Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004942.1 Corchorus capsularis cultivar CVL-1 contig04960, 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: 7322
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Found at i:350 original size:24 final size:24
Alignment explanation
Indices: 318--365 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
308 AGTTAAAAAT
318 TTAGAAAGTTAGAAATGATTTGAG
1 TTAGAAAGTTAGAAATGATTTGAG
342 TTAGAAAGTTAGAAATGATTTGAG
1 TTAGAAAGTTAGAAATGATTTGAG
366 AGAATTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (24 bp):
TTAGAAAGTTAGAAATGATTTGAG
Found at i:2260 original size:15 final size:15
Alignment explanation
Indices: 2240--2273 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2230 GTTCTTTATG
2240 TATATCTATACTATA
1 TATATCTATACTATA
2255 TATATCTATACTATA
1 TATATCTATACTATA
2270 TATA
1 TATA
2274 AAACTACGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATCTATACTATA
Found at i:2362 original size:13 final size:14
Alignment explanation
Indices: 2344--2388 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
2334 CTAAATTGAC
2344 ATTATTAAAATTT-
1 ATTATTAAAATTTA
2357 ATTATTTAAAATTTA
1 ATTA-TTAAAATTTA
2372 ATTA-TAAAATTTCA
1 ATTATTAAAATTT-A
2386 ATT
1 ATT
2389 TAGATGAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.41
14 13 0.45
15 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTATTAAAATTTA
Found at i:2894 original size:22 final size:21
Alignment explanation
Indices: 2838--3047 Score: 141
Period size: 22 Copynumber: 9.5 Consensus size: 21
2828 GTCTCTGTGT
**
2838 GGTTATCAAAATTTCATAATA
1 GGTTATCAAAATTTCATAGGA
* * *
2859 TGTTTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
2882 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* *
2904 GGTTACCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGG-A
*
2926 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* *
2948 GGTTACCAAAATTTAATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* * *
2972 TGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGG-A
** *
2994 GGTTATTGAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* *
3016 GGTTATCAAAATTTTATAGAAA
1 GGTTATCAAAATTTCATAG-GA
3038 GGTTATCAAA
1 GGTTATCAAA
3048 GAGATTATCA
Statistics
Matches: 144, Mismatches: 36, Indels: 16
0.73 0.18 0.08
Matches are distributed among these distances:
21 4 0.03
22 121 0.84
23 4 0.03
24 15 0.10
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:2917 original size:44 final size:44
Alignment explanation
Indices: 2869--2961 Score: 161
Period size: 44 Copynumber: 2.1 Consensus size: 44
2859 TGTTTATTAT
2869 AATTTCATGAGG-AGGTTATCAAAATTCCATAGTGTGGTTACCAA
1 AATTTCATG-GGAAGGTTATCAAAATTCCATAGTGTGGTTACCAA
*
2913 AATTTCATGGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAA
1 AATTTCATGGGAAGGTTATCAAAATTCCATAGTGTGGTTACCAA
2957 AATTT
1 AATTT
2962 AATAGGATCA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 2 0.04
44 45 0.96
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (44 bp):
