Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017820.1 Corchorus olitorius cultivar O-4 contig17853, 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: 70440
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:691 original size:21 final size:21
Alignment explanation
Indices: 656--697 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
646 TGTGTGTGTG
*
656 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
678 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
698 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:1596 original size:21 final size:21
Alignment explanation
Indices: 1561--1602 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1551 TGTGTGTGTG
*
1561 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
1583 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
1603 GATCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:3973 original size:467 final size:467
Alignment explanation
Indices: 3100--4039 Score: 1871
Period size: 467 Copynumber: 2.0 Consensus size: 467
3090 GTCTCCTTAT
3100 CTTTTGTATTTAAGGAGTCGGCGAGTTAATATTTGTCGGCGATCAATTTATCTATCTGCGTAAGG
1 CTTTTGTATTTAAGGAGTCGGCGAGTTAATATTTGTCGGCGATCAATTTATCTATCTGCGTAAGG
3165 GAAGCGTGAGATTTTAATGATCACATTTCTTGTACATTTTCACTTTAGCATAGTGGAGAAGTCGC
66 GAAGCGTGAGATTTTAATGATCACATTTCTTGTACATTTTCACTTTAGCATAGTGGAGAAGTCGC
3230 CTAGCCAGTTGTGCTCTCTCGGGCTACAGAACAACAACTTTTACATTTTGTTCAATTAAGGATAA
131 CTAGCCAGTTGTGCTCTCTCGGGCTACAGAACAACAACTTTTACATTTTGTTCAATTAAGGATAA
3295 ACTGTCGAAATTGGTGAAATTGACTATGGAGGAGTGGTGCGATTTCAACATGAAGCATACCTTGA
196 ACTGTCGAAATTGGTGAAATTGACTATGGAGGAGTGGTGCGATTTCAACATGAAGCATACCTTGA
3360 TGATCCTTGAACTTTATCAACCATTCTGGTGAAATGTCAGATCAATCCGACACAGTTGGAAAAAC
261 TGATCCTTGAACTTTATCAACCATTCTGGTGAAATGTCAGATCAATCCGACACAGTTGGAAAAAC
3425 TTTGTTGCGGTTTTCAATTAAGGATAGGTTATCGTTTTAAGGTGATCTGAGCCTAGATTTTGTGC
326 TTTGTTGCGGTTTTCAATTAAGGATAGGTTATCGTTTTAAGGTGATCTGAGCCTAGATTTTGTGC
3490 CAAGTGAGTCGGAATACTTTTATTACATTATTTTATGGCTAAGTGTCGAATTTGAGCCATTTCAT
391 CAAGTGAGTCGGAATACTTTTATTACATTATTTTATGGCTAAGTGTCGAATTTGAGCCATTTCAT
3555 GTTTCGGGCATA
456 GTTTCGGGCATA
3567 CTTTTGTATTTAAGGAGTCGGCGAGTTAATATTTGTCGGCGATCAATTTATCTATCTGCGTAAGG
1 CTTTTGTATTTAAGGAGTCGGCGAGTTAATATTTGTCGGCGATCAATTTATCTATCTGCGTAAGG
3632 GAAGCGTGAGATTTTAATGATCACATTTCTTGTACATTTTCACTTTAGCATAGTGGAGAAGTCGC
66 GAAGCGTGAGATTTTAATGATCACATTTCTTGTACATTTTCACTTTAGCATAGTGGAGAAGTCGC
3697 CTAGCCAGTTGTGCTCTCTCGGGCTACAGAACAACAACTTTTACATTTTGTTCAATTAAGGATAA
131 CTAGCCAGTTGTGCTCTCTCGGGCTACAGAACAACAACTTTTACATTTTGTTCAATTAAGGATAA
3762 ACTGTCGAAATTGGTGAAATTGACTATGGAGGAGTGGTGCGATTTCAACATGAAGCATACCTTGA
196 ACTGTCGAAATTGGTGAAATTGACTATGGAGGAGTGGTGCGATTTCAACATGAAGCATACCTTGA
3827 TGATCCTTGAACTTTATCAACCATTCTGGTGAAATGTCAGATCAATCCGACACAGTTGGAAAAAC
261 TGATCCTTGAACTTTATCAACCATTCTGGTGAAATGTCAGATCAATCCGACACAGTTGGAAAAAC
3892 TTTGTTGCGGTTTTCAATTAAGGATAGGTTATCGTTTTAAGGTGATCTGAGCCTAGATTTTGTGC
326 TTTGTTGCGGTTTTCAATTAAGGATAGGTTATCGTTTTAAGGTGATCTGAGCCTAGATTTTGTGC
*
