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

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:20487426-20487546 +	AAAGACC-----------------ATCCCAT--ATTCAGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGT-TAT-ATTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAGACATCG----------------------------------G----AGTTGAAA
droSim1	chr2L:20052694-20052814 +	AAAGACC-----------------ATCCCAT--CTTCAGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGT-TAT-ACTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAGACATCG----------------------------------G----AGTTGAAA
droSec1	super_18:365651-365771 +	AAGGACC-----------------ATCCCAT--CTTCAGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGT-TAT-ACTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAGACATCG----------------------------------G----AGTTGAAA
droYak2	chr2R:6842709-6842830 +	AAAGAAC-----------------ATCCCAC--CATCAGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATAT-ACTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAGTCATCG----------------------------------G----AGTTGAAA
droEre2	scaffold_4845:3954268-3954372 -	AAGGACC---------------------------TCCAGCCT-GTGAGAGTTCCATGCTTCCTTGCATTCAATAGT-TAT-ACTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAGACATCG----------------------------------G------------
droAna3	scaffold_12916:6985813-6985928 +	AAATATC-------------------------AAGAGAGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATAA-TATCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCAAGACTTCA----------------------------------A----GTTTAAAT
dp4	chr4_group3:7845311-7845422 -	GGAAA--------------------------TCAGAAGGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATAA-CATAAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCAAGACAGCG-----------------------------------------TCTACA
droPer1	super_1:9292009-9292126 -	AAAGACGG-A-------------A-------TCAGAAGGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATAA-CATAAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCAAGACATCG----------------------------------C------CTACAG
droWil1	scaffold_180708:1845911-1846049 +	ATAGATGGTAGATATATATGTAG--------CTACTTGGCCTCTTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATATTAAATAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGTCCGACATCA----------------------------------TCTACAATATAAT
droVir3	scaffold_12963:13613413-13613527 -	TGTGC--------------------------TTACTTGGCCT-TTGAGAGTTCCATGCTTCCTTACATTCAATAGTATTC-AAATAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAAACATCA----------------------------------C----AAAAACAA
droMoj3	scaffold_6500:24555167-24555325 +	TGGGTCTT-AAA--------TTGT-------TCATTGCGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATTT-ATATAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAAGCATCATACCAAACTGTAAAAAAAAACACATTATGAAATTG----TGTTTAAA
droGri2	scaffold_15126:6250403-6250508 +	ATTGT--------------------------TTACTTGGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATAT-AAATAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAAACATC------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:20487426-20487546 +	AAAGACC-----------------ATCCCAT--ATTCAGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGT-TAT-ATTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAGACATCG----------------------------------G----AGTTGAAA
droSim1	chr2L:20052694-20052814 +	AAAGACC-----------------ATCCCAT--CTTCAGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGT-TAT-ACTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAGACATCG----------------------------------G----AGTTGAAA
droSec1	super_18:365651-365771 +	AAGGACC-----------------ATCCCAT--CTTCAGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGT-TAT-ACTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAGACATCG----------------------------------G----AGTTGAAA
droYak2	chr2R:6842709-6842830 +	AAAGAAC-----------------ATCCCAC--CATCAGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATAT-ACTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAGTCATCG----------------------------------G----AGTTGAAA
droEre2	scaffold_4845:3954268-3954372 -	AAGGACC---------------------------TCCAGCCT-GTGAGAGTTCCATGCTTCCTTGCATTCAATAGT-TAT-ACTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAGACATCG----------------------------------G------------
droAna3	scaffold_12916:6985813-6985928 +	AAATATC-------------------------AAGAGAGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATAA-TATCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCAAGACTTCA----------------------------------A----GTTTAAAT
dp4	chr4_group3:7845311-7845422 -	GGAAA--------------------------TCAGAAGGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATAA-CATAAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCAAGACAGCG-----------------------------------------TCTACA
droPer1	super_1:9292009-9292126 -	AAAGACGG-A-------------A-------TCAGAAGGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATAA-CATAAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCAAGACATCG----------------------------------C------CTACAG
droWil1	scaffold_180708:1845911-1846049 +	ATAGATGGTAGATATATATGTAG--------CTACTTGGCCTCTTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATATTAAATAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGTCCGACATCA----------------------------------TCTACAATATAAT
droVir3	scaffold_12963:13613413-13613527 -	TGTGC--------------------------TTACTTGGCCT-TTGAGAGTTCCATGCTTCCTTACATTCAATAGTATTC-AAATAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAAACATCA----------------------------------C----AAAAACAA
droMoj3	scaffold_6500:24555167-24555325 +	TGGGTCTT-AAA--------TTGT-------TCATTGCGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATTT-ATATAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAAGCATCATACCAAACTGTAAAAAAAAACACATTATGAAATTG----TGTTTAAA
droGri2	scaffold_15126:6250403-6250508 +	ATTGT--------------------------TTACTTGGCCT-TTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATAT-AAATAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAAACATC------------------------------------------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AAAGACCATCCCATCTTCA----GCCTTTGAGAGTTCCATGCTTCCTTGCATTCAATAGTTATA--CTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAGACATCGGAGTTGAAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
............................................................................TGGAATGTAAAGAAGTATGGAG.............................	22	1	383333.00	383333	383333
............................................................................TGGAATGTAAAGAAGTATGGA..............................	21	1	2370.00	2370	2370
............................................................................TGGAATGTAAAGAAGTATGGAGC............................	23	1	484.00	484	484
.............................................................................GGAATGTAAAGAAGTATGGAG.............................	21	1	263.00	263	263
............................................................................TGGAATGTAAAGAAGTATGG...............................	20	1	166.00	166	166
..............................................................................GAATGTAAAGAAGTATGGAG.............................	20	1	119.00	119	119
................................................................................ATGTAAAGAAGTATGGAG.............................	18	1	13.00	13	13