AATTTCATGGGAAGGTTATCAAAATTCCATAGTGTGGTTACCAA
Found at i:3029 original size:112 final size:110
Alignment explanation
Indices: 2834--3047 Score: 279
Period size: 112 Copynumber: 1.9 Consensus size: 110
2824 TCTTGTCTCT
* * *
2834 GTGTGGTTATCAAAATTTCATAATATGTTTATTATAATTTCATGAGGAGGTTATCAAAATTCCAT
1 GTGTGGTTACCAAAATTTAATAATATGTTTATTAAAATTTCATGAGGAGGTTATCAAAATTCCAT
* *
2899 AGTGTGGTTACCAAAATTTCATGGGAAGGTTATCAAAATTTCATA
66 AGTGTGGTTACCAAAATTTCATAGAAAGGTTATCAAAATTTCATA
* **
2944 GTGTGGTTACCAAAATTTAATAGGATCATG-TTATTAAAATTTC-TTAGGAAGGTTATTGAAATT
1 GTGTGGTTACCAAAATTTAATA--AT-ATGTTTATTAAAATTTCATGAGG-AGGTTATCAAAATT
* * *
3007 TCATAGTGTGGTTATCAAAATTTTATAGAAAGGTTATCAAA
62 CCATAGTGTGGTTACCAAAATTTCATAGAAAGGTTATCAAA
3048 GAGATTATCA
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
110 20 0.22
111 4 0.04
112 62 0.70
113 3 0.03
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (110 bp):
GTGTGGTTACCAAAATTTAATAATATGTTTATTAAAATTTCATGAGGAGGTTATCAAAATTCCAT
AGTGTGGTTACCAAAATTTCATAGAAAGGTTATCAAAATTTCATA
Found at i:3172 original size:21 final size:22
Alignment explanation
Indices: 3138--3197 Score: 95
Period size: 21 Copynumber: 2.8 Consensus size: 22
3128 TTCACTGGGA
3138 GGTTATCAAAATTTCATTTTGT
1 GGTTATCAAAATTTCATTTTGT
**
3160 GGTTATC-AAATTTTTTTTTGT
1 GGTTATCAAAATTTCATTTTGT
3181 GGTTATCAAAATTTCAT
1 GGTTATCAAAATTTCAT
3198 ATGAAGGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (22 bp):
GGTTATCAAAATTTCATTTTGT
Found at i:3206 original size:22 final size:22
Alignment explanation
Indices: 3137--3442 Score: 77
Period size: 22 Copynumber: 13.9 Consensus size: 22
3127 TTTCACTGGG
*
3137 AGGTTATCAAAATTTCATTTTG-
1 AGGTTATCAAAATTTCA-TATGA
* * ** *
3159 TGGTTATCAAATTTTTTTTTG-
1 AGGTTATCAAAATTTCATATGA
*
3180 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
*
3202 AGGTTAT-AAAAGTCTCAATTTCAT-A
1 AGGTTATCAAAA-TTTC-A--T-ATGA
* ** *
3227 AGGAGTGCCAAAATTTGATA-GA
1 AGG-TTATCAAAATTTCATATGA
* *
3249 AGGTTATC-AAATCTCAGAGTG-
1 AGGTTATCAAAATTTCATA-TGA
*
3270 A--TTATCGAAATTTCATA-GA
1 AGGTTATCAAAATTTCATATGA
* *
3289 GATTGGATTATCAAAA-TTAATAGGA
1 -A--GG-TTATCAAAATTTCATATGA
*
3314 AGATTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
** *
3336 TTGTTATCAAAATTTCAAAGTG-
1 AGGTTATCAAAATTTCATA-TGA
* *
3358 AGGTTATCAAAATTACTAAAT-A
1 AGGTTATCAAAATTTC-ATATGA
* * *
3380 TGATTATCAAAATTTCGTA-GA
1 AGGTTATCAAAATTTCATATGA
* * * *
3401 GGGGTCAACAAAATTTTATA-GA
1 -AGGTTATCAAAATTTCATATGA
3423 GAGGTTATCAAAATTTCATA
1 -AGGTTATCAAAATTTCATA
3443 AAGAGGTTAT
Statistics
Matches: 208, Mismatches: 50, Indels: 52
0.67 0.16 0.17
Matches are distributed among these distances:
18 1 0.00
19 5 0.02
20 16 0.08
21 39 0.19
22 110 0.53
23 6 0.03
24 6 0.03
25 16 0.08
26 5 0.02
27 4 0.02
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:3371 original size:44 final size:45
Alignment explanation
Indices: 3235--3440 Score: 120
Period size: 44 Copynumber: 4.8 Consensus size: 45
3225 TAAGGAGTGC
* * *
