Secondary structure and small RNA-seq evidence for dme-mir-964

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:5642087-5642216 +	TCTAGTTGGTGATAC-----------------------CA-------ATA----A--CATATTGGTCCAACTTGCCTTAGAATAGGGGAGCTTAACTTATGTTT--TTGATGT-TTAAGTTAAAAGCCTCTGTTCTAAGACAATTTGATGATCAAAA------CAGC-----CGGAGAAA
droSim1	chr2L:5435151-5435306 +	TCTAGTGGGT-----AAATCCATGTGGTTATGACAAGTCAATC------A----A--AATCTTGGTCCAACTTGCCTTAGAATAGGGGAGCTTAACTTGTGTTT--TTAATGT-TTAAGTTAAAAGCCACTGTTCTAAGACAATTTGATGATCAAAACTTCAACT----TCATTTTGTAA
droSec1	super_5:3719805-3719957 +	TCTAGTGGGT-----AAATCCATGTGGTTATGATAAGTCAATC------A----A--AATCTTGGTCCAACTTGCCTTAGAATAGGGGAGCTTAACTTGTGTTT--TTAATGT-TTAAGTTAAAAGCCACTGTTCTAAGACAATTTGATGATCAAAA---C---CACCTG-ACAAAAAAA
droYak2	chr2L:13551054-13551191 -	TCAAGTT--------ATATCC-------TATGATCAATCAAT-------G----A--AATCTTGGTCCCACTTGTCTTAGAATAGGGGAGCTTAACTTATGTAT--ATCATGT-ATAAGTTAAGAACCTTTATTCTAAGACAATTCGACTACAAAAT------CAAC-----TGAAAAAC
droEre2	scaffold_4929:5730483-5730617 +	TCTAGTTGGTTA----CATCCTTGCGTTAGTGATCAATCAAT-------A----A--CGTTTTGGTCCCACTTGTCTTAGAATAGGGGAGCTTAACTTGTGTGT--GTTATGC-TTAAGTTAAGAGCCTTTATTCTAAGTCAATTCGACTGCCAA-------------------------
droAna3	scaffold_12916:11085546-11085681 +	AAGAATACGA-----GTGTTCGCGGGATGAGC-----------------A----TCGAATCAAAGTCAAACTTGTTTTAGAATAGGGGAGCTTAACTTATTGGAG-AGTTGATATTAAGTTAAGATCCCTAATTCTAAGATAATGTGACCATTAATG---C---AAC-----G------T
dp4	chr4_group4:3181498-3181623 -	AGGGATC-------C------CC------------------------GTG----C-CAAATAGAGCCAAAACTATCTTAGATCGAAGGTTCCTGGCTTACAGGG--ATTTGAT-GTAAGTTAAGAACCTCCGCTCTAAGCTAGTATGGCTATCAT-----CAACG----G-CCCTGAAAG
droPer1	super_10:2200424-2200549 -	AGGGATC-------C------CC------------------------GTG----C-CAAATAGAGCCAAAATTATCTTAGATCGAAGGTTCCTGGCTTACAGGG--ATTTGAT-GTAAGTTAAGAACCTCCGCTCTAAGCTAGTATGGCTATCAT-----CAACG----G-CCCTGAAAG
droWil1	scaffold_180708:8624927-8625071 -	TTTAAGCCCA-----ACACATTTGTTGTCTGTGT----CA---------G----T-TGAACAAGGTCAAACTTGTCTTAGAATAGGGGAGCTTAACTTATATTG--TTTTGCT-TAAAGTTAAGAGCCTCAATTCTAAGATAATGCGACTATCACCG---C---AGCA-G-TTC-AGATA
droVir3	scaffold_12963:3616457-3616573 +	TTCAAAAGTT----T------TC---------------ATATTG---AAAATAC-----ATTAAGTTTAACTTATCTTAGAATAGGGGAGCTTAACTTT-GT-A--TGAACAT-TTAAGCTAAGAGCCTCAATTCTTAGATAATGCGACTAACAA-------------------------
droMoj3	scaffold_6500:14019483-14019608 +	GATATATGATGA------------------TGATTTTCCAATTGTGATGAAATC-----ATTGAGTTCAACTTATCTTAGAATAGGGGAGCTTAACTTAA--TC--TGAACAC-TCAAGCTAAGAGCCTCGATTCTTCGATAATGCGACTAACA--------------------------
droGri2	scaffold_15252:3148300-3148427 +	TTCAGTTGATTA----GA-----------------------------AGAGTGC-----ATTATGTCAAACTTATCTTAGAATAGGGGAGCTTAACTTTTATCATATTAGCGC-TCGAGCTAAGATCCTCAATTCTTGGATAAGGCGACTAGCAA--------CT----G-CAGTAAAAA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:5642087-5642216 +	TCTAGTTGGTGATAC-----------------------CA-------ATA----A--CATATTGGTCCAACTTGCCTTAGAATAGGGGAGCTTAACTTATGTTT--TTGATGT-TTAAGTTAAAAGCCTCTGTTCTAAGACAATTTGATGATCAAAA------CAGC-----CGGAGAAA
droSim1	chr2L:5435151-5435306 +	TCTAGTGGGT-----AAATCCATGTGGTTATGACAAGTCAATC------A----A--AATCTTGGTCCAACTTGCCTTAGAATAGGGGAGCTTAACTTGTGTTT--TTAATGT-TTAAGTTAAAAGCCACTGTTCTAAGACAATTTGATGATCAAAACTTCAACT----TCATTTTGTAA
