Secondary structure and small RNA-seq evidence for dme-mir-965

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:243020-243156 -	TAATTGTACAATCTGGA-----CA-----ATATTGCTCAACA-TTTTGGGGGGTAAAACTGTACGTTATATGTGCCCTTCTG-TGATATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTATTGCAACGA----------AAAGT-----GTTTTTC
droSim1	chr2L:248245-248381 -	TACTTGTACAATCTGGA-----CA-----AAATTGCTCAACA-TTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCTG-TGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA----------AAAGT-----GGTTTTC
droSec1	super_14:240987-241123 -	TACTTGTACAATCTGGA-----CA-----AAATTGCTCAACA-TTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCTG-TGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA----------AAAGT-----GGTTTTC
droYak2	chr2L:236040-236180 -	TAATTGTACAATCACCATCTGACA-----AAATTGCTCAACA-TTTTAGGGGGTTAAACTGTACGTTATATGTGCCCTTT-T-GTAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAACAGCAACAA----------ATAGT-----GTATTTC
droEre2	scaffold_4929:289337-289472 -	TACTTGTAGAACCTG-A-----CA-----AAATTGCTCAACA-TTTTAGGGGGTGAAACTGTACGTTATATGTGTCCTTCTG-TAAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTACAGCAACAGCAACAA----------AAAGT-----GAATCTT
droAna3	scaffold_12943:4147952-4148086 +	TGGGTTTTCTGG--------------------AAGCTCAACCCTTTTGGGGGGTCAAACTGTACGTTCTATGTGGCAATCTT-AGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAAAGTCAACAAATCTCAACT-AAAGT-----GTT--TT
dp4	chr4_group1:4362148-4362281 +	TCATTTCCCCAT--------------------CTGCTCAAAA-ATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATATT-CGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAA-TCGCAACAACAATTCTA-------GC
droPer1	super_5:848159-848292 -	TCATTTCCCCAT--------------------CTGCTCAAAA-ATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATATT-CGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAA-TCGCAACAACAATTCTA-------GC
droWil1	scaffold_180764:130106-130233 -	TAT--GTAATAAATTAA-----AGAATCAATTCTACACAACA--TTTATGGGGTTAAACTGTACGTTGTATGTGCAAATCTTAAGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGTTAAATCAACAA---------------------------
droVir3	scaffold_12963:8856389-8856513 +	TTAGTGTAGAAAAAGAA-----AAAAACAC--ACACACAAAT-GTTTAGGGGGTCAAACTGTACGTTGTATGTGCAAATG-A-TGAAATTCATAAGCGTATAGCTTTTCCCCTTAAACGTTGATGTGACGACAAC-----------------------------
droMoj3	scaffold_6500:2474475-2474605 -	AATGTGAACAAA--------------------ACACTCAAAT-GTTTAGGGGGTCAAACTGTACGTTGTATGTGTAAACA-A-TGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGGAATCAACAG----------CAATTTAAGCATAGCTA
droGri2	scaffold_15252:12933990-12934109 -	G--------------GA-----AA-----ATAACACTCAAAT-GTTTAGGGGGTCAAACTGTACGTTATATGTGTAAATG-A-AGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGATAGCAACCT----------AAAAA-----GTC--TT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:243020-243156 -	TAATTGTACAATCTGGA-----CA-----ATATTGCTCAACA-TTTTGGGGGGTAAAACTGTACGTTATATGTGCCCTTCTG-TGATATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTATTGCAACGA----------AAAGT-----GTTTTTC
droSim1	chr2L:248245-248381 -	TACTTGTACAATCTGGA-----CA-----AAATTGCTCAACA-TTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCTG-TGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA----------AAAGT-----GGTTTTC
droSec1	super_14:240987-241123 -	TACTTGTACAATCTGGA-----CA-----AAATTGCTCAACA-TTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCTG-TGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA----------AAAGT-----GGTTTTC
droYak2	chr2L:236040-236180 -	TAATTGTACAATCACCATCTGACA-----AAATTGCTCAACA-TTTTAGGGGGTTAAACTGTACGTTATATGTGCCCTTT-T-GTAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAACAGCAACAA----------ATAGT-----GTATTTC
droEre2	scaffold_4929:289337-289472 -	TACTTGTAGAACCTG-A-----CA-----AAATTGCTCAACA-TTTTAGGGGGTGAAACTGTACGTTATATGTGTCCTTCTG-TAAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTACAGCAACAGCAACAA----------AAAGT-----GAATCTT
droAna3	scaffold_12943:4147952-4148086 +	TGGGTTTTCTGG--------------------AAGCTCAACCCTTTTGGGGGGTCAAACTGTACGTTCTATGTGGCAATCTT-AGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAAAGTCAACAAATCTCAACT-AAAGT-----GTT--TT
dp4	chr4_group1:4362148-4362281 +	TCATTTCCCCAT--------------------CTGCTCAAAA-ATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATATT-CGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAA-TCGCAACAACAATTCTA-------GC
