Secondary structure and small RNA-seq evidence for dme-mir-4950

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:3277158-3277280 +	TTTATACATTTG--TTTAT-----------------------AATGCACATAATAAATGCCAACC------ATTCATCATGA-AATTATAAATAGTAT--CATTTCAAGATGCATGG-TAAG-GCTT------TATTTT---------------------------------------------G--------TTTTGCA---ATCAAAGACATCTTTCTT
droSim1	chr3R:3321450-3321569 +	TTTATATATATT-ATTTAT-----------------------TATGCTCAGCATAAATGCCAAGC------ATTCGTCGTGA-AATTATAAATTATATATTA--TATAAATTCATGG-TAAG-GCTT------CATTTT---------------------------------------------T--------TAACGCA---GTCTAAGACATC----TT
droSec1	super_6:3368064-3368189 +	TTTATATATATT-ATTTAT-----------------------TATGCTCAGCATAAATGCCAAGC------ATTCGTCGTGA-AATTATAAATTATATATTATTTCTAGATTCATGG-TAAA-GTTT------CATTTT---------------------------------------------G--------TAACGCA---GTCTAAGACATCTTTCTC
droYak2	chr2L_random:3663454-3663574 -	TTTAGCCAAGTT-A-ATT--------------------------TGGTAAAAACAAAAACCAGAA------ACCGGCTACAC-GATGAAACGCTAAATGCCATTTTAGCAGTC--AG-GTAATTATA------TATT--------------------------------------------------T--AT-TTTTAAA---TTTAAACCCATTTTTTAT
droEre2	scaffold_4784:2237866-2237984 -	TTTCCAAATTTG-A-ATGC---AGA-TTTTT------------------AGACAATTGCTCCAGA------AACATT------------TAGAGGTATGCCACTTCAAAATACGA----TAATTGAAGGTTGAATTATG---------------------------------------------G-----AC--TTTAG----AACTTCAGCCTTCTTTTT
droAna3	scaffold_13340:2198726-2198841 +	TTAATAATTTTA--TTTAT-----------------------CGAAC------TAATT-AGGCTT------TTCATACAGATTTAAGCTTAATATTAAATTA--TAG-------------------------------------------------------AGCACTGGCTGCGGTGGTATATA--T--AT--TTTTC----AATAAACACATTTTTATG
dp4	chrXR_group6:912830-912970 -	TTTATACCACGC--ACTAGATTGGGTTCTCCAGATAACGAATGTTGTCCAGTAAAATCCCAATCCATTCAAATGGATTATGT-GACCA-------------GTGTTAAGATGCGTCG-AGGG-CAGT------CAGCTT---------------------------------------------G--------TGTTGCT---ATCTCGCTCCCCTCCGCC
droPer1	super_3:249021-249147 +	TTTTAAATCTGTTCCCTAAAATATACTTTTTGAAC------------------GAG-------------------------A---------------------------------------G-AGTA------TATATGTATGTATGCCGAGCAACTTCTAGTACCCCCTACTCAAT-A----TGTTTTTTTTTGGCTTAGTAAAATAATACATCTATATC
droWil1	scaffold_180708:152570-152690 -	TTTATATATATA-T-ATAT---GAT-GTAGA---TATA---TATTTTTTAT----ATTTAAATTTTT----------------------TTAAAGTGA--TTTTTGTCAA-GGCTAG-AAAA-GCTT------TATTTT-------------------------------------------TTGTTT-----TGTTTTA---GTTTATGCGATATTTCTT
droVir3	scaffold_135:841-956 -	TATATATATGTG-A-ACAT---AAC-TTATA-------------------TAATA------------------------------------CATATGA--CATACTGCCAGAC--AAATAAA-CGTA------ACTATTTATGTTTGAA-------ATCAAGATCACCAAAATAAATGATGATTT--T--AT--TT--------------------TACAA
droMoj3	scaffold_6308:1934837-1934961 -	TTTATATATTAT-A-AAAA---AAA-T-----------------TACTTAAATTAAAGCTTAGGA------AATATTTGTAT-CCATAAAAAATATGA--TATATTTTTATGCATGG-TAAA-TTTA------ATTTTT---------------------------------------------A--------ATTTCTA---ATAAAAAAAATTATATAT
droGri2	scaffold_14906:7885716-7885837 +	ATTATTATTTTT--TTTTT-----------------------A--TTTCAAGTTAATTTACAATT------ATCGAACCGGT-TAAACTAAATTTTAGCTTA--TAGATATTTATTG--------------------------------------------------------CTTAATTAACTGTTTTT---TTTTGTT----GTTAAAACATTTTTTTT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:3277158-3277280 +	TTTATACATTTG--TTTAT-----------------------AATGCACATAATAAATGCCAACC------ATTCATCATGA-AATTATAAATAGTAT--CATTTCAAGATGCATGG-TAAG-GCTT------TATTTT---------------------------------------------G--------TTTTGCA---ATCAAAGACATCTTTCTT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TTTATATAT----------------------ATTATTTATTATGCTCAGCATAAATGCCAAGCATTCGTCGTGAAATTATAAATTATATATTATATAAATTCATGGTAAGGCTTCATTTTTTAACGCAGTCTAAGACATCTT----	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

TTTATACCACGCACTAGATTGGGTTCTCCAGATAACGAATGTTGTCCAGTAAAATCCCAATCCATTCAAATGGATTATG-----TGACCAGTGTTAAGATGCGTCGAGGGCAGTCAGCTTGTGTTGCTATCTCGCTCCCCTCCGCC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

-26.6	-26.5	-26.0	-25.9

droSim1

-14.5	-14.5	-14.5	-14.3	-14.3	-14.2

droSec1

-13.9	-13.5	-13.4	-13.3	-13.2	-13.2

droYak2

-11.8	-11.7	-11.2	-11.1	-10.8

droEre2

-8.8	-8.8	-8.7	-8.5	-8.2	-8.2

droAna3

-14.9	-14.6	-14.5	-14.2	-14.2	-14.0

dp4

-23.6	-23.6	-23.6	-23.1	-23.1	-23.1

droPer1

-14.7	-14.6	-14.4	-14.3	-14.3	-14.0

droWil1

-10.6	-10.6	-10.6	-10.6	-10.4	-10.4

droVir3

-9.3	-9.3	-9.2	-8.9	-8.9	-8.8

droMoj3

-8.4	-8.3	-8.3	-8.1	-8.1	-8.1

droGri2

-11.8	-11.1	-11.0	-10.9

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