Secondary structure and small RNA-seq evidence for dme-mir-1000

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:21414566-21414695 -	TATACCATGAA----------------AT-------------CG-GACGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAACACTATATT--ATAGTTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCAACG--------AGCGG---------------------------------------------------------------------------------CGGACA-----G-
droSim1	chr3R:21243636-21243765 -	TATACCATGAA----------------AT-------------CG-GACGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTTACACTATATT--ATAGTTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCAACG--------AGCGG---------------------------------------------------------------------------------CGGACA-----G-
droSec1	super_13:202504-202633 -	TATACCATGAA----------------AT-------------CG-GACGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAACACTATATT--ATAGTTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCAACG--------AGCGG---------------------------------------------------------------------------------CGGACA-----G-
droYak2	chr3R:25064545-25064667 +	--------GAA----------------TT-------------GG-GACGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAACACTATATT--ATAGCTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCAACG--------AGAGG---------------------------------------------------------------------------------CGGCCA-----G-
droEre2	scaffold_4820:6627814-6627943 +	TATACCATGAA----------------AT-------------CG-GACGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAACACTATATT--ATAGCTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCAACG--------AGCGG---------------------------------------------------------------------------------CGGTCA-----G-
droAna3	scaffold_13340:3670416-3670527 -	TA-------------------------------------------GACGCTTGCCGATGATATTGTCCTGTCACAGCAGTATTGTAATTCTATACTATATAGCTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCAACG--------AGG----------------------------------------------------------------------------------------A-----G-
dp4	chr2:21158113-21158302 -	TATCGA----ATTACATACGGCGTCGGATCGGAGCAGATGAGAG-GGCGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAAC--TTAATT--ATAGCCTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGCCATTGGCAACA--------AAGAGAAGGAGAAGCTACAAAGCTACAAAGCTACGGAAAAATGCT--------------------------------------------ACA-----G-
droPer1	super_3:3932619-3932791 -	TATCGA----ATTACATACGGCGTCGGATCGGAGCAGATGAGAG-GGCGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAAC--TTAATT--ATAGCCTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGCCATTGGCAACA--------AAGAG-----------------CTACAAAGCTACGGAAAAATGCT--------------------------------------------ACA-----G-
droWil1	scaffold_181130:14638697-14638859 +	TCCATCTAACA----------------AA-------------AG-AGAGCTTGCCAGTGATATTGTCCTGTCACAGCAGTATAGTAAC--ATATTC--ATTTCGTACTGCTGAGCCGGGGCATTAACATTGTTGAGCGTCTGTGGCAACG--------AGCGGAAAACT--------------------------------CTACTTCTGATGATGATAATAATGATTCAA--------------GTCAA-----A-
droVir3	scaffold_12855:6810247-6810376 -	TATATCGTCG-----------------AT-------------CGTTGCGCTTGCCAGTGATATTGTCCTGTCACAGCAGTATTGTACG--TTAAGC--AATTGGTACTGCTGAGCCGGGGCATTAACATTGTTGAGCGTCGTTAGCAACCAA------AAAGC---------------------------------------------------------------------------------CAGAAA-----A-
droMoj3	scaffold_6540:25791543-25791693 +	TCTATTAT-------------------------------------AGCGCTTGCCAGTGATATTGTCCTGTCACAGCAGTATTGTAAA--TTAAGC--AATTGGTACTGCTGAGCCGGGGCATTAACATTGTTGAGCGTCGTTAGCAACC--------AGAAGAAATCTAA--------------------------------------------------------TCGAGTCGACTATGCGGCATACACAGAGG-
droGri2	scaffold_14906:2964690-2964824 -	TATAT---TTA----------------AT-------------CGTTGCGCTTGCCAGTGATATTGTCCTGTCACAGCAGTATTGTTAA--TTAAGC--AATTGGTACTGCTGAGCCGGGGCATTAACATTGTTGAGCGTTGCTAGCAACTAAAAAGCGAGCAG---------------------------------------------------------------------------------CGAGCA-----GC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:21414566-21414695 -	TATACCATGAA----------------AT-------------CG-GACGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAACACTATATT--ATAGTTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCAACG--------AGCGG---------------------------------------------------------------------------------CGGACA-----G-
droSim1	chr3R:21243636-21243765 -	TATACCATGAA----------------AT-------------CG-GACGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTTACACTATATT--ATAGTTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCAACG--------AGCGG---------------------------------------------------------------------------------CGGACA-----G-
droSec1	super_13:202504-202633 -	TATACCATGAA----------------AT-------------CG-GACGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAACACTATATT--ATAGTTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCAACG--------AGCGG---------------------------------------------------------------------------------CGGACA-----G-
