Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011693.1 Corchorus capsularis cultivar CVL-1 contig11714, 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: 11118
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Found at i:2841 original size:20 final size:20
Alignment explanation
Indices: 2816--2856 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2806 AAAAAGAGCA
*
2816 CCAATTTGCAAATCAAATGT
1 CCAATTCGCAAATCAAATGT
*
2836 CCAATTCGTAAATCAAATGT
1 CCAATTCGCAAATCAAATGT
2856 C
1 C
2857 TTGTATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (20 bp):
CCAATTCGCAAATCAAATGT
Found at i:3398 original size:27 final size:27
Alignment explanation
Indices: 3330--3401 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
3320 AAGTGAACTT
* *
3330 AAAATGACCAAAATACCCCTAAATGCA
1 AAAATGACCAAAATGCCCCTAAACGCA
* **
3357 AAAATGACCAAAATGCCCCTGAACGTG
1 AAAATGACCAAAATGCCCCTAAACGCA
3384 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
3402 TTATGTGACC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.47, C:0.26, G:0.12, T:0.14
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAAACGCA
Found at i:4032 original size:70 final size:68
Alignment explanation
Indices: 3858--4193 Score: 451
Period size: 70 Copynumber: 4.9 Consensus size: 68
3848 AAAGCTCTTT
* *
3858 CTTGGATGGAACC-AAGCTTGAATCT-CTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCTCCT
1 CTTGGATGGAACCAAAGCTTGAA-CTACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCT
*
3921 GATG
65 AATG
*
3925 CTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCT
1 CTTGGATGGAACCAAAGCTTGAACT-ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCT
3990 AAATG
65 -AATG
* * *
3995 TTTGGATGGAACAAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTCT
1 CTTGGATGGAACCAAAGCTTGAACT-ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCT
**
4060 GTTG
65 AATG
* *
4064 CTTGGATGGAACCAAAGCTTGATCTACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCTT
1 CTTGGATGGAACCAAAGCTTGAACTA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCT
4129 GAATG
65 -AATG
* * * * *
4134 CTTGGGTGGAACCAAAGTTTGAGCTACCTCGTATGGAAACGAGTTTGACTTATGGAAAAG
1 CTTGGATGGAACCAAAGCTTGAACTA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
4194 TCGAAGCATT
Statistics
Matches: 241, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
67 15 0.06
68 9 0.04
69 96 0.40
70 121 0.50
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (68 bp):
CTTGGATGGAACCAAAGCTTGAACTACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTA
ATG
Found at i:4032 original size:139 final size:137
Alignment explanation
Indices: 3858--4193 Score: 480
Period size: 139 Copynumber: 2.4 Consensus size: 137
3848 AAAGCTCTTT
*
3858 CTTGGATGGAACCAAGCTTGAATCT-CTCGTATGGAAACGAGTTTGACTTGTGGAAAAG-CTCCT
1 CTTGGATGGAACAAAGCTTGAA-CTACTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCCT-CT
*
3921 GATGCTTGGATGGAACCAAGGCTTGAACTGA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
64 GATGCTTGGATGGAACCAAAGCTTGAACT-ACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
