Secondary structure and small RNA-seq evidence for dme-mir-4946

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:18867030-18867176 -	TAAAAATAAAA----AAATG-------------CTC-----------------GATTGCTGCAA-----------------------------------------CTAAGAAACA--AATATTTTCAGTTGTTCAT----TGCAAATTAATTTA---TGTACATTGCTAT---------------GAAATCAATTGAAAATATAAT---TGTA--------------------TCCTAGGCTTATCAGCT-GCAATGCCTCTATGAAGGG
droSim1	chr2L:18557325-18557471 -	TAAAAATAACA----AAACG-------------CTC-----------------ATTTGCTGCAA-----------------------------------------ATAAGAAACA--AATATTTTCAGTTGTTCAT----TGCAAGTTAATTTA---TGTACATTGCTAT---------------GAAATCAATTGAAAATATAAT---TGTA--------------------TCCCAGGCTTATCAGCT-GCAATCCCCCCAAGAAGGG
droSec1	super_7:2494148-2494294 -	TAAAAATAACA----AAACG-------------TTC-----------------ATTTGCTGATA-----------------------------------------ATAAGAAACA--AATATCTTAAGATGTTCAT----TGCAAATTAATTTA---TGTACATTGCTAT---------------GAAATCAATTGAAAATATAAT---TGTA--------------------TCCTAGGCTTATCAGCT-GCAATCCCCCCAAGAAGGG
droYak2	chr2R:5382904-5383074 -	TAAAAATAACA----AAGCA-------------TAT-------------TAGCATATGCTGCAA-----------------------------------------ACAATAAATA--AATATTTTCAGCTGTGCAT----TGCAAATTAATGTA---TTTACATAGCTAT---------------GAAAGCAATTGAAACGACAAT---TGCAGGTCATTTTTATTGCACACATCCTAGGCTTATCAGTG-GCAATGCCCCTACGAAGAG
droEre2	scaffold_4845:5409251-5409398 +	TACAAGTAACA----AAGTG-------------CTA-----------------ATTCGCTGCAA-----------------------------------------ATAGGAAATA--AATATTTTCAT------------------------TATTAT-CACATTGCCA----------------GAAACCAATTGAAAAGATAAT---TGTAGGCCACTTTTGTTGCACGCATCCTAGGCTTATCAGCT-GATATGCCCCCACGAAGGG
droAna3	scaffold_13334:1096999-1097137 -	TAAATATTTTT----AAGTA-------------ATT-----------------AATTG-----------GGCTACTG----------------------------GCTTTAAAAAATAATATTTTCAAATGTTATT----GGTAATTTAATTTT---TTTATAATTTT-TAAA------------TACATTTTTTTAAACTAAAATCCTTGTT--------------------TTCT----------------GCTTCCTTT--TCAGCT
dp4	chrXR_group6:8932576-8932713 +	TTAAAATAAAA----ACATT--------------TC-----------------ATATTTAAATT-ACAAGGTTTTAT----------------------------ATTTTAAATA--AATAT------------ATTTCCCACAAATTAAAGAT---AATATATTTATTT---------------TAAAGTAATTTATAATTAAAT---TGAA--------------------TATGGGCCCTA----C---------TACAAAGACTTT
droPer1	super_1:5889084-5889218 +	GATAGGTT---------------------------T-----------------TTGCAACACAA-----------------------------------------AAAATAAACA--AAGATTAGTTTCCAGTTAT----TAAATATTAATATA---TATATTTGAAGCA---------------GAAATATGTATATTTTAGAAT---CGTT--------------------TCTGTGGGGTTTTCATT-GCAATACCTTT--TATGAA
droWil1	scaffold_180698:8557325-8557469 -	ACCAAAGAGAA----ATATCTCAAACTCAAACTCACAAACAAGACACATCAGCGC--------------------------------GCAAGAGCAACAACGCAAAGAACAAT--------------------------------------------TAAACAATTCTAT---------------TAAATTGATCGAAAATATAAA---CATT--------------------TCA-CAGCATAACAACA-ACAAA-----AGAAAAGGA
droVir3	scaffold_12855:7203873-7204022 +	TGAAAATGAAT----AAATA-------------TAT-------------------ATGCTCCAATTAAAATTGAAACTACTATCCGAT--------------------------------------CGAAGGTCTT-TG-TTCAAATTCATTTG---A--GGGGTTTTTC---------------GCACTTTTTGGAAAATCCATC---ACTC--------------------CCCGATGGAAATGGGCT-TCAATGACTTAGTGGGTGG
droMoj3	scaffold_6500:29247639-29247782 -	GGCCAATTAAC----AAACG-------------CAC-------------------GTGCAGCAG-----------------------------------------CTACAACAGC--ATCGTGTGCACACATACAT----TCAAACT-TCTTCT---GGAACATTCTTTTAATCACATCAGCTGTTAGTTTGGTTTAGTTTTGGTA---GATG--------------------G---------CGCTGCA-G------CACTGAATCTAT
droGri2	scaffold_14853:9426729-9426870 +	TCCACAAAGATATCAAAATC--------------TC-----------------AGATACTGCTT-GAAAGTTGACAT---------------------------------------------TT-----CCCTCAT----AGAATA-TCCTTTA---TGTACAGTAATAT---------------GAGT--GTTTGTATTTGAAGTCT-TCTT--------------------TTTCATCGTCATTTATCTCCATCCTCTCTTTGACTGC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:18867030-18867176 -	TAAAAATAAAAAAATGCTCGATTGCTGCAACTAAGAAACAAATATTTTCAGTTGTTCATTGCAAATTAATTTATGTACATTGCTATGAAATCAATTGAAAATATAATTGTATCCTAGGCTTATCAGCTGCAATGCCTCTATGAAGGG
droSim1	chr2L:18557325-18557471 -	TAAAAATAACAAAACGCTCATTTGCTGCAAATAAGAAACAAATATTTTCAGTTGTTCATTGCAAGTTAATTTATGTACATTGCTATGAAATCAATTGAAAATATAATTGTATCCCAGGCTTATCAGCTGCAATCCCCCCAAGAAGGG
droSec1	super_7:2494148-2494294 -	TAAAAATAACAAAACGTTCATTTGCTGATAATAAGAAACAAATATCTTAAGATGTTCATTGCAAATTAATTTATGTACATTGCTATGAAATCAATTGAAAATATAATTGTATCCTAGGCTTATCAGCTGCAATCCCCCCAAGAAGGG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TAAAAATAACAAAACGCTCATTTG-----------CTGCAAATAAGAAACAAATATTTTCAGTTGTTCATTGCAAGTTAATTTATGTACATTGCTATGAAATCAATTGAAAATATAATTGTATCCCAGGCTTATCAGCTGCAATCCCCCCAAGAAGGG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