droPer1	super_5:848159-848292 -	TCATTTCCCCAT--------------------CTGCTCAAAA-ATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATATT-CGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAA-TCGCAACAACAATTCTA-------GC
droWil1	scaffold_180764:130106-130233 -	TAT--GTAATAAATTAA-----AGAATCAATTCTACACAACA--TTTATGGGGTTAAACTGTACGTTGTATGTGCAAATCTTAAGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGTTAAATCAACAA---------------------------
droVir3	scaffold_12963:8856389-8856513 +	TTAGTGTAGAAAAAGAA-----AAAAACAC--ACACACAAAT-GTTTAGGGGGTCAAACTGTACGTTGTATGTGCAAATG-A-TGAAATTCATAAGCGTATAGCTTTTCCCCTTAAACGTTGATGTGACGACAAC-----------------------------
droMoj3	scaffold_6500:2474475-2474605 -	AATGTGAACAAA--------------------ACACTCAAAT-GTTTAGGGGGTCAAACTGTACGTTGTATGTGTAAACA-A-TGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGGAATCAACAG----------CAATTTAAGCATAGCTA
droGri2	scaffold_15252:12933990-12934109 -	G--------------GA-----AA-----ATAACACTCAAAT-GTTTAGGGGGTCAAACTGTACGTTATATGTGTAAATG-A-AGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGATAGCAACCT----------AAAAA-----GTC--TT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TACTTGTACAATCTGGACAAAATTGCTCAACATTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCTGTGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAAC---------GAAAAGTGGTTTT--C	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
......................................GGGGTGAAACTGTACGTTATATG.......................................................................................	23	1	364.00	364	364
................................................................................TAAGCGTATAGCTTTTCCCCTT..............................................	22	1	263.00	263	263
................................................................................TAAGCGTATAGCTTTTCCCCT...............................................	21	1	25.00	25	25
......................................GGGGTGAAACTGTACGTTATAT........................................................................................	22	1	18.00	18	18
......................................GGGGTGAAACTGTACGTTATA.........................................................................................	21	1	15.00	15	15
................................................................................TAAGCGTATAGCTTTTCCCCTTA.............................................	23	1	6.00	6	6
.............................................................TGCCCTTCTGTGAAATTCA....................................................................	19	1	2.00	2	2
.....................................GGGGGTGAAACTGTACGTTATATG.......................................................................................	24	1	2.00	2	2
......................................GGGGTGAAACTGTACGTTATATGT......................................................................................	24	1	2.00	2	2
................................................................................TAAGCGTATAGCTTTTCCCCTTAA............................................	24	1	2.00	2	2
......................................GGGGTGAAACTGTACGTTA...........................................................................................	19	1	2.00	2	2
.........................................GTGAAACTGTACGTTATAT........................................................................................	19	1	1.00	1	1
...................AAATTGCTCAACATTTTGG..............................................................................................................	19	1	1.00	1	1
.................................................................................AAGCGTATAGCTTTTCCCCTT..............................................	21	1	1.00	1	1
......................................GGGGTGAAACTGTACGTTAT..........................................................................................	20	1	1.00	1	1
......................................GGGGTGAAACTGTACGTTATATGTG.....................................................................................	25	1	1.00	1	1
................................................................................TAAGCGTATAGCTTTTCCCCTTAAAA..........................................	26	1	1.00	1	1

