Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006728.1 Corchorus capsularis cultivar CVL-1 contig06749, 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: 18770
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:2446 original size:27 final size:28
Alignment explanation
Indices: 2368--2446 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 28
2358 AGGTAAACTT
* *
2368 AAAAATGACTAAAATGCCCCTGAGTGCA
1 AAAAATGACCAAAATGCCCCTGGGTGCA
2396 AAAAATGACCAAAATGCCCCTGGGTGC-
1 AAAAATGACCAAAATGCCCCTGGGTGCA
* *
2423 AAAAATGACCAAAATACCCTTGGG
1 AAAAATGACCAAAATGCCCCTGGG
2447 CGACCCTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 22 0.47
28 25 0.53
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (28 bp):
AAAAATGACCAAAATGCCCCTGGGTGCA
Found at i:4703 original size:70 final size:69
Alignment explanation
Indices: 4374--4935 Score: 772
Period size: 70 Copynumber: 8.1 Consensus size: 69
4364 ACTTGGCCTA
* * *
4374 TGGAAAAGCCCCTTACTGCTTGGATGGAACCAAGGC-TAAACTGACTCGTATGGAAACGAGTTTG
1 TGGAAAAGCCCCTGA-TGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTG
4438 GCTTG
65 GCTTG
* * * * * *
4443 TGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGC-TAAACTAACTCGTATGGAAACAAGTTTTG
1 TGGAAAAGCCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGG
4507 CTTG
66 CTTG
* * * ** *
4511 TGGAAAAGCCCCTGTTGCTTGGATGGAACCAATGC-TAAACTGTGTCGTATGGAAACGAGTTTTG
1 TGGAAAAGCCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGG
4575 CTTG
66 CTTG
* * *
4579 TGGAAAAGCCCCTGCTGCTTGGATGGAACCAAAACTTGAACTGATTCGTATGGAAACGAGTTTGG
1 TGGAAAAGCCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGG
4644 CTTG
66 CTTG
* *
4648 TGGAAAAGTCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTAACTCGTATGGAAACGAGTTTG
1 TGGAAAAGCCCCTG-ATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTG
4713 GCTTG
65 GCTTG
* **
4718 TGGAAAAGCCCCTGAATGCTTGAATGGAACCAAAGCTTGAACTCTCTCGTATGGAAACGAGTTTG
1 TGGAAAAGCCCCTG-ATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTG
* *
4783 ACTTA
65 GCTTG
*
4788 TGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACT-ATCGCGTATGGAAACGAGTTT
1 TGGAAAAGCCCCTG-ATGCTTGGATGGAACCAAAGCTTGAACTGA-CTCGTATGGAAACGAGTTT
4852 GGCTTG
64 GGCTTG
* *
4858 TGGAAAAGCACCTGCATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTGTGGAAACGAGTTTG
1 TGGAAAAGCCCCTG-ATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTG
* *
4923 ACTTA
65 GCTTG
4928 TGGAAAAG
1 TGGAAAAG
4936 TCCAAGCATT
Statistics
Matches: 449, Mismatches: 40, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
68 144 0.32
69 55 0.12
70 249 0.55
71 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (69 bp):
TGGAAAAGCCCCTGATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGG
CTTG
Found at i:5470 original size:50 final size:50
Alignment explanation
Indices: 5406--5504 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
5396 AAAATGCCAT
*
5406 TTGAAAAGCAAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATC
1 TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAATGCAATCTTATC
* * *
5456 TTGAAAATCGAATTTTGATATTGGACTTACAAATGGAATGCAATCTTAT
1 TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAATGCAATCTTAT
5505 AAAACTTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (50 bp):
TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAATGCAATCTTATC
Found at i:5800 original size:6 final size:6
Alignment explanation
Indices: 5789--5815 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5779 TTCATTCTCT
5789 TTTTTC TTTTTC TTTTTC TTTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTT
5816 CATTTTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:5804 original size:13 final size:13
Alignment explanation
Indices: 5771--5815 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
5761 ACCCTAGAGC
*
5771 TTCTTTTCTTCATT
1 TTCTTTT-TTCTTT
*
5785 CTCTTTTTTCTTT
1 TTCTTTTTTCTTT
5798 TTC-TTTTTCTTT
1 TTCTTTTTTCTTT
5810 TTCTTT
1 TTCTTT
5816 CATTTTTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 12 0.44
13 9 0.33
14 6 0.22
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTTTTTTCTTT
Found at i:7020 original size:44 final size:44