3235 CAAAATTTGATAGA-A--GGTTATC-AAATCTCAGAGTGA-TTAT
1 CAAAATTTCATAGAGATTGGTTATCAAAATTTCAAAGTGAGTTAT
*
3275 CGAAATTTCATAGAGATTGGATTATCAAAA-TT-AATAG-GAAGATTAT
1 CAAAATTTCATAGAGATTGG-TTATCAAAATTTCAA-AGTG-AG-TTAT
*
3321 CAAAATTTCATAGTG-TT-GTTATCAAAATTTCAAAGTGAGGTTAT
1 CAAAATTTCATAGAGATTGGTTATCAAAATTTCAAAGTGA-GTTAT
* * * * * *
3365 CAAAATTAC-TA-A-ATATGATTATCAAAATTTCGTAGAG-GGGTCAA
1 CAAAATTTCATAGAGAT-TGGTTATCAAAATTTC--AAAGTGAGTTAT
*
3409 CAAAATTTTATAGAGA--GGTTATCAAAATTTCA
1 CAAAATTTCATAGAGATTGGTTATCAAAATTTCA
3441 TAAAGAGGTT
Statistics
Matches: 129, Mismatches: 16, Indels: 40
0.70 0.09 0.22
Matches are distributed among these distances:
40 12 0.09
41 1 0.01
42 2 0.02
43 16 0.12
44 64 0.50
45 12 0.09
46 21 0.16
47 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.33
Consensus pattern (45 bp):
CAAAATTTCATAGAGATTGGTTATCAAAATTTCAAAGTGAGTTAT
Found at i:3447 original size:22 final size:22
Alignment explanation
Indices: 3317--3486 Score: 112
Period size: 22 Copynumber: 7.7 Consensus size: 22
3307 AATAGGAAGA
** **
3317 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
*
3339 TTATCAAAATTTCA-AAGTGAGG
1 TTATCAAAATTTCATAA-AGAGG
* * *
3361 TTATCAAAATTAC-TAAATATGA
1 TTATCAAAATTTCATAAAGA-GG
* * *
3383 TTATCAAAATTTCGTAGAGGGG
1 TTATCAAAATTTCATAAAGAGG
* * * *
3405 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAAAGAGG
3427 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
* * * *
3449 TTATCGAATTTTCA-AAATGTGA
1 TTATCAAAATTTCATAAA-GAGG
*
3471 TTACCAAAATTTCATA
1 TTATCAAAATTTCATA
3487 GTGGTATTAC
Statistics
Matches: 114, Mismatches: 28, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
21 5 0.04
22 105 0.92
23 4 0.04
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:4017 original size:22 final size:22
Alignment explanation
Indices: 3992--4463 Score: 73
Period size: 22 Copynumber: 21.7 Consensus size: 22
3982 AGTTTAGTTT
3992 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAGGGTTA
* *
4014 TCAAAATTTCAT-AGTA-TGTAGA
1 TCAAAATTTCATAAG-AGGGT-TA
* *
4036 TTAGAATTTCAT-AG-GGAGATTA
1 TCAAAATTTCATAAGAGG-G-TTA
* *
4058 ACAAAATCTCATAATGA-GGTTA
1 TCAAAATTTCATAA-GAGGGTTA
** *
4080 TCAAAAAATCAT-AGGGAGGTTA
1 TCAAAATTTCATAAGAG-GGTTA
*
4102 TCAAAATTT-GT---A--GTTA
1 TCAAAATTTCATAAGAGGGTTA
* *
4118 TCAAGATTTCATAAG-GAAGTTA
1 TCAAAATTTCATAAGAG-GGTTA
* * *
4140 TCAAAATTTTATAGGAAGGTTTA
1 TCAAAATTTCATAAG-AGGGTTA
* * *
4163 TCAAAATTTTATAGAAAGGTTTA
1 TCAAAATTTCATA-AGAGGGTTA
** *
4186 TCTGAATTTCATAACGA-AGTTA
1 TCAAAATTTCATAA-GAGGGTTA
* * * *
4208 TCACAATTTTAT-AGTATGATTA
1 TCAAAATTTCATAAG-AGGGTTA
* * *
4230 TCAAAATTTCA-GAGTGTGATTA
1 TCAAAATTTCATAAGAG-GGTTA
* *
4252 -CTAACAA-TTCATATG-GAGGTTT
1 TC-AA-AATTTCATAAGAG-GGTTA
* * * *
4274 TTAAATTTTCATAACG-TGGTAA
1 TCAAAATTTCATAA-GAGGGTTA
* *
4296 TCAATATATT-ATATG-GAGGTTA
1 TCAAAAT-TTCATAAGAG-GGTTA
*
4318 TCAAAATTTCAT-AGTGAGG-TA
1 TCAAAATTTCATAAGAG-GGTTA
* * *
4339 TTCAAAA-TTCCTTAGGGAGGTTA
1 -TCAAAATTTCATAAGAG-GGTTA
* *
4362 ACAAAATTTCATAAGAAGGTT-
