Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012408.1 Corchorus olitorius cultivar O-4 contig12441, 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: 27299
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:2832 original size:42 final size:43
Alignment explanation
Indices: 2782--2875 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
2772 AGTGCATTAC
*
2782 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATAAAAAAAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATAAAAAAAAAG
* * *
2823 CTGATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATAAAAAAAAAG
2868 CTAATATT
1 CTAATATT
2876 AATTGTTGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 3 0.07
42 6 0.14
45 35 0.80
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.33
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATAAAAAAAAAG
Found at i:3531 original size:2 final size:2
Alignment explanation
Indices: 3524--3551 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3514 TGTTATACTG
3524 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
3552 AATTAGGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4348 original size:12 final size:12
Alignment explanation
Indices: 4331--4377 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
4321 TCTTGGCGGC
*
4331 CCAGCGCCTGGA
1 CCAGCGCTTGGA
*
4343 CCAGCGTTTGGA
1 CCAGCGCTTGGA
4355 CCAGCGCTTGGA
1 CCAGCGCTTGGA
4367 CCAGCGCTTGG
1 CCAGCGCTTGG
4378 TCTAGCCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.15, C:0.34, G:0.34, T:0.17
Consensus pattern (12 bp):
CCAGCGCTTGGA
Found at i:11172 original size:11 final size:11
Alignment explanation
Indices: 11156--11186 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
11146 TCTGTTTTTT
11156 GTTTTTGTTTC
1 GTTTTTGTTTC
*
11167 GTTTTTGTTTT
1 GTTTTTGTTTC
11178 GTTTTTGTT
1 GTTTTTGTT
11187 ACGCTGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.19, T:0.77
Consensus pattern (11 bp):
GTTTTTGTTTC
Found at i:12134 original size:28 final size:28
Alignment explanation
Indices: 12072--12146 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
12062 TAGGGATATA
* *
12072 AAATTACCGATTTACCCTTGGAGTTGAT
1 AAATTACCGATTTACCCTTAGAGTGGAT
12100 AAATTACC-ATTCTACCCTTAGAG-GGAT
1 AAATTACCGATT-TACCCTTAGAGTGGAT
* *
12127 AAAGTTACAGTTTTACCCTT
1 AAA-TTACCGATTTACCCTT
12147 TTAACCTTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 9 0.22
28 29 0.73
29 2 0.05
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (28 bp):
AAATTACCGATTTACCCTTAGAGTGGAT
Found at i:17657 original size:27 final size:27
Alignment explanation
Indices: 17592--17659 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 27
17582 AGTGTTATCC
* *
17592 AGGGGCATTTTGGTCATTTGCACGTCT
1 AGGGGTATTTTGGTCATTTGCACATCT
* *
17619 -GGGGTATTTTGGTCATTTGTACATTT
1 AGGGGTATTTTGGTCATTTGCACATCT
17645 AGGGGTATTTTGGTC
1 AGGGGTATTTTGGTC
17660 CTTTTCGTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 22 0.61
27 14 0.39
ACGTcount: A:0.15, C:0.12, G:0.31, T:0.43
Consensus pattern (27 bp):
AGGGGTATTTTGGTCATTTGCACATCT
Found at i:19708 original size:27 final size:27
Alignment explanation
Indices: 19678--19745 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 27
19668 CAACGAAAAG
*
19678 GACCAAAATACCCCTAAATGTACAAAT
1 GACCAAAATACCCCTAAACGTACAAAT
* * *
19705 GACCAAAATACCAC-AGACGTGCAAAT
1 GACCAAAATACCCCTAAACGTACAAAT
*
19731 GACCAAAATGCCCCT
1 GACCAAAATACCCCT
19746 GGATAACACT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 21 0.62
27 13 0.38
ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15
Consensus pattern (27 bp):
GACCAAAATACCCCTAAACGTACAAAT
Found at i:25523 original size:7 final size:7
Alignment explanation
Indices: 25504--25537 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
25494 AAAGTTAAGA
25504 AAAAAAC
1 AAAAAAC
25511 ACAAAAAC
1 A-AAAAAC
25519 AAAAAAC
1 AAAAAAC
25526 AAAAAAC
1 AAAAAAC
25533 AAAAA
1 AAAAA
25538 TATGAAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:25883 original size:29 final size:29