3957 CAAGTGAGTCGGAATACTTTTATTACATTATTTTATGGCTAATTGTCGAATTTGAGCCATTTCAT
391 CAAGTGAGTCGGAATACTTTTATTACATTATTTTATGGCTAAGTGTCGAATTTGAGCCATTTCAT
4022 GTTTCGGGCATA
456 GTTTCGGGCATA
4034 CTTTTG
1 CTTTTG
4040 CAAGTTATTC
Statistics
Matches: 472, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
467 472 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (467 bp):
CTTTTGTATTTAAGGAGTCGGCGAGTTAATATTTGTCGGCGATCAATTTATCTATCTGCGTAAGG
GAAGCGTGAGATTTTAATGATCACATTTCTTGTACATTTTCACTTTAGCATAGTGGAGAAGTCGC
CTAGCCAGTTGTGCTCTCTCGGGCTACAGAACAACAACTTTTACATTTTGTTCAATTAAGGATAA
ACTGTCGAAATTGGTGAAATTGACTATGGAGGAGTGGTGCGATTTCAACATGAAGCATACCTTGA
TGATCCTTGAACTTTATCAACCATTCTGGTGAAATGTCAGATCAATCCGACACAGTTGGAAAAAC
TTTGTTGCGGTTTTCAATTAAGGATAGGTTATCGTTTTAAGGTGATCTGAGCCTAGATTTTGTGC
CAAGTGAGTCGGAATACTTTTATTACATTATTTTATGGCTAAGTGTCGAATTTGAGCCATTTCAT
GTTTCGGGCATA
Found at i:9588 original size:34 final size:34
Alignment explanation
Indices: 9522--9588 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
9512 AACCATCTTT
* *****
9522 ATAAGACTATAATCATTCTTTTTTTTTTTGAAAA
1 ATAAGACTATAATCATTCTATTTGAACATGAAAA
9556 ATAAGACTATAATCATTCTATTTGAACATGAAA
1 ATAAGACTATAATCATTCTATTTGAACATGAAA
9589 GGTATAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (34 bp):
ATAAGACTATAATCATTCTATTTGAACATGAAAA
Found at i:18751 original size:11 final size:11
Alignment explanation
Indices: 18735--18769 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
18725 TTAGGTAAAC
18735 AGAAAAAAAAA
1 AGAAAAAAAAA
*
18746 AGAAAAAAAGA
1 AGAAAAAAAAA
*
18757 AGAAGAAAAAA
1 AGAAAAAAAAA
18768 AG
1 AG
18770 CCTTAAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:18762 original size:14 final size:13
Alignment explanation
Indices: 18737--18769 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
18727 AGGTAAACAG
18737 AAAAAA-AAAAGA
1 AAAAAAGAAAAGA
18749 AAAAAAGAAGAAGA
1 AAAAAAGAA-AAGA
18763 AAAAAAG
1 AAAAAAG
18770 CCTTAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 2 0.11
14 11 0.58
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAGA
Found at i:22384 original size:15 final size:16
Alignment explanation
Indices: 22364--22406 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
22354 AAACCTTAAA
22364 CCAAATTAAAAG-CAG
1 CCAAATTAAAAGTCAG
* *
22379 CCAAATTAATAGTTTAG
1 CCAAATTAAAAG-TCAG
22396 CCAAATTAAAA
1 CCAAATTAAAA
22407 TCCCAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 11 0.48
17 12 0.52
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.23
Consensus pattern (16 bp):
CCAAATTAAAAGTCAG
Found at i:35757 original size:37 final size:37
Alignment explanation
Indices: 35716--35790 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
35706 CAAGCCAACT
* *
35716 AGCCAA-GAGGCCAAATGTTAAGCATGCAGCTATATCA
1 AGCCAAGGA-GCCAAATGTGAACCATGCAGCTATATCA
* *
35753 AGCCAAGGAGCCAAATGTGCACCATGCAGCTCTATCA
1 AGCCAAGGAGCCAAATGTGAACCATGCAGCTATATCA
35790 A
1 A
35791 TTTCAATGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 31 0.94
38 2 0.06
