAAATGTTGCAT--TTA-TCAAATCATATCACAGCCATTTTGATGAGTTTCGTGTGG-AA-TGGCCA----GCA----------------------ATC
droPer1	super_0:10660066-10660165 -	CC-------C------------------CA-----TACTTACGTAACCCATCAAAC-GGTTGTGAAATGTTGCAT--TTA-TCAAATCATATCACAGCCATTTTGATGAGTTTCGTGTGG-AA-TGGCCA----GCA----------------------ATC
droWil1	scaffold_181089:2143204-2143324 -	CCGTT----CCGGCAAAAGATG-------GA--ATTTCTTACGTAACTCTTCAAGGGGGTTGTGAAATGTTGCCATTTTATTCAACTCATATCACAGCCATTTTGATGAGTTTCGTGCGAGTATT--CCT----GCA----------------------ACA
droVir3	scaffold_13047:13335625-13335725 +	CCACT----C-----------------------AATTCTTGCGTAACTCTTCAAGG-GGTTGTGAAATGTTGCCG--TTA-TCAAGTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-T--GCT----TAA----------------------ATT
droMoj3	scaffold_6540:10568336-10568468 +	CTCCG----C-----------------CCATTCAATTCTTGCGTAACTCTTCAAGG-GGTTGTGAAATGTAGCCA--TTA-TCAAGTCATATCACAGCCATTTTGATGAGTTTCGTGTGA-AT-T--GCTTTCAGCATTGTCCCATCCGTTTTGTGTCACTG
droGri2	scaffold_14906:4357674-4357778 -	CCAAG----C-----------------CCACCCAATTCTTGCGTAACTCTTCAAGG-GGTTGTGAAATGTGGGTA--TTA-TCAAGTCATATCACAGCCATTTTGATGAGTTTCGTGCGA-AT-T--GCTT---T-------------------------CA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CCAAGCCATAGTTCTTACGTAACTCCTCAAAGGGTTGTGAAATGTCGACTATTATCTACTCATATCACAGCCATTTTGATGAGTTTCGTGCG-AATCT-CGGCAGCG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..............................................................TATCACAGCCATTTTGATGAGTT......................	23	2	2427.00	4854	4854
..................................................................ACAGCCATTTTGATGAGTT......................	19	2	16.50	33	33
..............................................................TATCACAGCCATTTTGATGAGTTT.....................	24	2	6.50	13	13
..................................................................ACAGCCATTTTGATGAGT.......................	18	2	5.00	10	10
................................................................TCACAGCCATTTTGATGAGTT......................	21	2	3.50	7	7
.......................TCCTCAAAGGGTTGTGAAATG...............................................................	21	2	1.50	3	3
...............................................................ATCACAGCCATTTTGATGAGTT......................	22	2	1.00	2	2
..............................................................TATCACAGCCATTTTGATG..........................	19	2	0.50	1	1
.................................................................CACAGCCATTTTGATGAGT.......................	19	2	0.50	1	1
......................CTCCTCAAAGGGTTGTGAAATGT..............................................................	23	2	0.50	1	1
.................................................................CACAGCCATTTTGATGAGTT......................	20	2	0.50	1	1
.............................................................ATATCACAGCCATTTTGATGAGTT......................	24	2	0.50	1	1

dp4

CC---CCATA---CTTACGTAACCCATCAAACGGTTGTGAAATGTTGCAT-TTATCAAATCATATCACAGCCATTTTGATGAGTTTCGTGTGGAATGGCCAGCAATC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..............................................................TATCACAGCCATTTTGATGAGTT......................	23	2	7710.00	15420	8997	6423
..............................................................TATCACAGCCATTTTGATGAGT.......................	22	2	1888.50	3777	1277	2500
..............................................................TATCACAGCCATTTTGATGAGTTT.....................	24	2	93.50	187	39	148
..................................................................ACAGCCATTTTGATGAGTT......................	19	2	41.50	83	0	83
..............................................................TATCACAGCCATTTTGATGAG........................	21	2	24.50	49	49	0
................................................................TCACAGCCATTTTGATGAGTT......................	21	2	9.50	19	17	2
......................CCCATCAAACGGTTGTGAAATG...............................................................	22	2	5.00	10	0	10
.................................................................CACAGCCATTTTGATGAGTT......................	20	2	3.00	6	0	6
.......................CCATCAAACGGTTGTGAAATG...............................................................	21	2	2.00	4	4	0
..............................................................TATCACAGCCATTTTGATG..........................	19	2	2.00	4	0	4
...................................................................CAGCCATTTTGATGAGTT......................	18	2	2.00	4	2	2
..................................................................ACAGCCATTTTGATGAGTTT.....................	20	2	1.50	3	0	3
......................CCCATCAAACGGTTGTGAAAT................................................................	21	2	1.50	3	2	1

Secondary Structure

dm3

-26.6	-26.5	-26.2	-26.2	-26.1	-26.1

droSim1

-26.6	-26.5	-26.2	-26.2	-26.1	-26.1

droSec1

-26.6	-26.5	-26.2	-26.2	-26.1	-26.1

droYak2

-26.6	-26.2	-26.2	-25.8	-25.8

droEre2

-26.6	-26.5	-26.2	-26.2	-26.1	-26.1

droAna3

-29.1	-28.7	-28.7	-28.3	-28.3

dp4

-24.4	-24.0	-24.0	-24.0	-23.9	-23.6

droPer1

-24.4	-24.0	-24.0	-24.0	-23.9	-23.6

droWil1

-27.0	-26.8	-26.6	-26.6	-26.4	-26.4

droVir3

-26.6	-26.2	-26.2	-26.1	-25.9	-25.8

droMoj3

-26.6	-26.2	-25.9	-25.7	-25.7

droGri2

-27.4	-27.3	-27.1	-27.0	-26.9	-26.7

Generated: 01/05/2013 at 05:08 PM