Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016972.1 Corchorus olitorius cultivar O-4 contig17005, 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: 5534
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Found at i:3520 original size:14 final size:13
Alignment explanation
Indices: 3496--3530 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
3486 ATAATATTTA
*
3496 ATTATTATTTAGT
1 ATTAGTATTTAGT
3509 ATTTAGTATTTAGT
1 A-TTAGTATTTAGT
3523 ATTAGTAT
1 ATTAGTAT
3531 ATATATGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (13 bp):
ATTAGTATTTAGT
Found at i:3529 original size:6 final size:7
Alignment explanation
Indices: 3501--3530 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3491 ATTTAATTAT
3501 TATTTAG
1 TATTTAG
3508 TATTTAG
1 TATTTAG
3515 TATTTAG
1 TATTTAG
3522 TA-TTAG
1 TATTTAG
3528 TAT
1 TAT
3531 ATATATGGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (7 bp):
TATTTAG
Found at i:3702 original size:29 final size:29
Alignment explanation
Indices: 3642--3703 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
3632 TTGCTCCTTG
* *
3642 AAATAATTCTTCAAAGTCTTCAAATCTCC
1 AAATAAGTCTTCAAAGTCTTCAAATCTAC
3671 AAATAAGTCTTCAATGAGTCTTCAAA-C-AC
1 AAATAAGTCTTCAA--AGTCTTCAAATCTAC
3700 AAAT
1 AAAT
3704 TTCGAATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 18 0.62
30 1 0.03
31 10 0.34
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATAAGTCTTCAAAGTCTTCAAATCTAC
Found at i:5255 original size:35 final size:35
Alignment explanation
Indices: 5170--5532 Score: 199
Period size: 35 Copynumber: 10.5 Consensus size: 35
5160 TTTCAAATGC
* * *
5170 TTCAGTTCATTTCAAGTTGACCTAGAGCGGTCTTTA
1 TTCAATTCATTTC-AGTTGACCCAGGGCGGTCTTTA
* * * * *
5206 TTCAGTTTATTTCAGCTAACCCAGGGCGGTCTTTC
1 TTCAATTCATTTCAGTTGACCCAGGGCGGTCTTTA
* * * * *
5241 TTCAATTCACTTCAGTTGATCCAGGGTGATCCTTA
1 TTCAATTCATTTCAGTTGACCCAGGGCGGTCTTTA
*
5276 TTCAATTCATTTCAGTTGACCCAGGGTGGTC----
1 TTCAATTCATTTCAGTTGACCCAGGGCGGTCTTTA
* * *
5307 --C----CATTTCAGTTTGATCCAGGGCGATCCTTTC
1 TTCAATTCATTTCAG-TTGACCCAGGGCGGT-CTTTA
* * * *
5338 TTCAGTTTATTTCAGTTGGCCCAGGGCGGTCTTTC
1 TTCAATTCATTTCAGTTGACCCAGGGCGGTCTTTA
* * * * * *
5373 TTCAGTTTATTTCAATTGATCCAGGGCGATCTTTTC
1 TTCAATTCATTTCAGTTGACCCAGGGCGGTC-TTTA
* * * * * * *
5409 TTCAGTTTATTTCAATTGATCCAAGGCGATCTTTTC
1 TTCAATTCATTTCAGTTGACCCAGGGCGGTC-TTTA
* * * ** *
5445 TTCAGTTTATTTCAATTGAGGCAGGGCGGTCTTTC
1 TTCAATTCATTTCAGTTGACCCAGGGCGGTCTTTA
* * *
5480 TTCAGTTTATTTCAGTTGACCCA-GGCGGTCTTTC
1 TTCAATTCATTTCAGTTGACCCAGGGCGGTCTTTA
* *
5514 TTCAGTTTATTTCAGTTGA
1 TTCAATTCATTTCAGTTGA
5533 TC
Statistics
Matches: 276, Mismatches: 38, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
25 8 0.03
26 12 0.04
27 1 0.00
29 1 0.00
33 1 0.00
34 30 0.11
35 126 0.46
36 90 0.33
37 7 0.03
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.40
Consensus pattern (35 bp):
TTCAATTCATTTCAGTTGACCCAGGGCGGTCTTTA
Found at i:5395 original size:71 final size:70
Alignment explanation
Indices: 5317--5534 Score: 321
Period size: 71 Copynumber: 3.1 Consensus size: 70
