Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024269.1 Corchorus olitorius cultivar O-4 contig24302, 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: 19657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:347 original size:32 final size:32
Alignment explanation
Indices: 311--373 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
301 CAAAATCCAG
311 CCCGAACCCGAATCAACCTGATCCAAATTTAC
1 CCCGAACCCGAATCAACCTGATCCAAATTTAC
343 CCCGAACCCGAATCAACCTGATCCAAATTTA
1 CCCGAACCCGAATCAACCTGATCCAAATTTA
374 ACCTGACTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.37, G:0.10, T:0.19
Consensus pattern (32 bp):
CCCGAACCCGAATCAACCTGATCCAAATTTAC
Found at i:795 original size:2 final size:2
Alignment explanation
Indices: 790--827 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
780 AAAAAAAAAC
790 TA TA TA TA TA TA TA TA TA TA TA TA TA 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
828 ACCGGTCACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5545 original size:20 final size:21
Alignment explanation
Indices: 5520--6158 Score: 119
Period size: 22 Copynumber: 29.1 Consensus size: 21
5510 TTTTATGAAA
5520 TTTGATAA-TCACTATAAAAT
1 TTTGATAACTCACTATAAAAT
5540 TTTGATAACCTCTA-TATAAAAT
1 TTTGATAA-CTC-ACTATAAAAT
*
5562 TTTGATAATTACACTATAAAATACT
1 TTTGATAACT-CACTAT-AAA-A-T
* * * *
5587 TTTTATGACGAT-ATTATAGAAT
1 TTTGATAAC--TCACTATAAAAT
* *
5609 TTTGAGAAACTC-CATATGAAAT
1 TTTGA-TAACTCAC-TATAAAAT
* * * *
5631 CTTGTTAACTTCCCTCTAAAAT
1 TTTGATAAC-TCACTATAAAAT
* *
5653 TTTAATAAC-CACCTAATGAAAT
1 TTTGATAACTCA-CT-ATAAAAT
*
5675 TTTGATAACTACTCTATAAAAT
1 TTTGATAACT-CACTATAAAAT
* * *
5697 TTTGATAACCTCCCAATGAAAT
1 TTTGATAA-CTCACTATAAAAT
* * *
5719 GTTGGTAAGCGCA-TATTATGAAAT
1 TTTGATAA-CTCACTA-TA--AAAT
* *
5743 TTTGACAACTTTC-CGATAAAAT
1 TTTGATAAC--TCACTATAAAAT
*
5765 ATTTG-TAA-TCACATTATGAAAT
1 -TTTGATAACTCAC--TATAAAAT
* *
5787 TTTGATAAC-CATACCATGAAAT
1 TTTGATAACTC--ACTATAAAAT
* * *
5809 TGTGATACCTCACTATGAAAT
1 TTTGATAACTCACTATAAAAT
*
5830 TTTTATAAACCTC-CATATAAAAT
1 TTTGAT-AA-CTCAC-TATAAAAT
* **
5853 TTTGATAACCTC-CATTTGGAAT
1 TTTGATAA-CTCAC-TATAAAAT
* **
5875 TTTGATAAC-CTC-ATGGAAT
1 TTTGATAACTCACTATAAAAT
* * *
5894 TTCGAAAAC-CACTTCATGAAAT
1 TTTGATAACTCAC-T-ATAAAAT
* * * *
5916 TTTGA-CA-TCCCCATAAATT
1 TTTGATAACTCACTATAAAAT
*
5935 TTTTATAACCTC-CTTATAAAAT
1 TTTGATAA-CTCAC-TATAAAAT
* * * * *
5957 TTTGGTAACCCCCAATGAAAT
1 TTTGATAACTCACTATAAAAT
*** *
5978 TTTGATAAGAAAACTATTAAAT
1 TTTGATAA-CTCACTATAAAAT
* * * * *
6000 TTTGGTAACCCCCAATGAAAT
1 TTTGATAACTCACTATAAAAT
*
6021 TTTGATAATTAACTACACCATAAAAT
1 TTTG---A-TAACT-CACTATAAAAT
* *
6047 TATGATAACTTACCTATAAAAT
1 TTTGATAACTCA-CTATAAAAT
* *
6069 TTTGTTAATCTCCCTATAAAAT
1 TTTGATAA-CTCACTATAAAAT
* * *
6091 TTTGAGAACCACACTATCAAAT
1 TTTGATAA-CTCACTATAAAAT
*
6113 TTTGTTAATCTCACTAT-AAAT
1 TTTGATAA-CTCACTATAAAAT
* *
6134 TTTGATAAACTCATTATGAAAT
1 TTTGAT-AACTCACTATAAAAT
6156 TTT
1 TTT
6159 AATTACCACA
Statistics
Matches: 447, Mismatches: 114, Indels: 114
0.66 0.17 0.17
Matches are distributed among these distances:
19 26 0.06
20 12 0.03
21 75 0.17
22 252 0.56
23 36 0.08
24 17 0.04
25 17 0.04
26 11 0.02
27 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.37