droSec1	super_5:3719805-3719957 +	TCTAGTGGGT-----AAATCCATGTGGTTATGATAAGTCAATC------A----A--AATCTTGGTCCAACTTGCCTTAGAATAGGGGAGCTTAACTTGTGTTT--TTAATGT-TTAAGTTAAAAGCCACTGTTCTAAGACAATTTGATGATCAAAA---C---CACCTG-ACAAAAAAA
droYak2	chr2L:13551054-13551191 -	TCAAGTT--------ATATCC-------TATGATCAATCAAT-------G----A--AATCTTGGTCCCACTTGTCTTAGAATAGGGGAGCTTAACTTATGTAT--ATCATGT-ATAAGTTAAGAACCTTTATTCTAAGACAATTCGACTACAAAAT------CAAC-----TGAAAAAC
droEre2	scaffold_4929:5730483-5730617 +	TCTAGTTGGTTA----CATCCTTGCGTTAGTGATCAATCAAT-------A----A--CGTTTTGGTCCCACTTGTCTTAGAATAGGGGAGCTTAACTTGTGTGT--GTTATGC-TTAAGTTAAGAGCCTTTATTCTAAGTCAATTCGACTGCCAA-------------------------
droAna3	scaffold_12916:11085546-11085681 +	AAGAATACGA-----GTGTTCGCGGGATGAGC-----------------A----TCGAATCAAAGTCAAACTTGTTTTAGAATAGGGGAGCTTAACTTATTGGAG-AGTTGATATTAAGTTAAGATCCCTAATTCTAAGATAATGTGACCATTAATG---C---AAC-----G------T
dp4	chr4_group4:3181498-3181623 -	AGGGATC-------C------CC------------------------GTG----C-CAAATAGAGCCAAAACTATCTTAGATCGAAGGTTCCTGGCTTACAGGG--ATTTGAT-GTAAGTTAAGAACCTCCGCTCTAAGCTAGTATGGCTATCAT-----CAACG----G-CCCTGAAAG
droPer1	super_10:2200424-2200549 -	AGGGATC-------C------CC------------------------GTG----C-CAAATAGAGCCAAAATTATCTTAGATCGAAGGTTCCTGGCTTACAGGG--ATTTGAT-GTAAGTTAAGAACCTCCGCTCTAAGCTAGTATGGCTATCAT-----CAACG----G-CCCTGAAAG
droWil1	scaffold_180708:8624927-8625071 -	TTTAAGCCCA-----ACACATTTGTTGTCTGTGT----CA---------G----T-TGAACAAGGTCAAACTTGTCTTAGAATAGGGGAGCTTAACTTATATTG--TTTTGCT-TAAAGTTAAGAGCCTCAATTCTAAGATAATGCGACTATCACCG---C---AGCA-G-TTC-AGATA
droVir3	scaffold_12963:3616457-3616573 +	TTCAAAAGTT----T------TC---------------ATATTG---AAAATAC-----ATTAAGTTTAACTTATCTTAGAATAGGGGAGCTTAACTTT-GT-A--TGAACAT-TTAAGCTAAGAGCCTCAATTCTTAGATAATGCGACTAACAA-------------------------
droMoj3	scaffold_6500:14019483-14019608 +	GATATATGATGA------------------TGATTTTCCAATTGTGATGAAATC-----ATTGAGTTCAACTTATCTTAGAATAGGGGAGCTTAACTTAA--TC--TGAACAC-TCAAGCTAAGAGCCTCGATTCTTCGATAATGCGACTAACA--------------------------
droGri2	scaffold_15252:3148300-3148427 +	TTCAGTTGATTA----GA-----------------------------AGAGTGC-----ATTATGTCAAACTTATCTTAGAATAGGGGAGCTTAACTTTTATCATATTAGCGC-TCGAGCTAAGATCCTCAATTCTTGGATAAGGCGACTAGCAA--------CT----G-CAGTAAAAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TCTAGTGGGTAAATCCATGTGGTTATGACAAGTCAATCAAAATCTTGGTCCA-ACTTGCCTTAGAATAGGGGAGCTTAACTTGTGTTTTTAATGTTTAAGTTAAAAGCCACTGTTCTAAGACAATTTGATGATCAAAACTTCAACTTCATTTTGTAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
............................................................TTAGAATAGGGGAGCTTAACT............................................................................	21	1	2.00	2	2
............................................................TTAGAATAGGGGAGCTTAACTT...........................................................................	22	1	2.00	2	2
........................................AATCTTGGTCCA-ACTTGCC.................................................................................................	19	1	1.00	1	1
....................................................................................................TTAAAAGCCACTGTTCTAAGA....................................	21	1	1.00	1	1
....................................................................................................TTAAAAGCCACTGTTCTAAGAC...................................	22	1	1.00	1	1