Alignment explanation
Indices: 6911--7052 Score: 257
Period size: 44 Copynumber: 3.2 Consensus size: 44
6901 CACAACTTTG
*
6911 GAAAACCATTTTACCAAAACCTTTTGAAAACCATGACTCTTTTT
1 GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
*
6955 GAAAAACCGTTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
1 G-AAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
7000 GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
1 GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
7044 GAAAACCAT
1 GAAAACCAT
7053 CGTTGCTTTT
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
44 52 0.55
45 42 0.45
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (44 bp):
GAAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTT
Found at i:7063 original size:20 final size:19
Alignment explanation
Indices: 6977--7052 Score: 71
Period size: 19 Copynumber: 3.7 Consensus size: 19
6967 TATCAAAACC
6977 TTTTGAAAACCATGACTCT
1 TTTTGAAAACCATGACTCT
* * *
6996 TTTTGAAAACCATTTTATCAAAACC
1 TTTTGAAAACCA--TGA-C---TCT
7021 TTTTGAAAACCATGACTCT
1 TTTTGAAAACCATGACTCT
7040 TTTTGAAAACCAT
1 TTTTGAAAACCAT
7053 CGTTGCTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
19 26 0.58
21 2 0.04
22 2 0.04
23 2 0.04
25 13 0.29
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.37
Consensus pattern (19 bp):
TTTTGAAAACCATGACTCT
Found at i:7119 original size:11 final size:11
Alignment explanation
Indices: 7061--7111 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
7051 ATCGTTGCTT
*
7061 TTTCTCTTTTC
1 TTTCTTTTTTC
7072 TTTCTTTTTTC
1 TTTCTTTTTTC
*
7083 TTT-TATTATTC
1 TTTCT-TTTTTC
7094 -TTCTTCTTTTC
1 TTTCTT-TTTTC
7105 TTTCTTT
1 TTTCTTT
7112 CTTTTTTCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
10 4 0.12
11 24 0.73
12 5 0.15
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:7612 original size:75 final size:75
Alignment explanation
Indices: 7512--7657 Score: 220
Period size: 75 Copynumber: 1.9 Consensus size: 75
7502 CAATCACCTT
* * *
7512 GAAATCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACTCAACATCCTTTTG
1 GAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATTAAAACCCAACATCCTTTTG
7577 CTCACACCCC
66 CTCACACCCC
* * * * *
7587 GAAACCATTGCTTTGATTGAAACTGATTTTGAAACATGTTTTAATTAAAACCCATCATTCTTTTG
1 GAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATTAAAACCCAACATCCTTTTG
7652 CTCACA
66 CTCACA
7658 ATCCAGATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.36
Consensus pattern (75 bp):
GAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTAATTAAAACCCAACATCCTTTTG
CTCACACCCC
Found at i:9884 original size:17 final size:17
Alignment explanation
Indices: 9839--9885 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
9829 TAATAAGTTA
9839 TAATTAATATTTAGTAT
1 TAATTAATATTTAGTAT
* *
9856 TATTTAAATATTTA-TTT
1 TAATT-AATATTTAGTAT
9873 TAATTGAATATTT
1 TAATT-AATATTT
9886 GTGATCTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (17 bp):
TAATTAATATTTAGTAT
Found at i:10483 original size:16 final size:16
Alignment explanation
Indices: 10458--10489 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10448 AATTTGAGTC
*
10458 TCCCAGCTAGTTTGAA
1 TCCCAACTAGTTTGAA
10474 TCCCAACTAGTTTGAA
1 TCCCAACTAGTTTGAA
10490 ACCCGATCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (16 bp):
TCCCAACTAGTTTGAA
Found at i:13388 original size:23 final size:23
Alignment explanation
Indices: 13362--13407 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
13352 GAAAAACTTT
*
13362 TTTA-AAAAATCAAACAAAATAAA
1 TTTAGAAAAA-CAAAAAAAATAAA
13385 TTTAGAAAAACAAAAAAAATAAA
1 TTTAGAAAAACAAAAAAAATAAA
13408 GGAACTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.20
Consensus pattern (23 bp):
TTTAGAAAAACAAAAAAAATAAA
Found at i:14152 original size:187 final size:189
Alignment explanation
Indices: 13835--14210 Score: 657
Period size: 187 Copynumber: 2.0 Consensus size: 189
13825 GTATATGGTT
13835 ATATTAGTAATTAACAACTAAATAGCATTAATGTTAATTGATTTGTAATTGATCAAAATTTTCAT
1 ATATTAGTAATTAACAACTAAATAGCATTAATGTTAATTGATTTGTAATTGATCAAAATTTTCAT
* *
13900 TTTAACAATTAATTAAATAAAATAATTACTAATTGATTTTAATTGATCAAATTATTCAAATCAAC