Consensus pattern (21 bp):
TTTGATAACTCACTATAAAAT
Found at i:5828 original size:21 final size:22
Alignment explanation
Indices: 5779--5830 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
5769 GTAATCACAT
*
5779 TATGAAATTTTGATAACCATAC
1 TATGAAATTGTGATAACCATAC
*
5801 CATGAAATTGTGAT-ACC-TCAC
1 TATGAAATTGTGATAACCAT-AC
5822 TATGAAATT
1 TATGAAATT
5831 TTTATAAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 13 0.50
22 12 0.46
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (22 bp):
TATGAAATTGTGATAACCATAC
Found at i:5977 original size:21 final size:21
Alignment explanation
Indices: 5953--6024 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
5943 CCTCCTTATA
5953 AAATTTTGGTAACCCCCAATG
1 AAATTTTGGTAACCCCCAATG
* **** * *
5974 AAATTTTGATAAGAAAACTATT
1 AAATTTTGGTAA-CCCCCAATG
5996 AAATTTTGGTAACCCCCAATG
1 AAATTTTGGTAACCCCCAATG
6017 AAATTTTG
1 AAATTTTG
6025 ATAATTAACT
Statistics
Matches: 36, Mismatches: 14, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
21 22 0.61
22 14 0.39
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (21 bp):
AAATTTTGGTAACCCCCAATG
Found at i:6091 original size:44 final size:44
Alignment explanation
Indices: 6040--6141 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 44
6030 TAACTACACC
* * *
6040 ATAAAATTATGATAACTTAC-CTATAAAATTTTGTTAATCTCCCT
1 ATAAAATTTTGATAAC-CACACTATAAAATTTTGTTAATCTCACT
* *
6084 ATAAAATTTTGAGAACCACACTATCAAATTTTGTTAATCTCACT
1 ATAAAATTTTGATAACCACACTATAAAATTTTGTTAATCTCACT
6128 AT-AAATTTTGATAA
1 ATAAAATTTTGATAA
6142 ACTCATTATG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
43 13 0.25
44 38 0.75
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (44 bp):
ATAAAATTTTGATAACCACACTATAAAATTTTGTTAATCTCACT
Found at i:6228 original size:61 final size:58
Alignment explanation
Indices: 6145--6258 Score: 149
Period size: 61 Copynumber: 1.9 Consensus size: 58
6135 TTGATAAACT
*
6145 CATTATGAAATTTTAATTACCACACAATGAAAATTTGATAACCTCTCCCTCTGAAATACCA
1 CATTATGAAATTTTAATAACCACACAATGAAAATTTGATAA--TCTCCCTC-GAAATACCA
* * *
6206 CATTAT-AATATTTTGATAACCACACTATGAAATTTTGATAATCTCCCTCGAAA
1 CATTATGAA-ATTTTAATAACCACACAATGAAAATTTGATAATCTCCCTCGAAA
6259 ATATCGATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 4 0.08
59 8 0.17
60 2 0.04
61 34 0.71
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (58 bp):
CATTATGAAATTTTAATAACCACACAATGAAAATTTGATAATCTCCCTCGAAATACCA
Found at i:6240 original size:22 final size:22
Alignment explanation
Indices: 6202--6360 Score: 78
Period size: 22 Copynumber: 7.4 Consensus size: 22
6192 CCTCTGAAAT
*
6202 ACCACATTAT-AATATTTTGATA
1 ACCACACTATGAA-ATTTTGATA
6224 ACCACACTATGAAATTTTGATA
1 ACCACACTATGAAATTTTGATA
* * * * * *
6246 ATCTCCCT-CGAAAATATCGATA
1 ACCACACTATG-AAATTTTGATA
* *
6268 ACCTGC-CTATGAAATTTTGTTA
1 ACC-ACACTATGAAATTTTGATA
* * *
6290 A-C-CTCTATGAAATTGTGATT
1 ACCACACTATGAAATTTTGATA
*** * *
6310 GTTAAACTATGAAATTTTGGTA
1 ACCACACTATGAAATTTTGATA
*
6332 ACGACACT-TGAAATTTTGATA
1 ACCACACTATGAAATTTTGATA
*
6353 AGCACACT
1 ACCACACT
6361 CTATCTCACT
Statistics
Matches: 100, Mismatches: 30, Indels: 15
0.69 0.21 0.10
Matches are distributed among these distances:
19 1 0.01
20 13 0.13
21 20 0.20
