Secondary structure and small RNA-seq evidence for dme-mir-927

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:15859965-15860086 -	GGCAATATTAAATTGTGGTTGCTGTAGAGTTTTAGAATTCCTACGCTTTACCGTGGCA-TACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTACCGATCCATTATC-------------ATGTTAAAAAAAA
droSim1	chrX:12269402-12269519 -	GGCCATATTAAATTGTGGATGCTGTAGAGTTTTAGAATTCCTACGCTTTACCGTGGCA-TACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATCGATCCATTATC-------------ATGTTATTA----
droSec1	super_37:439539-439656 -	GGCAATATTAAATTGTGGATGCTGTAGAGTTTTAGAATTCCTACGCTTTACCGTCGCA-TACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATCGATCCATTATC-------------ATGTTATTA----
droYak2	chrX:10049094-10049217 -	GGCAGTTAAAAATTGTGGGCGCTGTAGAGTTTTAGAATTCCTACGCTTTACCGTCGCA-TACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTACCGATCCATTACCATTAC-------CATATTATTA----
droEre2	scaffold_4690:11188754-11188871 +	GGCAATAATAAATTGTGGGTGCTGCAGAGTTTTAGAATTCCTACGCTTTACCGTGGCA-TACGAAATTCGGCAAAGCGTTTGGATTCTGAAACTCTACCGATCCATTATC-------------ATATTATTA----
droAna3	scaffold_13250:3108664-3108783 +	TAA--------AAAAAGGGTATTGTGGAGTTTTAGAATTCCTACGCTTTACCGTTGCA-TATGAAATTAGGCAAAGCGTTTGGATTCTGGAACCCTATGTATTCATTTTTATAATGTGTTTTCA---TAAAT----
dp4	Unknown_group_79:17437-17552 +	ATAGATAG-ATAACGAGGATATTGTAGTGTTTTAGAATTCCTACGCTTTACCGTTGCAAAACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATGAGTCTGCATTC-------------A--ACAAAA----
droPer1	super_192:48564-48679 +	ATAGATAG-ATAACGAGGATATTGTAGTGTTTTAGAATTCCTACGCTTTACCGTTGCAAAACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATGAGTCTGCATTC-------------A--ACAAAA----
droWil1	scaffold_180777:2521614-2521709 -	CACAATCTGACATTG--------GTAGCGTTTTAGAATTCCTACGCTTTACCGTCGCC-TACGAAACTCGGCAAAGCGTTTGGATTCTGAAACATTATCTCTGCA-------------------------------
droVir3	scaffold_12970:3343518-3343635 -	AACTTTT---AATAATGTCCATCGTATCGTTTTAGAATTCCTACGCTTTACCGTCGTG-TCCGAAATTTGGCAAAGCGTTTGGATTCTGAAACGATATATGGTCGGTAAC-------------A--ACAAAAACAG
droMoj3	scaffold_6473:7790778-7790858 -	---------------TGGCCAGCGTATCGTTTTAGAATTCCTACGCTTTACCGTCGTA-TACGCAATTTGGCAAAGCGTTTGGATTCTGAAACAATA---------------------------------------
droGri2	scaffold_15203:10526906-10527015 +	GATAGTAGTTTACCGTGACTATTGTATTGTTTTAGAATTCCTACGCTTTACCGTCGTA-TACGAAATTTGGCAAAGCGTTTGGATTCTGAAACGGTATGTGGTCAGAAAC-------------A------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:15859965-15860086 -	GGCAATATTAAATTGTGGTTGCTGTAGAGTTTTAGAATTCCTACGCTTTACCGTGGCA-TACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTACCGATCCATTATC-------------ATGTTAAAAAAAA
droSim1	chrX:12269402-12269519 -	GGCCATATTAAATTGTGGATGCTGTAGAGTTTTAGAATTCCTACGCTTTACCGTGGCA-TACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATCGATCCATTATC-------------ATGTTATTA----
droSec1	super_37:439539-439656 -	GGCAATATTAAATTGTGGATGCTGTAGAGTTTTAGAATTCCTACGCTTTACCGTCGCA-TACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATCGATCCATTATC-------------ATGTTATTA----
droYak2	chrX:10049094-10049217 -	GGCAGTTAAAAATTGTGGGCGCTGTAGAGTTTTAGAATTCCTACGCTTTACCGTCGCA-TACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTACCGATCCATTACCATTAC-------CATATTATTA----
droEre2	scaffold_4690:11188754-11188871 +	GGCAATAATAAATTGTGGGTGCTGCAGAGTTTTAGAATTCCTACGCTTTACCGTGGCA-TACGAAATTCGGCAAAGCGTTTGGATTCTGAAACTCTACCGATCCATTATC-------------ATATTATTA----
droAna3	scaffold_13250:3108664-3108783 +	TAA--------AAAAAGGGTATTGTGGAGTTTTAGAATTCCTACGCTTTACCGTTGCA-TATGAAATTAGGCAAAGCGTTTGGATTCTGGAACCCTATGTATTCATTTTTATAATGTGTTTTCA---TAAAT----
dp4	Unknown_group_79:17437-17552 +	ATAGATAG-ATAACGAGGATATTGTAGTGTTTTAGAATTCCTACGCTTTACCGTTGCAAAACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATGAGTCTGCATTC-------------A--ACAAAA----
droPer1	super_192:48564-48679 +	ATAGATAG-ATAACGAGGATATTGTAGTGTTTTAGAATTCCTACGCTTTACCGTTGCAAAACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATGAGTCTGCATTC-------------A--ACAAAA----
droWil1	scaffold_180777:2521614-2521709 -	CACAATCTGACATTG--------GTAGCGTTTTAGAATTCCTACGCTTTACCGTCGCC-TACGAAACTCGGCAAAGCGTTTGGATTCTGAAACATTATCTCTGCA-------------------------------
droVir3	scaffold_12970:3343518-3343635 -	AACTTTT---AATAATGTCCATCGTATCGTTTTAGAATTCCTACGCTTTACCGTCGTG-TCCGAAATTTGGCAAAGCGTTTGGATTCTGAAACGATATATGGTCGGTAAC-------------A--ACAAAAACAG
droMoj3	scaffold_6473:7790778-7790858 -	---------------TGGCCAGCGTATCGTTTTAGAATTCCTACGCTTTACCGTCGTA-TACGCAATTTGGCAAAGCGTTTGGATTCTGAAACAATA---------------------------------------
droGri2	scaffold_15203:10526906-10527015 +	GATAGTAGTTTACCGTGACTATTGTATTGTTTTAGAATTCCTACGCTTTACCGTCGTA-TACGAAATTTGGCAAAGCGTTTGGATTCTGAAACGGTATGTGGTCAGAAAC-------------A------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GGCCATATTAAATTGTGGATGCTGTAGAGTTTTAGAATTCCTACGCTTTACCGTGGCA-TACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATCGATCCATTATCATGTTATT----A	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..............................TTTAGAATTCCTACGCTTTACC.......................................................................	22	1	152.00	152	152
.......................................................................CAAAGCGTTTGGATTCTGAAAC..............................	22	1	20.00	20	20
....................................................GTGGCA-TACGAAATTCGG....................................................	18	1	17.00	17	17
..............................TTTAGAATTCCTACGCTTTACCG......................................................................	23	1	11.00	11	11
..............................TTTAGAATTCCTACGCTTTAC........................................................................	21	1	6.00	6	6
......................................................................GCAAAGCGTTTGGATTCTGAAA...............................	22	1	2.00	2	2
.......................................................................CAAAGCGTTTGGATTCTGAAA...............................	21	1	1.00	1	1