3985 CCCCTAAATG
128 CCCCTAAATG
* *
3995 TTTGGATGGAACAAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTCT
1 CTTGGATGGAAC-AAAGCTTGAACT-ACTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCCTCT
* *
4060 GTTGCTTGGATGGAACCAAAGCTTGATCTACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGC
64 GATGCTTGGATGGAACCAAAGCTTGAACTACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGC
* *
4125 CCTTGAATG
129 CCCTAAATG
* * * *
4134 CTTGGGTGGAACCAAAGTTTGAGCTACCTCGTATGGAAACGAGTTTGACTTATGGAAAAG
1 CTTGGATGGAA-CAAAGCTTGAACTA-CTCGTATGGAAACGAGTTTGACTTGTGGAAAAG
4194 TCGAAGCATT
Statistics
Matches: 178, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
137 13 0.07
138 11 0.06
139 151 0.85
140 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (137 bp):
CTTGGATGGAACAAAGCTTGAACTACTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCCTCTGA
TGCTTGGATGGAACCAAAGCTTGAACTACCTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCC
CTAAATG
Found at i:6154 original size:29 final size:29
Alignment explanation
Indices: 6122--6179 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
6112 TTTTAGGCCA
6122 ATTTTTT-TTCT-TCTCTTTCTTCTTCTCTT
1 ATTTTTTCTTCTCTCTCTTT-TT-TTCTCTT
6151 ATTTTTTCTTCTCTCTCTTTTTTTCTCTT
1 ATTTTTTCTTCTCTCTCTTTTTTTCTCTT
6180 GAGTTGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 14 0.52
30 6 0.22
31 7 0.26
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.72
Consensus pattern (29 bp):
ATTTTTTCTTCTCTCTCTTTTTTTCTCTT
Found at i:6165 original size:17 final size:18
Alignment explanation
Indices: 6137--6176 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
6127 TTTTCTTCTC
6137 TTTCTTCTTCTCT-TATTT
1 TTTCTTCTTCTCTCT-TTT
6155 TTTCTTC-TCTCTCTTTT
1 TTTCTTCTTCTCTCTTTT
6172 TTTCT
1 TTTCT
6177 CTTGAGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCTTCTTCTCTCTTTT
Found at i:6852 original size:14 final size:13
Alignment explanation
Indices: 6833--6881 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
6823 TAAAAACCTC
6833 TTTGAAAACTCATT
1 TTTGAAAAC-CATT
6847 TTTGAAAACC-TT
1 TTTGAAAACCATT
*
6859 TCCTTGAAAACAATT
1 T--TTGAAAACCATT
6874 TTTGAAAA
1 TTTGAAAA
6882 ACGTTTCTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 3 0.10
13 8 0.26
14 17 0.55
15 3 0.10
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (13 bp):
TTTGAAAACCATT
Found at i:7731 original size:34 final size:34
Alignment explanation
Indices: 7688--7758 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
7678 CAGGCTCCCA
7688 TTTCCCTTCGTCACTGCTTTGGGATTGTCAAGTT
1 TTTCCCTTCGTCACTGCTTTGGGATTGTCAAGTT
7722 TTTCCCTTCGTCACTGCTTTGGGATTGTCAAGTT
1 TTTCCCTTCGTCACTGCTTTGGGATTGTCAAGTT
7756 TTT
1 TTT
7759 TCATGCGATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (34 bp):
TTTCCCTTCGTCACTGCTTTGGGATTGTCAAGTT
Found at i:9656 original size:28 final size:26
Alignment explanation
Indices: 9575--9768 Score: 167
Period size: 27 Copynumber: 7.2 Consensus size: 26
9565 TATTTTTTGA
*
9575 TTACTAATTACCA-TTTTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
* *
