Secondary structure and small RNA-seq evidence for dme-mir-959

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:5640925-5641052 +	CGAATTAA-ATTGATTTTAACTTT-----------------------------------------GTTCTATATTCTTAGTACTCGGGTTGATAAAGACCTTTTCT---TCAG--GGAGCCTTTGTCATCGGGGGTATTATGAAATA---------TAGTTTAAAGAAACTGCAATGATT------------ATCG----------------------------------
droSim1	chr2L:5434012-5434138 +	A--ATTAA-ATAGATTTTAACTTT-----------------------------------------GTTCTATATTCTTAGTACTCGGGTTGATAAAGACCTTTTCT---TTGC--GGAGCCTTTGTCATCGGGGGTATTATGAAATA---------TAGTTTAAAGAAGCTGCAAGGATC------------ATCG----------------------------------
droSec1	super_5:3718667-3718793 +	A--ATTAA-ATAGATTTTAACTTT-----------------------------------------GTTCTATATTCTTAGTACTCGGGTTGATAAAGACCTTTTCT---TTGC--GGAGCCTTTGTCATCGGGGGTATTATGAAATA---------TAGTTTAAAGAAGCTGCAAGGATC------------ATCG----------------------------------
droYak2	chr2L:13552255-13552381 -	CGAGTTAA-ATTGATTTTAACTTT-----------------------------------------GTTCTATATTCTTAGTACTCGGGTTGACAAAGACCTTTCCT----TGC--GGCGCCTTTGTCATCGGGGGTATTATGAAATA---------TAGCTCAAAGAAACTGCAAGGATC------------ATCG----------------------------------
droEre2	scaffold_4929:5729400-5729526 +	CGAGTTAA-ATTGATTTTAACTTT-----------------------------------------GTTCTATATTCTTAGTACTCGGGTTGACAAAGAGCTTTCCT----TGC--GGCGCCTTTGTCATCGGGGGTATTATGAAATA---------TAGCTCAAAGAAACTGCAAGGAGC------------AACG----------------------------------
droAna3	scaffold_12916:11084702-11084849 +	GAAGTTAA-ATTTATTTCAATTTT-----------------------------------------GTTCTATATTCTTAGTACTCGGGTTGATAAAGACCTTTCCT----GGA--GCCGCCTTTGTCATCGGGGGTATTATGAAATA---------TAGCTCAAAAAACCAGCACAATGT------------ATCGGCCAATAGGCCAATTAACCCG-------------
dp4	chr4_group4:3182582-3182745 -	TGGTTTTC-GTTTA------------------------CGTTTTTT-TTTT--------GTTTTGGTTCTATGTTCTTAGTACTTGGGTTGATAAAGACCACTCGTAGTGTGA--GAAGCCTTTGTCATCGCGGGTATTATGCAACA---------TAGCTCAAAAGCGCAACAAAATACACA-------------AAA--------AATATACACGTAAATGTGTGTGG
droPer1	super_10:2201518-2201669 -	TGGTTTTC-GTTCA------------------------CGTTTTTTTTTTT--------GTTTTGGTTCTATGTTCTTAGTACTTGGGTTGATAAAGACCACTCGTAGTGTGA--GAAGCCTTTGTCATCGCGGGTATTATGCAACA---------TAGCTCAAAAGCGCAACAAAATACACA-------------AAA--------AATATACACG-------------
droWil1	scaffold_180708:8626283-8626424 -	AGTGAAAA-AGTGACTTAAGTTTT-----------------------------------------GTTCTATATTCTTAGTACTCGGGTTGATAAAGACAAAATGT---TTACCAATCGCCTTTGTCATCGGGGGTATTATGAAATA---------TAGCTCAAAAGTTCAACATAATAATTAAGAATTAACTTTG----------------------------------
droVir3	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6500:14018136-14018207 +	TGATGTAATAAGTGTTTTAGCTTT-----------------------------------------AAGTTGTGCCATT-------------------------------------------------------------TTAAATTG---------AAAAAAGTG-AAGATTGAAAATTG------------ACTA----------------------------------
droGri2	scaffold_15252:3146904-3147001 +	CAAAGAGT-AGCAGGAGTAGTTAAGTTGTAGTTTCTTACGGTTTTTTTTTTAATAACATGCT--------------TTAGTGCT--------------------------------------------------------------TCAATGTAGGTGGCTCAA---------GATATTT------------GTTG----------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:5640925-5641052 +	CGAATTAAATTGA---------TTTTAACTTTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCTTTTCT---TCAG--GGAGCCTTTGTCATCGGGGGTATTATGAAATATAGTTTAAAGAAACTGCAATGATTATCG-----------------------------------
droSim1	chr2L:5434012-5434138 +	A--ATTAAATAGA---------TTTTAACTTTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCTTTTCT---TTGC--GGAGCCTTTGTCATCGGGGGTATTATGAAATATAGTTTAAAGAAGCTGCAAGGATCATCG-----------------------------------
droSec1	super_5:3718667-3718793 +	A--ATTAAATAGA---------TTTTAACTTTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCTTTTCT---TTGC--GGAGCCTTTGTCATCGGGGGTATTATGAAATATAGTTTAAAGAAGCTGCAAGGATCATCG-----------------------------------
droYak2	chr2L:13552255-13552381 -	CGAGTTAAATTGA---------TTTTAACTTTGTTCTATATTCTTAGTACTCGGGTTGACAAAGACCTTTCCT----TGC--GGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAAGGATCATCG-----------------------------------
droEre2	scaffold_4929:5729400-5729526 +	CGAGTTAAATTGA---------TTTTAACTTTGTTCTATATTCTTAGTACTCGGGTTGACAAAGAGCTTTCCT----TGC--GGCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAGAAACTGCAAGGAGCAACG-----------------------------------
droAna3	scaffold_12916:11084702-11084849 +	GAAGTTAAATTTA---------TTTCAATTTTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCTTTCCT----GGA--GCCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAAAACCAGCACAATGTATCGGCCAATAGGCCAATTA-ACCCG-------------
dp4	chr4_group4:3182582-3182745 -	TGGTTTTCGTTTACGTTTTT-TTTTTGTTTTGGTTCTATGTTCTTAGTACTTGGGTTGATAAAGACCACTCGTAGTGTGA--GAAGCCTTTGTCATCGCGGGTATTATGCAACATAGCTCAAAAGCGCAACAAAATACACA-AAA--------AA-TATACACGTAAATGTGTGTGG
droPer1	super_10:2201518-2201669 -	TGGTTTTCGTTCACGTTTTTTTTTTTGTTTTGGTTCTATGTTCTTAGTACTTGGGTTGATAAAGACCACTCGTAGTGTGA--GAAGCCTTTGTCATCGCGGGTATTATGCAACATAGCTCAAAAGCGCAACAAAATACACA-AAA--------AA-TATACACG-------------
droWil1	scaffold_180708:8626283-8626424 -	AGTGAAAAAGTGA---------CTTAAGTTTTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACAAAATGT---TTACCAATCGCCTTTGTCATCGGGGGTATTATGAAATATAGCTCAAAAGTTCAACATAATAATTA-AGA--------AT-TAACTTTG-------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