droYak2	chr3R:25064545-25064667 +	--------GAA----------------TT-------------GG-GACGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAACACTATATT--ATAGCTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCAACG--------AGAGG---------------------------------------------------------------------------------CGGCCA-----G-
droEre2	scaffold_4820:6627814-6627943 +	TATACCATGAA----------------AT-------------CG-GACGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAACACTATATT--ATAGCTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCAACG--------AGCGG---------------------------------------------------------------------------------CGGTCA-----G-
droAna3	scaffold_13340:3670416-3670527 -	TA-------------------------------------------GACGCTTGCCGATGATATTGTCCTGTCACAGCAGTATTGTAATTCTATACTATATAGCTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCAACG--------AGG----------------------------------------------------------------------------------------A-----G-
dp4	chr2:21158113-21158302 -	TATCGA----ATTACATACGGCGTCGGATCGGAGCAGATGAGAG-GGCGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAAC--TTAATT--ATAGCCTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGCCATTGGCAACA--------AAGAGAAGGAGAAGCTACAAAGCTACAAAGCTACGGAAAAATGCT--------------------------------------------ACA-----G-
droPer1	super_3:3932619-3932791 -	TATCGA----ATTACATACGGCGTCGGATCGGAGCAGATGAGAG-GGCGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAAC--TTAATT--ATAGCCTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGCCATTGGCAACA--------AAGAG-----------------CTACAAAGCTACGGAAAAATGCT--------------------------------------------ACA-----G-
droWil1	scaffold_181130:14638697-14638859 +	TCCATCTAACA----------------AA-------------AG-AGAGCTTGCCAGTGATATTGTCCTGTCACAGCAGTATAGTAAC--ATATTC--ATTTCGTACTGCTGAGCCGGGGCATTAACATTGTTGAGCGTCTGTGGCAACG--------AGCGGAAAACT--------------------------------CTACTTCTGATGATGATAATAATGATTCAA--------------GTCAA-----A-
droVir3	scaffold_12855:6810247-6810376 -	TATATCGTCG-----------------AT-------------CGTTGCGCTTGCCAGTGATATTGTCCTGTCACAGCAGTATTGTACG--TTAAGC--AATTGGTACTGCTGAGCCGGGGCATTAACATTGTTGAGCGTCGTTAGCAACCAA------AAAGC---------------------------------------------------------------------------------CAGAAA-----A-
droMoj3	scaffold_6540:25791543-25791693 +	TCTATTAT-------------------------------------AGCGCTTGCCAGTGATATTGTCCTGTCACAGCAGTATTGTAAA--TTAAGC--AATTGGTACTGCTGAGCCGGGGCATTAACATTGTTGAGCGTCGTTAGCAACC--------AGAAGAAATCTAA--------------------------------------------------------TCGAGTCGACTATGCGGCATACACAGAGG-
droGri2	scaffold_14906:2964690-2964824 -	TATAT---TTA----------------AT-------------CGTTGCGCTTGCCAGTGATATTGTCCTGTCACAGCAGTATTGTTAA--TTAAGC--AATTGGTACTGCTGAGCCGGGGCATTAACATTGTTGAGCGTTGCTAGCAACTAAAAAGCGAGCAG---------------------------------------------------------------------------------CGAGCA-----GC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TATACCATGAAAT------------C-------------GGACGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTTACACTATATTATAGTTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTCATTAGCAACG----------------------------AGCGGCGG---------ACAG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
......................................................ATATTGTCCTGTCACAGCAGTA....................................................................................................................	22	1	4519.00	4519	4519
......................................................ATATTGTCCTGTCACAGCAGT.....................................................................................................................	21	1	1421.00	1421	1421
...................................................................................................CTGCTGGGTCGGGGCATTAACA.......................................................................	22	1	82.00	82	82
......................................................ATATTGTCCTGTCACAGCAG......................................................................................................................	20	1	20.00	20	20
...................................................................................................CTGCTGGGTCGGGGCATTAAC........................................................................	21	1	18.00	18	18
.......................................................TATTGTCCTGTCACAGCAGTA....................................................................................................................	21	1	4.00	4	4
.........................................................TTGTCCTGTCACAGCAGTA....................................................................................................................	19	1	3.00	3	3
........................................................ATTGTCCTGTCACAGCAGTA....................................................................................................................	20	1	3.00	3	3
............................................................................TTGTTACACTATATTATAGTTTA.............................................................................................	23	1	3.00	3	3

