Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006849.1 Corchorus capsularis cultivar CVL-1 contig06870, 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: 28521
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:2923 original size:58 final size:58
Alignment explanation
Indices: 2856--2965 Score: 202
Period size: 58 Copynumber: 1.9 Consensus size: 58
2846 TGAAAAAACG
* *
2856 TATAAGAAGATTAGAGATGGAATGTGAGACGAAAACTAAAGCGTCTTCAAAACGTCTC
1 TATAAGAAGATTAGAGATGGAATCTGAGACGAAAACTAAAGCGGCTTCAAAACGTCTC
2914 TATAAGAAGATTAGAGATGGAATCTGAGACGAAAACTAAAGCGGCTTCAAAA
1 TATAAGAAGATTAGAGATGGAATCTGAGACGAAAACTAAAGCGGCTTCAAAA
2966 GTGAGGTCGC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (58 bp):
TATAAGAAGATTAGAGATGGAATCTGAGACGAAAACTAAAGCGGCTTCAAAACGTCTC
Found at i:6184 original size:13 final size:13
Alignment explanation
Indices: 6166--6190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6156 AGAGAATCAA
6166 CTATCAAGAAAAC
1 CTATCAAGAAAAC
6179 CTATCAAGAAAA
1 CTATCAAGAAAA
6191 GTAAATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (13 bp):
CTATCAAGAAAAC
Found at i:14469 original size:104 final size:104
Alignment explanation
Indices: 14235--14469 Score: 344
Period size: 104 Copynumber: 2.3 Consensus size: 104
14225 CTGTCAGAAA
* *
14235 AGTATTAGTCGATGAAAACTTCAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAATCTTTA
1 AGTATTAATCGATGAAAACTTCAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAATCTTCA
* *
14300 CTTTGAAAAAGTGGCAGTGTTGACAGCTAACCCGGAGTC
66 CTTTGAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * * ** *
14339 GGTATTAATCGATGAAAACTCCAGTTTTAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
1 AGTATTAATCGATGAAAACTTCAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAATCTTCA
*
14404 CTTTGAAAAAGTGGCGGTGTTGACAGCGAACCCGGAGCC
66 CTTTGAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * *
14443 AGTATTAATTGATGAATACTTAAGTTT
1 AGTATTAATCGATGAAAACTTCAGTTT
14470 CATGTTTCAA
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
104 115 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (104 bp):
AGTATTAATCGATGAAAACTTCAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAATCTTCA
CTTTGAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
Found at i:20076 original size:54 final size:54
Alignment explanation
Indices: 19994--20102 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
19984 GATGATGGAG
19994 GATCATTTATACAAAGGATTTGTTTGATCCGGTGTTGGGTGATTCGGGTAAGCC
1 GATCATTTATACAAAGGATTTGTTTGATCCGGTGTTGGGTGATTCGGGTAAGCC
20048 GATCATTTATACAAAGGATTTGTTTGATCCGGTGTTGGGTGATTCGGGTAAGCC
1 GATCATTTATACAAAGGATTTGTTTGATCCGGTGTTGGGTGATTCGGGTAAGCC
20102 G
1 G
20103 CACAATAAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (54 bp):
GATCATTTATACAAAGGATTTGTTTGATCCGGTGTTGGGTGATTCGGGTAAGCC
Found at i:23444 original size:36 final size:35
Alignment explanation
Indices: 23402--23520 Score: 149
Period size: 36 Copynumber: 3.4 Consensus size: 35
23392 CTCTTTTTAG
*
