Secondary structure and small RNA-seq evidence for dme-mir-970

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:12530354-12530478 +	AAAGTGCCCAT-------------------AA------TCGAAAGGCATCTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGTAATG--A-TTTG---AATCTATCATAAGACACACGCGGCTATAACCGTT--GTCT--AAGAGCTTCAAA---A-------------------TC------GAT
droSim1	chrX_random:3444234-3444357 +	AAAGTGAACGT-------------------AA------TCGAAAGGCATCTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGAATTG--A-TTTG---AATCTATCATAAGACACACGCGGCTATAACCGAT--GTCT--AAATGCTTCAAA-----------------------TC------GAC
droSec1	super_21:285079-285202 +	AAAGTGAACGT-------------------AA------TCGAAAGGCATCTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGAATTG--A-TTTG---AATCTATCATAAGACACACGCGGCTATAACCGAT--GTCT--AAATGCTTCAAA---A--------------------T------GAT
droYak2	chrX:6807144-6807273 +	ATAGTGCATTT-------------------AA------TCGAAAGGCATCTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGTAATG--A-TTTG---AATCTATCATAAGACACACGCGGCTATAACCGAT--GTCA--C---------ACATGCGACACA--------------CACATTAGAT
droEre2	scaffold_4690:14328958-14329082 -	AAAGTGC-CTT-------------------AA------TCGAAAGGCATCCGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGTAATG--A-TTTG---AATCTATCATAAGACACACGCGGCTATAACCGAT--GTCT--AAACGCTTCAAA---G----TG--------------C------AAT
droAna3	scaffold_13117:3438231-3438350 +	TTAGTGGA-------------------------------AGAAAGGCATTTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGATATC--G-AAAG---AATCTATCATAAGACACACGCGGCTATAATCGAT--GTCCTTAGAGTCTACAAG---C--------------------T------AAA
dp4	chrXL_group1a:3316403-3316556 +	ATCACCC---CAAAAAGTGAGCAGACA-----TCGCG-A--CATGGCATCTGTTGCAGCTAGCGGGTGTTTTATCTGGTAGCTGTACCC--T-TTTG---AATCTATCATAAGACACACGCGGCTATGACCGAT--GCCC--AAACCATCCAAG---A----TTCAATAATTAGTAATC------AAT
droPer1	super_77:191839-191992 -	ATCACCC---CAAAAAGTGAGCAGACA-----TCGCG-A--CATGGCATCTGTTGCAGCTAGCGGGTGTTTTATCTGGTAGCTGTACCC--T-TTTG---AATCTATCATAAGACACACGCGGCTATGACCGAT--GCCC--AAACCATCCAAG---A----TTCAATAATTAGTAATC------AAT
droWil1	scaffold_181096:1892772-1892900 +	AGAGTGTAC---------------------AATCGTATT--CAGGGCATTTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGCACTA-AAATTTCAATAATCTATCATAAGACACACGCGGCTATGACCGAT--GTCTTT-----CT----------------------TAGCCAAC------AAT
droVir3	scaffold_13042:2658865-2658967 +	--------------------------------------------GACGTCTGTTGTAGCCAGCGGATGTTTTATTTGGTAGTTGCGCTT--T-ATTA---AATCTATCATAAGACACACGCGGCTATAACAGTGCCG--TTCA---------ACAAGCAA------------------C------GTC
droMoj3	scaffold_6328:939989-940116 -	TAAACCC---CA----GTGATCGACTATGAAA------ACAATTGACGTCTGTTGTAGCCAGCGGATGTTTTATTTGGTAGTTGTATTT--T-ATAA---AGTCTATCATAAGACACACGCGGCTATAACAGAACTG--TTCA---------ATA------------------------------AGC
droGri2	scaffold_15203:5475247-5475378 +	AAAGTCTGCCC-------------------AA------AAAATTGACGTCTGTTGTAGCCTGCGTATGTTTTATTTGGTAGTTGTAACTAAA-ATCG---AATCTATCATAAGACACACGCGGCTATCACAGTTCCG--TTCA---------ACAATCAACGTA--------------C-CATT-ACA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:12530354-12530478 +	AAAGTGCCCAT-------------------AA------TCGAAAGGCATCTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGTAATG--A-TTTG---AATCTATCATAAGACACACGCGGCTATAACCGTT--GTCT--AAGAGCTTCAAA---A-------------------TC------GAT
droSim1	chrX_random:3444234-3444357 +	AAAGTGAACGT-------------------AA------TCGAAAGGCATCTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGAATTG--A-TTTG---AATCTATCATAAGACACACGCGGCTATAACCGAT--GTCT--AAATGCTTCAAA-----------------------TC------GAC
droSec1	super_21:285079-285202 +	AAAGTGAACGT-------------------AA------TCGAAAGGCATCTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGAATTG--A-TTTG---AATCTATCATAAGACACACGCGGCTATAACCGAT--GTCT--AAATGCTTCAAA---A--------------------T------GAT
droYak2	chrX:6807144-6807273 +	ATAGTGCATTT-------------------AA------TCGAAAGGCATCTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGTAATG--A-TTTG---AATCTATCATAAGACACACGCGGCTATAACCGAT--GTCA--C---------ACATGCGACACA--------------CACATTAGAT
droEre2	scaffold_4690:14328958-14329082 -	AAAGTGC-CTT-------------------AA------TCGAAAGGCATCCGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGTAATG--A-TTTG---AATCTATCATAAGACACACGCGGCTATAACCGAT--GTCT--AAACGCTTCAAA---G----TG--------------C------AAT
droAna3	scaffold_13117:3438231-3438350 +	TTAGTGGA-------------------------------AGAAAGGCATTTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGATATC--G-AAAG---AATCTATCATAAGACACACGCGGCTATAATCGAT--GTCCTTAGAGTCTACAAG---C--------------------T------AAA
dp4	chrXL_group1a:3316403-3316556 +	ATCACCC---CAAAAAGTGAGCAGACA-----TCGCG-A--CATGGCATCTGTTGCAGCTAGCGGGTGTTTTATCTGGTAGCTGTACCC--T-TTTG---AATCTATCATAAGACACACGCGGCTATGACCGAT--GCCC--AAACCATCCAAG---A----TTCAATAATTAGTAATC------AAT
droPer1	super_77:191839-191992 -	ATCACCC---CAAAAAGTGAGCAGACA-----TCGCG-A--CATGGCATCTGTTGCAGCTAGCGGGTGTTTTATCTGGTAGCTGTACCC--T-TTTG---AATCTATCATAAGACACACGCGGCTATGACCGAT--GCCC--AAACCATCCAAG---A----TTCAATAATTAGTAATC------AAT
droWil1	scaffold_181096:1892772-1892900 +	AGAGTGTAC---------------------AATCGTATT--CAGGGCATTTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGCACTA-AAATTTCAATAATCTATCATAAGACACACGCGGCTATGACCGAT--GTCTTT-----CT----------------------TAGCCAAC------AAT
droVir3	scaffold_13042:2658865-2658967 +	--------------------------------------------GACGTCTGTTGTAGCCAGCGGATGTTTTATTTGGTAGTTGCGCTT--T-ATTA---AATCTATCATAAGACACACGCGGCTATAACAGTGCCG--TTCA---------ACAAGCAA------------------C------GTC
droMoj3	scaffold_6328:939989-940116 -	TAAACCC---CA----GTGATCGACTATGAAA------ACAATTGACGTCTGTTGTAGCCAGCGGATGTTTTATTTGGTAGTTGTATTT--T-ATAA---AGTCTATCATAAGACACACGCGGCTATAACAGAACTG--TTCA---------ATA------------------------------AGC
droGri2	scaffold_15203:5475247-5475378 +	AAAGTCTGCCC-------------------AA------AAAATTGACGTCTGTTGTAGCCTGCGTATGTTTTATTTGGTAGTTGTAACTAAA-ATCG---AATCTATCATAAGACACACGCGGCTATCACAGTTCCG--TTCA---------ACAATCAACGTA--------------C-CATT-ACA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