dp4

TATCGAATTACATACGGCGTCGGATCGGAGCAGATGAGAGGGCGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAA--CTTAATTATAGCCTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGCCATTGGCAACAAAGAGAAGGAGAAGCTACAAAGCTACAAAGCTACGGAAAAATGCTACAG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
......................................................ATATTGTCCTGTCACAGCAGT.....................................................................................................................	21	1	12382.00	12382	2055	10327
......................................................ATATTGTCCTGTCACAGCAGTA....................................................................................................................	22	1	9294.00	9294	8201	1093
......................................................ATATTGTCCTGTCACAGCAG......................................................................................................................	20	1	1049.00	1049	20	1029
......................................................ATATTGTCCTGTCACAGCA.......................................................................................................................	19	1	377.00	377	9	368
...................................................................................................CTGCTGGGTCGGGGCATTAACA.......................................................................	22	1	120.00	120	95	25
...................................................................................................CTGCTGGGTCGGGGCATTAAC........................................................................	21	1	34.00	34	25	9
......................................................ATATTGTCCTGTCACAGCAGTAT...................................................................................................................	23	1	19.00	19	8	11
.......................................................TATTGTCCTGTCACAGCAGT.....................................................................................................................	20	1	13.00	13	5	8
.......................................................TATTGTCCTGTCACAGCAGTA....................................................................................................................	21	1	13.00	13	11	2
............................................................................TTGTAA--CTTAATTATAGCCTA.............................................................................................	21	1	10.00	10	9	1
...................................................................................................CTGCTGGGTCGGGGCATTA..........................................................................	19	1	7.00	7	3	4
..................................................................................................ACTGCTGGGTCGGGGCATTAAC........................................................................	22	1	5.00	5	2	3
.......................................................TATTGTCCTGTCACAGCAGTAT...................................................................................................................	22	1	4.00	4	0	4
........................................................ATTGTCCTGTCACAGCAGTA....................................................................................................................	20	1	3.00	3	3	0

Secondary Structure

dm3

-38.8	-38.7	-38.7	-38.6	-38.4	-38.3

droSim1

-37.3	-37.2	-37.1	-37.0	-36.9	-36.8

droSec1

-38.8	-38.7	-38.7	-38.6	-38.4	-38.3

droYak2

-38.7	-38.6	-38.3	-38.2	-38.2	-38.1

droEre2

-38.7	-38.6	-38.3	-38.2	-38.2	-38.1

droAna3

-40.4	-40.3	-40.3	-40.2	-40.0	-40.0

dp4

-41.1	-41.0	-40.7	-40.6	-40.6	-40.5

droPer1

-41.1	-41.0	-40.7	-40.6	-40.6	-40.5

droWil1

-34.3	-33.9	-33.4

droVir3

-37.9	-37.7	-37.6	-37.5	-37.3	-37.3

droMoj3

-37.9	-37.8	-37.5	-37.4	-37.4	-37.3

droGri2

-38.4	-38.0	-37.9	-37.7	-37.5	-37.4

Generated: 01/05/2013 at 05:04 PM