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.17
Consensus pattern (37 bp):
AGCCAAGGAGCCAAATGTGAACCATGCAGCTATATCA
Found at i:37297 original size:73 final size:72
Alignment explanation
Indices: 37175--37326 Score: 223
Period size: 73 Copynumber: 2.1 Consensus size: 72
37165 GGTATGCATC
* * *
37175 TTGTTATATCTGTGATACGGTTAAAAGGACAGATAATTTGCAACGAACGGAGTATATAACCGAAT
1 TTGTTATATCCGTGATACGGTTAAAAGGACAGATAATTTGCAACAAACGGAGTATAAAACCGAAT
37240 TCCTGAA
66 TCCTGAA
* * * * *
37247 TTTTTATATCCGTGATATGGTTAAATGGGACAGATAATTTGCCACAAACGGAGTTTAAAACCGAA
1 TTGTTATATCCGTGATACGGTTAAA-AGGACAGATAATTTGCAACAAACGGAGTATAAAACCGAA
37312 TTCCTGAA
65 TTCCTGAA
37320 TTGTTAT
1 TTGTTAT
37327 GTTTTTTCAG
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 22 0.31
73 48 0.69
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (72 bp):
TTGTTATATCCGTGATACGGTTAAAAGGACAGATAATTTGCAACAAACGGAGTATAAAACCGAAT
TCCTGAA
Found at i:44130 original size:56 final size:56
Alignment explanation
Indices: 44029--44137 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 56
44019 CAGAGTAAAG
* * * *
44029 TCAGGCTCAGGCAGAAGTCGATCCTTTTACCACATTTCAACAGTAATTATCTTTAC
1 TCAGGCTCAGGCAGAAGTCGATCATTTAACCACATTTAAACAGTAATAATCTTTAC
* *
44085 TCAGGCTCAGGTAGAAG-CAGATCATTTAACCATC-TTTAAAGAGTAATAATCTT
1 TCAGGCTCAGGCAGAAGTC-GATCATTTAACCA-CATTTAAACAGTAATAATCTT
44138 ACAACATTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 1 0.02
56 43 0.96
57 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (56 bp):
TCAGGCTCAGGCAGAAGTCGATCATTTAACCACATTTAAACAGTAATAATCTTTAC
Found at i:44463 original size:93 final size:93
Alignment explanation
Indices: 44304--44488 Score: 282
Period size: 93 Copynumber: 2.0 Consensus size: 93
44294 ACTGTACAAT
* * *
44304 CAGCCTAGACATTTATAGTCTGTTATCTGTCATCTGCTTCATTGACTAATAAGGAACATTTGTCA
1 CAGCCTAGACATATATAGTCTGTCATCTCTCATCTGCTTCATTGACTAATAAGGAACATTTGTCA
* *
44369 CTTGGTGAGTATAGTAAGTAAAAACTAG
66 CTTGGTGAATAGAGTAAGTAAAAACTAG
* *
44397 CAGCCTAGACATATATAG-CTTGTCATCTCTTATCTGCTTCATTGACTAATAAGGGACATTTGTC
1 CAGCCTAGACATATATAGTC-TGTCATCTCTCATCTGCTTCATTGACTAATAAGGAACATTTGTC
*
44461 ACTTGGTGAATAGAGTAAGTAGAAACTA
65 ACTTGGTGAATAGAGTAAGTAAAAACTA
44489 ACTGCAGCAT
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 1 0.01
93 82 0.99
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (93 bp):
CAGCCTAGACATATATAGTCTGTCATCTCTCATCTGCTTCATTGACTAATAAGGAACATTTGTCA
CTTGGTGAATAGAGTAAGTAAAAACTAG
Found at i:50627 original size:48 final size:47
Alignment explanation
Indices: 50569--50665 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 47
50559 GTTATTGACC
*
50569 ATGTGGTTGAACC-AGTTTTGATTAATGTTAAAAAAATAAATGTTAATT
1 ATGTGATTGAACCGA-TTTTGATTAATGTTAAAAAAATAAATGTT-ATT
*
50617 ATGTGATTGAACCGATTTTGATTAATGTTAAAAAATTAAATGTTATT
1 ATGTGATTGAACCGATTTTGATTAATGTTAAAAAAATAAATGTTATT
50664 AT
1 AT
50666 TAGAATTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
47 5 0.11
48 40 0.87
49 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.41
