Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024749.1 Corchorus olitorius cultivar O-4 contig24782, 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: 68911
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:471 original size:26 final size:26
Alignment explanation
Indices: 435--540 Score: 106
Period size: 26 Copynumber: 3.9 Consensus size: 26
425 TTAAGAGTGT
**
435 ACTTAAAATGACCAACGTGCCCCTGA
1 ACTTAAAATGACCAAAATGCCCCTGA
461 ACTTAAAATGACCAAAATGCCCCTGA
1 ACTTAAAATGACCAAAATGCCCCTGA
* *
487 A-TATGCAAATGACTAAAATGCCCCTAGA
1 ACT-T-AAAATGACCAAAATGCCCCT-GA
* *
515 TTCTTGAGAATGACCAAAATGCCCCT
1 -ACTT-AAAATGACCAAAATGCCCCT
541 AGTTGATCCT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
25 1 0.01
26 26 0.39
27 18 0.27
28 2 0.03
29 19 0.28
30 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (26 bp):
ACTTAAAATGACCAAAATGCCCCTGA
Found at i:534 original size:29 final size:28
Alignment explanation
Indices: 466--542 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
456 CCTGAACTTA
466 AAATGACCAAAATGCCCCT-GAATATGC
1 AAATGACCAAAATGCCCCTAGAATATGC
* * *
493 AAATGACTAAAATGCCCCTAGATTCTTG-
1 AAATGACCAAAATGCCCCTAGAAT-ATGC
521 AGAATGACCAAAATGCCCCTAG
1 A-AATGACCAAAATGCCCCTAG
543 TTGATCCTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 18 0.42
28 4 0.09
29 21 0.49
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.21
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTAGAATATGC
Found at i:6265 original size:2 final size:2
Alignment explanation
Indices: 6260--6298 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6250 TCTTTCTCGG
6260 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6299 TTGTTGCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11152 original size:49 final size:49
Alignment explanation
Indices: 11099--11197 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
11089 AGCAAAAAGG
*
11099 GCCTGGCACGACCCGCGCGCAGGTAGCTTGTCTTGAGACACGGAAATTT
1 GCCTGGCACGACCCGCCCGCAGGTAGCTTGTCTTGAGACACGGAAATTT
* * * * *
11148 GCCTGGCACTAGCCGCCCGCGGGTAGCTTGTCTTGAGACGCGGAGATTT
1 GCCTGGCACGACCCGCCCGCAGGTAGCTTGTCTTGAGACACGGAAATTT
11197 G
1 G
11198 TCTTGAGACA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.21
Consensus pattern (49 bp):
GCCTGGCACGACCCGCCCGCAGGTAGCTTGTCTTGAGACACGGAAATTT
Found at i:12380 original size:20 final size:18
Alignment explanation
Indices: 12338--12392 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 18
12328 CTGCCACGTC
12338 ATATTTTTATAAAAAAAAT
1 ATATTTTT-TAAAAAAAAT
12357 -TATTTTTTAAAAAATATAT
1 ATATTTTTTAAAAAA-A-AT
12376 ATATTTTTTAAAAAAAA
1 ATATTTTTTAAAAAAAA
12393 AATTGGGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
17 7 0.21
18 9 0.27
19 3 0.09
20 14 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATTTTTTAAAAAAAAT
Found at i:12445 original size:31 final size:30
Alignment explanation
Indices: 12402--12469 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
12392 AAATTGGGTG
12402 AGGGACCTAATTGCTTAATTAA-CTCAACTTC
1 AGGGACCTAATTGC-TAATTAAGCTC-ACTTC
* *
12433 AGGGA-CTCAATTGCTCATTAAGTTCACTTC
1 AGGGACCT-AATTGCTAATTAAGCTCACTTC
12463 AGGGACC
1 AGGGACC
12470 CATTTGCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (30 bp):
AGGGACCTAATTGCTAATTAAGCTCACTTC
Found at i:16823 original size:31 final size:31
Alignment explanation
Indices: 16785--16845 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
16775 GAAGAGATAT
16785 ATCACAATAAAACTAATAATAGTAAGACAAG
1 ATCACAATAAAACTAATAATAGTAAGACAAG
16816 ATCACAATAAAACTAATAATAGTAAGACAA
1 ATCACAATAAAACTAATAATAGTAAGACAA
16846 CATCTCAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.20
Consensus pattern (31 bp):
ATCACAATAAAACTAATAATAGTAAGACAAG
Found at i:23847 original size:44 final size:44
Alignment explanation
Indices: 23773--23892 Score: 150
Period size: 44 Copynumber: 2.7 Consensus size: 44
23763 TCCATGAAAC
* * * **