A----------AAGTGAAC-------GTAATCGAAAGGCATCTGTTGCAGCTAGCGGGTGTTTTATTTGGTAGCTGAATTGATTTGAATCTATCATAAGACACACGCGGCTATAACCGATGTCTAAATGCTTCAA----------------ATCGAC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
............................................................................................TCATAAGACACACGCGGCTAT............................................	21	1	804.00	804	804
............................................................................................TCATAAGACACACGCGGCTA.............................................	20	1	30.00	30	30
................................................AGCTAGCGGGTGTTTTATTTGGTA.....................................................................................	24	1	26.00	26	26
...........................................................................................ATCATAAGACACACGCGGCTAT............................................	22	1	16.00	16	16
............................................................................................TCATAAGACACACGCGGCTATA...........................................	22	1	12.00	12	12
..............................................................................................ATAAGACACACGCGGCTAT............................................	19	1	6.00	6	6
................................................AGCTAGCGGGTGTTTTATTTGGT......................................................................................	23	1	3.00	3	3
............................................................................................TCATAAGACACACGCGGCT..............................................	19	1	3.00	3	3
............................................................................................TCATAAGACACACGCGGCTATAA..........................................	23	1	2.00	2	2
...........................................................................................ATCATAAGACACACGCGGCT..............................................	20	1	1.00	1	1
...........................................................................................ATCATAAGACACACGCGGCTA.............................................	21	1	1.00	1	1