23402 ATTAAGTTCTTTATTGATTTCACTTAATTACCTTGA
1 ATTAAGTTCTTTATTGATCTCACTTAATTACC-TGA
23438 ATTAAGTTCTTTA-T--TCT-ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGATCTCACTTAATTA-CCTGA
*
23470 ATTAAG-TCTTTTATTGACCTCACTTAATTACACTGA
1 ATTAAGTTC-TTTATTGATCTCACTTAATTAC-CTGA
23506 ATTAAGTTCTTTATT
1 ATTAAGTTCTTTATT
23521 TTACTTAATT
Statistics
Matches: 73, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
31 2 0.03
32 22 0.30
33 5 0.07
35 4 0.05
36 38 0.52
37 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.48
Consensus pattern (35 bp):
ATTAAGTTCTTTATTGATCTCACTTAATTACCTGA
Found at i:23464 original size:32 final size:32
Alignment explanation
Indices: 23423--23535 Score: 131
Period size: 32 Copynumber: 3.4 Consensus size: 32
23413 TATTGATTTC
23423 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
1 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
*
23455 ACTTAATTACCCTGAATTAAG-TCTTTTATTGACCT
1 ACTTAATTACCTTGAATTAAGTTC-TTTATT---CT
*
23490 CACTTAATTACAC-TGAATTAAGTTCTTTATTTT
1 -ACTTAATTAC-CTTGAATTAAGTTCTTTATTCT
*
23523 ACTTAATTTCCTT
1 ACTTAATTACCTT
23536 TCCTGAAATT
Statistics
Matches: 70, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
31 3 0.04
32 36 0.51
33 1 0.01
35 2 0.03
36 25 0.36
37 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (32 bp):
ACTTAATTACCTTGAATTAAGTTCTTTATTCT
Found at i:23483 original size:68 final size:68
Alignment explanation
Indices: 23402--23530 Score: 199
Period size: 68 Copynumber: 1.9 Consensus size: 68
23392 CTCTTTTTAG
**
23402 ATTAAGTTCTTTATTGATTTCACTTAATTAC-CTTGAATTAAGTTCTTTATTCTACTTAATTACC
1 ATTAAGTTCTTTATTGACCTCACTTAATTACAC-TGAATTAAGTTCTTTATTCTACTTAATTACC
23466 CTGA
65 CTGA
*
23470 ATTAAG-TCTTTTATTGACCTCACTTAATTACACTGAATTAAGTTCTTTATTTTACTTAATT
1 ATTAAGTTC-TTTATTGACCTCACTTAATTACACTGAATTAAGTTCTTTATTCTACTTAATT
23531 TCCTTTCCTG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
67 2 0.04
68 53 0.95
69 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (68 bp):
ATTAAGTTCTTTATTGACCTCACTTAATTACACTGAATTAAGTTCTTTATTCTACTTAATTACCC
TGA
Found at i:23593 original size:21 final size:21
Alignment explanation
Indices: 23569--23629 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
23559 TTTACTTAAT
23569 TTCCTTGAAATTAAGCCAGTC
1 TTCCTTGAAATTAAGCCAGTC
*
23590 TTCCCT----TT-A-CCTAGT-
1 TTCCTTGAAATTAAGCC-AGTC
23605 TTCCTTGAAATTAAGCCAGTC
1 TTCCTTGAAATTAAGCCAGTC
23626 TTCC
1 TTCC
23630 CTTTACCTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 16
0.62 0.04 0.33
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
17 2 0.07
19 2 0.07
20 4 0.13
21 11 0.37
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.38
Consensus pattern (21 bp):
TTCCTTGAAATTAAGCCAGTC
Found at i:23608 original size:36 final size:34
Alignment explanation
Indices: 23554--23840 Score: 297
Period size: 36 Copynumber: 8.1 Consensus size: 34
23544 TTAAGCTTGT
*
23554 GTCTT-TTTACTTAATTTCCTTGAAATTAAGCCA
1 GTCTTCTTTACCTAATTTCCTTGAAATTAAGCCA
*
23587 GTCTTCCCTTTACCTAGTTTCCTTGAAATTAAGCCA
