Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012144.1 Corchorus olitorius cultivar O-4 contig12177, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51082
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:10612 original size:21 final size:19
Alignment explanation
Indices: 10588--10646 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 19
10578 CGTTGCTCTA
10588 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
* *
10607 ACATAATCTAATCTGTACGGT
1 --ATAATCTCATCTGTACAGT
*
10628 GTAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
10647 TGTTAAACAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:19694 original size:17 final size:15
Alignment explanation
Indices: 19674--19710 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
19664 GTTCATGTAT
19674 TATTATTATTTATATTA
1 TATTATTA-TTATA-TA
19691 TATTATTATTATATA
1 TATTATTATTATATA
19706 TATTA
1 TATTA
19711 ATTCAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.35
16 5 0.25
17 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTATTATATA
Found at i:19694 original size:20 final size:20
Alignment explanation
Indices: 19671--19710 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19661 ATTGTTCATG
*
19671 TATTATTATTATTTATATTA
1 TATTATTATTATATATATTA
19691 TATTATTATTATATATATTA
1 TATTATTATTATATATATTA
19711 ATTCAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTATTATTATATATATTA
Found at i:28312 original size:61 final size:61
Alignment explanation
Indices: 28215--28333 Score: 177
Period size: 61 Copynumber: 2.0 Consensus size: 61
28205 CACAGTTCTT
*
28215 ATATGCTTCACATACTGTACCTAATATCCGACACCCTATTCCGAGTCCAAGTATTCTTGTA
1 ATATGCTTCACATAATGTACCTAATATCCGACACCCTATTCCGAGTCCAAGTATTCTTGTA
* * * *
28276 ATATGCTTTACATAATGTATCGT-ATATCGGAGACCCTATTCCGAGTCCAAGTATTCTT
1 ATATGCTTCACATAATGTA-CCTAATATCCGACACCCTATTCCGAGTCCAAGTATTCTT
28334 TATACGCTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
61 50 0.96
62 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (61 bp):
ATATGCTTCACATAATGTACCTAATATCCGACACCCTATTCCGAGTCCAAGTATTCTTGTA
Found at i:38635 original size:31 final size:30
Alignment explanation
Indices: 38597--38682 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 30
38587 AACTTTTTGT
38597 AACCTTATACCCTGAATTGCATTTTCAGGCA
1 AACCTTATACCCTGAATTGCATTTT-AGGCA
* * *
38628 AACCTTATATCATGAAGTGCAATTTTAGGCA
1 AACCTTATACCCTGAATTGC-ATTTTAGGCA
38659 AACCTTATACCCTGAATTG-ATTTT
1 AACCTTATACCCTGAATTGCATTTT
38683 TAAACACAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.10
31 38 0.79
32 5 0.10
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (30 bp):
AACCTTATACCCTGAATTGCATTTTAGGCA
Found at i:40413 original size:14 final size:13
Alignment explanation
Indices: 40393--40431 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
40383 TTTGTTCTTG
*
40393 GAAAAAGGAAAAA
1 GAAAAAAGAAAAA
40406 GAAAAAAGAGAAAA
1 GAAAAAAGA-AAAA
40420 GAAAAAAGAAAA
1 GAAAAAAGAAAA
40432 GGAGAGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
GAAAAAAGAAAAA
Found at i:42866 original size:70 final size:70
Alignment explanation
Indices: 42771--42915 Score: 290
Period size: 70 Copynumber: 2.1 Consensus size: 70
42761 TATACACTAA
42771 ATTTGAAGGGACAATCAATAAAAATAAATAAATAAATAAATATAGTTGTACATATCTTCCTTAAG
1 ATTTGAAGGGACAATCAATAAAAATAAATAAATAAATAAATATAGTTGTACATATCTTCCTTAAG
42836 TTTGG
66 TTTGG
42841 ATTTGAAGGGACAATCAATAAAAATAAATAAATAAATAAATATAGTTGTACATATCTTCCTTAAG
1 ATTTGAAGGGACAATCAATAAAAATAAATAAATAAATAAATATAGTTGTACATATCTTCCTTAAG
42906 TTTGG
66 TTTGG
42911 ATTTG
1 ATTTG
42916 GCAGGAAAGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 75 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (70 bp):
ATTTGAAGGGACAATCAATAAAAATAAATAAATAAATAAATATAGTTGTACATATCTTCCTTAAG
TTTGG
Found at i:43315 original size:32 final size:32
Alignment explanation
Indices: 43279--43364 Score: 127
Period size: 32 Copynumber: 2.7 Consensus size: 32
43269 AAATTGAACG
*
43279 GGGGACAAATTTCCAATGCATTAATTACAAAT
1 GGGGACAAATTTACAATGCATTAATTACAAAT
**
43311 GGGGACAAATTTACAATGCATTAATTGTAAAT
1 GGGGACAAATTTACAATGCATTAATTACAAAT
* *
43343 GGGGACAAATTTGCAATTCATT
1 GGGGACAAATTTACAATGCATT
43365 TAAGTATATG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (32 bp):
GGGGACAAATTTACAATGCATTAATTACAAAT
Found at i:46477 original size:107 final size:107
Alignment explanation
Indices: 46291--46558 Score: 362
Period size: 107 Copynumber: 2.5 Consensus size: 107
46281 AATTTTTCTA
* **
46291 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGACTAAACTTAGTG-AATTAGTTATATAGTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTATATAGTTTA
* *
46354 TTTCTAAAATCCTATAACAATAAATTATTAATCATGGAATTT
66 TTTATAAAATCCTATAACAATAAATTATTAATCATGAAATTT
* * * * *
46396 ACTCTTAAAATAAAAATAAAATTTTAATTTGGGCCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTATATAGTTTA
* **
46461 TTTATAAAA-CCTTATAATAATAAATTATTAATTTTGAAATTT
66 TTTATAAAATCC-TATAACAATAAATTATTAATCATGAAATTT
* *
46503 ACCCTTAAAAGAAAAAATAAAATTTTAATTTGGAACTAAACTTAGTGAAATTAGTT
1 ACCCTTAAAA-TAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTT
46559 CTGATAAAAA
Statistics
Matches: 142, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
105 26 0.18
106 16 0.11
107 58 0.41
108 42 0.30
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (107 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTATATAGTTTA
TTTATAAAATCCTATAACAATAAATTATTAATCATGAAATTT
Found at i:47976 original size:29 final size:29
Alignment explanation
Indices: 47934--47992 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
47924 CACTGTCAGG
47934 CAAGCAGAACATAACACCTCATAAAACAC
1 CAAGCAGAACATAACACCTCATAAAACAC
47963 CAAGCAGAACATAACACCTCATAAAACAC
1 CAAGCAGAACATAACACCTCATAAAACAC
47992 C
1 C
47993 GAGAGCAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.51, C:0.32, G:0.07, T:0.10
Consensus pattern (29 bp):
CAAGCAGAACATAACACCTCATAAAACAC
Found at i:48319 original size:1 final size:1
Alignment explanation
Indices: 48315--48339 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
48305 ACCTTTTTTC
48315 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
48340 TTAGCTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.