Secondary structure and small RNA-seq evidence for dme-mir-4957

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:15213971-15214085 -	CTTTTTTTT--------------CTCTGCTC----GT-----------------------T--GTA--------TTTTACGCA--CTCTGCTGGCAGCG---CTGTCGGC---GTCGCTGCCAGCTGCCAGCAGCGAGCGGTACACTT--------GCAACTATC-----CTGT-GCACCCTACAATT
droSim1	chrX:11736931-11737042 -	CTTTTTTTTTTTT----------CTCTGCTC----GT-----------------------T--GCA--------TTTTACGCA--CTCTGCTGGCAGCG---ACGCCGAC---AGCGCTGCCA-------GCAGCGAGCGGTACACTT--------GCAACTATC-----CTGC-GCACCCTACAATT
droSec1	super_56:101687-101796 -	CTTTTTTTTT--T----------CTCTGCTC----GT-----------------------T--GCA--------TTTTACGCA--CTCTGCTGGCAGCG---ACGCCGAC---AGCGGTGCCA-------GCAGCGAGCGGTACACTT--------GCAACTATC-----CTGC-ACACCCTACAATT
droYak2	chrX:9414156-9414285 -	TTTTTTT----------------CTCTGCTC----GTTTTTCTCTCTTTTTCTTCTCGCCT--GCA--------TTTTACGCA--CTCTGCTAGCAGCG---ACGCCGAC---TGCGCTGCCA-------ACAGCAAGCGGTACACTT--------GCAACTATT-----CTAT-GCACCCTACAATT
droEre2	scaffold_4690:11807313-11807440 +	TTTTTT-----------------CTCCGCTC----GTTTTTCTCTCCTTTTCTGCTCGCCT--GCA--------TTTTACGCA--CTCTGCTGGCAGCG---ACGCCGAC---TGCGCTGCAA-------ACAGCGAGCGGTACACTT--------GCAACTATT-----CTGT-GCACCCTACAATT
droAna3	scaffold_13117:1427273-1427395 -	ATTTTTCTTC---CCATGCAACC-TGTGTCC----AT-----------------------TGTACG--------TTTTACGCA--CTCTCC--CCAGCA---ACACCGCC---GCCGATAGCG-------ACTGCGACGAGTACGTTG--------GCAGCGGCACTTGACTCT-TTTTGCGGCAATT
dp4	chrXL_group1e:12152468-12152588 -	CTTTAGCTTT---TTG--------------CGTTTGCGTTTGCCCCGATTTCAATGCA-AT--GTG--------TTGTACGCA--CACGGGTT---TTT---ATCTCAGC---TGTGGGATGA-------ACGGC--CCGAGACACTT--------GC--CGATG-----CGGC-GA-CCC--CAGGC
droPer1	super_14:1456573-1456693 +	CTTTAGCTTT---TTG--------------CGTTTGCGTTTGCCCCGATTTCAATGCA-AT--GTG--------TTGTACGCA--CACGGGTT---TTT---ATCTCAGC---TGTGGGATGA-------ACGGC--CCGAGACACTT--------GC--CGATG-----CGGC-GA-CCC--CAGGC
droWil1	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12928:4095173-4095244 -	CTCTTTATTG---CAA--------------------------------TGCGAC-----------------------TACGCATGATTTAGGCGCAGGT---TGGTCG----------------------------------ACACTT--------GCATTGGTT-----GC--------AAGTACTT
droMoj3	scaffold_6680:3750941-3751063 -	TTTGTTTTTG---TTT-----------TCTT----TT-----------------------T--GTAGCCTAGGAATTTACC-----TCTTGTGGCATATCAGCTGTTGGC---TTTGGTTGCA-------AACACACG--TTGACTTTTCACACACAGAATTCTG-----TTGAAATGTTTAACACTT
droGri2	scaffold_14853:566008-566117 +	CTCTTTTATT----------------------------------GCAATGAGACTGCG-AC--GCA--------TGATTTGGG--CGCAGG-------T---CTATCACCACTTGCACTGACG-------ACTGCTTTTGCTTTTGCT--------ACTACTTTT-----ACTT-GCCAGCGGAACTT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:15213971-15214085 -	CTTTTTTTTCTCTGCTCGTTGTATTTTACGCACTCTGCTGGCAGCGCTGTCGGCGTCGCTGCCAGCTGCCAGCAGCGAGCGGTACACTTGCAACTATCCTGTGCACCCTACAATT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CTTTTTTTTTTTTC-------------------TCTGCTCGTTGCATTTTACGCACTCTGCTGG-CAGCGACGCCGACAGCGCTG-------------------CCAGCAGCGAGCGGTACACTTGCAACTATCCTGCGCACCCTACAATT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

CTTTAGCTTTTTGCGTTTGCGTTTGCCCCGATTTCAATGCAATGTGTTGTACGCACACGGGTTTTTATC----------------TCAGCTGTGGGATGAACGGC---------CCGAGACACTTGC--CGATGCGGCGACCC---CAGGC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
................................................................TTATC----------------TCAGCTGTGGGATGA...................................................	20	1	1.00	1	1	0
......CTTTTTGCGTTTGCGTTTGCC............................................................................................................................	21	1	1.00	1	0	1

Secondary Structure

dm3

dG=-31.1, p-value=0.009901	dG=-31.1, p-value=0.009901	dG=-30.3, p-value=0.009901	dG=-30.3, p-value=0.009901

droSim1

dG=-28.5, p-value=0.009901

droSec1

dG=-24.4, p-value=0.009901

droYak2

dG=-16.3, p-value=0.009901	dG=-15.6, p-value=0.009901

droEre2

dG=-18.2, p-value=0.009901	dG=-17.9, p-value=0.009901	dG=-17.9, p-value=0.009901	dG=-17.6, p-value=0.009901	dG=-17.5, p-value=0.009901

droAna3

dG=-9.8, p-value=0.009901	dG=-9.5, p-value=0.009901	dG=-9.4, p-value=0.009901	dG=-9.1, p-value=0.009901

dp4

dG=-18.2, p-value=0.009901	dG=-17.2, p-value=0.009901

droPer1

dG=-18.2, p-value=0.009901	dG=-17.2, p-value=0.009901

droWil1

No secondary structure predictions returned

droVir3

dG=-2.3, p-value=0.019802	dG=-2.2, p-value=0.019802	dG=-2.2, p-value=0.009901	dG=-2.1, p-value=0.019802	dG=-1.8, p-value=0.009901

droMoj3

dG=-9.2, p-value=0.009901	dG=-8.9, p-value=0.009901	dG=-8.5, p-value=0.009901	dG=-8.4, p-value=0.009901	dG=-7.7, p-value=0.009901

droGri2

dG=-9.6, p-value=0.009901	dG=-8.9, p-value=0.009901	dG=-7.8, p-value=0.009901

Generated: 03/07/2013 at 06:00 PM