Secondary structure and small RNA-seq evidence for dme-mir-2c

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:11243451-11243582 -	TGCGT----CG-----------ACGTTACCTCGTAT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTCTGCATTTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCAGCG------ATAGCA-AA-------------------------------------------ATGTG--------------ACC
droSim1	chr3R:10237596-10237727 +	TGCGT----CG-----------ACGTTACCTCGTAT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTCTGCATTTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCAGCG------ATAGCA-AA-------------------------------------------GTGTG--------------ACC
droSec1	super_0:10704829-10704960 +	TGCGT----CG-----------ACGTTACCTCGTAT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTCTGCATTTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCAGCG------ATAGCA-AA-------------------------------------------GTGTG--------------ACC
droYak2	chr3R:15188346-15188476 +	TTCGT----CG-----------ACGTTACCTCGTAT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTCTGCATTTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCATCG------ATAGTA--A-------------------------------------------GTGCG--------------ACC
droEre2	scaffold_4770:10769593-10769723 -	TGTGT----CG-----------ACGTTACCTCGTAT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTCTGCATTTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCATCG------ATGGCA--A-------------------------------------------GTGTG--------------ACC
droAna3	scaffold_13340:12827820-12827951 -	TGCGTTTAGCG-----------ACGTATCTACGAAT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAG--AGATATTTCTGCATTTGAAGTGTATCACAGCCAGCTTTGATGGGCATTGCAATAAGCCTAGATTCCGATTGAA-----------------------------------------------------------------A-C
dp4	chr2:9824664-9824803 +	TGCGT----GCGTGCTTGCGTATCGGCACTTGGTATCCTTACTTTCAGTGTCATCAAAAATGGCTGAAGAAAGATATATTTGCATTTGAAGCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCATCG------ATTGCA------------------------------------------------GTT--------------TCG
droPer1	super_0:10660285-10660410 -	TGCGT----AT------------CGGCACTTGGTATCCTTACTTTCAGTGTCATCAAAAATGGCTGAAGAAAGATATATTTGCATTTGAAGCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCATCG------ATTGCA-GT---------------------------------------------TT------------------
droWil1	scaffold_181089:2143458-2143641 -	TGTGT----GT---------------GA-ATTGCGT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTTTGCATTTGAAGCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCATCGTT-----TTGCA-TTTTTCCCCTCATTATTCGCCACACACTCTGGGAGTACCAGCCAACAGAGACAGAGAGCGAGCGAC-
droVir3	scaffold_13047:13335413-13335531 +	TGT---------------------------ACATGT-CTTACTTTCAATGTCATCAAAAAGGGCTGA-GAATGATATATCTGCAATTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAAAGGGCAACG-------TAGCAGAA-------------------------------------------AAGTA--------------ACA
droMoj3	scaffold_6540:10568085-10568205 +	CATGC-------------------------TTG-GT-CTTACTTTCAGTGTCATCAAAAAGGGCTGA-GAATGATATTTCTGTAATTGAATTGTATCACAGCCAGCTTTGATGGGCACTGCGAAGGGCGAAG-------TAACA-GT-----------------------------------------AACATTA--------------ACA
droGri2	scaffold_14906:4357869-4357995 -	TGTGT----GT-----------TTGTGTGTACATGT-CTTACTTTCAATGTCATCAAAAAGGGCTGA-GAATGATATATCTGCAATTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAAAGGGCAATG-------TAGCA-AA-------------------------------------------AAGAG-----------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:11243451-11243582 -	TGCGT----CG-----------ACGTTACCTCGTAT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTCTGCATTTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCAGCG------ATAGCA-AA-------------------------------------------ATGTG--------------ACC
droSim1	chr3R:10237596-10237727 +	TGCGT----CG-----------ACGTTACCTCGTAT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTCTGCATTTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCAGCG------ATAGCA-AA-------------------------------------------GTGTG--------------ACC
droSec1	super_0:10704829-10704960 +	TGCGT----CG-----------ACGTTACCTCGTAT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTCTGCATTTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCAGCG------ATAGCA-AA-------------------------------------------GTGTG--------------ACC
droYak2	chr3R:15188346-15188476 +	TTCGT----CG-----------ACGTTACCTCGTAT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTCTGCATTTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCATCG------ATAGTA--A-------------------------------------------GTGCG--------------ACC
droEre2	scaffold_4770:10769593-10769723 -	TGTGT----CG-----------ACGTTACCTCGTAT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTCTGCATTTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCATCG------ATGGCA--A-------------------------------------------GTGTG--------------ACC
droAna3	scaffold_13340:12827820-12827951 -	TGCGTTTAGCG-----------ACGTATCTACGAAT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAG--AGATATTTCTGCATTTGAAGTGTATCACAGCCAGCTTTGATGGGCATTGCAATAAGCCTAGATTCCGATTGAA-----------------------------------------------------------------A-C
dp4	chr2:9824664-9824803 +	TGCGT----GCGTGCTTGCGTATCGGCACTTGGTATCCTTACTTTCAGTGTCATCAAAAATGGCTGAAGAAAGATATATTTGCATTTGAAGCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCATCG------ATTGCA------------------------------------------------GTT--------------TCG