23773 AAAGTTTGGTTTAAAAACAATCATATTTAACAGCTACAATCAAAA
1 AAAGTTTGG-TTAAAAACAACCCTAATTAACAAATACAATCAAAA
* * *
23818 AAAGTTTGGTTAAAAACAACCCTAATTAACAAATACCATGAAAC
1 AAAGTTTGGTTAAAAACAACCCTAATTAACAAATACAATCAAAA
*
23862 AAAGTTTGGTTAAAAACAACCCTAATCAACA
1 AAAGTTTGGTTAAAAACAACCCTAATTAACA
23893 TATAGTTAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
44 57 0.86
45 9 0.14
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (44 bp):
AAAGTTTGGTTAAAAACAACCCTAATTAACAAATACAATCAAAA
Found at i:28710 original size:250 final size:250
Alignment explanation
Indices: 28267--28743 Score: 828
Period size: 250 Copynumber: 1.9 Consensus size: 250
28257 TAATGTTTTT
28267 AGTCTAGAACATTTGGCAGATTATGAATTTCCTTGGATTGAACATATCTTCCAATTTTTGAAGCC
1 AGTCTAGAACATTTGGCAGATTATGAATTTCCTTGGATTGAACATATCTTCCAATTTTTGAAGCC
*
28332 TTTTTATGATATAACCATGTTGTTTTCTGGATCTGACTATCGTACTGCAAACTTGTATATTGAGA
66 TTTTTATGATATAACCATGTTGTTTTCTGGATCTGACTATCCTACTGCAAACTTGTATATTGAGA
* *
28397 ATGTGATCATCATTCAAAAGAATATTGAGAATGAGCTTTTGTCGAATGATGTTGCTCTTAGAGAA
131 ATGTGATCATCATTCAAAAGAATATTGAGAAGGAGCATTTGTCGAATGATGTTGCTCTTAGAGAA
* *
28462 TTGGCTTTAAACATGAAAAACAAGTTTTCAAACTTGTTTTTCAGATGATGGTTAA
196 ATGGCTCTAAACATGAAAAACAAGTTTTCAAACTTGTTTTTCAGATGATGGTTAA
* *
28517 AGTCTAGAATATTTGGCAGATTATGAATTTCCTTGGATTGAACATATCTTCCAATTTTTGAAGGC
1 AGTCTAGAACATTTGGCAGATTATGAATTTCCTTGGATTGAACATATCTTCCAATTTTTGAAGCC
* * *
28582 TTTTTATGATATAAGCATGTTGTTTTCTGGATTTGACTATCCTACTGCAAACTTGTATTTTGAGA
66 TTTTTATGATATAACCATGTTGTTTTCTGGATCTGACTATCCTACTGCAAACTTGTATATTGAGA
* * * *
28647 ATGTGTTCATCATTCAGAAGATTATTGAGAAGGAGCATTTGTCGAATGATGTTGCTTTTAGAGAA
131 ATGTGATCATCATTCAAAAGAATATTGAGAAGGAGCATTTGTCGAATGATGTTGCTCTTAGAGAA
28712 ATGGCTCTAAACATGAAAAACAAGTTTTCAAA
196 ATGGCTCTAAACATGAAAAACAAGTTTTCAAA
28744 GTATTGGGAT
Statistics
Matches: 213, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
250 213 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (250 bp):
AGTCTAGAACATTTGGCAGATTATGAATTTCCTTGGATTGAACATATCTTCCAATTTTTGAAGCC
TTTTTATGATATAACCATGTTGTTTTCTGGATCTGACTATCCTACTGCAAACTTGTATATTGAGA
ATGTGATCATCATTCAAAAGAATATTGAGAAGGAGCATTTGTCGAATGATGTTGCTCTTAGAGAA
ATGGCTCTAAACATGAAAAACAAGTTTTCAAACTTGTTTTTCAGATGATGGTTAA
Found at i:29481 original size:43 final size:44
Alignment explanation
Indices: 29397--29482 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 44
29387 TACAAACATT
29397 CATGAAACAAAGTTTGGTTAAAAACAATCCTAATTAACAGATAC
1 CATGAAACAAAGTTTGGTTAAAAACAATCCTAATTAACAGATAC
* * * *
29441 CATGAGACAAAGTTTGG-TCAAACCAATCTTAATTAACAGATA
1 CATGAAACAAAGTTTGGTTAAAAACAATCCTAATTAACAGATA
29483 GTTTATGTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
43 22 0.58
44 16 0.42
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (44 bp):
CATGAAACAAAGTTTGGTTAAAAACAATCCTAATTAACAGATAC
Found at i:45772 original size:37 final size:37
Alignment explanation
Indices: 45721--45798 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
45711 ATATAATTAT
*
45721 TCATAAAGTCATGTCTATTTGGAAAGACATG-TGTTGA
1 TCATAAAGTCATGTCTATAT-GAAAGACATGATGTTGA
*
45758 TCATAAAGTTATGTCTATATGAAAGACATGTATGTTGA
1 TCATAAAGTCATGTCTATATGAAAGACATG-ATGTTGA
45796 TCA
1 TCA
45799 AGTATATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 10 0.27
37 18 0.49
38 9 0.24
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (37 bp):
TCATAAAGTCATGTCTATATGAAAGACATGATGTTGA
Found at i:47140 original size:20 final size:20
Alignment explanation
Indices: 47115--47169 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
47105 TCCGGGGGTG
47115 ACCCGGCCCCGGGTACCCCT
1 ACCCGGCCCCGGGTACCCCT
47135 ACCCGGCCCCGGGTACCCCT
1 ACCCGGCCCCGGGTACCCCT
* *
47155 ACCCGCCCCCAGGTA
1 ACCCGGCCCCGGGTA
47170 GCCTCAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.13, C:0.55, G:0.24, T:0.09
Consensus pattern (20 bp):
ACCCGGCCCCGGGTACCCCT
Found at i:56386 original size:5 final size:5
Alignment explanation