TTAAAATAAAAACATTTCATATTTAAATTACAAGGTTTTATATTTTAAATAAATATATT--------TCCCACAAATTAAAGATAATATATTTATTTTAAAGTAATTTATAATTAAATTGAATATGGGCCCT------------ACTACAAAGACTTT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

-27.4	-27.0	-26.8	-26.7	-26.7	-26.6

droSim1

-28.0	-27.6	-27.4	-27.4	-27.2	-27.2

droSec1

-17.6	-17.3	-17.2	-17.2	-17.0	-17.0

droYak2

-26.2	-26.0	-26.0	-25.8	-25.7	-25.7

droEre2

-18.2	-17.7	-17.7	-17.2	-17.2	-17.2

droAna3

-9.4	-8.9	-8.9	-8.8	-8.7	-8.6

dp4

-15.9	-15.9	-15.9	-15.9	-15.9	-15.9

droPer1

-15.2	-15.1	-15.0	-15.0	-14.9	-14.8

droWil1

-3.1	-2.9	-2.9	-2.7	-2.6	-2.6

droVir3

-20.2	-19.9	-19.8	-19.7	-19.7	-19.5

droMoj3

-21.0	-20.9	-20.9	-20.8	-20.7	-20.7

droGri2

-11.9	-11.6	-11.5	-11.4	-11.3	-11.3

Generated: 01/05/2013 at 05:22 PM