dp4

ATAGATAGA-TAACGAGGATATTGTAGTGTTTTAGAATTCCTACGCTTTACCGTTGCAAAACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATGAGTCTGCATTC------AACAAAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..............................TTTAGAATTCCTACGCTTTACC.......................................................................	22	1	527.00	527	228	299
.......................................................................CAAAGCGTTTGGATTCTGAAAC..............................	22	1	435.00	435	112	323
..............................TTTAGAATTCCTACGCTTTAC........................................................................	21	1	197.00	197	36	161
..............................TTTAGAATTCCTACGCTTTACCG......................................................................	23	1	26.00	26	21	5
.......................................................................CAAAGCGTTTGGATTCTGAAA...............................	21	1	19.00	19	11	8
..............................TTTAGAATTCCTACGCTTTA.........................................................................	20	1	12.00	12	2	10
......................................................................GCAAAGCGTTTGGATTCTGAAAC..............................	23	1	12.00	12	3	9
.......................................................................CAAAGCGTTTGGATTCTGAAACC.............................	23	1	10.00	10	4	6
..............................TTTAGAATTCCTACGCTTT..........................................................................	19	1	8.00	8	2	6
.......................................................................CAAAGCGTTTGGATTCTGAA................................	20	1	8.00	8	2	6
..............................TTTAGAATTCCTACGCTTTACCGT.....................................................................	24	1	7.00	7	1	6
.......................................................................CAAAGCGTTTGGATTCTGA.................................	19	1	4.00	4	2	2
........................................................................AAAGCGTTTGGATTCTGAAAC..............................	21	1	2.00	2	1	1
....................................................GTTGCAAAACGAAATTCGG....................................................	19	1	2.00	2	1	1
......................................................................GCAAAGCGTTTGGATTCTGAA................................	21	1	2.00	2	1	1
...............................TTAGAATTCCTACGCTTTAC........................................................................	20	1	1.00	1	0	1
...............................TTAGAATTCCTACGCTTTACC.......................................................................	21	1	1.00	1	0	1
................................TAGAATTCCTACGCTTTAC........................................................................	19	1	1.00	1	0	1
...........AACGAGGATATTGTAGTGT.............................................................................................	19	1	1.00	1	0	1
.......GA-TAACGAGGATATTGTAGTGT.............................................................................................	22	1	1.00	1	1	0
..............................................................GAAATTCGGCAAAGCGTTTGGATTCT...................................	26	1	1.00	1	0	1
..........TAACGAGGATATTGTAGTGT.............................................................................................	20	1	1.00	1	0	1

Secondary Structure

dm3

-34.6	-34.1	-33.6

droSim1

-35.2	-34.6	-34.2

droSec1

-36.7	-36.1

droYak2

-37.1	-36.5

droEre2

-36.6	-36.0	-35.6

droAna3

-31.8	-31.5

dp4

-33.7	-33.0	-32.9	-32.8

droPer1

-33.7	-33.0	-32.9	-32.8

droWil1

-29.8

droVir3

-39.9	-38.9

droMoj3

-25.0	-25.0	-24.8	-24.8	-24.0	-24.0

droGri2

-38.8	-38.8	-38.5	-37.8

Generated: 01/05/2013 at 05:30 PM