Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014753.1 Corchorus olitorius cultivar O-4 contig14786, 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: 15762
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4065 original size:19 final size:18
Alignment explanation
Indices: 4041--4080 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
4031 AGAATAAATG
*
4041 AAAAATGAAAAGAAAGGGA
1 AAAAATG-AAAGAAACGGA
4060 AAAAATGAAAGAAACGGA
1 AAAAATGAAAGAAACGGA
4078 AAA
1 AAA
4081 GAATCAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.70, C:0.03, G:0.23, T:0.05
Consensus pattern (18 bp):
AAAAATGAAAGAAACGGA
Found at i:5126 original size:30 final size:30
Alignment explanation
Indices: 5068--6276 Score: 1223
Period size: 30 Copynumber: 40.1 Consensus size: 30
5058 TGATGAGGCC
5068 ATGATCCT-AAACCAGGATTAAAAAATAAAGCA
1 ATGATCCTCAAA-CAGGATT--AAAATAAAGCA
* *
5100 ATGAT-CTTAAACCAGGAATT-AAATAAAGCG
1 ATGATCCTCAAA-CAGG-ATTAAAATAAAGCA
*
5130 ATGATCCTCAACCAGGATTAAAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* *
5160 ATGATCCTCAACCAGGATTAAAAGTGAAGCA
1 ATGATCCTCAAACAGGATTAAAA-TAAAGCA
* *
5191 ATGATCCTCAAACAGGATTAAAATAGAGCG
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* * *
5221 ATGATCCTCAAATAGGATTAAAATAGAGCG
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* * *
5251 ATGATCCTCAAACAAGATTAAAATGAAGTA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* * * * *
5281 ATGATCCTCAACCAGGACTGACATAGAGCAA
1 ATGATCCTCAAACAGGATTAAAATAAAGC-A
* * *
5312 AT-ATTCTCAACCAGGATAAAAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
**
5341 ATGATCCTCAAACAGGACAAAAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
** *
5371 ATGATCCTCAAACAGGACAAAAATAAAACA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* *
5401 ATGATCCTCAAACAAGATTAAAA-AAAGTA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
5430 ATGATCCTCAAACAGGATTAAAAT--A--A
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* * *
5456 A-GATCCTTAATCAGGATTGAAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* * **
5485 ACGATCCTCAAACATGACAAAAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* *
5515 ATGATCCTAAAACAGGATTAAAATAAAGTA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* **
5545 ATGAACCTCAAACAGGATTAAAAGGAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* * * *
5575 ATGATCCTCGACCAGTATAAAAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* *
5605 ATAAACCTCAAACAGGATTAAAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* * *
5635 ACGATCCTCAAATAGGATAAAAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
*
5665 ATGATCCTCAAACAGGATTAAAATGAAGTGAAGTA
1 ATGATCCTCAAACAGGATTAAAAT--A---AAGCA
* *
5700 ATGATCTTCAACCAGGATTAAAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* **
5730 ACGATCCTCAAACAGGACAAAAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* *
5760 ATGATCCTCAAATAGGATTAAAATAAAGTA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
*
5790 ATGATCCTCAGAA-AGGACTAAAAT--A--A
1 ATGATCCTCA-AACAGGATTAAAATAAAGCA
* * *
5816 A-GATCCTTAATCAGGATTAAAATAAATCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* * **
5845 ACGATCCTCAAACATGACAAAAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
*
5875 ATGATCCTCAAACAGGATTAAAATAAAGTA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* **
5905 ATGATCCTCGAACAGGATTAAAAGGAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* * *