1 TCAAAATTTCATAAGAGGGTTA
* * * *
4383 TAAAAAATTT-ATAAAAAGGTTC
1 T-CAAAATTTCATAAGAGGGTTA
* **
4405 TCGAAATTTCAT-AGTATCGTTA
1 TCAAAATTTCATAAG-AGGGTTA
* * *
4427 TTAAAATTTCATAAGAAGGATA
1 TCAAAATTTCATAAGAGGGTTA
4449 TCAAAATTTCATAAG
1 TCAAAATTTCATAAG
4464 GAGGTCGTAA
Statistics
Matches: 323, Mismatches: 83, Indels: 88
0.65 0.17 0.18
Matches are distributed among these distances:
16 12 0.04
17 1 0.00
20 2 0.01
21 37 0.11
22 215 0.67
23 53 0.16
24 3 0.01
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
TCAAAATTTCATAAGAGGGTTA
Found at i:4165 original size:23 final size:21
Alignment explanation
Indices: 4113--4238 Score: 99
Period size: 22 Copynumber: 5.7 Consensus size: 21
4103 CAAAATTTGT
* *
4113 AGTTATCAAGATTTCATAAGGA
1 AGTTATCAAAATTTTAT-AGGA
4135 AGTTATCAAAATTTTATAGGA
1 AGTTATCAAAATTTTATAGGA
*
4156 AGGTTTATCAAAATTTTATAGAA
1 A-G-TTATCAAAATTTTATAGGA
** * *
4179 AGGTTTATCTGAATTTCATAACGA
1 A-G-TTATCAAAATTTTAT-AGGA
* *
4203 AGTTATCACAATTTTATAGTA
1 AGTTATCAAAATTTTATAGGA
*
4224 TGATTATCAAAATTT
1 AG-TTATCAAAATTT
4239 CAGAGTGTGA
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
21 8 0.09
22 39 0.46
23 35 0.41
24 3 0.04
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (21 bp):
AGTTATCAAAATTTTATAGGA
Found at i:4396 original size:21 final size:23
Alignment explanation
Indices: 4359--4403 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
4349 CTTAGGGAGG
*
4359 TTAACAAAATTTCATAAGAAGGT
1 TTAACAAAATTTCATAAAAAGGT
4382 TTAA-AAAATTT-ATAAAAAGGT
1 TTAACAAAATTTCATAAAAAGGT
4403 T
1 T
4404 CTCGAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 7 0.33
23 4 0.19
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.33
Consensus pattern (23 bp):
TTAACAAAATTTCATAAAAAGGT
Found at i:5441 original size:146 final size:149
Alignment explanation
Indices: 5279--5568 Score: 408
Period size: 146 Copynumber: 2.0 Consensus size: 149
5269 ATTAATTTAT
5279 TTTTACTATTTTTCATTAAAAA-TTAGGATATATTAAAATTTTTTAATATACAGTTTTATCCTAC
1 TTTTACTATTTTTCATTAAAAACTT-GGATATATTAAAATTTTTTAATATACAGTTTTATCCTAC
* * *
5343 TATAAATTCTA-TTTCATTTAATTAAATTCAACAATTTCATAATTA-T-TTTTCACCATTTTAAT
65 TAAAAATGCTATTTTCATTGAATTAAATTCAACAATTTCATAATTATTATTTTCACCATTTTAAT
*
5405 TTAAAAGTTTATTTTTGCCA
130 TTAAAACTTTATTTTTGCCA
* * * * *
5425 TTTTACTATTTTTCATTAAAAACTTGGATATTTTAAAATTTTTTACTATATAGTTTTATTCTATT
1 TTTTACTATTTTTCATTAAAAACTTGGATATATTAAAATTTTTTAATATACAGTTTTATCCTACT
* * * *
5490 AAAAATGCTATTTTCATTGAATTAAATTCAATATTTTTATAATTATTTTATTTTTACCATTTTAA
66 AAAAATGCTATTTTCATTGAATTAAATTCAACAATTTCATAATTA--TTATTTTCACCATTTTAA
5555 TTTAAAACTTTATT
129 TTTAAAACTTTATT
5569 GTGATTGACC
Statistics
Matches: 125, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
146 65 0.52
147 32 0.26
150 1 0.01
151 27 0.22
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.52
Consensus pattern (149 bp):
TTTTACTATTTTTCATTAAAAACTTGGATATATTAAAATTTTTTAATATACAGTTTTATCCTACT
AAAAATGCTATTTTCATTGAATTAAATTCAACAATTTCATAATTATTATTTTCACCATTTTAATT
TAAAACTTTATTTTTGCCA
Done.