dp4

ATCACCCCAAAAAGTGAGCAGACATCGCGA---CATGGCATCTGTTGCAGCTAGCGGGTGTTTTATCTGGTAGCTGTACCCTTTTGAATCTATCATAAGACACACGCGGCTATGACCGATGCCCAAACCATCCAAGATTCAATAATTAGTAATCAAT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
............................................................................................TCATAAGACACACGCGGCTAT............................................	21	1	5657.00	5657	1053	4604
............................................................................................TCATAAGACACACGCGGCTA.............................................	20	1	323.00	323	58	265
............................................................................................TCATAAGACACACGCGGCT..............................................	19	1	120.00	120	7	113
................................................AGCTAGCGGGTGTTTTATCTGGTA.....................................................................................	24	1	97.00	97	28	69
...........................................................................................ATCATAAGACACACGCGGCTAT............................................	22	1	60.00	60	13	47
..............................................................................................ATAAGACACACGCGGCTAT............................................	19	1	44.00	44	8	36
...........................................................................................ATCATAAGACACACGCGGCT..............................................	20	1	13.00	13	0	13
................................................AGCTAGCGGGTGTTTTATCTGGT......................................................................................	23	1	13.00	13	7	6
...........................................................................................ATCATAAGACACACGCGGCTA.............................................	21	1	11.00	11	1	10
.............................................................................................CATAAGACACACGCGGCTAT............................................	20	1	9.00	9	1	8
.........................................................................................CTATCATAAGACACACGCGGCT..............................................	22	1	7.00	7	0	7
................................................AGCTAGCGGGTGTTTTATCTG........................................................................................	21	1	6.00	6	5	1
................................................AGCTAGCGGGTGTTTTATCTGG.......................................................................................	22	1	4.00	4	1	3
.............................................................................................CATAAGACACACGCGGCTA.............................................	19	1	3.00	3	1	2
........................................................................GCTGTACCCTTTTGAATCTA.................................................................	20	1	2.00	2	2	0
............................................................................................TCATAAGACACACGCGGC...............................................	18	1	1.00	1	1	0
..........................................................................................TATCATAAGACACACGCGGCTA.............................................	22	1	1.00	1	0	1
..........................................................TGTTTTATCTGGTAGCTGTACCC............................................................................	23	1	1.00	1	1	0
.........................................................................................CTATCATAAGACACACGCGG................................................	20	1	1.00	1	0	1
................................................AGCTAGCGGGTGTTTTATCT.........................................................................................	20	1	1.00	1	0	1
..............................................................................................ATAAGACACACGCGGCTA.............................................	18	1	1.00	1	0	1
...............................................................................................TAAGACACACGCGGCTAT............................................	18	1	1.00	1	1	0
.........................................................................................CTATCATAAGACACACGCGGC...............................................	21	1	1.00	1	1	0

Secondary Structure

dm3

dG=-23.9, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-23.1, p-value=0.009901

droSim1

dG=-22.3, p-value=0.009901	dG=-22.3, p-value=0.009901	dG=-21.8, p-value=0.009901	dG=-21.8, p-value=0.009901	dG=-21.8, p-value=0.009901

droSec1

dG=-22.3, p-value=0.009901	dG=-22.3, p-value=0.009901	dG=-21.8, p-value=0.009901	dG=-21.8, p-value=0.009901	dG=-21.8, p-value=0.009901

droYak2

dG=-23.9, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-23.1, p-value=0.009901

droEre2

dG=-23.9, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-23.1, p-value=0.009901

droAna3

dG=-21.1, p-value=0.009901	dG=-21.0, p-value=0.009901	dG=-20.8, p-value=0.009901	dG=-20.7, p-value=0.009901	dG=-20.6, p-value=0.009901

dp4

dG=-21.3, p-value=0.009901	dG=-20.9, p-value=0.009901	dG=-20.8, p-value=0.009901	dG=-20.7, p-value=0.009901	dG=-20.5, p-value=0.009901

droPer1

dG=-21.3, p-value=0.009901	dG=-20.9, p-value=0.009901	dG=-20.8, p-value=0.009901	dG=-20.7, p-value=0.009901	dG=-20.5, p-value=0.009901

droWil1

dG=-20.6, p-value=0.009901	dG=-20.1, p-value=0.009901	dG=-20.0, p-value=0.009901	dG=-19.8, p-value=0.009901

droVir3

dG=-28.8, p-value=0.009901	dG=-28.4, p-value=0.009901	dG=-28.3, p-value=0.009901	dG=-27.9, p-value=0.009901

droMoj3

dG=-29.2, p-value=0.009901	dG=-28.8, p-value=0.009901	dG=-28.7, p-value=0.009901	dG=-28.7, p-value=0.009901	dG=-28.4, p-value=0.009901

droGri2

dG=-25.1, p-value=0.009901	dG=-25.1, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.6, p-value=0.009901

Generated: 03/07/2013 at 07:16 PM