Secondary structure and small RNA-seq evidence for dme-mir-282

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:3251007-3251133 +	CCGTTCTTT---------AACTATAGTTTCCTTCTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTCGAA-AGCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACAATCAGC------------------GAAAACGGA
droSim1	chr3L:2784381-2784507 +	CCGTTCTTA---------AACTAAAGTTTCCTTTTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTCGAA-AGCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACAATCAGC------------------GAAAACGGA
droSec1	super_2:3244745-3244871 +	CCGTTCTTA---------AAATAAAGTTTCCTTTTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTCGAA-AGCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGTGAACAATCAGC------------------GAAAACGGA
droYak2	chr3L:3795918-3796050 +	TCGTTCTATATCCGTTATAT---CAGTTTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TACGAA-AGCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGTGAAAAATCAGC------------------GAAAACGGA
droEre2	scaffold_4784:5933708-5933834 +	TCGTTCTAT---------CACCACAGTTTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTCAAA-AGCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACAAGCAGC------------------GAAAACGGA
droAna3	scaffold_13337:7556585-7556720 +	CCGTTCTAA-TTCGAAA-ATCGAAAATTTCCTTATAGATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTCGAA-AGTCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGACAAGACATC----------------ACAAAAACGGA
dp4	chrXR_group8:3299974-3300083 -	---------------------------TGCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTTGAAAACCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGAAGAAATGCATC------------------AAAAGCGGA
droPer1	super_65:103931-104040 -	---------------------------TGCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTTGAAAACCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGAAGAAATGCATC------------------AAAAGCGGA
droWil1	scaffold_181136:1999668-1999787 +	TTTTCCTTTAT--GTAA-TATTAATATATCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTTGGA------TTCAGACATAGCCTATGAGAGGTTAGGTGTACCAAGGAGAAAATACAAC------------------A--------
droVir3	scaffold_12758:910696-910814 -	GCGTCCGAC--------------AAATTTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTCGAT-ATACGGTCAGACATAGCCTATGAGAGGTTAGGTGTACCAAGGGG-ACAAGCAGC------------------GAGGGCG--
droMoj3	scaffold_6680:1963284-1963406 -	ATTTTTTTT-TGCG------GT-GCATTTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTTGAT-ATAAGATCAGACATAGCCTATGAGAGGTTAGGTGTAGCAAGGGG-TCAAACAGC------------------AGA----GA
droGri2	scaffold_15110:607073-607202 +	---------------------------TTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCACTTTTTCA-ATTCAATCAGACATAGCCTATGAGAGGTTAGGTGTACAAATGGATCAAAGCAACAAGGCTGCTGTCGGGGACTAAAAATGA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:3251007-3251133 +	CCGTTCTTT---------AACTATAGTTTCCTTCTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTCGAA-AGCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACAATCAGC------------------GAAAACGGA
droSim1	chr3L:2784381-2784507 +	CCGTTCTTA---------AACTAAAGTTTCCTTTTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTCGAA-AGCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACAATCAGC------------------GAAAACGGA
droSec1	super_2:3244745-3244871 +	CCGTTCTTA---------AAATAAAGTTTCCTTTTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTCGAA-AGCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGTGAACAATCAGC------------------GAAAACGGA
droYak2	chr3L:3795918-3796050 +	TCGTTCTATATCCGTTATAT---CAGTTTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TACGAA-AGCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGTGAAAAATCAGC------------------GAAAACGGA
droEre2	scaffold_4784:5933708-5933834 +	TCGTTCTAT---------CACCACAGTTTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTCAAA-AGCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACAAGCAGC------------------GAAAACGGA
droAna3	scaffold_13337:7556585-7556720 +	CCGTTCTAA-TTCGAAA-ATCGAAAATTTCCTTATAGATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTCGAA-AGTCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGACAAGACATC----------------ACAAAAACGGA
dp4	chrXR_group8:3299974-3300083 -	---------------------------TGCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTTGAAAACCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGAAGAAATGCATC------------------AAAAGCGGA
droPer1	super_65:103931-104040 -	---------------------------TGCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTTGAAAACCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGAAGAAATGCATC------------------AAAAGCGGA
droWil1	scaffold_181136:1999668-1999787 +	TTTTCCTTTAT--GTAA-TATTAATATATCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTTGGA------TTCAGACATAGCCTATGAGAGGTTAGGTGTACCAAGGAGAAAATACAAC------------------A--------
droVir3	scaffold_12758:910696-910814 -	GCGTCCGAC--------------AAATTTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTCGAT-ATACGGTCAGACATAGCCTATGAGAGGTTAGGTGTACCAAGGGG-ACAAGCAGC------------------GAGGGCG--
droMoj3	scaffold_6680:1963284-1963406 -	ATTTTTTTT-TGCG------GT-GCATTTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCA--TTTGAT-ATAAGATCAGACATAGCCTATGAGAGGTTAGGTGTAGCAAGGGG-TCAAACAGC------------------AGA----GA
droGri2	scaffold_15110:607073-607202 +	---------------------------TTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCACTTTTTCA-ATTCAATCAGACATAGCCTATGAGAGGTTAGGTGTACAAATGGATCAAAGCAACAAGGCTGCTGTCGGGGACTAAAAATGA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CCGTTCTTAAACTAAAGTTTCCTTTTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCGAAAGC-CGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACAATCAGCGAAAACGGA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...............................TAGCCTCTACTAGGCTTTGTCT...........................................................................	22	2	345.00	690	690
...........................................................................ACATAGCCTATAAGAGGTTAGG...............................	22	2	197.00	394	394
...........................................................................ACATAGCCTATAAGAGGTTAGGT..............................	23	2	8.50	17	17
...................................CTCTACTAGGCTTTGTCT...........................................................................	18	2	1.50	3	3
..........................................................................GACATAGCCTATAAGAGGTTAGG...............................	23	2	1.50	3	3
...............................TAGCCTCTACTAGGCTTTGT.............................................................................	20	2	1.50	3	3
...........................................................................ACATAGCCTATAAGAGGTTA.................................	20	2	1.00	2	2
..............................CTAGCCTCTACTAGGCTTTGTCT...........................................................................	23	2	1.00	2	2
..................................CCTCTACTAGGCTTTGTCT...........................................................................	19	2	0.50	1	1
.....................................................GTGCATTCGAAAGC-CGATCAG.....................................................	21	2	0.50	1	1