Alignment explanation
Indices: 25823--25903 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
25813 GGCTAAATAC
* *
25823 ACAAAAAAATCCGTTATGTTTGCTTTTGGG
1 ACAAAATAATCCCTTATGTTT-CTTTTGGG
25853 ACAAAATAATCCCTTATGTTT-TTTTGGGG
1 ACAAAATAATCCCTTATGTTTCTTTT-GGG
* *
25882 ACAAATTAATCCCTTACGTTTC
1 ACAAAATAATCCCTTATGTTTC
25904 AAAAATGAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 4 0.09
29 22 0.49
30 19 0.42
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (29 bp):
ACAAAATAATCCCTTATGTTTCTTTTGGG
Found at i:26062 original size:30 final size:30
Alignment explanation
Indices: 26026--26120 Score: 154
Period size: 31 Copynumber: 3.1 Consensus size: 30
26016 AAGGGACTGA
26026 TTTGTCCCAAAAGAAAAACATAAGGGATTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTT
26056 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGA-TTT
* *
26087 TTTGTCCCAAAAGAAAAATATAAGAGAATTT
1 TTTGTCCCAAAAGAAAAACATAAG-GGATTT
26118 TTT
1 TTT
26121 TAGTATTTAG
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
30 27 0.44
31 32 0.52
32 2 0.03
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.31
Consensus pattern (30 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTT
Found at i:26091 original size:31 final size:31
Alignment explanation
Indices: 26026--26121 Score: 158
Period size: 30 Copynumber: 3.1 Consensus size: 31
26016 AAGGGACTGA
26026 TTTGTCCCAAAAGAAAAACATAAGGGA-TTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
26056 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
* *
26087 TTTGTCCCAAAAGAAAAATATAAGAGAATTTT
1 TTTGTCCCAAAAGAAAAACATAAG-GGATTTT
26119 TTT
1 TTT
26122 AGTATTTAGT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
30 27 0.44
31 26 0.42
32 9 0.15
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Found at i:26832 original size:126 final size:125
Alignment explanation
Indices: 26727--26960 Score: 305
Period size: 126 Copynumber: 1.9 Consensus size: 125
26717 TTCCTACCCT
* * **
26727 TATTTT-TCAAATATATTT-TTAAATGCCATT-TTTATACTTTTACAATTTTACTCAATTAAAAA
1 TATTTTATCAAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTACTCAACCAAAAA
**
26789 CTCTATTTTTATTTAATCAAA-TCTAATATATTTATAACTATTTTATTTTTACCATTTTAC
66 CTCTATTTTTATTTAATCAAATTC-AATATATTTATAACTATTTTATTAATACCATTTTAC
* * * **
26849 TATTTTAATTAAATATATTTCTTAAATGACATTATTTAAACTTTTACAGTTTTATTTTACCAAAA
1 TATTTT-ATCAAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTACTCAACCAAAA
* *
26914 ATTCTATTTTTATTTAATTAAATTCAATATATTTATAACTATTTTAT
65 ACTCTATTTTTATTTAATCAAATTCAATATATTTATAACTATTTTAT
26961 CTTTACCATT
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
122 6 0.06
124 11 0.11
125 11 0.11
126 66 0.69
127 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.53
Consensus pattern (125 bp):
TATTTTATCAAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTACTCAACCAAAAA
CTCTATTTTTATTTAATCAAATTCAATATATTTATAACTATTTTATTAATACCATTTTAC
Found at i:27072 original size:7 final size:7
Alignment explanation
Indices: 27060--27101 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
27050 GGAGTAGAGG
27060 GAAAAAA
1 GAAAAAA
27067 GAAAAAA
1 GAAAAAA
27074 GAAAAAA
1 GAAAAAA
27081 GAAAAAA
1 GAAAAAA
*
27088 GAAAGAA
1 GAAAAAA
27095 GAAAAAA
1 GAAAAAA
27102 AAATCAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:27203 original size:32 final size:32
Alignment explanation
Indices: 27146--27234 Score: 112
Period size: 31 Copynumber: 2.9 Consensus size: 32
27136 ACTAAATACT
* *
27146 AAAAAAATCCCTAATG-TTTTCTTTTGGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGGAA
*
27177 AAATAAATCCCTTATGTTTTTCTTTT-GGGAA
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGGAA
* *
27208 AAAAAAATCCC-TACGTTTTTTTTTTGG
1 AAAAAAATCCCTTATGTTTTTCTTTTGG
27235 ACAAATTAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.24
31 29 0.58
32 9 0.18
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (32 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGGAA
Done.