Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017028.1 Corchorus olitorius cultivar O-4 contig17061, 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: 29609
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:646 original size:26 final size:27
Alignment explanation
Indices: 617--667 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
607 AAATTATAAG
*
617 TGAACATA-AAGTGACCAAAATGCCTC
1 TGAACATACAAATGACCAAAATGCCTC
**
643 TGAATGTACAAATGACCAAAATGCC
1 TGAACATACAAATGACCAAAATGCC
668 CCTGGATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.20
Consensus pattern (27 bp):
TGAACATACAAATGACCAAAATGCCTC
Found at i:3300 original size:31 final size:32
Alignment explanation
Indices: 3225--3326 Score: 143
Period size: 32 Copynumber: 3.2 Consensus size: 32
3215 TTTCCGTACA
*
3225 GAAACGCCGCTAAATAGTGGCATTTTTGAAAG
1 GAAACGCCGCTAAATAGTGGCGTTTTTGAAAG
*
3257 GAAACGCCGCTAAATAGTGGCGTTTTT-AATG
1 GAAACGCCGCTAAATAGTGGCGTTTTTGAAAG
* * * *
3288 TAAATGCCGCTAAATAGTGGCGTTTTTGTACG
1 GAAACGCCGCTAAATAGTGGCGTTTTTGAAAG
3320 GAAACGC
1 GAAACGC
3327 TGCAATTCCT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 28 0.46
32 33 0.54
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (32 bp):
GAAACGCCGCTAAATAGTGGCGTTTTTGAAAG
Found at i:5436 original size:22 final size:22
Alignment explanation
Indices: 5418--5462 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5408 TCCTCTTGAG
5418 ATAATTCTTCAATAA-TCTTCAA
1 ATAA-TCTTCAATAAGTCTTCAA
*
5440 ATTATCTTCAATAAGTCTTCAA
1 ATAATCTTCAATAAGTCTTCAA
5462 A
1 A
5463 CACGAACTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAATCTTCAATAAGTCTTCAA
Found at i:14330 original size:20 final size:21
Alignment explanation
Indices: 14277--14330 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
14267 TTTTCTTCTT
* *
14277 TTGCTTTGATTTGATTGATTA
1 TTGCCTTGATTTGATTGACTA
* *
14298 TTGCTTTGA-TTGATTGCCTA
1 TTGCCTTGATTTGATTGACTA
14318 TT-CCTTGATTTGA
1 TTGCCTTGATTTGA
14331 ATTAGTTGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.17
20 15 0.52
21 9 0.31
ACGTcount: A:0.17, C:0.11, G:0.19, T:0.54
Consensus pattern (21 bp):
TTGCCTTGATTTGATTGACTA
Found at i:15003 original size:18 final size:18
Alignment explanation
Indices: 14980--15016 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
14970 AAAAGGTAAT
**
14980 TAAAAAAATTTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
14998 TAAAAAAAAGTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
15016 T
1 T
15017 GATAAGAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTCA
Found at i:24316 original size:10 final size:10
Alignment explanation
Indices: 24301--24329 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
24291 CCATATTAAC
24301 AATTTTATTT