Consensus pattern (47 bp):
ATGTGATTGAACCGATTTTGATTAATGTTAAAAAAATAAATGTTATT
Found at i:57114 original size:13 final size:13
Alignment explanation
Indices: 57096--57121 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57086 AAGGTAACAA
57096 CAAAAATCATCAC
1 CAAAAATCATCAC
57109 CAAAAATCATCAC
1 CAAAAATCATCAC
57122 TCATGCCAAG
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:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:58081 original size:17 final size:17
Alignment explanation
Indices: 58059--58098 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
58049 ATCACCCCCC
*
58059 AGATCACTAGTGAT-CTA
1 AGATCACCAGTGATGC-A
58076 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
58093 AGATCA
1 AGATCA
58099 ATGGTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:58810 original size:14 final size:14
Alignment explanation
Indices: 58791--58838 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
58781 GTCAAGCATG
58791 ACAGGAAAATCAAA
1 ACAGGAAAATCAAA
*
58805 ACAGGAAGAA--AAT
1 ACAGGAA-AATCAAA
*
58818 CCAGGAAAATCAAA
1 ACAGGAAAATCAAA
58832 ACAGGAA
1 ACAGGAA
58839 GAAAAATCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 2 0.07
13 8 0.30
14 15 0.56
15 2 0.07
ACGTcount: A:0.60, C:0.15, G:0.19, T:0.06
Consensus pattern (14 bp):
ACAGGAAAATCAAA
Found at i:58826 original size:27 final size:27
Alignment explanation
Indices: 58792--58843 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
58782 TCAAGCATGA
58792 CAGGAAAATCAAAACAGGAAGAAAATC
1 CAGGAAAATCAAAACAGGAAGAAAATC
58819 CAGGAAAATCAAAACAGGAAGAAAA
1 CAGGAAAATCAAAACAGGAAGAAAA
58844 ATCTGACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.62, C:0.13, G:0.19, T:0.06
Consensus pattern (27 bp):
CAGGAAAATCAAAACAGGAAGAAAATC
Found at i:58860 original size:15 final size:15
Alignment explanation
Indices: 58840--58871 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
58830 AAACAGGAAG
58840 AAAAATCTGACACAA
1 AAAAATCTGACACAA
*
58855 AAAAATCTGACATAA
1 AAAAATCTGACACAA
58870 AA
1 AA
58872 CAGAAACAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.16, G:0.06, T:0.16
Consensus pattern (15 bp):
AAAAATCTGACACAA
Found at i:62805 original size:22 final size:22
Alignment explanation
Indices: 62756--62806 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
62746 AAATATTACC
* **
62756 ATAATTATTTTTGGCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
62778 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
62801 A-AATTA
1 ATAATTA
62807 GGGAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Found at i:70276 original size:17 final size:18
Alignment explanation
Indices: 70239--70276 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
70229 ACCCTTGCCT
*
70239 AAAACTAGAAGAAAACTA
1 AAAACTAGAAGAAAACGA
*
70257 AAAACTATAAGAAAA-GA
1 AAAACTAGAAGAAAACGA
70274 AAA
1 AAA
70277 TATCTATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.71, C:0.08, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAACTAGAAGAAAACGA
Done.