dp4

TCATTTCCCCATCT----------GCTCAAAAATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATATTCGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAATCGCAACAACAA----TTCTAGC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
................................................................................TAAGCGTATAGCTTTTCCCCTT..............................................	22	1	580.00	580	379	201
......................................GGGGTCAAACTGTACGTTCTATG.......................................................................................	23	1	91.00	91	87	4
................................................................................TAAGCGTATAGCTTTTCCCCT...............................................	21	1	83.00	83	61	22
................................................................................TAAGCGTATAGCTTTTCCCCTTA.............................................	23	1	16.00	16	15	1
................................................................................TAAGCGTATAGCTTTTCCCC................................................	20	1	6.00	6	2	4
.............................................................TGACAATATTCGAAATTCA....................................................................	19	1	6.00	6	5	1
................................................................................TAAGCGTATAGCTTTTCCCCTTAA............................................	24	1	5.00	5	5	0
.................................................................................AAGCGTATAGCTTTTCCCCTT..............................................	21	1	4.00	4	1	3
......................................GGGGTCAAACTGTACGTTCTAT........................................................................................	22	1	2.00	2	2	0
......................................GGGGTCAAACTGTACGTTCTATGT......................................................................................	24	1	1.00	1	1	0
................................................................................TAAGCGTATAGCTTTTCCCCTTAAA...........................................	25	1	1.00	1	1	0
......................................GGGGTCAAACTGTACGTTCTA.........................................................................................	21	1	1.00	1	1	0
.....................................AGGGGTCAAACTGTACGTTCTATG.......................................................................................	24	1	1.00	1	1	0

Secondary Structure

dm3

dG=-24.8, p-value=0.009901	dG=-24.5, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-23.9, p-value=0.009901

droSim1

dG=-25.4, p-value=0.009901	dG=-25.2, p-value=0.009901	dG=-24.8, p-value=0.009901	dG=-24.5, p-value=0.009901

droSec1

dG=-25.4, p-value=0.009901	dG=-25.2, p-value=0.009901	dG=-24.8, p-value=0.009901	dG=-24.5, p-value=0.009901

droYak2

dG=-25.2, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.3, p-value=0.009901

droEre2

dG=-25.8, p-value=0.009901	dG=-25.6, p-value=0.009901	dG=-24.9, p-value=0.009901

droAna3

dG=-23.7, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.1, p-value=0.009901	dG=-23.0, p-value=0.009901	dG=-22.8, p-value=0.009901

dp4

dG=-24.5, p-value=0.009901	dG=-24.5, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-24.0, p-value=0.009901

droPer1

dG=-24.5, p-value=0.009901	dG=-24.5, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-24.0, p-value=0.009901

droWil1

dG=-20.8, p-value=0.009901	dG=-20.4, p-value=0.009901	dG=-20.3, p-value=0.009901	dG=-19.9, p-value=0.009901	dG=-19.8, p-value=0.009901

droVir3

dG=-23.6, p-value=0.009901	dG=-23.3, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.1, p-value=0.009901	dG=-23.0, p-value=0.009901

droMoj3

dG=-23.8, p-value=0.009901	dG=-23.6, p-value=0.009901	dG=-23.3, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.1, p-value=0.009901

droGri2

dG=-24.3, p-value=0.009901	dG=-24.2, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.7, p-value=0.009901	dG=-23.7, p-value=0.009901

Generated: 03/07/2013 at 07:12 PM