1 AATTTTATTT
24311 AATTTTATTT
1 AATTTTATTT
24321 AA-TTTATTT
1 AATTTTATTT
24330 CCTTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
AATTTTATTT
Found at i:25842 original size:26 final size:27
Alignment explanation
Indices: 25785--25851 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
25775 CAGACTCTGG
* *
25785 ATTTTGAGTTTCGAACATGACATGCAA
1 ATTTTGAGTTTTGAACATGAAATGCAA
*
25812 ATTTTGAGTTTTGAA-ATTAAATGCAA
1 ATTTTGAGTTTTGAACATGAAATGCAA
*
25838 ATTTTGAATTTTGA
1 ATTTTGAGTTTTGA
25852 CTTTTGAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 22 0.61
27 14 0.39
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.42
Consensus pattern (27 bp):
ATTTTGAGTTTTGAACATGAAATGCAA
Found at i:26050 original size:7 final size:7
Alignment explanation
Indices: 25909--26047 Score: 197
Period size: 7 Copynumber: 19.9 Consensus size: 7
25899 GAGCCATGAA
*
25909 TTTTGAA
1 TTTTGAG
25916 TTTTGAG
1 TTTTGAG
25923 TTTTGAG
1 TTTTGAG
25930 TTTTGAG
1 TTTTGAG
25937 TTTTGAG
1 TTTTGAG
*
25944 TTTTGCG
1 TTTTGAG
*
25951 TTTTGAA
1 TTTTGAG
*
25958 TTTTGAA
1 TTTTGAG
*
25965 TTTTGAA
1 TTTTGAG
25972 TTTTGAG
1 TTTTGAG
*
25979 TTTTGAA
1 TTTTGAG
25986 TTTTGAG
1 TTTTGAG
25993 TTTTGAG
1 TTTTGAG
26000 TTTTGAG
1 TTTTGAG
26007 TTTTGAG
1 TTTTGAG
26014 TTTTGAG
1 TTTTGAG
26021 TTTTGAG
1 TTTTGAG
*
26028 TTTTGAA
1 TTTTGAG
* *
26035 CTTTGAA
1 TTTTGAG
26042 TTTTGA
1 TTTTGA
26048 ATTGCCTATT
Statistics
Matches: 122, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 122 1.00
ACGTcount: A:0.19, C:0.01, G:0.23, T:0.57
Consensus pattern (7 bp):
TTTTGAG
Found at i:26257 original size:34 final size:34
Alignment explanation
Indices: 26203--26281 Score: 115
Period size: 34 Copynumber: 2.4 Consensus size: 34
26193 AGAAACTGTG
* * *
26203 GATTTTGAAC-TTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTTGAATTTTGAAATGAAATGCA
26236 GATTTTGAACTTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTTGAATTTTGAAATGAAATGCA
*
26270 AATTTTGAACTT
1 GATTTTGAACTT
26282 CTTAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 10 0.24
34 31 0.76
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (34 bp):
GATTTTGAACTTTTGAATTTTGAAATGAAATGCA
Found at i:26379 original size:56 final size:55
Alignment explanation
Indices: 26319--26428 Score: 150
Period size: 55 Copynumber: 2.0 Consensus size: 55
26309 AATTCAACCT
* * *
26319 TGATCATGGAAATATTTCTTGGAACGACCGCACTGGATCAA-TTTAGAGATCAACTC
1 TGATCATCGAAA-ACTTCTTGGAACGACCACACTGGATCAACTTTA-AGATCAACTC
* *
26375 TGATCATCGTAAACTTCTTGGAATGACCACACTGGATCAACTTTAAGATCAACT
1 TGATCATCGAAAACTTCTTGGAACGACCACACTGGATCAACTTTAAGATCAACT
26429 TAGACTTCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
55 34 0.71
56 14 0.29