1 GTCTT--CTTTACCTAATTTCCTTGAAATTAAGCCA
* *
23623 GTCTTCCCTTTACCTAGTTTCCTTGAAACTAAGCCAA
1 GTCTT--CTTTACCTAATTTCCTTGAAATTAAGCC-A
* * *
23660 TTCTTTTTTACTTAATTTCCTTGAAATTAAGCCA
1 GTCTTCTTTACCTAATTTCCTTGAAATTAAGCCA
* * *
23694 ATCTTGTTTTACTTAATTTCCTTGAAATTAAGCCA
1 GTCTT-CTTTACCTAATTTCCTTGAAATTAAGCCA
** *
23729 GTCTTTTCTTTACCTAGCTTCCTTGAAACTAAGCCA
1 GTC--TTCTTTACCTAATTTCCTTGAAATTAAGCCA
* * *
23765 ATCTATCTTTACTTAATTTCTTTGAAATTAAGCCA
1 GTCT-TCTTTACCTAATTTCCTTGAAATTAAGCCA
* * *
23800 GTCTATTCTTTACCTAGTTTCCTTGAAACTAAGCTA
1 GTC--TTCTTTACCTAATTTCCTTGAAATTAAGCCA
23836 GTCTT
1 GTCTT
23841 TTATCAGTCT
Statistics
Matches: 217, Mismatches: 27, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
33 5 0.02
34 8 0.04
35 82 0.38
36 114 0.53
37 8 0.04
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.43
Consensus pattern (34 bp):
GTCTTCTTTACCTAATTTCCTTGAAATTAAGCCA
Found at i:23614 original size:71 final size:70
Alignment explanation
Indices: 23559--23833 Score: 347
Period size: 71 Copynumber: 3.9 Consensus size: 70
23549 CTTGTGTCTT
* *
23559 TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTCCCTTTACCTAGTTTCCTTGAAATTAAGCCAG
1 TTTACTTAATTTCCTTGAAATTAAGCCAGTCTT-TCTTTACCTAGTTTCCTTGAAATTAAGCCAA
*
23624 TCTTCCC
65 TC-TCTC
* * * * * *
23631 TTTACCTAGTTTCCTTGAAACTAAGCCAATTCTTT-TTTACTTAATTTCCTTGAAATTAAGCCAA
1 TTTACTTAATTTCCTTGAAATTAAGCC-AGTCTTTCTTTACCTAGTTTCCTTGAAATTAAGCCAA
*
23695 TCT-TGT
65 TCTCT-C
* *
23701 TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGCTTCCTTGAAACTAAGCCAA
1 TTTACTTAATTTCCTTGAAATTAAGCCAGTC-TTTCTTTACCTAGTTTCCTTGAAATTAAGCCAA
*
23766 TCTATC
65 TCTCTC
* *
23772 TTTACTTAATTTCTTTGAAATTAAGCCAGTCTATTCTTTACCTAGTTTCCTTGAAACTAAGC
1 TTTACTTAATTTCCTTGAAATTAAGCCAGTCT-TTCTTTACCTAGTTTCCTTGAAATTAAGC
23834 TAGTCTTTTA
Statistics
Matches: 176, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
69 3 0.02
70 29 0.16
71 114 0.65
72 25 0.14
73 5 0.03
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (70 bp):
TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTCTTTACCTAGTTTCCTTGAAATTAAGCCAAT
CTCTC
Found at i:23731 original size:106 final size:105
Alignment explanation
Indices: 23557--23840 Score: 408
Period size: 106 Copynumber: 2.7 Consensus size: 105
23547 AGCTTGTGTC
*
23557 TTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTCCCTTTACCTAGTTTCCTTGAAATTAAGCC
1 TTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTT--TTTTACCTAGTTTCCTTGAAATTAAGCC
*
23622 AGTCTTCCCTTTACCTAGTTTCCTTGAAACTAAGCCAATTCT-
64 AGTCTTCCCTTTACCTAGCTTCCTTGAAACTAAGCCAA-TCTA
* * *
23664 TTTTTACTTAATTTCCTTGAAATTAAGCCAATCTTGTTTTACTTAATTTCCTTGAAATTAAGCCA
1 TTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTT-TTTTACCTAGTTTCCTTGAAATTAAGCCA
**
23729 GTCTTTTCTTTACCTAGCTTCCTTGAAACTAAGCCAATCTA
65 GTCTTCCCTTTACCTAGCTTCCTTGAAACTAAGCCAATCTA
* * * *
23770 TCTTTACTTAATTTCTTTGAAATTAAGCCAGTCTATTCTTTACCTAGTTTCCTTGAAACTAAGCT
1 TTTTTACTTAATTTCCTTGAAATTAAGCCAGTCT-TT-TTTACCTAGTTTCCTTGAAATTAAGCC
23835 AGTCTT
64 AGTCTT
23841 TTATCAGTCT
Statistics
