Secondary structure and small RNA-seq evidence for dme-mir-275

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:7425780-7425907 +	TGATGTTCCCCCGACTGTA--AAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGG-CAGACATATAT----CTCCATCTT-------------------CACC--AT
droSim1	chr2L:7217350-7217477 +	TGATGTTCCCCCGACTGAA--AAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGG-CAGACATATAT----CTCCATCTC-------------------CGCC--AT
droSec1	super_3:2941240-2941367 +	TGATGTTCCCCCGACTGAA--AAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTTGTTTT-----TTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGG-CAGACATATAT----CTCCATCTC-------------------CGTC--AT
droYak2	chr2L:5473766-5473897 -	TGATGTTCCCCCGACTGAACAGAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGC-CAGACATATAT----CTCCAACTC-------------------CACGATAT
droEre2	scaffold_4929:16344506-16344633 +	TGATGTTCCCCCGACTGAA--AAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGC-CAGACATATAT----CTCCATCTC-------------------CACC--AT
droAna3	scaffold_12916:15333987-15334092 +	-------------ACTCTC--CAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TGCA-----ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGG-CAGACATATAT----C---------------------------CGCC--AT
dp4	chr4_group1:4175726-4175840 +	CCACCTTC-------TTGA--AAGTCTCCTACCATGCGCGCTAATCAGAGACCGGGGCTGGTTTT-----TTCACT---GCAGTCAGGTACCTGAAGTAGCGCGCGTGGTGC-TAGACACGAA--CATC--TGT----------------------------GT
droPer1	super_5:1086449-1086563 -	CCACCTTC-------TTGA--AAGTCTCCTACCATGCGCGCTAATCAGAGACCGGGGCTGGTTTT-----TTCACT---GCAGTCAGGTACCTGAAGTAGCGCGCGTGGTGC-TAGACACGAA--CATC--TGT----------------------------GT
droWil1	scaffold_180772:5257564-5257692 -	-----------------------GTCTCTTACCTTGCGCGCTAATCAGTGACCAGGGCTGAGTAATTTTATTCAAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTTT-TAGACCAAGATTCATC------GCACGACGACGGCGACAACGACGAC--AC
droVir3	scaffold_12963:15419953-15420067 -	--------------CTGCG--CCGTCTTTTACCGTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----GGTTATCCCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCCAGACGTATT--CATC------TT-------------------AAGC--TT
droMoj3	scaffold_6500:18399386-18399492 -	-----------------------GTCTTTTACCGTGCGCGCTAATCAGTGACCGGGGCTGGTTTC-----GATTATCTCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCTAGACGCATT--CAAC------GCTC-----------------T-----GC
droGri2	scaffold_15126:5008400-5008494 +	-----------------------GTCGTTTACCGCGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----GATTATCCCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCCAGACGCAT------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:7425780-7425907 +	TGATGTTCCCCCGACTGTA--AAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGG-CAGACATATAT----CTCCATCTT-------------------CACC--AT
droSim1	chr2L:7217350-7217477 +	TGATGTTCCCCCGACTGAA--AAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGG-CAGACATATAT----CTCCATCTC-------------------CGCC--AT
droSec1	super_3:2941240-2941367 +	TGATGTTCCCCCGACTGAA--AAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTTGTTTT-----TTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGG-CAGACATATAT----CTCCATCTC-------------------CGTC--AT
droYak2	chr2L:5473766-5473897 -	TGATGTTCCCCCGACTGAACAGAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGC-CAGACATATAT----CTCCAACTC-------------------CACGATAT
droEre2	scaffold_4929:16344506-16344633 +	TGATGTTCCCCCGACTGAA--AAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGC-CAGACATATAT----CTCCATCTC-------------------CACC--AT
droAna3	scaffold_12916:15333987-15334092 +	-------------ACTCTC--CAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TGCA-----ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGG-CAGACATATAT----C---------------------------CGCC--AT
dp4	chr4_group1:4175726-4175840 +	CCACCTTC-------TTGA--AAGTCTCCTACCATGCGCGCTAATCAGAGACCGGGGCTGGTTTT-----TTCACT---GCAGTCAGGTACCTGAAGTAGCGCGCGTGGTGC-TAGACACGAA--CATC--TGT----------------------------GT
droPer1	super_5:1086449-1086563 -	CCACCTTC-------TTGA--AAGTCTCCTACCATGCGCGCTAATCAGAGACCGGGGCTGGTTTT-----TTCACT---GCAGTCAGGTACCTGAAGTAGCGCGCGTGGTGC-TAGACACGAA--CATC--TGT----------------------------GT
droWil1	scaffold_180772:5257564-5257692 -	-----------------------GTCTCTTACCTTGCGCGCTAATCAGTGACCAGGGCTGAGTAATTTTATTCAAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTTT-TAGACCAAGATTCATC------GCACGACGACGGCGACAACGACGAC--AC
droVir3	scaffold_12963:15419953-15420067 -	--------------CTGCG--CCGTCTTTTACCGTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----GGTTATCCCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCCAGACGTATT--CATC------TT-------------------AAGC--TT
droMoj3	scaffold_6500:18399386-18399492 -	-----------------------GTCTTTTACCGTGCGCGCTAATCAGTGACCGGGGCTGGTTTC-----GATTATCTCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCTAGACGCATT--CAAC------GCTC-----------------T-----GC
droGri2	scaffold_15126:5008400-5008494 +	-----------------------GTCGTTTACCGCGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----GATTATCCCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCCAGACGCAT------------------------------------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGATGTTCCCCCGACTGAAAAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTTTTATATACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCAGACATATATCTCCATCTCCGCCAT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.........................................................................TCAGGTACCTGAAGTAGCGCG..................................	21	2	2389.00	4778	4778
.........................................................................TCAGGTACCTGAAGTAGCGCGCG................................	23	2	525.50	1051	1051
.........................................................................TCAGGTACCTGAAGTAGCGC...................................	20	2	176.00	352	352
..................................CGCGCTAATCAGTGACCGGGGCT.......................................................................	23	2	16.00	32	32
..................................CGCGCTAATCAGTGACCGGGGC........................................................................	22	2	14.50	29	29
...........................................................................AGGTACCTGAAGTAGCGCGC.................................	20	2	11.50	23	23
.........................................................................TCAGGTACCTGAAGTAGCG....................................	19	2	6.00	12	12
...........................................................................AGGTACCTGAAGTAGCGCGCG................................	21	2	4.50	9	9
..................................CGCGCTAATCAGTGACCGGGG.........................................................................	21	2	2.00	4	4
..................................CGCGCTAATCAGTGACCGGG..........................................................................	20	2	0.50	1	1