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (55 bp):
TGATCATCGAAAACTTCTTGGAACGACCACACTGGATCAACTTTAAGATCAACTC
Found at i:26497 original size:20 final size:18
Alignment explanation
Indices: 26477--26518 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
26467 CATTTTAAAC
*
26477 ACAAAACATGAATTTTGA
1 ACAAAAAATGAATTTTGA
* *
26495 ACAAGAAATGGATTTTGA
1 ACAAAAAATGAATTTTGA
26513 ACAAAA
1 ACAAAA
26519 TTTTGATAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (18 bp):
ACAAAAAATGAATTTTGA
Found at i:26546 original size:37 final size:37
Alignment explanation
Indices: 26504--26699 Score: 94
Period size: 37 Copynumber: 5.3 Consensus size: 37
26494 AACAAGAAAT
26504 GGATTTTGAACAAAATTTTGATAAGAAACCTAAACTG
1 GGATTTTGAACAAAATTTTGATAAGAAACCTAAACTG
* * ** ** **
26541 GGATTTTGAAGAGACACCTAAAT-AGGTACCTAAACAT-
1 GGATTTTGAACA-AAATTTTGATAAGAAACCTAAAC-TG
* * * *
26578 GAATTTTGAACAAGATTTTGATGAGACACCTAAA-TAG
1 GGATTTTGAACAAAATTTTGATAAGAAACCTAAACT-G
** * * * * *
26615 GGACCTTAAATAAAGA-TTTAATAAGAAGCCTAAACAG
1 GGATTTTGAACAAA-ATTTTGATAAGAAACCTAAACTG
* * * * * *
26652 GAATGTTGAACAAGATTTTGATGAGACACCTAAACAG
1 GGATTTTGAACAAAATTTTGATAAGAAACCTAAACTG
*
26689 GGATCTTGAAC
1 GGATTTTGAAC
26700 CAGATTTCGA
Statistics
Matches: 111, Mismatches: 40, Indels: 16
0.66 0.24 0.10
Matches are distributed among these distances:
35 1 0.01
36 6 0.05
37 97 0.87
38 7 0.06
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (37 bp):
GGATTTTGAACAAAATTTTGATAAGAAACCTAAACTG
Found at i:26705 original size:37 final size:36
Alignment explanation
Indices: 26568--26923 Score: 297
Period size: 37 Copynumber: 9.7 Consensus size: 36
26558 CTAAATAGGT
* * * * *
26568 ACCTAAACATGAATTTTGAACAAGATTTTGATGAGAC
1 ACCTAAACAGGGATCTTAAACAAGA-TTTGATAAGAC
* * * *
26605 ACCTAAATAGGGACCTTAAATAAAGATTTAATAAGA-
1 ACCTAAACAGGGATCTTAAA-CAAGATTTGATAAGAC
* * * *
26641 AGCCTAAACAGGAATGTTGAACAAGATTTTGATGAGAC
1 A-CCTAAACAGGGATCTTAAACAAGA-TTTGATAAGAC
* *
26679 ACCTAAACAGGGATCTTGAACCAGATTTCGATGAA-AC
1 ACCTAAACAGGGATCTTAAACAAGATTT-GAT-AAGAC
* * *
26716 ACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAC
1 ACCTAAACAGGGATCTTAAACAA-GATTTGATAAGAC
* * * *
26753 ACCTAAATAGGGA-CTTTAAATAAGAATTAATAAGAC
1 ACCTAAACAGGGATC-TTAAACAAGATTTGATAAGAC
*
26789 ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAC
1 ACCTAAACAGGGATCTTAAACAA-GATTTGATAAGAC
* *
26826 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAA-AC
1 ACCTAAACAGGGATCTTAAACAAGA-TTTGAT-AAGAC
* * *
26863 ACCTAAACAGGGACCTTAAATAAGGACTTGATAAGAC
1 ACCTAAACAGGGATCTTAAACAA-GATTTGATAAGAC
** *
26900 ACCTAAACAGAAATCTTGAACAAG
1 ACCTAAACAGGGATCTTAAACAAG
26924 GTTTTGATGA
Statistics
Matches: 259, Mismatches: 45, Indels: 31
0.77 0.13 0.09
