Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016093.1 Corchorus olitorius cultivar O-4 contig16126, 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: 26984
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Found at i:556 original size:20 final size:18
Alignment explanation
Indices: 531--583 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
521 CCGAGAAATC
*
531 AAAAACCAGCTCCTGCAGCT
1 AAAAACCAGCTCC-GC-GCA
**
551 AAAAACTTGCTCCGCGCA
1 AAAAACCAGCTCCGCGCA
569 AAAAACCAAGCTCCG
1 AAAAACC-AGCTCCG
584 TGCTTATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 8 0.30
19 8 0.30
20 11 0.41
ACGTcount: A:0.38, C:0.34, G:0.15, T:0.13
Consensus pattern (18 bp):
AAAAACCAGCTCCGCGCA
Found at i:3877 original size:43 final size:43
Alignment explanation
Indices: 3829--3946 Score: 121
Period size: 43 Copynumber: 2.7 Consensus size: 43
3819 ATTTATTCTT
* *
3829 TTACAAATTCCATACCAATCTTTTCAGGCCCAAGT-CTTTTTCC
1 TTACAAATTCCATACCAATCTTTTCAGGCCCAAATAC-TTTCCC
* ** * *
3872 TTACAAATGCTTTACAAATCTTTTCGGGCCCAAATACTTTCCC
1 TTACAAATTCCATACCAATCTTTTCAGGCCCAAATACTTTCCC
* * * *
3915 TTACAAACTCCATACCAAGCTTTACAAGCCCA
1 TTACAAATTCCATACCAATCTTTTCAGGCCCA
3947 GATTTTCTTT
Statistics
Matches: 58, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
43 57 0.98
44 1 0.02
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.32
Consensus pattern (43 bp):
TTACAAATTCCATACCAATCTTTTCAGGCCCAAATACTTTCCC
Found at i:6113 original size:10 final size:10
Alignment explanation
Indices: 6094--6136 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
6084 TTTAAGTAAC
6094 AATTAAAAAA
1 AATTAAAAAA
6104 AA-TAAAAAA
1 AATTAAAAAA
*
6113 AATTAAAAGA
1 AATTAAAAAA
*
6123 AATTTAAAAA
1 AATTAAAAAA
6133 AATT
1 AATT
6137 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 9 0.31
10 20 0.69
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (10 bp):
AATTAAAAAA
Found at i:6513 original size:26 final size:26
Alignment explanation
Indices: 6450--6519 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
6440 TTTTTGATCA
* *
6450 TATTTT-TGTTGGGCCTTTGTTTTTTT
1 TATTTTCTGTTGGG-CTTTGCTTTTCT
***
6476 TAGACTCT-TTGGGCTTTGCTTTTCT
1 TATTTTCTGTTGGGCTTTGCTTTTCT
6501 TATTTTCTGTTGGGCTTTG
1 TATTTTCTGTTGGGCTTTG
6520 TTTGTTACTT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
25 15 0.44
26 18 0.53
27 1 0.03
ACGTcount: A:0.06, C:0.13, G:0.21, T:0.60
Consensus pattern (26 bp):
TATTTTCTGTTGGGCTTTGCTTTTCT
Found at i:7308 original size:33 final size:34
Alignment explanation
Indices: 7265--7417 Score: 211
Period size: 33 Copynumber: 4.5 Consensus size: 34
7255 AGTTTTGTTT
7265 ATTGGGAAAGTTCCCACCAGTTTTAAGTTTT-TA
1 ATTGGGAAAGTTCCCACCAGTTTTAAGTTTTCTA
*
7298 ATTAGGAAAGTTCCCACCAGTTTTAAGTTTT-TA
1 ATTGGGAAAGTTCCCACCAGTTTTAAGTTTTCTA
*
7331 ATTGGGAAAGTTCCTACCAGTTTTAAGTTTTTCTAA
1 ATTGGGAAAGTTCCCACCAGTTTTAAG-TTTTCT-A
** * *
7367 ATTGGGAAAGTTCCCGTCAGCTTGTAAGTTTTCAA
1 ATTGGGAAAGTTCCCACCAG-TTTTAAGTTTTCTA
7402 ATTGGGAAAGTTCCCA
1 ATTGGGAAAGTTCCCA
7418 TTCGGTTTTT
Statistics
Matches: 107, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
33 57 0.53
34 4 0.04
35 17 0.16
36 23 0.21
37 6 0.06
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (34 bp):
ATTGGGAAAGTTCCCACCAGTTTTAAGTTTTCTA
Found at i:18867 original size:13 final size:13
Alignment explanation
Indices: 18849--18874 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18839 CTTGGCATGA
18849 GTGATGATTTTTG
1 GTGATGATTTTTG
18862 GTGATGATTTTTG
1 GTGATGATTTTTG
18875 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:19251 original size:18 final size:18
Alignment explanation
Indices: 19228--19287 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
19218 ACGGGCTGAA
* *
19228 ATTAATTAATTATTAATT
1 ATTAATTAAATAATAATT
19246 ATTAATTAAATAATAATT
1 ATTAATTAAATAATAATT
* * *
19264 ATTTTATTGAATAATTATT
1 A-TTAATTAAATAATAATT
19283 ATTAA
1 ATTAA
19288 AAATCTCACA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 20 0.57
19 15 0.43
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTAATTAAATAATAATT
Found at i:19278 original size:19 final size:19
Alignment explanation
Indices: 19229--19285 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
19219 CGGGCTGAAA
* *
19229 TTAATTAATTATTAATTA-
1 TTAATTAAATAATAATTAT
19247 TTAATTAAATAATAATTAT
1 TTAATTAAATAATAATTAT
* * *
19266 TTTATTGAATAATTATTAT
1 TTAATTAAATAATAATTAT
19285 T
1 T
19286 AAAAATCTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
18 16 0.48
19 17 0.52
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TTAATTAAATAATAATTAT
Found at i:23448 original size:93 final size:93
Alignment explanation
Indices: 23363--23539 Score: 300
Period size: 93 Copynumber: 1.9 Consensus size: 93
23353 ACTTTTTAAT
* *
23363 TAAATTAGTAATATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
23428 AGTTTTTAGTTGAGTAAAACTATAAAAG
66 AGTTTTTAGCTGAGTAAAACTATAAAAG
* *
23456 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
23521 AGTTTTTAGCTGATTAAAA
66 AGTTTTTAGCTGAGTAAAA
23540 AAATAAAAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGCTGAGTAAAACTATAAAAG
Found at i:23465 original size:22 final size:22
Alignment explanation
Indices: 23440--23486 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
23430 TTTTTAGTTG
*
23440 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
23462 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
23484 AGT
1 AGT
23487 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:23860 original size:31 final size:31
Alignment explanation
Indices: 23825--23886 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
23815 ATATTCGAAA
*
23825 AATAAGGGTATGATAGGCAATTCAAAAGTTT
1 AATAAGGGTATAATAGGCAATTCAAAAGTTT
*
23856 AATAAGGGTATAATAGGCGATTCAAAAGTTT
1 AATAAGGGTATAATAGGCAATTCAAAAGTTT
23887 TACAAAACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (31 bp):
AATAAGGGTATAATAGGCAATTCAAAAGTTT
Done.