5935 ATGATCCTCGACCAGGATAAAAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* *
5965 ATGATCCTCAAACAGGATTAAAATAGAGCG
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* *
5995 ATGATCCTCAAACAGGATTAAAATGAAGTA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* *
6025 ATGATCCT-AAACCAGGATTAACATAGAGCAA
1 ATGATCCTCAAA-CAGGATTAAAATAAAGC-A
* * **
6056 AT-ATCCTCAACCAGGATAAAAATAAAATA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* *
6085 ATGATCCTCAAACAGGATTAAAATGAAGTA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
6115 ATGATCCTCAAACAGGATTTAAAATAAAGCA
1 ATGATCCTCAAACAGGA-TTAAAATAAAGCA
*
6146 ATGATCCTCAAACATGATTAAAATAAAACTGATAAAGCA
1 ATGATCCTCAAACAGGA-T----T-AAA---ATAAAGCA
*
6185 ATGATCCT-AAATAGGATTTAAAATAAAGCA
1 ATGATCCTCAAACAGGA-TTAAAATAAAGCA
* * *
6215 ATGATCCTCGAACAGGATTAAAATGAAGCC
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
* * *
6245 ATGATCCTTAACCAGGATTAAAATAAAACA
1 ATGATCCTCAAACAGGATTAAAATAAAGCA
6275 AT
1 AT
6277 CACGCAATGA
Statistics
Matches: 982, Mismatches: 156, Indels: 80
0.81 0.13 0.07
Matches are distributed among these distances:
24 1 0.00
25 36 0.04
26 4 0.00
27 2 0.00
28 2 0.00
29 42 0.04
30 740 0.75
31 79 0.08
32 14 0.01
33 7 0.01
34 1 0.00
35 27 0.03
36 3 0.00
38 8 0.01
39 16 0.02
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (30 bp):
ATGATCCTCAAACAGGATTAAAATAAAGCA
Found at i:5481 original size:25 final size:25
Alignment explanation
Indices: 5394--5482 Score: 79
Period size: 25 Copynumber: 3.4 Consensus size: 25
5384 AGGACAAAAA
* * *
5394 TAAAACAATGATCCTCAAACAAGAT
1 TAAAATAAAGATCCTCAAACAGGAT
*
5419 TAAAAAAAGTAATGATCCTCAAACAGGAT
1 T---AAAA-TAAAGATCCTCAAACAGGAT
* *
5448 TAAAATAAAGATCCTTAATCAGGAT
1 TAAAATAAAGATCCTCAAACAGGAT
*
5473 TGAAATAAAG
1 TAAAATAAAG
5483 CAACGATCCT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
25 27 0.50
26 4 0.07
28 4 0.07
29 19 0.35
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.22
Consensus pattern (25 bp):
TAAAATAAAGATCCTCAAACAGGAT
Found at i:6709 original size:156 final size:156
Alignment explanation
Indices: 6425--6746 Score: 599
Period size: 156 Copynumber: 2.1 Consensus size: 156
6415 TGATGAGAAA
*
6425 TTTGATGAAATCAAATGGTACCCGGAGGTTTTACCGATTGCCTGGAGGACTTATCAGAATTACTA
1 TTTGATGAAATCAAATGGTACCCGGAGGTTTTACCGATTGCCCGGAGGACTTATCAGAATTACTA
6490 CCCGGAGGTTTCTGAAGTTGTGCCCGGAGGACTTACCAACGCAAACTCTGAATAGAGACCTTAAA
66 CCCGGAGGTTTCTGAAGTTGTGCCCGGAGGACTTACCAACGCAAACTCTGAATAGAGACCTTAAA
6555 AAAGGATTTTAAAATTAAACATGAAT
131 AAAGGATTTTAAAATTAAACATGAAT
* *
6581 TTTGATGAAATGAAATGGTACCTGGAGGTTTTACCGATTGCCCGGAGGACTTATCAGAATTACTA
1 TTTGATGAAATCAAATGGTACCCGGAGGTTTTACCGATTGCCCGGAGGACTTATCAGAATTACTA
*
6646 CCCGGAGGTTTCTGAAGTTGTGCCCGGAGGACTTATCAACGCAAACTCTGAATAGAGACCTTAAA
66 CCCGGAGGTTTCTGAAGTTGTGCCCGGAGGACTTACCAACGCAAACTCTGAATAGAGACCTTAAA
*
6711 CAAGGATTTTAAAATTAAACATGAAT
131 AAAGGATTTTAAAATTAAACATGAAT
6737 TTTGATGAAA
1 TTTGATGAAA
6747 AACTTGATGA
Statistics
Matches: 161, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 161 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (156 bp):
TTTGATGAAATCAAATGGTACCCGGAGGTTTTACCGATTGCCCGGAGGACTTATCAGAATTACTA
CCCGGAGGTTTCTGAAGTTGTGCCCGGAGGACTTACCAACGCAAACTCTGAATAGAGACCTTAAA
AAAGGATTTTAAAATTAAACATGAAT
Found at i:6770 original size:15 final size:15
Alignment explanation
Indices: 6731--6777 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
6721 AAAATTAAAC
