Secondary structure and small RNA-seq evidence for dme-bantam

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:642193-642303 +	TTTGT---------------------------A-ACTCCAATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droSim1	chr3L:290535-290645 +	TTTGT---------------------------A-ACTCCAATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droSec1	super_2:662642-662752 +	TTTGT---------------------------A-ACTCCAATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droYak2	chr3L:629639-629749 +	TTTGT---------------------------A-ACTCCAATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droEre2	scaffold_4784:648329-648439 +	TTTGT---------------------------A-ACTCCAATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droAna3	scaffold_13337:6520579-6520690 -	TTTGT---------------------------AAACTCCAATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTTATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
dp4	chrXR_group8:4603895-4604015 -	TTTGGGAC-------T-----ACTCCACCAAT---A---TATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTTATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droPer1	super_29:844606-844726 -	TTTGGGAC-------T-----ACTCCACCAAT---A---TATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTTATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droWil1	scaffold_180698:10172097-10172254 +	TTTTTTTCATACATTTT-------------------TTTGATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACAGAAAAAAAAAGAAGAAAAAAAAATAACGATCATCATCTTGCC
droVir3	scaffold_13049:5805300-5805416 +	TTTGTGTG-------T-----CGTCT------A-TCTC---TGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTAT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droMoj3	scaffold_6680:4143306-4143408 +	CT--------------------------------------ATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTTTTTTATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATAACCACA--------------------------------------TTCC
droGri2	scaffold_15110:13265206-13265333 -	TGTGCGTC-------TCTCTGTCTCCATCACT---A-CCTATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCAGACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:642193-642303 +	TTTGT---------------------------A-ACTCCAATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droSim1	chr3L:290535-290645 +	TTTGT---------------------------A-ACTCCAATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droSec1	super_2:662642-662752 +	TTTGT---------------------------A-ACTCCAATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droYak2	chr3L:629639-629749 +	TTTGT---------------------------A-ACTCCAATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droEre2	scaffold_4784:648329-648439 +	TTTGT---------------------------A-ACTCCAATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droAna3	scaffold_13337:6520579-6520690 -	TTTGT---------------------------AAACTCCAATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTTATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
dp4	chrXR_group8:4603895-4604015 -	TTTGGGAC-------T-----ACTCCACCAAT---A---TATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTTATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droPer1	super_29:844606-844726 -	TTTGGGAC-------T-----ACTCCACCAAT---A---TATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTTATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droWil1	scaffold_180698:10172097-10172254 +	TTTTTTTCATACATTTT-------------------TTTGATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACAGAAAAAAAAAGAAGAAAAAAAAATAACGATCATCATCTTGCC
droVir3	scaffold_13049:5805300-5805416 +	TTTGTGTG-------T-----CGTCT------A-TCTC---TGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTAT-TTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC
droMoj3	scaffold_6680:4143306-4143408 +	CT--------------------------------------ATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTTTTTTATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATAACCACA--------------------------------------TTCC
droGri2	scaffold_15110:13265206-13265333 -	TGTGCGTC-------TCTCTGTCTCCATCACT---A-CCTATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTT-TTCAGACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATA-CCACA--------------------------------------TTCC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TTTGTAACT---CCA-------ATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTTTTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATACCACATTCC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
............................................................................TGAGATCATTTTGAAAGCTGAT.......................	22	1	103826.00	103826	103826
............................................................................TGAGATCATTTTGAAAGCTGATT......................	23	1	80118.00	80118	80118
.......................................CCGGTTTTCGATTTGGTTTGACT...........................................................	23	1	2555.00	2555	2555
............................................................................TGAGATCATTTTGAAAGCTGATTT.....................	24	1	1261.00	1261	1261
............................................................................TGAGATCATTTTGAAAGCTGA........................	21	1	437.00	437	437
........................................CGGTTTTCGATTTGGTTTGACT...........................................................	22	1	287.00	287	287
............................................................................TGAGATCATTTTGAAAGCT..........................	19	1	124.00	124	124
.......................................CCGGTTTTCGATTTGGTTTGAC............................................................	22	1	100.00	100	100
...........................................................................GTGAGATCATTTTGAAAGCTGAT.......................	23	1	65.00	65	65
............................................................................TGAGATCATTTTGAAAGCTG.........................	20	1	58.00	58	58
.............................................................................GAGATCATTTTGAAAGCTGAT.......................	21	1	30.00	30	30
.............................................................................GAGATCATTTTGAAAGCTGATT......................	22	1	28.00	28	28
........................................CGGTTTTCGATTTGGTTTGAC............................................................	21	1	16.00	16	16
.......................................CCGGTTTTCGATTTGGTTTGA.............................................................	21	1	14.00	14	14
..............................................................................AGATCATTTTGAAAGCTGAT.......................	20	1	9.00	9	9

