Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022769.1 Corchorus olitorius cultivar O-4 contig22802, 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: 11731
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:5171 original size:27 final size:27
Alignment explanation
Indices: 5131--5208 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
5121 AGTGGAGTGA
* *
5131 AAATGACCACAATGTCTCCTGAA-GTAC
1 AAATGACCAAAATG-CCCCTGAATGTAC
5158 AAATGACCAAAATGCCCCTGAATGTAC
1 AAATGACCAAAATGCCCCTGAATGTAC
*
5185 AAATGACCAAAATGCCCATGAATG
1 AAATGACCAAAATGCCCCTGAATG
5209 ACCTTAATGC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 7 0.15
27 40 0.85
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.19
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAATGTAC
Found at i:5694 original size:30 final size:30
Alignment explanation
Indices: 5651--6052 Score: 496
Period size: 30 Copynumber: 14.0 Consensus size: 30
5641 CAGAGTGATA
* * * * *
5651 ATCCTAAATCAGGATTGAAATAAAGTACTG
1 ATCCTCAACCAGGATTAAAATAAAGCAATG
*
5681 ATCCTCAACCAGGATTAAAATAAAGCATTG
1 ATCCTCAACCAGGATTAAAATAAAGCAATG
* * * *
5711 ATCTTCAGCCAGGATTAGAATGAAGC-A--
1 ATCCTCAACCAGGATTAAAATAAAGCAATG
5738 AT--T-AACCAGGATTAAAATAAA-CAATG
1 ATCCTCAACCAGGATTAAAATAAAGCAATG
*
5764 ATCCTAAACCAGG------AT----CAATG
1 ATCCTCAACCAGGATTAAAATAAAGCAATG
* *
5784 ATCCTCAACTAGGATTAAAATGAAGCAATG
1 ATCCTCAACCAGGATTAAAATAAAGCAATG
5814 ATCCTCAACCAGGATTAAAATAAAGCAATG
1 ATCCTCAACCAGGATTAAAATAAAGCAATG
*
5844 ATCCTCAACCAGGATTAAAATAAAGCGATG
1 ATCCTCAACCAGGATTAAAATAAAGCAATG
* *
5874 ATCCTTAACCGGGATTAAAATAAAGCAATG
1 ATCCTCAACCAGGATTAAAATAAAGCAATG
*
5904 ATCTTCAACCAGGATTAAAATAAAGCAATG
1 ATCCTCAACCAGGATTAAAATAAAGCAATG
5934 ATCCTCAACCAGGATTAAAATAAAGCAATG
1 ATCCTCAACCAGGATTAAAATAAAGCAATG
*
5964 ATCCTCAACCAGGATTAAAATAAAGCGATG
1 ATCCTCAACCAGGATTAAAATAAAGCAATG
*
5994 ATCCTTAACCAGGATTAAAATAAAGCAATG
1 ATCCTCAACCAGGATTAAAATAAAGCAATG
* *
6024 ATCGTCAACCGGGATTAAAATAAAGCAAT
1 ATCCTCAACCAGGATTAAAATAAAGCAAT
6053 AACGCAATGA
Statistics
Matches: 325, Mismatches: 31, Indels: 32
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.05
23 3 0.01
24 16 0.05
25 1 0.00
26 4 0.01
27 2 0.01
28 1 0.00
29 7 0.02
30 275 0.85
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.22
Consensus pattern (30 bp):
ATCCTCAACCAGGATTAAAATAAAGCAATG
Found at i:5784 original size:20 final size:20
Alignment explanation
Indices: 5759--5798 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5749 TTAAAATAAA
5759 CAATGATCCTAAACCAGGAT
1 CAATGATCCTAAACCAGGAT
* *
5779 CAATGATCCTCAACTAGGAT
1 CAATGATCCTAAACCAGGAT
5799 TAAAATGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.23
Consensus pattern (20 bp):
CAATGATCCTAAACCAGGAT
Found at i:6083 original size:38 final size:38
Alignment explanation
Indices: 6012--6085 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
6002 CCAGGATTAA
* * * *
6012 AATAAAGCAATGATCGTCAACCGGGATTAAAATAAAGC
1 AATAAAGCAATGATCCTAAACCAGGATCAAAATAAAGC
* *
6050 AATAACGCAATGATCCTAAACCAGGATCGAAATAAA