dp4

------------------TGCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTTGAAAACCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGAAGAAATGCATCAAAAGCGGA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...........................................................................ACATAGCCTATAAGAGGTTAGG...............................	22	2	56.50	113	113	0
...........................................................................ACATAGCCTATAAGAGGTTAGGT..............................	23	2	19.00	38	6	32
...............................TAGCCTCTACTAGGCTTTGTC............................................................................	21	2	8.00	16	16	0
...................................CTCTACTAGGCTTTGTCT...........................................................................	18	2	4.50	9	9	0
..........................................................................GACATAGCCTATAAGAGGTTAGG...............................	23	2	2.50	5	5	0
..........................................................................GACATAGCCTATAAGAGGTTAG................................	22	2	2.00	4	4	0
..............................CTAGCCTCTACTAGGCTTTGTCT...........................................................................	23	2	2.00	4	4	0
...............................TAGCCTCTACTAGGCTTTGT.............................................................................	20	2	1.50	3	3	0
.................................GCCTCTACTAGGCTTTGTCT...........................................................................	20	2	0.50	1	0	1
..............................CTAGCCTCTACTAGGCTTTGTCTG..........................................................................	24	2	0.50	1	0	1
................................AGCCTCTACTAGGCTTTGTCTGT.........................................................................	23	2	0.50	1	1	0
...............................TAGCCTCTACTAGGCTTTGTCTG..........................................................................	23	2	0.50	1	1	0
.....................................................GTGCATTTGAAAACCCGATCA......................................................	21	2	0.50	1	1	0
..........................................................................GACATAGCCTATAAGAGGTTAGGT..............................	24	2	0.50	1	1	0

Secondary Structure

dm3

dG=-34.2, p-value=0.009901	dG=-34.1, p-value=0.009901

droSim1

dG=-34.2, p-value=0.009901	dG=-34.1, p-value=0.009901

droSec1

dG=-34.2, p-value=0.009901	dG=-34.1, p-value=0.009901

droYak2

dG=-34.2, p-value=0.009901

droEre2

dG=-34.2, p-value=0.009901

droAna3

dG=-34.8, p-value=0.009901	dG=-34.1, p-value=0.009901

dp4

dG=-33.1, p-value=0.009901	dG=-32.3, p-value=0.009901

droPer1

dG=-33.1, p-value=0.009901	dG=-32.3, p-value=0.009901

droWil1

dG=-33.9, p-value=0.009901

droVir3

dG=-33.9, p-value=0.009901	dG=-33.8, p-value=0.009901	dG=-33.5, p-value=0.009901	dG=-33.2, p-value=0.009901

droMoj3

dG=-34.4, p-value=0.009901	dG=-33.6, p-value=0.009901	dG=-33.5, p-value=0.009901

droGri2

dG=-33.4, p-value=0.009901

Generated: 03/07/2013 at 05:03 PM