Secondary structure and small RNA-seq evidence for dme-mir-79

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:16698539-16698665 +	AT---GAGTGCCT----TAGAGTGAAG--------------------------CTGACTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCTGCAGGTCAA-TCGTCA----------GAAACA----AT
droSim1	wck39a12.g1:600-726 -	AT---GAGTGCGT----CAGAGTGTAG--------------------------CTGACTTACCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTGTGCAGATCAA-TCGTCA----------GAAACA----A-
droSec1	super_7:345550-345676 +	AT---GAGTGCCT----CAGAGTGTAG--------------------------CTGACTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTGTGCAGATCAA-TCGTCA----------GAAACA----AA
droYak2	chr2R:4404406-4404531 -	AT---AAGTGAAT---TGAGAGTGTAG--------------------------CTGCCTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTATACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCTGCAGATCAA-TCATCA------------GACA----AA
droEre2	scaffold_4845:19768185-19768311 +	AT---AAGTGACT----TAGAGTGCAG--------------------------CTGCCTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCTGCAGATCAA-TCTTCA----------GAAAGA----AA
droAna3	scaffold_12916:15864702-15864823 -	TA---TAGTGTTC----TA-----TAG--------------------------CTGCTTAACCGATGCTTTGGCGCTTTAGCTGTATGATAGATTTAAA-TACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCCGCAGGCCTG-TCTTCAA---------GGAATA----AA
dp4	chr4_group3:8443957-8444103 +	GA---AAGTGTTT----AAAAGTACAACAATCTAATCTGTGCTTAA----GCCCTGCTCTGCTTCTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAAATACTTCATAAAGCTAGATTACCAAAGCATTGGCTC-TGTGGAAACT-TCATCC-----------AAACA----AT
droPer1	super_1:9895076-9895222 +	GA---AAGTGTTT----AAAAGTACGACAATCTAATCTGTGCTTAA----GCCCTGCTCTGCTTCTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAAATACTTCATAAAGCTAGATTACCAAAGCATTGGCTC-TGTGGAAACT-TCATCC-----------AAACA----AT
droWil1	scaffold_181061:28846-28963 -	GT---AAT-------------GGATAA--------------------------TGGTCTTGCCTATGCTTTGGCGCTTTAGCTGTATGATAGATTTGA-CTACTTCATAAAGCTAGATTACCAAAGCATGGGCTCTGGCTGA--CT-TAATCA-----------ACGCAAGTGTT
droVir3	scaffold_12963:12863019-12863151 -	AT---AGCC---AGGATTAGA-TGAA-------------------------CGCCGCACTGCCGTTGCTTTGGCGCTTTAGCTGTATGATAGATTTGAA-TACTTCATAAAGCTAGATTACCAAAGCATTGGCTC-TGTGGC-CAGCTTAGCA---AAGTTGTGAAACG----AT
droMoj3	scaffold_6500:7202098-7202247 +	A------GTGTCT----TGTAATGTAA-------ACGTGTTTTTAAATATTCGCCCCATTGCCGTTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAA-TACTTCATAAAGCTAGATTACCAAAGCATTGGCTC-TGTGG-CCAA-ACCCCAGCGAACTTGTGAAATA----AT
droGri2	scaffold_14978:831072-831198 +	ATTTAAAGTGCTT----CTTCTTGGTG--------------------------CCACATTGCCGTCGCTTTGGCGCTTTAGCTGTATGATAGATTTGAA-TACTTCATAAAGCTAGATTACCAAAGCATCGGCGCCTGTGGC-CA--GCTTAA----------CAAACG----TT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:16698539-16698665 +	AT---GAGTGCCT----TAGAGTGAAG--------------------------CTGACTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCTGCAGGTCAA-TCGTCA----------GAAACA----AT
droSim1	wck39a12.g1:600-726 -	AT---GAGTGCGT----CAGAGTGTAG--------------------------CTGACTTACCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTGTGCAGATCAA-TCGTCA----------GAAACA----A-
droSec1	super_7:345550-345676 +	AT---GAGTGCCT----CAGAGTGTAG--------------------------CTGACTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTGTGCAGATCAA-TCGTCA----------GAAACA----AA
droYak2	chr2R:4404406-4404531 -	AT---AAGTGAAT---TGAGAGTGTAG--------------------------CTGCCTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTATACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCTGCAGATCAA-TCATCA------------GACA----AA
droEre2	scaffold_4845:19768185-19768311 +	AT---AAGTGACT----TAGAGTGCAG--------------------------CTGCCTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCTGCAGATCAA-TCTTCA----------GAAAGA----AA
droAna3	scaffold_12916:15864702-15864823 -	TA---TAGTGTTC----TA-----TAG--------------------------CTGCTTAACCGATGCTTTGGCGCTTTAGCTGTATGATAGATTTAAA-TACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCCGCAGGCCTG-TCTTCAA---------GGAATA----AA
dp4	chr4_group3:8443957-8444103 +	GA---AAGTGTTT----AAAAGTACAACAATCTAATCTGTGCTTAA----GCCCTGCTCTGCTTCTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAAATACTTCATAAAGCTAGATTACCAAAGCATTGGCTC-TGTGGAAACT-TCATCC-----------AAACA----AT
droPer1	super_1:9895076-9895222 +	GA---AAGTGTTT----AAAAGTACGACAATCTAATCTGTGCTTAA----GCCCTGCTCTGCTTCTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAAATACTTCATAAAGCTAGATTACCAAAGCATTGGCTC-TGTGGAAACT-TCATCC-----------AAACA----AT
droWil1	scaffold_181061:28846-28963 -	GT---AAT-------------GGATAA--------------------------TGGTCTTGCCTATGCTTTGGCGCTTTAGCTGTATGATAGATTTGA-CTACTTCATAAAGCTAGATTACCAAAGCATGGGCTCTGGCTGA--CT-TAATCA-----------ACGCAAGTGTT
droVir3	scaffold_12963:12863019-12863151 -	AT---AGCC---AGGATTAGA-TGAA-------------------------CGCCGCACTGCCGTTGCTTTGGCGCTTTAGCTGTATGATAGATTTGAA-TACTTCATAAAGCTAGATTACCAAAGCATTGGCTC-TGTGGC-CAGCTTAGCA---AAGTTGTGAAACG----AT
droMoj3	scaffold_6500:7202098-7202247 +	A------GTGTCT----TGTAATGTAA-------ACGTGTTTTTAAATATTCGCCCCATTGCCGTTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAA-TACTTCATAAAGCTAGATTACCAAAGCATTGGCTC-TGTGG-CCAA-ACCCCAGCGAACTTGTGAAATA----AT
droGri2	scaffold_14978:831072-831198 +	ATTTAAAGTGCTT----CTTCTTGGTG--------------------------CCACATTGCCGTCGCTTTGGCGCTTTAGCTGTATGATAGATTTGAA-TACTTCATAAAGCTAGATTACCAAAGCATCGGCGCCTGTGGC-CA--GCTTAA----------CAAACG----TT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ATGAGTGCGTCAGAGTGTAGCT----------------------GACTTACCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTGTGCAGATCAATCGTCAGAAACAA-	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
................................................................................................TAAAGCTAGATTACCAAAGCAT...............................	22	1	817.00	817	817
...............................................................................................ATAAAGCTAGATTACCAAAGCAT...............................	23	1	398.00	398	398
.......................................................GCTTTGGCGCTTTAGCTGTATG........................................................................	22	1	93.00	93	93
................................................................................................TAAAGCTAGATTACCAAAGCA................................	21	1	15.00	15	15
.......................................................GCTTTGGCGCTTTAGCTGTATGA.......................................................................	23	1	15.00	15	15
................................................................................................TAAAGCTAGATTACCAAAGC.................................	20	1	14.00	14	14
...............................................................................................ATAAAGCTAGATTACCAAAGCA................................	22	1	8.00	8	8
................................................................................................TAAAGCTAGATTACCAAAG..................................	19	1	6.00	6	6
.......................................................GCTTTGGCGCTTTAGCTGTAT.........................................................................	21	1	3.00	3	3
................................................................................................TAAAGCTAGATTACCAAAGCATT..............................	23	1	2.00	2	2
.................................................................................................AAAGCTAGATTACCAAAGCATT..............................	22	1	2.00	2	2
.............AGTGTAGCT----------------------GACTTACCATT..............................................................................................	20	1	1.00	1	1
....................................................................................................GCTAGATTACCAAAGCAT...............................	18	1	1.00	1	1
........................................................CTTTGGCGCTTTAGCTGTATG........................................................................	21	1	1.00	1	1
...............................................................................................ATAAAGCTAGATTACCAAAGCATT..............................	24	1	1.00	1	1
...............................................................................................ATAAAGCTAGATTACCAAAG..................................	20	1	1.00	1	1
.................................................................................................AAAGCTAGATTACCAAAGCA................................	20	1	1.00	1	1
........................................................CTTTGGCGCTTTAGCTGTATGA.......................................................................	22	1	1.00	1	1
.................................................................................................AAAGCTAGATTACCAAAGCAT...............................	21	1	1.00	1	1
...............................................................................................ATAAAGCTAGATTACCAAA...................................	19	1	1.00	1	1