1 AATAAAGCAATGATCCTAAACCAGGATCAAAATAAA
6086 TTGATAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.18
Consensus pattern (38 bp):
AATAAAGCAATGATCCTAAACCAGGATCAAAATAAAGC
Found at i:6429 original size:168 final size:168
Alignment explanation
Indices: 6175--6576 Score: 569
Period size: 168 Copynumber: 2.4 Consensus size: 168
6165 AAACAAGGAT
* *
6175 CTTAAACATGAAATTTTGATGAAAAACTTGATGAAATCG-AATGGTACCCGGAGGTTTTATCAAT
1 CTTAAACATG-AATTTTGATGAAAAACTTGATGAAAT-GAAATGATACCCGGAGGTTTTACCAAT
*
6239 TGCTCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCC-GTAGGACTTACC
64 TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCAG-AGGACTTACC
* * * *
6303 -AATGCGATCTTTGAA-ATGAGACCTTAAACAAGGATTTTAAA
128 GAATG-AAACTCTGAATA-GAGACCTTAAACAAGGATTATAAA
* *
6344 CTTAAACATGAATTTTGATGAAAAACTTAATGAAATGAAATGATACCCGGAGGTTTTACCGATTG
1 CTTAAACATGAATTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTACCAATTG
* *
6409 CCCGGAGGACTTATCAGAATTACTACCCGGAGGTTTCTGAATTTGTGCCCAGAGGACTTACCGAT
66 CCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCAGAGGACTTACCGAA
* *
6474 TGAAACTCTGAATAGAGACCTTGACCAAGGATTATAAA
131 TGAAACTCTGAATAGAGACCTTAAACAAGGATTATAAA
* * * *
6512 CTTAAACATGAACTTTTAATGACAAACTTGATGAAATGAAATGATACCCAGAGGTTTTATCAATT
1 CTTAAACATGAA-TTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTACCAATT
6577 CAAACTCTGA
Statistics
Matches: 209, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
167 1 0.00
168 147 0.70
169 61 0.29
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (168 bp):
CTTAAACATGAATTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTACCAATTG
CCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCAGAGGACTTACCGAA
TGAAACTCTGAATAGAGACCTTAAACAAGGATTATAAA
Found at i:6684 original size:103 final size:102
Alignment explanation
Indices: 6476--6717 Score: 367
Period size: 103 Copynumber: 2.4 Consensus size: 102
6466 TTACCGATTG
* * * *
6476 AAACTCTGAATAGAGACCTTGACCAAGGATTATAAACTTAAACATGAACTTTTAATGACAAACTT
1 AAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTTAATAAAAAACTT
* *
6541 GATGAAATGAAATGATACCCAGAGGTTTTATCAATTC
66 GATAAAATGAAATGATACCCAGAGGTTTTATCAATGC
* * *
6578 AAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGGATTTTTGATAAAAAAACT
1 AAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTTAAT-AAAAAACT
*
6643 TGATAAAATGAAATGGTACCCAGAGGTTTTATCAATGC
65 TGATAAAATGAAATGATACCCAGAGGTTTTATCAATGC
* *
6681 AAACTCTGAACAGAGACCTTGAGCAAGGATTTTAAAC
1 AAACTCTGAATAGAGACCTTGAACAAGGATTTTAAAC
6718 ATGGAAAACT
Statistics
Matches: 127, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
102 51 0.40
103 76 0.60
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (102 bp):
AAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTTAATAAAAAACTT
GATAAAATGAAATGATACCCAGAGGTTTTATCAATGC
Found at i:6895 original size:69 final size:69
Alignment explanation
Indices: 6807--6981 Score: 298
Period size: 69 Copynumber: 2.5 Consensus size: 69
6797 GTAAGGCTTA
* *