5307 CCATTTCAGT
*
5317 TTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGGCCCAGGGCGGTCTTTCTTCAGTTTA
1 TTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGACCCA-GGCGGTCTTTCTTCAGTTTA
5382 TTTCAA
65 TTTCAA
* * * *
5388 TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAAGGCGATCTTTTCTTCAGTTT
1 TTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGA-CCCAGGCGGTC-TTTCTTCAGTTT
5453 ATTTCAA
64 ATTTCAA
** *
5460 TTGAGGCAGGGCGGT-CTTTCTTCAGTTTATTTCAGTTGACCCAGGCGGTCTTTCTTCAGTTTAT
1 TTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGACCCAGGCGGTCTTTCTTCAGTTTAT
*
5524 TTCAG
66 TTCAA
5529 TTGATC
1 TTGATC
Statistics
Matches: 130, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
69 22 0.17
70 9 0.07
71 65 0.50
72 34 0.26
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.42
Consensus pattern (70 bp):
TTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGACCCAGGCGGTCTTTCTTCAGTTTAT
TTCAA
Found at i:5416 original size:36 final size:35
Alignment explanation
Indices: 5317--5534 Score: 294
Period size: 36 Copynumber: 6.2 Consensus size: 35
5307 CCATTTCAGT
*
5317 TTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAG
1 TTGATCCAGGGCGAT-CTTTCTTCAGTTTATTTCAA
** *
5353 TTGGCCCAGGGCGGTCTTTCTTCAGTTTATTTCAA
1 TTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAA
5388 TTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAA
1 TTGATCCAGGGCGATC-TTTCTTCAGTTTATTTCAA
*
5424 TTGATCCAAGGCGATCTTTTCTTCAGTTTATTTCAA
1 TTGATCCAGGGCGATC-TTTCTTCAGTTTATTTCAA
** * *
5460 TTGAGGCAGGGCGGTCTTTCTTCAGTTTATTTCAG
1 TTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAA
* * *
5495 TTGACCCA-GGCGGTCTTTCTTCAGTTTATTTCAG
1 TTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAA
5529 TTGATC
1 TTGATC
Statistics
Matches: 165, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
34 31 0.19
35 56 0.34
36 78 0.47
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.42
Consensus pattern (35 bp):
TTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAA
Found at i:5470 original size:107 final size:105
Alignment explanation
Indices: 5317--5534 Score: 330
Period size: 107 Copynumber: 2.1 Consensus size: 105
5307 CCATTTCAGT
* *
5317 TTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGGCCCAGGGCGGTCTTTCTTCAGTTTA
1 TTGATCCAAGGCGATCCTTTCTTCAGTTTATTTCAATTGGCCCAGGGCGGTCTTTCTTCAGTTTA
*
5382 TTTCAATTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAA
66 TTTCAATTGACCCA-GGCGATC-TTTCTTCAGTTTATTTCAA
* *
5424 TTGATCCAAGGCGATCTTTTCTTCAGTTTATTTCAATTGAG-GCAGGGCGGTCTTTCTTCAGTTT
1 TTGATCCAAGGCGATCCTTTCTTCAGTTTATTTCAATTG-GCCCAGGGCGGTCTTTCTTCAGTTT
* * *
5488 ATTTCAGTTGACCCAGGCGGTCTTTCTTCAGTTTATTTCAG
65 ATTTCAATTGACCCAGGCGATCTTTCTTCAGTTTATTTCAA
5529 TTGATC
1 TTGATC
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
105 24 0.24
106 6 0.06
107 71 0.70
108 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.42
Consensus pattern (105 bp):
TTGATCCAAGGCGATCCTTTCTTCAGTTTATTTCAATTGGCCCAGGGCGGTCTTTCTTCAGTTTA
TTTCAATTGACCCAGGCGATCTTTCTTCAGTTTATTTCAA
Done.