droPer1	super_0:10660285-10660410 -	TGCGT----AT------------CGGCACTTGGTATCCTTACTTTCAGTGTCATCAAAAATGGCTGAAGAAAGATATATTTGCATTTGAAGCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCATCG------ATTGCA-GT---------------------------------------------TT------------------
droWil1	scaffold_181089:2143458-2143641 -	TGTGT----GT---------------GA-ATTGCGT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTTTGCATTTGAAGCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCATCGTT-----TTGCA-TTTTTCCCCTCATTATTCGCCACACACTCTGGGAGTACCAGCCAACAGAGACAGAGAGCGAGCGAC-
droVir3	scaffold_13047:13335413-13335531 +	TGT---------------------------ACATGT-CTTACTTTCAATGTCATCAAAAAGGGCTGA-GAATGATATATCTGCAATTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAAAGGGCAACG-------TAGCAGAA-------------------------------------------AAGTA--------------ACA
droMoj3	scaffold_6540:10568085-10568205 +	CATGC-------------------------TTG-GT-CTTACTTTCAGTGTCATCAAAAAGGGCTGA-GAATGATATTTCTGTAATTGAATTGTATCACAGCCAGCTTTGATGGGCACTGCGAAGGGCGAAG-------TAACA-GT-----------------------------------------AACATTA--------------ACA
droGri2	scaffold_14906:4357869-4357995 -	TGTGT----GT-----------TTGTGTGTACATGT-CTTACTTTCAATGTCATCAAAAAGGGCTGA-GAATGATATATCTGCAATTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAAAGGGCAATG-------TAGCA-AA-------------------------------------------AAGAG-----------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGCGT--------------CGACGTTACCTCGTAT-CTTACTTTCAATGTCATCAAAAAGGGCTGAAGAAAGATATTTCTGCATTTGAATCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCAGCGATAGCAAAGTGTGACC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..............................................................................................TCACAGCCAGCTTTGATGGGCA...............................	22	1	1511.00	1511	1511
................................................................................................ACAGCCAGCTTTGATGGGCA...............................	20	1	24.00	24	24
.................................................TCATCAAAAAGGGCTGAAGAAAGAT.........................................................................	25	1	18.00	18	18
.................................................TCATCAAAAAGGGCTGAAGAAAGA..........................................................................	24	1	15.00	15	15
............................................................................................TATCACAGCCAGCTTTGATGGGC................................	23	1	14.00	14	14
..............................................................................................TCACAGCCAGCTTTGATGGG.................................	20	1	14.00	14	14
............................................................................................TATCACAGCCAGCTTTGATGGGCA...............................	24	1	14.00	14	14
..............................................................................................TCACAGCCAGCTTTGATGGGCAT..............................	23	1	13.00	13	13
.................................................TCATCAAAAAGGGCTGAAGAAAGATA........................................................................	26	1	10.00	10	10
............................................................................................TATCACAGCCAGCTTTGATGGG.................................	22	1	9.00	9	9
..............................................................................................TCACAGCCAGCTTTGATGGGC................................	21	1	7.00	7	7
...............................................................................................CACAGCCAGCTTTGATGGGCA...............................	21	1	4.00	4	4
..................................................................................................AGCCAGCTTTGATGGGCA...............................	18	1	3.00	3	3
.................................................................................................CAGCCAGCTTTGATGGGCA...............................	19	1	2.00	2	2
.................................................TCATCAAAAAGGGCTGAAGA..............................................................................	20	1	2.00	2	2
.................................................TCATCAAAAAGGGCTGAAGAAA............................................................................	22	1	2.00	2	2
...............................................................................................CACAGCCAGCTTTGATGGGCAT..............................	22	1	2.00	2	2
.................................................TCATCAAAAAGGGCTGAAGAAAGATAT.......................................................................	27	1	1.00	1	1
...................................................ATCAAAAAGGGCTGAAGAAAGAT.........................................................................	23	1	1.00	1	1
.............................................................................................ATCACAGCCAGCTTTGATGGGC................................	22	1	1.00	1	1
................................................................................................ACAGCCAGCTTTGATGGGC................................	19	1	1.00	1	1
..............................................................................................TCACAGCCAGCTTTGATGG..................................	19	1	1.00	1	1
.................................................TCATCAAAAAGGGCTGAAGAAAG...........................................................................	23	1	1.00	1	1