6731 ATGAATTTTGATGAA
1 ATGAATTTTGATGAA
*
6746 A--AA-CTTGATGAA
1 ATGAATTTTGATGAA
6758 ATGAATTTTGATGAA
1 ATGAATTTTGATGAA
6773 ATGAA
1 ATGAA
6778 ATGGTACCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 2 0.07
15 14 0.52
ACGTcount: A:0.45, C:0.02, G:0.19, T:0.34
Consensus pattern (15 bp):
ATGAATTTTGATGAA
Found at i:6817 original size:138 final size:138
Alignment explanation
Indices: 6644--6900 Score: 392
Period size: 138 Copynumber: 1.9 Consensus size: 138
6634 TCAGAATTAC
*
6644 TACCCGGAGGTTTCTGAAGTTGTGCCCGGAGGACTTATCAACGCAAACTCTGAATAGAGACCTTA
1 TACCCGGAGGTTTCTGAAGTTGTGCCCGGAGGACTTACCAACGCAAACTCTGAATAGAGACCTTA
*
6709 AACAAGGATTTTAAAATTAAACAT-GAATTTTGA-TGAAAAACTTGATGAAATGAATTTTGATGA
66 AACAAGGATTTT-AAATCAAACATGGAATTTT-ACTGAAAAACTTGATGAAATGAATTTTGATGA
6772 AATGAAATGG
129 AATGAAATGG
* * * *
6782 TACCCGGAGGTTTCTGAAGTTGTGCCCGGAGGACTTACCAATGCAAATTTTGAATTGAGACCTTA
1 TACCCGGAGGTTTCTGAAGTTGTGCCCGGAGGACTTACCAACGCAAACTCTGAATAGAGACCTTA
* * * *
6847 AACAAGGATTTTGACTCAAATATGGACTTTTACTGAAAAACTTGATGAAATGAA
66 AACAAGGATTTTAAATCAAACATGGAATTTTACTGAAAAACTTGATGAAATGAA
6901 AGGATACCCG
Statistics
Matches: 107, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
137 8 0.07
138 99 0.93
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (138 bp):
TACCCGGAGGTTTCTGAAGTTGTGCCCGGAGGACTTACCAACGCAAACTCTGAATAGAGACCTTA
AACAAGGATTTTAAATCAAACATGGAATTTTACTGAAAAACTTGATGAAATGAATTTTGATGAAA
TGAAATGG
Found at i:7093 original size:69 final size:69
Alignment explanation
Indices: 6965--7141 Score: 291
Period size: 69 Copynumber: 2.6 Consensus size: 69
6955 AAGTAAGGCT
* ** *
6965 TGACTCATATGGAAATAAGTTTGGCTTGTGGGAAAAGCCTATATGGCTTGGATGGAACCAAGGCT
1 TGACTCGTATGGAAACGAGTTTGGCTTGT-GGAAAAGCCTATATGGCTTAGATGGAACCAAGGCT
7030 TGAAC
65 TGAAC
*
7035 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTAGATGGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTAGATGGAACCAAGGCTT
7100 GAAC
66 GAAC
*
7104 TGACTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
7142 AAAGCATTCG
Statistics
Matches: 101, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
69 75 0.74
70 26 0.26
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (69 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTAGATGGAACCAAGGCTT
GAAC
Found at i:8741 original size:6 final size:6
Alignment explanation
Indices: 8730--8772 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
8720 TCAATTCTCT
* * *
8730 TTTTGA TTTTGA TTTTAA TTTTGA TTTT-T TTTTGT TTTTGA TT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TT
8773 GAATTTCTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.14, C:0.00, G:0.12, T:0.74
Consensus pattern (6 bp):
TTTTGA
Found at i:9175 original size:17 final size:17
Alignment explanation
Indices: 9150--9186 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
9140 AGTGCCATGA
*
9150 TTTTAATTTTTTCATTT
1 TTTTAATTTTATCATTT
*
9167 TTTTCATTTTATCATTT
1 TTTTAATTTTATCATTT
9184 TTT
1 TTT
9187 ATGGGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTAATTTTATCATTT
Found at i:15191 original size:15 final size:15
Alignment explanation
Indices: 15161--15202 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
15151 TTACTTTGTT
15161 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
15177 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
15192 TTGCTTTCTGT
1 TTGTTTTCTGT
15203 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Done.