Matches: 159, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
105 3 0.02
106 92 0.58
107 64 0.40
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (105 bp):
TTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTTTACCTAGTTTCCTTGAAATTAAGCCAG
TCTTCCCTTTACCTAGCTTCCTTGAAACTAAGCCAATCTA
Found at i:23860 original size:22 final size:22
Alignment explanation
Indices: 23835--23963 Score: 98
Period size: 22 Copynumber: 5.6 Consensus size: 22
23825 AAACTAAGCT
23835 AGTCTTTTATCAGTCTAATTTC
1 AGTCTTTTATCAGTCTAATTTC
* * *
23857 AGTCTTCTATCAATCTGATTTAATATC
1 AGTCTT-T-T--ATCAG-TCTAATTTC
*
23884 AGTCTTATATCAGTCTAATATT-
1 AGTCTTTTATCAGTCTAAT-TTC
* *
23906 AGTCTTTTTTTAGTCTAATTTC
1 AGTCTTTTATCAGTCTAATTTC
* * **
23928 AGTTTTTTTTCAGTCTTCTTTC
1 AGTCTTTTATCAGTCTAATTTC
*
23950 AGTCTTTTGTCAGT
1 AGTCTTTTATCAGT
23964 AATCTTTCAG
Statistics
Matches: 84, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
21 2 0.02
22 57 0.68
23 6 0.07
24 1 0.01
25 1 0.01
26 4 0.05
27 13 0.15
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (22 bp):
AGTCTTTTATCAGTCTAATTTC
Found at i:23969 original size:22 final size:22
Alignment explanation
Indices: 23924--23977 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
23914 TTTAGTCTAA
* * **
23924 TTTCAGTTTTTTTTCAGTCTTC
1 TTTCAGTCTTTTGTCAGTAATC
23946 TTTCAGTCTTTTGTCAGTAATC
1 TTTCAGTCTTTTGTCAGTAATC
23968 TTTCAGTCTT
1 TTTCAGTCTT
23978 CTTTTGCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.13, C:0.19, G:0.11, T:0.57
Consensus pattern (22 bp):
TTTCAGTCTTTTGTCAGTAATC
Found at i:23980 original size:11 final size:11
Alignment explanation
Indices: 23924--23981 Score: 64
Period size: 11 Copynumber: 5.3 Consensus size: 11
23914 TTTAGTCTAA
* *
23924 TTTCAGTTTTT
1 TTTCAGTCTTC
23935 TTTCAGTCTTC
1 TTTCAGTCTTC
23946 TTTCAGTCTT-
1 TTTCAGTCTTC
**
23956 TTGTCAGTAATC
1 TT-TCAGTCTTC
23968 TTTCAGTCTTC
1 TTTCAGTCTTC
23979 TTT
1 TTT
23982 TGCCTAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 2 0.05
11 35 0.90
12 2 0.05
ACGTcount: A:0.12, C:0.19, G:0.10, T:0.59
Consensus pattern (11 bp):
TTTCAGTCTTC
Found at i:27101 original size:87 final size:88
Alignment explanation
Indices: 26955--27130 Score: 311
Period size: 87 Copynumber: 2.0 Consensus size: 88
26945 CTTTTACTCT
* *
26955 ATTATCTTCCGCAGTTCATAAAGATTGCTCTTATCACATCATGGCATGCCTGACCTTGCGGGCCG
1 ATTATCTTCCGCAGTTCATAAAGATTGCTCTTAACACATCATGGCACGCCTGACCTTGCGGGCCG
27020 ATCTT-GGACAAAGAGGGAGAAG
66 ATCTTGGGACAAAGAGGGAGAAG
27042 ATTATCTTCCGCAGTTCAT-AAGAATTGCTCTTAACACATCATGGCACGCCTGACCTTGCGGGCC
1 ATTATCTTCCGCAGTTCATAAAG-ATTGCTCTTAACACATCATGGCACGCCTGACCTTGCGGGCC
27106 GATCTTGGGACAAAGAGGGAGAAG
65 GATCTTGGGACAAAGAGGGAGAAG
27130 A
1 A
27131 CTTAGCTGGG
Statistics
Matches: 85, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
86 3 0.04
87 64 0.75
88 18 0.21
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.25
Consensus pattern (88 bp):
ATTATCTTCCGCAGTTCATAAAGATTGCTCTTAACACATCATGGCACGCCTGACCTTGCGGGCCG
ATCTTGGGACAAAGAGGGAGAAG
Done.