66 ATTAACAATTAATTAAATAAAATAATTACTAAATGATTTTAATTGATCAAATTATTCAAATCAAC
*
13965 TAATTAATCAATCAAAAGAAATTAATATATTTCCTAATCAACCTAAAGTAATTAATTTA
131 TAATTAATCAATCAAAAGAAATTAATATATTTCCCAATCAACCTAAAGTAATTAATTTA
*
14024 ATATTAGTAATTAACAACTAAATAGCATTAATGTTAATTGA-TTGTGATTGATCAAAATTTTCA-
1 ATATTAGTAATTAACAACTAAATAGCATTAATGTTAATTGATTTGTAATTGATCAAAATTTTCAT
* * *
14087 ATTAACAATTGATTAAATAGAATTATTACTAAATGATTTTAATTGATCAAATTATTCAAATCAAC
66 ATTAACAATTAATTAAATAAAATAATTACTAAATGATTTTAATTGATCAAATTATTCAAATCAAC
**
14152 TAATTAATCAATCAAAAGTGATTAATATATTTCCCAATCAACCTAAAGTAATTAATTTA
131 TAATTAATCAATCAAAAGAAATTAATATATTTCCCAATCAACCTAAAGTAATTAATTTA
14211 TTTCCTTTTA
Statistics
Matches: 178, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
187 116 0.65
188 21 0.12
189 41 0.23
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (189 bp):
ATATTAGTAATTAACAACTAAATAGCATTAATGTTAATTGATTTGTAATTGATCAAAATTTTCAT
ATTAACAATTAATTAAATAAAATAATTACTAAATGATTTTAATTGATCAAATTATTCAAATCAAC
TAATTAATCAATCAAAAGAAATTAATATATTTCCCAATCAACCTAAAGTAATTAATTTA
Found at i:14191 original size:30 final size:30
Alignment explanation
Indices: 14157--14215 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
14147 TCAACTAATT
* *
14157 AATCAATCAAAAGTGATTAATATATTTCCC
1 AATCAACCAAAAGTAATTAATATATTTCCC
* *
14187 AATCAACCTAAAGTAATTAATTTATTTCC
1 AATCAACCAAAAGTAATTAATATATTTCC
14216 TTTTATCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (30 bp):
AATCAACCAAAAGTAATTAATATATTTCCC
Found at i:14247 original size:2 final size:2
Alignment explanation
Indices: 14240--14266 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14230 CTCAGTTTTA
14240 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
14267 CTTGTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14785 original size:140 final size:139
Alignment explanation
Indices: 14527--14855 Score: 496
Period size: 140 Copynumber: 2.4 Consensus size: 139
14517 TACAACTTTG
* * * *
14527 ATTACATAATCATCATTCAATTACAACTTTAATTGGCAAAATTAACTAATGACATATTCAATAAT
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATATTCAATAAT
* *
14592 TTATTTTTTGGTAACATAATTACTAGTTGATTTATTTATTTATGGTAATTTTTTTGGTGGCAATT
66 TTATTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGCAA-T
14657 TTATGGTAAA
130 TTATGGTAAA
* * * *
14667 ATTATATAATCATCAATCAATTACAATTTTGATTGACAAAATTAACTAACGACATGTTCAATAAT
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATATTCAATAAT
* * * *
14732 TTATTTTTTTGGTAACATAATTACTAATTTATTTATTTCTTTATGTTAATTTTTTTGGTAGCGAT
66 TTA-TTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGCAAT
14797 TTATGGTAAA
130 TTATGGTAAA
* *
14807 ATTAAATAATTATCAATCAATTACGACTTTGATTGGCAAAATTAACTAA
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAA
14856 TGATCACTAA
Statistics
Matches: 170, Mismatches: 18, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
140 116 0.68
141 54 0.32
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (139 bp):
ATTAAATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATATTCAATAAT
TTATTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATTTTTTTGGTAGCAATT
TATGGTAAA
Found at i:17510 original size:20 final size:19
Alignment explanation
Indices: 17474--17516 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
17464 ACATTATAAG
* *
17474 TTTTTAAATAAATAAAAAT
1 TTTTTAAAAAAACAAAAAT
17493 TTTTATAAAAAAACAAAAAT
1 TTTT-TAAAAAAACAAAAAT
17513 TTTT
1 TTTT
17517 CCATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTTTAAAAAAACAAAAAT
Found at i:18483 original size:37 final size:38
Alignment explanation
Indices: 18414--18509 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 38
18404 AATTTGGCTT
*
18414 TTTGTTTCCAACGTCCTATTTAATTTTGTC-TTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTGTCTTTTTGTA
**
18451 TTTGTTTCCAATCGTTGTATTTAATTTT-TCTTTTTGTA
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGTCTTTTTGTA
*
18489 TTTGTCTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
18510 GGGCTTAGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
37 21 0.41
38 30 0.59
ACGTcount: A:0.15, C:0.18, G:0.10, T:0.57
Consensus pattern (38 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGTCTTTTTGTA
Done.