Secondary structure and small RNA-seq evidence for dme-mir-280

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:4185596-4185720 +	CTGACGT-------------------G--------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTATGCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATA--TGCAA-------------------------------------GTCGA------GGTCCTCCA-----------CACT-------GCACTCGC-CGC-CTCGA
droSim1	zee54c10.b1:599-724 +	CTGACGT-------------------G--------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTGCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATA--TGCAA-------------------------------------GTCGA------GGTCCTGCA-----------CACT-------GCACTCGC-CGC-CTCGA
droSec1	super_1:1832273-1832397 +	CTGACGT-------------------G--------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTGCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATA--TGCAA-------------------------------------GTCGA------GGTCCTGCA-----------CACT-------GCACTCGC-CGC-CTCGA
droYak2	chr2L:16840791-16840915 +	CTGACGT-------------------G--------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTGCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATA--TGCAA-------------------------------------CTTGA------GGTCCTGCA-----------CACT-------GCACTCTC-CCG-CTCGA
droEre2	scaffold_4929:18446687-18446817 -	CTGACGT-------------------G--------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTGCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATA--TGCAA-------------------------------------GTCGA------GGTCCAGCA-----------CACTGCACACTGCACTTGC-C-C-CTCGA
droAna3	scaffold_13266:1806990-1807233 -	TTGAAAT-------------------G-----TGTGTATGTGGG--------TG----------GGTG----GGTGTGTGTGCACTTTCTGCCATCCAGACTGCCAGCCAGCCATCTAGCCAGCCTGCCTGACTGCTTTCCTTGCCACTT-----GTGTGTATGTGTGTGTG-----------------TGTATGAGCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATA--TGCAA-------------------------------------G-------------CCTGAACAACTTTGGAACACT-------GCAATCGC-CTT-CTGGA
dp4	chr3:2170016-2170201 +	TTGATGC-------------------C-----tgtgtgtgtgtg--------------------------tgtgtgtgtgtCCAGTCGGTGTCATGA-GG-------------------------------------------------CGTATGCC----GTGTGTGTGTG-----------------TGTGTGAGACGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATG--TGCAG-------------------------------------CTGAA------GAGCCTGTC-----------CATT-------GCACAATC-C-C-CACCC
droPer1	super_2:2339680-2339867 +	TTGATGC-------------------C-----TGTGTGTGTGTG----------------------------TGTGTGCGTCCAGTCGGTGTCATGA-GG-------------------------------------------------CGTATGCCgtgtgtgtgtgtgtg-----------------tgtgtgAGACGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATG--TGCAG-------------------------------------CTGAA------GAGCCTGTC-----------CATT-------GCACAATC-C-C-CTCCC
droWil1	scaffold_180701:589914-590141 +	TTGATGCCCCAACACACACCCACCTCC-----TATCTATCTATCTATCTCTGTCTCACCATAACTGAg------------------------------------------------------------------------------------------tgtgtgtgtgtgtg-----------------tgtgtatgtTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATG--TGCAACCGAAGCAGCAGAAGCCAGGCC--CAA----------GTAGAAGCAAAAGGCCTGAA-----------CATT-------GCACTTGGGC-CATACGC
droVir3	scaffold_12875:9206154-9206327 +	TTGATGT-------------------CGTCTTTGTGTG-----CCAT------------------GTGTGTGTGTGTGTGTCCATT-------------------------------------------------------------------------------------T-----------------TGTGTGTGTTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATACATGCCA------------------GA----GCAGTGCATGCAACTG------------C-CCA-----------CAAT-------GCACATTT-C-TATCCGC
droMoj3	scaffold_6496:17934933-17935113 -	TTGATGT-------------------CGTCGTTGTGTA-----CCATGCATTCG----------TGTG------------------------------------------------------------------------------------------TGCCTGTGTGTGTG-----------------CGTGTGTGTTAGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATACATGCCA------------------GGCCGGCCAGTGCATGCAACTT------------C-TCT-----------CAAT-------GCATATTC-C-AATCCAC
droGri2	scaffold_15245:2520625-2520797 +	TTGATGT-------------------TGTCGTTGAGT------CTAtgtctgtg----------tgtg------------------------------------------------------------------------------------------tgtgtgtgtgtgtgtgtgcgagtgtCCAGTTCGTGTGTGTTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATACATGCAA-------------------------------------CTC------------CTTCT-----------CAAT-------GGATCCCC--------AC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:4185596-4185720 +	CTGACGT-------------------G--------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTATGCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATA--TGCAA-------------------------------------GTCGA------GGTCCTCCA-----------CACT-------GCACTCGC-CGC-CTCGA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CTGACG--------------------------------------------------------------TGTGTGTGCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATATGCAAGTCGAGGTCCTGCACACTGCACTCGCCGCCTCGA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

TTGATGCCtgtgtgtgtgtgtgtgtgtgtgtCCAGTCGGTGTCATGAGGCGTATGCCGTGTGTGTGTGTGTGTGAGACGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATGTGCAGCTGAAGAGCCTGTCCATTGCACA-ATCCCCACCC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..............TGTGTGTGTGTGTGTGTCC..........................................................................................................................................................	19	1	1.00	1	0	1
......CCTGTGTGTGTGTGTGTGT..................................................................................................................................................................	19	1	1.00	1	0	1
......CCTGTGTGTGTGTGTGTGTGTGTG.............................................................................................................................................................	24	1	1.00	1	0	1
.......CTGTGTGTGTGTGTGTGTGTGTG.............................................................................................................................................................	23	2	0.50	1	0	1
........TGTGTGTGTGTGTGTGTGTG...............................................................................................................................................................	20	13	0.08	1	0	1

Secondary Structure

dm3

-25.3	-25.2	-24.5	-24.4	-24.4	-24.4

droSim1

-25.3	-25.2	-24.5	-24.4	-24.4	-24.3

droSec1

-25.3	-25.2	-24.5	-24.4	-24.4	-24.3

droYak2

-25.9	-25.8	-25.1	-25.0	-25.0	-24.9

droEre2

-26.6	-26.5	-26.3	-26.2	-26.2	-26.1

droAna3

-25.8	-25.7	-25.1	-25.0	-25.0	-24.9

dp4

-28.0	-28.0	-27.9	-27.9	-27.3	-27.2

droPer1

-28.0	-28.0	-27.9	-27.9	-27.3	-27.2

droWil1

-37.1	-37.0	-36.5	-36.4	-36.3	-36.3

droVir3

-30.3	-30.2	-30.1	-30.0	-29.7	-29.6

droMoj3

-23.8	-23.7	-23.7	-23.6	-23.6	-23.5

droGri2

-20.3	-20.2	-20.1	-20.0	-19.9	-19.8

Generated: 01/05/2013 at 05:13 PM