dp4

GAAAGTGTTTAAAAGTACAACAATCTAATCTGTGCTTAAGCCCTGCTCTGCTTCTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAAATACTTCATAAAGCTAGATTACCAAAGCATTGGCT-CTGTGGAAACTTCATCCAAA-CAAT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
................................................................................................TAAAGCTAGATTACCAAAGCAT...............................	22	1	3548.00	3548	1475	2073
...............................................................................................ATAAAGCTAGATTACCAAAGCAT...............................	23	1	1991.00	1991	707	1284
.......................................................GCTTTGGCGCTTTAGCTGTATG........................................................................	22	1	193.00	193	161	32
................................................................................................TAAAGCTAGATTACCAAAGCA................................	21	1	110.00	110	17	93
...............................................................................................ATAAAGCTAGATTACCAAAGCA................................	22	1	74.00	74	14	60
................................................................................................TAAAGCTAGATTACCAAAGC.................................	20	1	49.00	49	12	37
.................................................................................................AAAGCTAGATTACCAAAGCAT...............................	21	1	35.00	35	9	26
...............................................................................................ATAAAGCTAGATTACCAAAGC.................................	21	1	35.00	35	8	27
.......................................................GCTTTGGCGCTTTAGCTGTATGA.......................................................................	23	1	29.00	29	18	11
...............................................................................................ATAAAGCTAGATTACCAAAG..................................	20	1	15.00	15	11	4
................................................................................................TAAAGCTAGATTACCAAAGCATT..............................	23	1	12.00	12	2	10
...............................................................................................ATAAAGCTAGATTACCAAA...................................	19	1	4.00	4	1	3
................................................................................................TAAAGCTAGATTACCAAAG..................................	19	1	4.00	4	2	2
.......................................................GCTTTGGCGCTTTAGCTGTA..........................................................................	20	1	4.00	4	3	1
...............................................................................................ATAAAGCTAGATTACCAAAGCATT..............................	24	1	3.00	3	3	0
.......................................................GCTTTGGCGCTTTAGCTGTAT.........................................................................	21	1	3.00	3	1	2