Matches are distributed among these distances:
36 47 0.18
37 197 0.76
38 15 0.06
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (36 bp):
ACCTAAACAGGGATCTTAAACAAGATTTGATAAGAC
Found at i:26718 original size:111 final size:109
Alignment explanation
Indices: 26568--26936 Score: 343
Period size: 111 Copynumber: 3.3 Consensus size: 109
26558 CTAAATAGGT
* * * * *
26568 ACCTAAACATGAATTTTGAACAAGATTTTGATGAGACACCTAAATAGGGACCTTAAATAAAGATT
1 ACCTAAACAGGGATCTTGAACAAGA-TTTGATGAAACACCTAAACAGGGACCTTAAATAAAGATT
* * * *
26633 TAATAAGA-AGCCTAAACA-GGAATGTTGAACAAGATTTTGATGAGAC
65 TAATAAGACA-CCTAAACAGGGAAT-TTAAACAAGA-ATTAATAAGAC
* *
26679 ACCTAAACAGGGATCTTGAACCAGATTTCGATGAAACACCTAAACAGGGACCTTAAATAAGGATT
1 ACCTAAACAGGGATCTTGAACAAGATTT-GATGAAACACCTAAACAGGGACCTTAAATAAAGATT
* * *
26744 TAATAAGACACCTAAATAGGGACTTTAAATAAGAATTAATAAGAC
65 TAATAAGACACCTAAACAGGGAATTTAAACAAGAATTAATAAGAC
* * * * * *
26789 ACCTAAACAGGGACCTTAAACAAGGATTTGAT-AAGACACCTAAACAGGAATCTTGAA-CAAGAT
1 ACCTAAACAGGGATCTTGAACAA-GATTTGATGAA-ACACCTAAACAGGGACCTTAAATAAAGA-
* ** * * *
26852 TTTGATGAA-ACACCTAAACAGGGACCTTAAATAAGGACTTGATAAGAC
63 TTTAAT-AAGACACCTAAACAGGGAATTTAAACAA-GAATTAATAAGAC
** *
26900 ACCTAAACAGAAATCTTGAACAAGGTTTTGATGAAAC
1 ACCTAAACAGGGATCTTGAACAA-GATTTGATGAAAC
26937 TGAATTTTGA
Statistics
Matches: 217, Mismatches: 32, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
109 5 0.02
110 81 0.37
111 124 0.57
112 7 0.03
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (109 bp):
ACCTAAACAGGGATCTTGAACAAGATTTGATGAAACACCTAAACAGGGACCTTAAATAAAGATTT
AATAAGACACCTAAACAGGGAATTTAAACAAGAATTAATAAGAC
Found at i:26721 original size:74 final size:73
Alignment explanation
Indices: 26586--26936 Score: 345
Period size: 74 Copynumber: 4.8 Consensus size: 73
26576 ATGAATTTTG
* * * * * *
26586 AACAA-GATTTTGATGAGACACCTAAATAGGGACCTTAAATAAAGATTTAAT-AAGA-AGCCTAA
1 AACAAGGA-TTTGATAAGACACCTAAACAGGGATCTTGAA-CAAGATTTGATGAA-ACA-CCTAA
* ** *
26648 ACAGGAATGTTG
62 ACAGGGACCTTA
* *
26660 AACAA-GATTTTGATGAGACACCTAAACAGGGATCTTGAACCAGATTTCGATGAAACACCTAAAC
1 AACAAGGA-TTTGATAAGACACCTAAACAGGGATCTTGAACAAGATTT-GATGAAACACCTAAAC
26724 AGGGACCTTA
64 AGGGACCTTA
* * * * * * *
26734 AATAAGGATTTAATAAGACACCTAAATAGGGA-CTTTAAATAAGAATTAAT-AAGACACCTAAAC
1 AACAAGGATTTGATAAGACACCTAAACAGGGATC-TTGAACAAGATTTGATGAA-ACACCTAAAC
26797 AGGGACCTTA
64 AGGGACCTTA
*
26807 AACAAGGATTTGATAAGACACCTAAACAGGAATCTTGAACAAGATTTTGATGAAACACCTAAACA
1 AACAAGGATTTGATAAGACACCTAAACAGGGATCTTGAACAAGA-TTTGATGAAACACCTAAACA
26872 GGGACCTTA
65 GGGACCTTA
* * ** *
26881 AATAAGGACTTGATAAGACACCTAAACAGAAATCTTGAACAAGGTTTTGATGAAAC
1 AACAAGGATTTGATAAGACACCTAAACAGGGATCTTGAACAA-GATTTGATGAAAC
26937 TGAATTTTGA
Statistics
Matches: 236, Mismatches: 31, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