--AATTAAATAG--------ATTTTAACTTTGTTCTATATTCTTAGTACTCGGGTTGATAAAGACCTTTTCT---TTGCGGAGCCTTTGTCATCGGGGGTATTATGAAATATAGTTTAAAGAAGCTGCAA-------------------------GGATCATCG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
......................................................................................TTGTCATCGGGGGTATTATGAA........................................................	22	1	1.00	1	1
......................................................................................TTGTCATCGGGGGTATTATGA.........................................................	21	1	1.00	1	1

dp4

TGGTTTTCGTTTACGTTTTTTTTTTGTTTTGGTTCTATGTTCTTAGTACTTGGGTTGATAAAGACCACTCGTAGTGTGAGAAGCCTTTGTCATCGCGGGTATTATGCAACATAGCTCAAAAGCGCAACAAAATACACAAAAAATATACACGTAAATGTGTGTGG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
......................................................................................TTGTCATCGCGGGTATTATGC.........................................................	21	1	31.00	31	0	31
......................................................................................TTGTCATCGCGGGTATTATGCA........................................................	22	1	24.00	24	0	24
..........................................TTAGTACTTGGGTTGATAAAGA....................................................................................................	22	1	17.00	17	0	17
......................................................................................TTGTCATCGCGGGTATTATG..........................................................	20	1	17.00	17	0	17
..........................................TTAGTACTTGGGTTGATAAAG.....................................................................................................	21	1	16.00	16	2	14
......................................................................................TTGTCATCGCGGGTATTATGCAA.......................................................	23	1	4.00	4	0	4
..........................................TTAGTACTTGGGTTGATAAA......................................................................................................	20	1	3.00	3	0	3
.........................................CTTAGTACTTGGGTTGATAA.......................................................................................................	20	1	2.00	2	0	2
.........................................CTTAGTACTTGGGTTGATAAAG.....................................................................................................	22	1	2.00	2	0	2
..........................................TTAGTACTTGGGTTGATAA.......................................................................................................	19	1	1.00	1	0	1
.....................................................................................TTTGTCATCGCGGGTATTATG..........................................................	21	1	1.00	1	0	1
.......................................................................................TGTCATCGCGGGTATTATGCA........................................................	21	1	1.00	1	0	1

Secondary Structure

dm3

dG=-21.2, p-value=0.009901	dG=-20.6, p-value=0.009901	dG=-20.6, p-value=0.009901	dG=-20.6, p-value=0.009901

droSim1

dG=-18.7, p-value=0.009901	dG=-18.5, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-17.9, p-value=0.009901

droSec1

dG=-18.7, p-value=0.009901	dG=-18.5, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-17.9, p-value=0.009901

droYak2

dG=-20.7, p-value=0.009901	dG=-20.1, p-value=0.009901	dG=-20.1, p-value=0.009901

droEre2

dG=-24.4, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.7, p-value=0.009901

droAna3

dG=-17.7, p-value=0.009901	dG=-17.6, p-value=0.009901	dG=-17.5, p-value=0.009901	dG=-17.4, p-value=0.009901	dG=-17.2, p-value=0.009901

dp4

dG=-19.6, p-value=0.009901	dG=-19.6, p-value=0.009901	dG=-19.3, p-value=0.009901	dG=-19.3, p-value=0.009901	dG=-19.3, p-value=0.009901

droPer1

dG=-19.6, p-value=0.009901	dG=-19.6, p-value=0.009901	dG=-19.3, p-value=0.009901	dG=-19.3, p-value=0.009901	dG=-19.3, p-value=0.009901

droWil1

dG=-17.1, p-value=0.009901	dG=-16.5, p-value=0.009901	dG=-16.5, p-value=0.009901	dG=-16.3, p-value=0.009901

droVir3

No secondary structure predictions returned

droMoj3

dG=0.0, p-value=1.0

droGri2

dG=-0.9, p-value=0.009901	dG=0.0, p-value=0.009901

Generated: 03/07/2013 at 07:08 PM