.............................................................................................ATCACAGCCAGCTTTGATGGGCA...............................	23	1	1.00	1	1
.................................................................................................CAGCCAGCTTTGATGGGCAT..............................	20	1	1.00	1	1
............................................................................................TATCACAGCCAGCTTTGATGG..................................	21	1	1.00	1	1

dp4

TGCGTGCGTGCTTGCGTATCGG---CACTTGGTATCCTTACTTTCAGTGTCATCAAAAATGGCTGAAGAAAGATATATTTGCATTTGAAGCGTATCACAGCCAGCTTTGATGGGCATTGCAATGAGCATCGATTGCA----GTTTCG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..............................................................................................TCACAGCCAGCTTTGATGGGCA...............................	22	1	1141.00	1141	1035	106
............................................................................................TATCACAGCCAGCTTTGATGGG.................................	22	1	48.00	48	34	14
..............................................................................................TCACAGCCAGCTTTGATGGGC................................	21	1	40.00	40	28	12
............................................................................................TATCACAGCCAGCTTTGATGGGC................................	23	1	39.00	39	33	6
..............................................................................................TCACAGCCAGCTTTGATGGG.................................	20	1	26.00	26	16	10
............................................................................................TATCACAGCCAGCTTTGATGGGCA...............................	24	1	22.00	22	18	4
................................................................................................ACAGCCAGCTTTGATGGGCA...............................	20	1	16.00	16	15	1
..............................................................................................TCACAGCCAGCTTTGATGGGCAT..............................	23	1	9.00	9	6	3
.................................................TCATCAAAAATGGCTGAAG...............................................................................	19	1	5.00	5	0	5
............................................................................................TATCACAGCCAGCTTTGA.....................................	18	5	4.60	23	23	0
..............................................................................................TCACAGCCAGCTTTGATGG..................................	19	1	4.00	4	3	1
.............................................................................................ATCACAGCCAGCTTTGATGGGC................................	22	1	4.00	4	2	2
.................................................TCATCAAAAATGGCTGAAGA..............................................................................	20	1	3.00	3	0	3
.................................................TCATCAAAAATGGCTGAAGAAAG...........................................................................	23	1	3.00	3	0	3
.................................................TCATCAAAAATGGCTGAAGAAAGATA........................................................................	26	1	3.00	3	3	0
............................................................................................TATCACAGCCAGCTTTGATGG..................................	21	1	3.00	3	3	0
...............................................................................................CACAGCCAGCTTTGATGGGCA...............................	21	1	3.00	3	3	0
.................................................TCATCAAAAATGGCTGAAGAAAGA..........................................................................	24	1	3.00	3	3	0
.................................................................................................CAGCCAGCTTTGATGGGCA...............................	19	1	2.00	2	2	0
.................................................TCATCAAAAATGGCTGAAGAAAGAT.........................................................................	25	1	2.00	2	2	0
..................................................................................................AGCCAGCTTTGATGGGCA...............................	18	1	2.00	2	2	0
...............................................................................................CACAGCCAGCTTTGATGGGCAT..............................	22	1	2.00	2	2	0
.................................................TCATCAAAAATGGCTGAAGAAA............................................................................	22	1	2.00	2	0	2
.............................................................................................ATCACAGCCAGCTTTGATGGGCA...............................	23	1	2.00	2	2	0
................................................................................................ACAGCCAGCTTTGATGGGC................................	19	1	1.00	1	1	0
...........................................................................TATTTGCATTTGAAGCGTA.....................................................	19	1	1.00	1	1	0
................................................................................................ACAGCCAGCTTTGATGGG.................................	18	1	1.00	1	1	0
..................................................CATCAAAAATGGCTGAAGAAAGATA........................................................................	25	1	1.00	1	1	0