Secondary structure and small RNA-seq evidence for dme-mir-6-1

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:15548493-15548604 -	AACTTAA-----------------------TCACAGCCTTTAATGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATATACC---ATATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CTAACATC----------------ATT
droSim1	chr2R:14253929-14254041 -	AACTTAA-----------------------TCACAGCCTTTAAAGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATATACC---ATATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAG-GCATTTTACATC----------------ATT
droSec1	super_1:13063224-13063336 -	AACTTAA-----------------------TCACAGCCTTTAAAGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATATACC---ATATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAG-GCATTTTACATC----------------ATT
droYak2	chr2R:13624186-13624297 +	AGTTTAA-----------------------TCACAGCCTTTAACGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATAACAA---ATATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CTAACATC----------------ATT
droEre2	scaffold_4845:9748744-9748855 -	AGCTAAA-----------------------TCGCAGCCTTTAAAGTAGAGGGAATAGTTGCCGTGCTGTAAGTTAATATATC---ATATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CTAACATC----------------ATC
droAna3	scaffold_13266:9731810-9731917 +	---------------------------------CCGCCTTTAAAGTAGAGAGAATAGTGGCTGTGCTGTAAGTTT------C--AAAATCTATATCACAGTGGCTGTTCTTTTTGCACCTAAAGTGC--CAAACAGCCAAACCCGAG------AAT
dp4	chr3:12677072-12677187 -	AC-----------------------------ACCAGCCTTTGAAGTAGAGAGAATAGTTGCTGTGCTATATGTCC----TTCG-ACTCTATATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CAAACAGCCAAG-----GAATCGCGTT
droPer1	super_2:8906485-8906600 +	AC-----------------------------ACCAGCCTTTGAAGTAGAGAGAATAGTTGCTGTGCTATATGTCC----TTCG-ACTCTATATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CAAACAGCCAAG-----GAATCGCGTT
droWil1	scaffold_180701:1651298-1651414 -	T---CAA-----------------------C--CAGCCTTTAAAGTAGAGAGAATAGTTGCTGTGTTTTATGCCC----TTTT-CAATTTCATATCACAGTGGCTGTTCTTTTTGTGCCTAAAGTGC--CCCACAACAACA-----ACAACAACAC
droVir3	scaffold_12875:4112589-4112722 +	GACTTAAAACTATATCGCCCAGTTATCTGTTTATAGCCTTTAAAGTAGAGAGAATAGACGCTGTGCTGTATGTTT----TGCGTATGGTCTATATCACAGTGGCTGTTCTTTTTGTACCTGAAGCGC--CGTACAAC----------------GTT
droMoj3	scaffold_6496:20936294-20936412 -	TATTTATTTCTCTAGTGT-----------TTTTTCGCCTTTAAAGTAGAGAGAATAGATGCTGTG-----AGTATATCTGTT---GCATTTATATCACAGTGGCTGTTCTTTTTGTACCTAAATGGC--CAGACAGC----------------ATT
droGri2	scaffold_5621:3389-3488 +	A----------------------------------GCCTTTAATGTAAAGAGAATAGATGCTGTGCTGTATGTTG----AACGTATTGTCTATATCACAGTGGCTGTTCTTTTTGTACCAAAAGTGC--CGTACAAC----------------AAA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:15548493-15548604 -	AACTTAA-----------------------TCACAGCCTTTAATGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATATACC---ATATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CTAACATC----------------ATT
droSim1	chr2R:14253929-14254041 -	AACTTAA-----------------------TCACAGCCTTTAAAGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATATACC---ATATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAG-GCATTTTACATC----------------ATT
droSec1	super_1:13063224-13063336 -	AACTTAA-----------------------TCACAGCCTTTAAAGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATATACC---ATATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAG-GCATTTTACATC----------------ATT
droYak2	chr2R:13624186-13624297 +	AGTTTAA-----------------------TCACAGCCTTTAACGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATAACAA---ATATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CTAACATC----------------ATT
droEre2	scaffold_4845:9748744-9748855 -	AGCTAAA-----------------------TCGCAGCCTTTAAAGTAGAGGGAATAGTTGCCGTGCTGTAAGTTAATATATC---ATATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CTAACATC----------------ATC
droAna3	scaffold_13266:9731810-9731917 +	---------------------------------CCGCCTTTAAAGTAGAGAGAATAGTGGCTGTGCTGTAAGTTT------C--AAAATCTATATCACAGTGGCTGTTCTTTTTGCACCTAAAGTGC--CAAACAGCCAAACCCGAG------AAT
dp4	chr3:12677072-12677187 -	AC-----------------------------ACCAGCCTTTGAAGTAGAGAGAATAGTTGCTGTGCTATATGTCC----TTCG-ACTCTATATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CAAACAGCCAAG-----GAATCGCGTT
droPer1	super_2:8906485-8906600 +	AC-----------------------------ACCAGCCTTTGAAGTAGAGAGAATAGTTGCTGTGCTATATGTCC----TTCG-ACTCTATATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CAAACAGCCAAG-----GAATCGCGTT
droWil1	scaffold_180701:1651298-1651414 -	T---CAA-----------------------C--CAGCCTTTAAAGTAGAGAGAATAGTTGCTGTGTTTTATGCCC----TTTT-CAATTTCATATCACAGTGGCTGTTCTTTTTGTGCCTAAAGTGC--CCCACAACAACA-----ACAACAACAC
droVir3	scaffold_12875:4112589-4112722 +	GACTTAAAACTATATCGCCCAGTTATCTGTTTATAGCCTTTAAAGTAGAGAGAATAGACGCTGTGCTGTATGTTT----TGCGTATGGTCTATATCACAGTGGCTGTTCTTTTTGTACCTGAAGCGC--CGTACAAC----------------GTT
droMoj3	scaffold_6496:20936294-20936412 -	TATTTATTTCTCTAGTGT-----------TTTTTCGCCTTTAAAGTAGAGAGAATAGATGCTGTG-----AGTATATCTGTT---GCATTTATATCACAGTGGCTGTTCTTTTTGTACCTAAATGGC--CAGACAGC----------------ATT
droGri2	scaffold_5621:3389-3488 +	A----------------------------------GCCTTTAATGTAAAGAGAATAGATGCTGTGCTGTATGTTG----AACGTATTGTCTATATCACAGTGGCTGTTCTTTTTGTACCAAAAGTGC--CGTACAAC----------------AAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AACTTAATCACAGCCTTTAAAGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATATACCATATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAG-GCA--------------TTTTACATCATT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.........................AGGGAATAGTTGCTGTGCTGTA.................................................................................	22	1	15.00	15	15
.........................AGGGAATAGTTGCTGTGCTG...................................................................................	20	1	5.00	5	5
.........................AGGGAATAGTTGCTGTGCTGT..................................................................................	21	1	3.00	3	3
..........................GGGAATAGTTGCTGTGCTGTA.................................................................................	21	1	1.00	1	1
......................TAGAGGGAATAGTTGCTGTGCT....................................................................................	22	1	1.00	1	1
.........................AGGGAATAGTTGCTGTGCTGTAA................................................................................	23	1	1.00	1	1
..........................GGGAATAGTTGCTGTGCTG...................................................................................	19	1	1.00	1	1