22 62 0.62
23 4 0.04
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (22 bp):
ACCACACTATGAAATTTTGATA
Found at i:6551 original size:21 final size:22
Alignment explanation
Indices: 6393--6742 Score: 207
Period size: 22 Copynumber: 15.8 Consensus size: 22
6383 TAAAGCACAC
*
6393 TATGAAATTTTGATAATCTTCC-
1 TATGAAATTTTGATAA-CCTCCT
* * * *
6415 TATGAAATTTCGATAATCGCCA
1 TATGAAATTTTGATAACCTCCT
* * *
6437 TATGAAATTTTGTTAGCCTCCC
1 TATGAAATTTTGATAACCTCCT
* ****
6459 TATGAGATTTTGATAACCAGAG
1 TATGAAATTTTGATAACCTCCT
** *
6481 TATGAAATGCT-AGTAACCTCCC
1 TATGAAATTTTGA-TAACCTCCT
* * * *
6503 TGTGAAAATTTCATAACCTTCT
1 TATGAAATTTTGATAACCTCCT
* *
6525 AATG-AATTTTGATAGCCTCCT
1 TATGAAATTTTGATAACCTCCT
*
6546 TATGAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCT
*
6568 TATGAAATTTTGATAACATCCT
1 TATGAAATTTTGATAACCTCCT
*
6590 TATGAAATTTTATTTTAATAACCTCCT
1 TATG-AA----ATTTTGATAACCTCCT
*
6617 TATGAAATTTTGATAACATCC-
1 TATGAAATTTTGATAACCTCCT
* * *
6638 CAAGAAATTGTGATAA-CTACAC-
1 TATGAAATTTTGATAACCT-C-CT
*
6660 TATAAAATTTTGAT-ACCTACC-
1 TATGAAATTTTGATAACCT-CCT
*
6681 TATGAAATTTTGGTAACCTCAC-
1 TATGAAATTTTGATAACCTC-CT
* *
6703 TATAAAATTTTGATAACCACAC-
1 TATGAAATTTTGATAACCTC-CT
* *
6725 TATAAAATTTTGAGAACC
1 TATGAAATTTTGATAACC
6743 ACACTATAAA
Statistics
Matches: 255, Mismatches: 59, Indels: 28
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.00
21 48 0.19
22 183 0.72
23 3 0.01
26 2 0.01
27 18 0.07
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCT
Found at i:6562 original size:43 final size:44
Alignment explanation
Indices: 6393--6719 Score: 163
Period size: 43 Copynumber: 7.4 Consensus size: 44
6383 TAAAGCACAC
* * *
6393 TATGAAATTTTGATAATCTTCC-TATGAAA-TTTCGATAATCGCCA
1 TATGAAATTTTGATAA-CATCCTTATGAAATTTTC-ATAACCTCCA
* * * * * * **
6437 TATGAAATTTTGTTAGCCTCCCTATGAGATTTTGATAACC-AGA
1 TATGAAATTTTGATAACATCCTTATGAAATTTTCATAACCTCCA
** * * * * *
6480 GTATGAAATGCT-AGTAACCTCCCTGTGAAAATTTCATAACCTTC-
1 -TATGAAATTTTGA-TAACATCCTTATGAAATTTTCATAACCTCCA
* * *
6524 TAATG-AATTTTGATAGCCTCCTTATGAAATTTTGATAACCTCCA
1 T-ATGAAATTTTGATAACATCCTTATGAAATTTTCATAACCTCCA
* *
6568 TATGAAATTTTGATAACATCCTTATGAAATTTTATTTTAATAACCTCCT
1 TATGAAATTTTGATAACATCCTTATG-AA----ATTTTCATAACCTCCA
* * * * *
6617 TATGAAATTTTGATAACATCC-CAAGAAATTGTGATAA-CTACA
1 TATGAAATTTTGATAACATCCTTATGAAATTTTCATAACCTCCA
* * **
6659 CTATAAAATTTTGAT-ACCTACC-TATGAAATTTTGGTAACCT-CA
1 -TATGAAATTTTGATAACAT-CCTTATGAAATTTTCATAACCTCCA
*
6702 CTATAAAATTTTGATAAC
1 -TATGAAATTTTGATAAC
6720 CACACTATAA
Statistics
Matches: 223, Mismatches: 42, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
42 6 0.03
43 89 0.40
44 84 0.38
45 5 0.02
47 2 0.01
48 2 0.01
49 35 0.16
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAACATCCTTATGAAATTTTCATAACCTCCA
Found at i:6616 original size:27 final size:27
Alignment explanation
Indices: 6574--6627 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
6564 TCCATATGAA
*
6574 ATTTTGATAACATCCTTATGAAATTTT
1 ATTTTAATAACATCCTTATGAAATTTT
*
6601 ATTTTAATAACCTCCTTATGAAATTTT
1 ATTTTAATAACATCCTTATGAAATTTT
6628 GATAACATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (27 bp):
ATTTTAATAACATCCTTATGAAATTTT
Found at i:6742 original size:22 final size:22