dp4

-------AGGGATCCCCG-------------------TGCCAAATAGAGCCAAAACTATCTTAGATCGAAGGTTCCTGGCTTACAGGGATTTGATGTAAGTTAAGAACCTCCGCTCTAAGCTAGTATGGCTATCA-----TCAACGGCC-CTGAAAG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
................................................................................................TAAGTTAAGAACCTCCGCTCTA.......................................	22	1	27.00	27	1	26
................................................................................................TAAGTTAAGAACCTCCGCTCT........................................	21	1	14.00	14	0	14
..............................................................AGATCGAAGGTTCCTGGCTTAC.........................................................................	22	1	3.00	3	0	3
................................................................................................TAAGTTAAGAACCTCCGCTCTAA......................................	23	1	3.00	3	0	3
................................................................................................TAAGTTAAGAACCTCCGCTC.........................................	20	1	3.00	3	0	3
..............................................................AGATCGAAGGTTCCTGGCTT...........................................................................	20	1	1.00	1	0	1
................................................................ATCGAAGGTTCCTGGCTTA..........................................................................	19	1	1.00	1	0	1
.................................................................................................AAGTTAAGAACCTCCGCTCTA.......................................	21	1	1.00	1	0	1

Secondary Structure

dm3

dG=-25.3, p-value=0.009901	dG=-25.0, p-value=0.009901

droSim1

dG=-20.7, p-value=0.009901	dG=-20.4, p-value=0.009901	dG=-20.2, p-value=0.009901	dG=-19.9, p-value=0.009901

droSec1

dG=-20.7, p-value=0.009901	dG=-20.4, p-value=0.009901	dG=-20.2, p-value=0.009901	dG=-19.9, p-value=0.009901

droYak2

dG=-34.4, p-value=0.009901	dG=-34.1, p-value=0.009901	dG=-33.6, p-value=0.009901

droEre2

dG=-31.1, p-value=0.009901	dG=-30.8, p-value=0.009901	dG=-30.2, p-value=0.009901

droAna3

dG=-27.6, p-value=0.009901	dG=-27.5, p-value=0.009901	dG=-27.3, p-value=0.009901	dG=-27.2, p-value=0.009901	dG=-26.6, p-value=0.009901

dp4

dG=-29.3, p-value=0.009901

droPer1

dG=-27.3, p-value=0.009901

droWil1

dG=-27.1, p-value=0.009901	dG=-26.8, p-value=0.009901	dG=-26.6, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.3, p-value=0.009901

droVir3

dG=-20.3, p-value=0.009901	dG=-20.0, p-value=0.009901	dG=-19.6, p-value=0.009901	dG=-19.4, p-value=0.009901	dG=-19.3, p-value=0.009901

droMoj3

dG=-17.2, p-value=0.009901	dG=-17.2, p-value=0.009901	dG=-16.9, p-value=0.009901	dG=-16.9, p-value=0.009901	dG=-16.5, p-value=0.009901

droGri2

dG=-19.7, p-value=0.009901	dG=-19.0, p-value=0.009901	dG=-18.9, p-value=0.009901	dG=-18.8, p-value=0.009901	dG=-18.7, p-value=0.009901

Generated: 03/07/2013 at 07:11 PM