Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016465.1 Corchorus olitorius cultivar O-4 contig16498, 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: 61317
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1070 original size:15 final size:15
Alignment explanation
Indices: 1033--1071 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1023 ACCAAAAGCT
*
1033 GAGAAGAAGCCGGCA
1 GAGAAGAAGCCAGCA
*
1048 GAGAAGAAGCCAGCG
1 GAGAAGAAGCCAGCA
*
1063 GAGGAGAAG
1 GAGAAGAAG
1072 AAGACGACTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.44, T:0.00
Consensus pattern (15 bp):
GAGAAGAAGCCAGCA
Found at i:10804 original size:17 final size:16
Alignment explanation
Indices: 10754--10804 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
10744 AAACAAAATT
*
10754 AAAAGGAAAAAAGAAA
1 AAAAGGAAGAAAGAAA
* *
10770 AAAAAG-AGAGAGAGAA
1 AAAAGGAAGAAAGA-AA
10786 AAAAGGAAGACAAGAAA
1 AAAAGGAAGA-AAGAAA
10803 AA
1 AA
10805 TTAAATAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
15 5 0.19
16 12 0.44
17 7 0.26
18 3 0.11
ACGTcount: A:0.75, C:0.02, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAAGGAAGAAAGAAA
Found at i:18060 original size:19 final size:18
Alignment explanation
Indices: 18031--18066 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18021 AGCCATTTTC
18031 TAAGGCTAAATGCTCAAA
1 TAAGGCTAAATGCTCAAA
*
18049 TAAGGACTAAATGTTCAA
1 TAAGG-CTAAATGCTCAA
18067 GATTTATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (18 bp):
TAAGGCTAAATGCTCAAA
Found at i:26016 original size:13 final size:13
Alignment explanation
Indices: 25985--26017 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
25975 TAAATTGAAA
25985 ATTTTCTTTTTTCT
1 ATTTTC-TTTTTCT
25999 A-TTTCTTTTTCT
1 ATTTTCTTTTTCT
26011 ATTTTCT
1 ATTTTCT
26018 GTTTGGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.44
13 9 0.50
14 1 0.06
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTCTTTTTCT
Found at i:31484 original size:57 final size:57
Alignment explanation
Indices: 31415--31532 Score: 236
Period size: 57 Copynumber: 2.1 Consensus size: 57
31405 TAGGCTGTCC
31415 AAATTGATCTCTTTTTCTGTGGCATTATGTTCAAATTGATCTCTTAAAAGAAAAGAA
1 AAATTGATCTCTTTTTCTGTGGCATTATGTTCAAATTGATCTCTTAAAAGAAAAGAA
31472 AAATTGATCTCTTTTTCTGTGGCATTATGTTCAAATTGATCTCTTAAAAGAAAAGAA
1 AAATTGATCTCTTTTTCTGTGGCATTATGTTCAAATTGATCTCTTAAAAGAAAAGAA
31529 AAAT
1 AAAT
31533 ATCTCATAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (57 bp):
AAATTGATCTCTTTTTCTGTGGCATTATGTTCAAATTGATCTCTTAAAAGAAAAGAA
Found at i:33310 original size:29 final size:29
Alignment explanation
Indices: 33268--33339 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
33258 ATAATGTAGT
33268 GAGAACAGGAGTAAGATGGCGAAAAAAAA
1 GAGAACAGGAGTAAGATGGCGAAAAAAAA
33297 GAGAACAGGAGTAAGATGGCGAAAAAAAA
1 GAGAACAGGAGTAAGATGGCGAAAAAAAA
33326 GAGAACAGGAGTAA
1 GAGAACAGGAGTAA
33340 ACATGATTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.54, C:0.07, G:0.32, T:0.07
Consensus pattern (29 bp):
GAGAACAGGAGTAAGATGGCGAAAAAAAA
Found at i:42287 original size:30 final size:31
Alignment explanation
Indices: 42253--42312 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
42243 TGATGTTGCT
*
42253 ATGTCACGT-AGCATGTTCGATGATATTTTC
1 ATGTCACGTCAGCATGTTAGATGATATTTTC
* * *
42283 ATGTCATGTCATCATGTTAGGTGATATTTT
1 ATGTCACGTCAGCATGTTAGATGATATTTT
42313 AGATGATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.43
Consensus pattern (31 bp):
ATGTCACGTCAGCATGTTAGATGATATTTTC
Found at i:46459 original size:31 final size:31
Alignment explanation
Indices: 46423--46576 Score: 146
Period size: 31 Copynumber: 5.0 Consensus size: 31
46413 TTTGTGCACG
* * *
46423 TGACATGCCACGTGTCACTTTTGGGTACACA
1 TGACATGACACATGTCACTTTTTGGTACACA
* *
46454 TGACATGATACATGTCACTTTTTGATACACA
1 TGACATGACACATGTCACTTTTTGGTACACA
* * *
46485 TGACATGATACACGTCACTTTTTGGTATACA
1 TGACATGACACATGTCACTTTTTGGTACACA
* * * * *
46516 TGGCATGCCACATGTCGCTTTTTGGTATACG
1 TGACATGACACATGTCACTTTTTGGTACACA
* * * * *
46547 TGGCGTGTCATATGTCGCTTTTTGGTACAC
1 TGACATGACACATGTCACTTTTTGGTACAC
46577 GTGGCATGTC
Statistics
Matches: 105, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (31 bp):
TGACATGACACATGTCACTTTTTGGTACACA
Found at i:46579 original size:31 final size:31
Alignment explanation
Indices: 46502--46588 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
46492 ATACACGTCA
* * *
46502 CTTTTTGGTATACATGGCATGCCACATGTCG
1 CTTTTTGGTATACGTGGCATGTCATATGTCG
*
46533 CTTTTTGGTATACGTGGCGTGTCATATGTCG
1 CTTTTTGGTATACGTGGCATGTCATATGTCG
*
46564 CTTTTTGGTACACGTGGCATGTCAT
1 CTTTTTGGTATACGTGGCATGTCAT
46589 GTCGGACACC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (31 bp):
CTTTTTGGTATACGTGGCATGTCATATGTCG
Found at i:48093 original size:31 final size:31
Alignment explanation
Indices: 48055--48159 Score: 156
Period size: 31 Copynumber: 3.4 Consensus size: 31
48045 ACGGTGTCCG
*
48055 ATGTGGCATGCCATGTGTACCAAAAAGCGAC
1 ATGTGGCATGCCATGTGTACCAAAAAGTGAC
* *
48086 ATGTGGCAAGCCACGTGTACCAAAAAGTGAC
1 ATGTGGCATGCCATGTGTACCAAAAAGTGAC
** *
48117 ATGTATCACGCCATGTGTACCAAAAAGTGAC
1 ATGTGGCATGCCATGTGTACCAAAAAGTGAC
48148 ATGTGGCATGCC
1 ATGTGGCATGCC
48160 TCATGCACAA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 64 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (31 bp):
ATGTGGCATGCCATGTGTACCAAAAAGTGAC
Found at i:58292 original size:17 final size:18
Alignment explanation
Indices: 58270--58306 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
58260 CTAGTACTGA
58270 TATTATTTT-ATTTCCTT
1 TATTATTTTCATTTCCTT
*
58287 TATTATTTTCATTTTCTT
1 TATTATTTTCATTTCCTT
58305 TA
1 TA
58307 ATTTATACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTATTTTCATTTCCTT
Done.