dp4

GGAAA-----------TCAGAAGGCCTTTGAGAGTTCCATGCTTCCTTGCATTCAATAGT-ATAACATAAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCAAGACA---GCGTCTACA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
............................................................................TGGAATGTAAAGAAGTATGGAG.............................	22	1	635117.00	635117	246218	388899
............................................................................TGGAATGTAAAGAAGTATGGA..............................	21	1	19848.00	19848	2175	17673
............................................................................TGGAATGTAAAGAAGTATGG...............................	20	1	2776.00	2776	196	2580
............................................................................TGGAATGTAAAGAAGTATGGAGC............................	23	1	611.00	611	349	262
.............................................................................GGAATGTAAAGAAGTATGGAG.............................	21	1	411.00	411	145	266
............................................................................TGGAATGTAAAGAAGTATG................................	19	1	334.00	334	27	307
..............................................................................GAATGTAAAGAAGTATGGAG.............................	20	1	235.00	235	94	141
...............................................................................AATGTAAAGAAGTATGGAG.............................	19	1	35.00	35	20	15
...........................................................................ATGGAATGTAAAGAAGTATGGAG.............................	23	1	26.00	26	12	14
............................................................................TGGAATGTAAAGAAGTAT.................................	18	1	24.00	24	1	23

Secondary Structure

dm3

dG=-29.0, p-value=0.009901	dG=-28.3, p-value=0.009901

droSim1

dG=-29.0, p-value=0.009901	dG=-28.3, p-value=0.009901

droSec1

dG=-29.0, p-value=0.009901	dG=-28.3, p-value=0.009901

droYak2

dG=-27.9, p-value=0.009901	dG=-27.4, p-value=0.009901	dG=-27.2, p-value=0.009901

droEre2

dG=-29.0, p-value=0.009901	dG=-28.3, p-value=0.009901

droAna3

dG=-27.9, p-value=0.009901	dG=-27.4, p-value=0.009901	dG=-27.2, p-value=0.009901

dp4

dG=-27.9, p-value=0.009901	dG=-27.4, p-value=0.009901	dG=-27.2, p-value=0.009901

droPer1

dG=-27.9, p-value=0.009901	dG=-27.4, p-value=0.009901	dG=-27.2, p-value=0.009901

droWil1

dG=-28.5, p-value=0.009901	dG=-27.8, p-value=0.009901	dG=-27.8, p-value=0.009901	dG=-27.7, p-value=0.009901

droVir3

dG=-27.9, p-value=0.009901	dG=-27.4, p-value=0.009901	dG=-27.2, p-value=0.009901	dG=-26.9, p-value=0.009901

droMoj3

dG=-27.9, p-value=0.009901	dG=-27.8, p-value=0.009901	dG=-27.4, p-value=0.009901	dG=-27.2, p-value=0.009901	dG=-27.1, p-value=0.009901

droGri2

dG=-27.9, p-value=0.009901	dG=-27.8, p-value=0.009901	dG=-27.4, p-value=0.009901	dG=-27.2, p-value=0.009901	dG=-27.1, p-value=0.009901

Generated: 03/07/2013 at 04:44 PM