9600 GTACTGATTACCATATTTTACTCTTTT
1 TTACTGATTACCATTTTTTACTC-TTT
*
9627 TTACTGATTACCCATTTTCTTACTGTTT
1 TTACTGATTA-CCATTTT-TTACTCTTT
* * *
9655 TTACTGAATATCACTTTTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
* * *
9681 TTATTTAATTACCATTTCTTACTCTTT
1 TTA-CTGATTACCATTTTTTACTCTTT
* *
9708 ATTACTAATTACTC-TCTTTTACTCTTTT
1 -TTACTGATTAC-CATTTTTTACTC-TTT
* *
9736 TTACTGATCACCACTTTTTACTCATTT
1 TTACTGATTACCATTTTTTACTC-TTT
9763 CTTACT
1 -TTACT
9769 CTTTTTACTG
Statistics
Matches: 135, Mismatches: 24, Indels: 17
0.77 0.14 0.10
Matches are distributed among these distances:
25 11 0.08
26 20 0.15
27 69 0.51
28 30 0.22
29 5 0.04
ACGTcount: A:0.22, C:0.21, G:0.03, T:0.54
Consensus pattern (26 bp):
TTACTGATTACCATTTTTTACTCTTT
Found at i:9660 original size:55 final size:52
Alignment explanation
Indices: 9575--9768 Score: 180
Period size: 55 Copynumber: 3.6 Consensus size: 52
9565 TATTTTTTGA
*
9575 TTACTAATTACCATTT-TTACTCTTTGTACTGATTACCATATTTTACTCTTTT
1 TTACTAATTACCATTTCTTACTCTTTTTACTGATTACCAT-TTTTACTCTTTT
* * * *
9627 TTACTGATTACCCATTTTCTTACTGTTTTTACTGAATATCACTTTTTACTC-TTT
1 TTACTAATTA-CCA-TTTCTTACTCTTTTTACTGATTACCA-TTTTTACTCTTTT
* *
9681 TTATTTAATTACCATTTCTTACTCTTTATTACTAATTACTC-TCTTTTACTCTTTT
1 TTA-CTAATTACCATTTCTTACTCTTT-TTACTGATTAC-CAT-TTTTACTCTTTT
* *
9736 TTACTGATCACCACTTT-TTACTCATTTCTTACT
1 TTACTAATTACCA-TTTCTTACTC-TTT-TTACT
9769 CTTTTTACTG
Statistics
Matches: 116, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
52 9 0.08
53 16 0.14
54 41 0.35
55 49 0.42
56 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.03, T:0.54
Consensus pattern (52 bp):
TTACTAATTACCATTTCTTACTCTTTTTACTGATTACCATTTTTACTCTTTT
Found at i:9987 original size:166 final size:165
Alignment explanation
Indices: 9771--10090 Score: 459
Period size: 166 Copynumber: 1.9 Consensus size: 165
9761 TTCTTACTCT
* * *
9771 TTTTACTGATTACTCTTTTCTCTTTCAATTTAATTACTGACTATCATTTTACTCTTTACTGATTA
1 TTTTACTGACTACTCTTTTCTCTTTCAACTAAATTACTGACTATCATTTTACTCTTTACTGATTA
* *
9836 TTTTTTTTTACTTTTTATTGATTACTA-TTTCACACTTACTGATTACCATTAC-TTTTTGAACTT
66 --TTTCTTTACTTTTTATTAATTACTACTTT-ACACTTACTGATTACCATTACTTTTTTGAACTT
9899 GAACACTGATTA-CCTTTTTACTTTTCTTCTTTTTCTC
128 GAACACTGATTACCCTTTTTACTTTTCTTCTTTTTCTC
*
9936 TTTTACTGACTAC-CATTTTACTCTTTGAACTAAATTACTGACTATCATTTTACTCTTTACTGAT
1 TTTTACTGACTACTC-TTTT-CTCTTTCAACTAAATTACTGACTATCATTTTACTCTTTACTGAT
* *
10000 TATTTCTTTACTTTTTATTAATTACTACTTTACTCTTACTGATTATCATTACTTTTTTTGAACTT
64 TATTTCTTTACTTTTTATTAATTACTACTTTACACTTACTGATTACCATTAC-TTTTTTGAACTT
***
10065 GGTTACTGATTACCCTTTTTACTTTT
128 GAACACTGATTACCCTTTTTACTTTT
10091 ACTGTTTACT
Statistics
Matches: 138, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
164 43 0.31
165 19 0.14
166 63 0.46
167 13 0.09
ACGTcount: A:0.22, C:0.18, G:0.05, T:0.54
Consensus pattern (165 bp):
TTTTACTGACTACTCTTTTCTCTTTCAACTAAATTACTGACTATCATTTTACTCTTTACTGATTA
TTTCTTTACTTTTTATTAATTACTACTTTACACTTACTGATTACCATTACTTTTTTGAACTTGAA
CACTGATTACCCTTTTTACTTTTCTTCTTTTTCTC
Found at i:10009 original size:22 final size:22
Alignment explanation