dp4

AC------ACCAGCCTTTGAAGTAGAGAGAATAGTTGCTGTGCTATATGTCCTTCGAC--TCTATATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGCCAAACAGCCAAGGAAT-----CGCGTT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.........................AGAGAATAGTTGCTGTGCTATA.................................................................................	22	1	739.00	739	739	0
.........................AGAGAATAGTTGCTGTGCTAT..................................................................................	21	1	262.00	262	262	0
.........................AGAGAATAGTTGCTGTGCTATAT................................................................................	23	1	48.00	48	48	0
.........................AGAGAATAGTTGCTGTGCTA...................................................................................	20	1	26.00	26	26	0
..........................GAGAATAGTTGCTGTGCTATAT................................................................................	22	1	16.00	16	16	0
..........................GAGAATAGTTGCTGTGCTAT..................................................................................	20	1	7.00	7	7	0
..........................GAGAATAGTTGCTGTGCTATA.................................................................................	21	1	6.00	6	6	0
..........................GAGAATAGTTGCTGTGCTA...................................................................................	19	1	1.00	1	1	0
...........................AGAATAGTTGCTGTGCTATAT................................................................................	21	1	1.00	1	1	0
.........................AGAGAATAGTTGCTGTGCT....................................................................................	19	1	1.00	1	1	0

Secondary Structure

dm3

dG=-24.2, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-23.2, p-value=0.009901

droSim1

dG=-24.2, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-23.4, p-value=0.009901

droSec1

dG=-24.2, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-23.4, p-value=0.009901

droYak2

dG=-24.2, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-23.4, p-value=0.009901

droEre2

dG=-19.5, p-value=0.009901	dG=-19.3, p-value=0.009901	dG=-19.1, p-value=0.009901	dG=-18.8, p-value=0.009901	dG=-18.7, p-value=0.009901

droAna3

dG=-30.0, p-value=0.009901	dG=-29.3, p-value=0.009901

dp4

dG=-28.7, p-value=0.009901	dG=-28.0, p-value=0.009901

droPer1

dG=-28.7, p-value=0.009901	dG=-28.0, p-value=0.009901

droWil1

dG=-23.9, p-value=0.009901	dG=-23.2, p-value=0.009901

droVir3

dG=-26.2, p-value=0.009901	dG=-25.6, p-value=0.009901	dG=-25.5, p-value=0.009901

droMoj3

dG=-23.9, p-value=0.009901	dG=-23.3, p-value=0.009901	dG=-23.3, p-value=0.009901	dG=-23.2, p-value=0.009901

droGri2

dG=-21.3, p-value=0.009901	dG=-21.0, p-value=0.009901	dG=-20.8, p-value=0.009901	dG=-20.7, p-value=0.009901	dG=-20.6, p-value=0.009901

Generated: 03/07/2013 at 06:59 PM