6807 ACTCATATGGAAATGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAA
1 ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAA
*
6872 ATTG
66 ACTG
6876 ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAA
1 ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAA
6941 ACTG
66 ACTG
*
6945 ACAT-GTATGGAAACGAGTTTGACTTGTGGAAAAGCCT
1 AC-TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCT
6982 GAGTATTCGG
Statistics
Matches: 101, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
69 100 0.99
70 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.27
Consensus pattern (69 bp):
ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAA
ACTG
Found at i:8290 original size:8 final size:7
Alignment explanation
Indices: 8266--8298 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
8256 TTTTCTTCTC
8266 TTTTCAT
1 TTTTCAT
8273 TTTTCAT
1 TTTTCAT
8280 TTTTCAT
1 TTTTCAT
8287 TTTTCAAT
1 TTTTC-AT
8295 TTTT
1 TTTT
8299 TTTTTTGCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTCAT
Found at i:8618 original size:11 final size:11
Alignment explanation
Indices: 8602--8650 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
8592 TCGATTTTGA
8602 TTTTTTTTGTT
1 TTTTTTTTGTT
8613 TTTTTTTTG-T
1 TTTTTTTTGTT
** *
8623 TTTTTGATGAT
1 TTTTTTTTGTT
*
8634 TTTTTTTTATT
1 TTTTTTTTGTT
8645 TTTTTT
1 TTTTTT
8651 GATTTTTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
10 8 0.26
11 23 0.74
ACGTcount: A:0.06, C:0.00, G:0.08, T:0.86
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:8637 original size:31 final size:31
Alignment explanation
Indices: 8599--8661 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
8589 TTTTCGATTT
*
8599 TGATTTTTTTTGTTTTTTTTTTG-TTTTTTGA
1 TGATTTTTTTT-TATTTTTTTTGATTTTTTGA
8630 TGATTTTTTTTTATTTTTTTTGATTTTTTGA
1 TGATTTTTTTTTATTTTTTTTGATTTTTTGA
8661 T
1 T
8662 TTTTTTGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.10, C:0.00, G:0.11, T:0.79
Consensus pattern (31 bp):
TGATTTTTTTTTATTTTTTTTGATTTTTTGA
Found at i:8655 original size:10 final size:10
Alignment explanation
Indices: 8596--8667 Score: 78
Period size: 10 Copynumber: 7.3 Consensus size: 10
8586 TCTTTTTCGA
8596 TTTTGATTTT
1 TTTTGATTTT
*
8606 TTTTGTTTTTT
1 TTTTG-ATTTT
8617 TTTTG-TTTT
1 TTTTGATTTT
*
8626 TTGATGATTTT
1 TT-TTGATTTT
*
8637 TTTTTATTTT
1 TTTTGATTTT
8647 TTTTGA--TT
1 TTTTGATTTT
8655 TTTTGATTTT
1 TTTTGATTTT
8665 TTT
1 TTT
8668 GGAATTTCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
8 8 0.15
9 6 0.12
10 23 0.44
11 15 0.29
ACGTcount: A:0.08, C:0.00, G:0.10, T:0.82
Consensus pattern (10 bp):
TTTTGATTTT
Found at i:8674 original size:19 final size:18
Alignment explanation
Indices: 8635--8680 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
8625 TTTGATGATT
* *
8635 TTTTTTTATTTTTTTTGA
1 TTTTTTGATTTTTTTGGA
8653 TTTTTTGATTTTTTTGGAA
1 TTTTTTGATTTTTTTGG-A
*
8672 TTTCTTGAT
1 TTTTTTGAT
8681 GGAGTAGACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.13, C:0.02, G:0.11, T:0.74
Consensus pattern (18 bp):
TTTTTTGATTTTTTTGGA
Done.