Indices: 9970--10045 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
9960 TTGAACTAAA
* * *
9970 TTACTGACTATCATTTTACTCT
1 TTACTGATTATTACTTTACTCT
* *
9992 TTACTGATTATTTCTTTACTTT
1 TTACTGATTATTACTTTACTCT
* * *
10014 TTATTAATTACTACTTTACTC-
1 TTACTGATTATTACTTTACTCT
10035 TTACTGATTAT
1 TTACTGATTAT
10046 CATTACTTTT
Statistics
Matches: 41, Mismatches: 13, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
21 8 0.20
22 33 0.80
ACGTcount: A:0.24, C:0.17, G:0.04, T:0.55
Consensus pattern (22 bp):
TTACTGATTATTACTTTACTCT
Found at i:10092 original size:22 final size:20
Alignment explanation
Indices: 10067--10340 Score: 136
Period size: 20 Copynumber: 13.0 Consensus size: 20
10057 TTGAACTTGG
10067 TTACTGATTACCCTTTTTACTT
1 TTACTGATTA-CC-TTTTACTT
* *
10089 TTACTGTTTA-CTATTACTT
1 TTACTGATTACCTTTTACTT
* *
10108 CTTATTGATTACC-ATTACTCT
1 -TTACTGATTACCTTTTACT-T
10129 TTACTGATTATCAC-TTTACTCT
1 TTACTGATTA-C-CTTTTACT-T
* *
10151 TTACTAATTACCATTTTACCCT
1 TTACTGATTACC-TTTTA-CTT
*
10173 TT-CAGA-TACCTTTTTACTTT
1 TTACTGATTACC-TTTTAC-TT
10193 TTACTGATTACCTTTTTACTTTT
1 TTACTGATTACC-TTTTAC--TT
* *
10216 TTACTGTTTA-CTATTACTT
1 TTACTGATTACCTTTTACTT
* *
10235 CTTACTGATT-TCTATTACTCT
1 -TTACTGATTACCTTTTACT-T
10256 TTACTGATTATCAC-TTTACTCT
1 TTACTGATTA-C-CTTTTACT-T
* *
10278 TTACTAATTACCATTTTACCCT
1 TTACTGATTACC-TTTTA-CTT
*
10300 TTACAGA-TACCCTTTTTAC-T
1 TTACTGATTA-CC-TTTTACTT
10320 TTACTGATTACCTTTTTACTT
1 TTACTGATTACC-TTTTACTT
10341 CTTTTGACTG
Statistics
Matches: 204, Mismatches: 24, Indels: 49
0.74 0.09 0.18
Matches are distributed among these distances:
19 10 0.05
20 79 0.39
21 22 0.11
22 78 0.38
23 15 0.07
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.52
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTT
Found at i:10230 original size:127 final size:127
Alignment explanation
Indices: 10067--10350 Score: 468
Period size: 127 Copynumber: 2.2 Consensus size: 127
10057 TTGAACTTGG
*
10067 TTACTGATTACCCTTTTTAC--TTTTACTGTTTACTATTACTTCTTATTGATTACCATTACTCTT
1 TTACTGATTA-CCTTTTTACTTTTTTACTGTTTACTATTACTTCTTACTGATTACCATTACTCTT
10130 TACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTT-CAGATA-CCTTTTTACTTT
65 TACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTTACAGATACCCTTTTTAC--T
* *
10193 TTACTGATTACCTTTTTACTTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTT
1 TTACTGATTACCTTTTTACTTTTTTACTGTTTACTATTACTTCTTACTGATTACCATTACTCTTT
10258 ACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTTACAGATACCCTTTTTACT
66 ACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTTACAGATACCCTTTTTACT
10320 TTACTGATTACCTTTTTACTTCTTTTGACTG
1 TTACTGATTACCTTTTTACTT-TTTT-ACTG
10351 ACCCCATTTT
Statistics
Matches: 149, Mismatches: 3, Indels: 9
0.93 0.02 0.06
Matches are distributed among these distances:
125 9 0.06
126 10 0.07
127 107 0.72
128 10 0.07
129 13 0.09
ACGTcount: A:0.21, C:0.22, G:0.05, T:0.52
Consensus pattern (127 bp):
TTACTGATTACCTTTTTACTTTTTTACTGTTTACTATTACTTCTTACTGATTACCATTACTCTTT
ACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTTACAGATACCCTTTTTACT
Done.