Alignment explanation
Indices: 6642--6767 Score: 134
Period size: 22 Copynumber: 5.8 Consensus size: 22
6632 ACATCCCAAG
* * *
6642 AAATTGTGATAACTACACTATA
1 AAATTTTGAGAACCACACTATA
* *
6664 AAATTTTGA-TACCTAC-CTATG
1 AAATTTTGAGAACC-ACACTATA
*
6685 AAATTTTG-GTAACCTCACTATA
1 AAATTTTGAG-AACCACACTATA
*
6707 AAATTTTGATAACCACACTATA
1 AAATTTTGAGAACCACACTATA
6729 AAATTTTGAGAACCACACTATA
1 AAATTTTGAGAACCACACTATA
6751 AAATTTT-AGTAACCACA
1 AAATTTTGAG-AACCACA
6768 ATGAATTTTG
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
21 17 0.19
22 71 0.81
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (22 bp):
AAATTTTGAGAACCACACTATA
Found at i:6748 original size:44 final size:44
Alignment explanation
Indices: 6642--6767 Score: 152
Period size: 44 Copynumber: 2.9 Consensus size: 44
6632 ACATCCCAAG
* * * *
6642 AAATTGTGATAACTACACTATAAAATTTTGAT-ACCTAC-CTATG
1 AAATTTTGAGAACCACACTATAAAATTTTGATAACC-ACACTATA
*
6685 AAATTTTG-GTAACCTCACTATAAAATTTTGATAACCACACTATA
1 AAATTTTGAG-AACCACACTATAAAATTTTGATAACCACACTATA
6729 AAATTTTGAGAACCACACTATAAAATTTT-AGTAACCACA
1 AAATTTTGAGAACCACACTATAAAATTTTGA-TAACCACA
6768 ATGAATTTTG
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
43 30 0.42
44 41 0.57
45 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (44 bp):
AAATTTTGAGAACCACACTATAAAATTTTGATAACCACACTATA
Found at i:6965 original size:2 final size:2
Alignment explanation
Indices: 6958--6989 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6948 AACCTGTAAC
*
6958 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6990 TAAGATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9904 original size:16 final size:16
Alignment explanation
Indices: 9883--9917 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
9873 CTTACTTTAT
9883 TTTTTATTAATTTGTA
1 TTTTTATTAATTTGTA
9899 TTTTTATTAATTTGTA
1 TTTTTATTAATTTGTA
9915 TTT
1 TTT
9918 AGAAAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTTATTAATTTGTA
Found at i:10612 original size:2 final size:2
Alignment explanation
Indices: 10605--10640 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10595 CTAAAACAGG
10605 TA TA TA TA TA TA TA TA TA TA TA TA 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
10641 ACACCCTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16331 original size:13 final size:13
Alignment explanation
Indices: 16306--16345 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
16296 ATATCATATT
16306 TTATATT-TATAA
1 TTATATTATATAA
16318 TTATATTATATAA
1 TTATATTATATAA
16331 TTA-ATTAATATAA
1 TTATATT-ATATAA
16344 TT
1 TT
16346 TAATTCTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATATTATATAA
Found at i:16832 original size:24 final size:24
Alignment explanation
Indices: 16788--16851 Score: 119
Period size: 24 Copynumber: 2.6 Consensus size: 24
16778 GAAAATCAAA
16788 CGGCCACATAGTTGGTCGTGAGATT
1 CGGCCACATAG-TGGTCGTGAGATT
16813 CGGCCACATAGTGGTCGTGAGATT
1 CGGCCACATAGTGGTCGTGAGATT
16837 CGGCCACATAGTGGT
1 CGGCCACATAGTGGT
16852 TGTGGGAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
24 28 0.72
25 11 0.28
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.25
Consensus pattern (24 bp):
CGGCCACATAGTGGTCGTGAGATT
Done.