Indices: 56376--56420 Score: 65
Period size: 5 Copynumber: 8.8 Consensus size: 5
56366 AAGACATTGC
56376 TATAA TATAA TATAA TATAA TATAA TAT-A TATATA TATATA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA-A TATA-A TATA
56421 TGAATGTACC
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.11
5 23 0.61
6 11 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:56407 original size:2 final size:2
Alignment explanation
Indices: 56376--56421 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
56366 AAGACATTGC
56376 TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56413 TA TA TA TA T
1 TA TA TA TA T
56422 GAATGTACCA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 5 0.13
2 34 0.87
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:60001 original size:29 final size:29
Alignment explanation
Indices: 59959--60016 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
59949 ATCAAACGTA
59959 AGAACTTACTTTTGGCCAAAAAGGAAATT
1 AGAACTTACTTTTGGCCAAAAAGGAAATT
59988 AGAACTTACTTTTGGCCAAAAAGGAAATT
1 AGAACTTACTTTTGGCCAAAAAGGAAATT
60017 TCTTAAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (29 bp):
AGAACTTACTTTTGGCCAAAAAGGAAATT
Found at i:61073 original size:31 final size:31
Alignment explanation
Indices: 61036--61176 Score: 156
Period size: 31 Copynumber: 4.5 Consensus size: 31
61026 ACGGTGTTCG
*
61036 ACGTGGCATGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
* *
61067 ATGTGGCACGCCACGTGTACAAAAAAGCGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
* * * * *
61098 ATGTGACACGTCACGTGTACTAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
** * * *
61129 ACGTATCACGCCATGTGTACCCAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
*
61160 ACGTGGCATGCCACGTG
1 ACGTGGCACGCCACGTG
61177 CACAAAAGGA
Statistics
Matches: 92, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 92 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGCGAC
Found at i:65528 original size:11 final size:11
Alignment explanation
Indices: 65512--65537 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
65502 TCCAATTCCT
65512 TTCTTTTCTTC
1 TTCTTTTCTTC
65523 TTCTTTTCTTC
1 TTCTTTTCTTC
65534 TTCT
1 TTCT
65538 ACCTCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TTCTTTTCTTC
Found at i:66724 original size:13 final size:14
Alignment explanation
Indices: 66701--66734 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
66691 TCTTTGTCTC
66701 TTTTTGTTTTTTTT
1 TTTTTGTTTTTTTT
66715 TTTTTGTTTTTTTT
1 TTTTTGTTTTTTTT
66729 TATTTT
1 T-TTTT
66735 ATAGTAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.91
Consensus pattern (14 bp):
TTTTTGTTTTTTTT
Found at i:68553 original size:52 final size:51
Alignment explanation
Indices: 68487--68824 Score: 439
Period size: 52 Copynumber: 6.6 Consensus size: 51
68477 ATTGAAAACT
* *
68487 AAAACCTGGTGGGAACTTTCCCAATTTGCAAAAGAGCTAGATTGAATACTTTG
1 AAAA-CTGATGGGAACTTTCCCAATTTG-AAAAGAGCTAAATTGAATACTTTG
* *
68540 AAAACTGATGGGAACTTTCCCAAGTTGAAAAGAGCTAGATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
* *
68591 AAAACTTGATGGGAACTTTCCCAATTTAAAAAGAGCTAAATTGAATACTTTA
1 AAAAC-TGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
* * *
68643 AAAACTGGTGGGAACTTTCCCGACTTGCAAAAGAGCTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTG-AAAAGAGCTAAATTGAATACTTTG
* ** * **
68695 AAGACTGATGGGAACTTTCCGGACTTGAAAA-ATTTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
* * ** *
68745 AAGACTGATGGGAACTTTCCCGATTTGAAAA-ATTTAAATTGAATAC-TTA
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
68794 AAAACTGATGGGAACTTTCCCAATTTGAAAA
1 AAAACTGATGGGAACTTTCCCAATTTGAAAA
68825 CTTAAACATG
Statistics
Matches: 262, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
49 31 0.12
50 61 0.23
51 51 0.19
52 115 0.44
53 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (51 bp):
AAAACTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTTTG
Done.