dp4

TTTGGGACTACTCCACCAATATATGATTTGACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTTTTTATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATACCACATTCC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
............................................................................TGAGATCATTTTGAAAGCTGATT......................	23	1	141453.00	141453	47921	93532
............................................................................TGAGATCATTTTGAAAGCTGAT.......................	22	1	139018.00	139018	78544	60474
............................................................................TGAGATCATTTTGAAAGCTGATTT.....................	24	1	6775.00	6775	1877	4898
............................................................................TGAGATCATTTTGAAAGCTGA........................	21	1	6431.00	6431	703	5728
.......................................CCGGTTTTCGATTTGGTTTGACT...........................................................	23	1	2120.00	2120	1762	358
............................................................................TGAGATCATTTTGAAAGCTG.........................	20	1	1135.00	1135	72	1063
........................................CGGTTTTCGATTTGGTTTGACT...........................................................	22	1	539.00	539	456	83
............................................................................TGAGATCATTTTGAAAGCT..........................	19	1	421.00	421	113	308
.......................................CCGGTTTTCGATTTGGTTTGAC............................................................	22	1	99.00	99	47	52
...........................................................................GTGAGATCATTTTGAAAGCTGAT.......................	23	1	60.00	60	56	4
.......................................CCGGTTTTCGATTTGGTTTGA.............................................................	21	1	51.00	51	10	41
.............................................................................GAGATCATTTTGAAAGCTGATT......................	22	1	49.00	49	18	31
.............................................................................GAGATCATTTTGAAAGCTGAT.......................	21	1	32.00	32	25	7
............................................................................TGAGATCATTTTGAAAGCTGATTTT....................	25	1	29.00	29	0	29
............................................................................TGAGATCATTTTGAAAGC...........................	18	1	26.00	26	11	15
........................................CGGTTTTCGATTTGGTTTGAC............................................................	21	1	20.00	20	18	2
.......................................CCGGTTTTCGATTTGGTTTG..............................................................	20	1	19.00	19	1	18
................................................................................ATCATTTTGAAAGCTGATT......................	19	1	13.00	13	6	7

Secondary Structure

dm3

-26.0	-26.0	-25.7	-25.7	-25.4	-25.3

droSim1

-26.0	-26.0	-25.7	-25.7	-25.4	-25.3

droSec1

-26.0	-26.0	-25.7	-25.7	-25.4	-25.3

droYak2

-26.0	-26.0	-25.7	-25.7	-25.4	-25.3

droEre2

-26.0	-26.0	-25.7	-25.7	-25.4	-25.3

droAna3

-26.0	-26.0	-25.7	-25.7	-25.4	-25.3

dp4

-26.0	-26.0	-25.7	-25.7	-25.4	-25.3

droPer1

-26.0	-26.0	-25.7	-25.7	-25.4	-25.3

droWil1

-26.0	-26.0	-25.7	-25.7	-25.4	-25.3

droVir3

-27.6	-27.6	-27.3	-27.3	-26.9	-26.9

droMoj3

-26.5	-26.5	-26.2	-26.2	-25.8	-25.8

droGri2

-27.1	-27.1	-26.9	-26.9	-26.8	-26.8

Generated: 01/05/2013 at 05:04 PM