72 2 0.01
73 65 0.28
74 161 0.68
75 8 0.03
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.23
Consensus pattern (73 bp):
AACAAGGATTTGATAAGACACCTAAACAGGGATCTTGAACAAGATTTGATGAAACACCTAAACAG
GGACCTTA
Found at i:26842 original size:147 final size:148
Alignment explanation
Indices: 26601--26906 Score: 465
Period size: 147 Copynumber: 2.1 Consensus size: 148
26591 GATTTTGATG
* ** *
26601 AGACACCTAAATAGGGACCTTAAATAAAGATTTAATAAGAAGCCTAAACAGGAATGTTGAACAAG
1 AGACACCTAAATAGGGACCTTAAATAAAGAATTAATAAGAAGCCTAAACAGGAACCTTAAACAAG
* * *
26666 ATTTTGATGAGACACCTAAACAGGGATCTTGAACCAGATTTCGATGAAACACCTAAACAGGGACC
66 ATTTTGATAAGACACCTAAACAGGAATCTTGAACAAGATTTCGATGAAACACCTAAACAGGGACC
*
26731 TTAAATAAGGATTTAATA
131 TTAAATAAGGACTTAATA
* *
26749 AGACACCTAAATAGGGACTTTAAAT-AAGAATTAATAAGACA-CCTAAACAGGGACCTTAAACAA
1 AGACACCTAAATAGGGACCTTAAATAAAGAATTAATAAGA-AGCCTAAACAGGAACCTTAAACAA
*
26812 GGA-TTTGATAAGACACCTAAACAGGAATCTTGAACAAGATTTTGATGAAACACCTAAACAGGGA
65 -GATTTTGATAAGACACCTAAACAGGAATCTTGAACAAGATTTCGATGAAACACCTAAACAGGGA
*
26876 CCTTAAATAAGGACTTGATA
129 CCTTAAATAAGGACTTAATA
26896 AGACACCTAAA
1 AGACACCTAAA
26907 CAGAAATCTT
Statistics
Matches: 144, Mismatches: 12, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
147 117 0.81
148 27 0.19
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.22
Consensus pattern (148 bp):
AGACACCTAAATAGGGACCTTAAATAAAGAATTAATAAGAAGCCTAAACAGGAACCTTAAACAAG
ATTTTGATAAGACACCTAAACAGGAATCTTGAACAAGATTTCGATGAAACACCTAAACAGGGACC
TTAAATAAGGACTTAATA
Found at i:27917 original size:10 final size:11
Alignment explanation
Indices: 27893--27919 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
27883 AACCTTTTGA
27893 TTTTTCTTTCT
1 TTTTTCTTTCT
27904 TTTTTCTTTCT
1 TTTTTCTTTCT
27915 TTTTT
1 TTTTT
27920 TTTTGCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:27922 original size:16 final size:16
Alignment explanation
Indices: 27887--27939 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
27877 GATTTGAACC
* *
27887 TTTTGATTTTTCTTTCT
1 TTTTGCTTTCTCTTT-T
* *
27904 TTTTTCTTTCTTTTTT
1 TTTTGCTTTCTCTTTT
27920 TTTTGCTTTCTCTTTT
1 TTTTGCTTTCTCTTTT
27936 TTTT
1 TTTT
27940 AGATTGCTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 19 0.63
17 11 0.37
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (16 bp):
TTTTGCTTTCTCTTTT
Found at i:28611 original size:13 final size:13
Alignment explanation
Indices: 28576--28614 Score: 69
Period size: 14 Copynumber: 2.9 Consensus size: 13
28566 ACTCAAAACC
28576 TTTTTGAAAATCA
1 TTTTTGAAAATCA
28589 TTTCTTGAAAATCA
1 TTT-TTGAAAATCA
28603 TTTTTGAAAATC
1 TTTTTGAAAATC
28615 GTCCTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTTTGAAAATCA
Done.