dp4

CCACCTTC-------TTGAAAGTCTCCTACCATGCGCGCTAATCAGAGACCGGGGCTGGTTTTTTCACTGCAGTCAGGTACCTGAAGTAGCGCGCGTGGTGCTAGACACGAACATCTGT-------GT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.........................................................................TCAGGTACCTGAAGTAGCGCG..................................	21	2	1344.00	2688	2688	0
.........................................................................TCAGGTACCTGAAGTAGCGCGC.................................	22	2	833.50	1667	0	1667
.........................................................................TCAGGTACCTGAAGTAGCGC...................................	20	2	366.50	733	386	347
.........................................................................TCAGGTACCTGAAGTAGCG....................................	19	2	102.00	204	28	176
.........................................................................TCAGGTACCTGAAGTAGCGCGCG................................	23	2	70.50	141	141	0
.........................................................................TCAGGTACCTGAAGTAGCGCGCGT...............................	24	2	2.00	4	4	0
..................................CGCGCTAATCAGAGACCGGGGC........................................................................	22	2	2.00	4	4	0
...........................................................................AGGTACCTGAAGTAGCGCGCGT...............................	22	2	1.50	3	0	3
..........................................................................CAGGTACCTGAAGTAGCGCGC.................................	21	2	1.50	3	3	0

Secondary Structure

dm3

-43.7	-42.9

droSim1

-43.7

droSec1

-40.8	-40.8	-40.2

droYak2

-39.7

droEre2

-39.7

droAna3

-43.9	-42.9

dp4

-44.9	-44.4

droPer1

-44.9	-44.4

droWil1

-36.5	-36.5	-36.5	-36.2	-36.2

droVir3

-43.7	-43.5	-42.9	-42.7	-42.7

droMoj3

-41.5

droGri2

-45.0	-44.3

Generated: 01/05/2013 at 05:12 PM