Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014910.1 Corchorus capsularis cultivar CVL-1 contig14931, 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: 11734
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:2639 original size:201 final size:201
Alignment explanation
Indices: 2294--2876 Score: 990
Period size: 201 Copynumber: 2.9 Consensus size: 201
2284 ATGCTTCCAT
* * *
2294 AAAATTTATACAATACATCGTCAGTGGAGTTTAGCAAACTGCACGTGTGGAGTTTAACTTTAAGG
1 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAAACTGCACGTGAGGGGTTTAACTTTAAGG
* *
2359 GTTGACATATGTACCCTTA-GGAAGTATGTATTAATATTAAATATTTAATTATGAAATGGGGTAT
66 GTTGACATGTGTACCCTTAGGGAA-TATGTATTAATATTAAATATTTAATTATGAAATAGGGTAT
* *
2423 GTGTTAACTTCTTAACCCGCTTATGGAGTCTAAAATTTACACTAACAGTGTATTGTATAACAATC
130 GTGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAACAATC
2488 CTATAAG
195 CTATAAG
* ** *
2495 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCATACTATACGTGAGGGGTTTAATTTTAAGG
1 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAAACTGCACGTGAGGGGTTTAACTTTAAGG
2560 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGTATG
66 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGTATG
2625 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAACAATCC
131 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAACAATCC
2690 TATAAG
196 TATAAG
* * * *
2696 AAAAATTATATAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGG-TTAACTTTAAGG
1 AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAAACTGCACGTGAGGGGTTTAACTTTAAGG
*
2760 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATATGGTATG
66 GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGTATG
*
2825 TGTTAACTTCTTAACCCTCTTATGGAGTCCAAAATTTACACTGACAGTGTAT
131 TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTAT
2877 ATAATACACC
Statistics
Matches: 361, Mismatches: 20, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
200 126 0.35
201 231 0.64
202 4 0.01
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (201 bp):
AAAATTTATACAATACACCGTCAGTGGAGTTTAGCAAACTGCACGTGAGGGGTTTAACTTTAAGG
GTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATAGGGTATG
TGTTAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAACAATCC
TATAAG
Found at i:3213 original size:173 final size:172
Alignment explanation
Indices: 2702--3221 Score: 934
Period size: 172 Copynumber: 3.0 Consensus size: 172
2692 TAAGAAAAAT
2702 TATATAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTAACTTTAAGGGTTGACA
1 TATATAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTAACTTTAAGGGTTGACA
2767 TGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATATGGTATGTGTTAAC
66 TGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATATGGTATGTGTTAAC
2832 TTCTTAACCCTCTTATGGAGTCCAAAATTTACACTGACAGTG
131 TTCTTAACCCTCTTATGGAGTCCAAAATTTACACTGACAGTG
2874 TATATAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTAACTTTAAGGGTTGACA
1 TATATAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTAACTTTAAGGGTTGACA
2939 TGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATATGGTATGTGTTAAC
66 TGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATATGGTATGTGTTAAC
3004 TTCTTAACCCTCTTATGGAGTCCAAAATTTACACTGACAGTG
131 TTCTTAACCCTCTTATGGAGTCCAAAATTTACACTGACAGTG
*
3046 TATATAATACACCGTCAGTGGAGTTTAGCAGACTGCATGTGCGGGGTTTAACTTTAAGGGTTGAC
1 TATATAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGG-TTAACTTTAAGGGTTGAC
* * * * ** *
3111 ATGTTTAGCCTTAGGGAGTATGTATTAGTATTAAATATTTAATTATGAAATGGGGTATGTGTCAA
65 ATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATATGGTATGTGTTAA
*
3176 CTTCTTAACCCGT-TTATGGAGTCCAAAATTCACACTGACAGTG
130 CTTCTTAACCC-TCTTATGGAGTCCAAAATTTACACTGACAGTG
3219 TAT
1 TAT
3222 TGTATAATAA
Statistics
Matches: 337, Mismatches: 9, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
172 217 0.64
173 119 0.35
174 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (172 bp):
TATATAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTAACTTTAAGGGTTGACA
TGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATATGGTATGTGTTAAC
TTCTTAACCCTCTTATGGAGTCCAAAATTTACACTGACAGTG
Found at i:3448 original size:198 final size:198
Alignment explanation
Indices: 3098--3632 Score: 683
Period size: 198 Copynumber: 2.7 Consensus size: 198
3088 GGGGTTTAAC
* ** * * *
3098 TTTAAGGGTTGACATGTTTAGCCTTAGGGAGTATGTATTAGTATTAAATA--T--TTAATTATGA
1 TTTAAGGGTTGACATGTGTCCCCTTAGAGAATATGTATTAATATTAAATATTTAATTAATTATGA
* *
3159 AATGGGGTATGTGTCAACTTCTTAACCCGTTTATGGAGTCCAAAATTCACACTGACAGTGTATTG
66 AATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTG
* * * * *
3224 TATAATAATCATATAAAAAAATTATACAATACACCGTTAGTGAAATTTAGC-GACTGCACGCGC-
131 TATAATAATCTTATAAAAAAATTATACAATACACCATCAGTGAAATTTAGCAAACTGCACACGCA
3287 GGG
196 GGG
** * **
3290 ATTTTGGGGGTTGACATGTGTCCTCTTAGAGAATATGTATTAATATTTTATATTTAATTAATTAT
1 --TTTAAGGGTTGACATGTGTCCCCTTAGAGAATATGTATTAATATTAAATATTTAATTAATTAT
* * * * * *
3355 GAAATAGGATATGTGTCAACTTCTTATCCCGCTTATGGAGTTCAGAATTTAC-CTAACAGTGTAT
64 GAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTAT
* * *
3419 TGTATAATAATCTTATAAAAAAGATTATACAATACACCATCAGTGGAGTTTAGCAAACTGCACAT
129 TGTATAATAATCTTATAAAAAA-ATTATACAATACACCATCAGTGAAATTTAGCAAACTGCACAC
*
3484 GCATGG
193 GCAGGG
*
3490 TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGA
1 TTTAAGGGTTGACATGTGTCCCCTTAGAGAATATGTATTAATATTAAATATTTAATTAATTATGA
* * *
3555 AATGGGGTATGTGTCAACTTTTTAACCCGCTTAT-G-GTCCAAAATTTACATTGACATTGTATTG
66 AATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTG
3618 TATAATAATCCTTAT
131 TATAATAAT-CTTAT
3633 TATAAAGCTT
Statistics
Matches: 289, Mismatches: 43, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
194 39 0.13
196 12 0.04
197 53 0.18
198 174 0.60
199 9 0.03
200 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (198 bp):
TTTAAGGGTTGACATGTGTCCCCTTAGAGAATATGTATTAATATTAAATATTTAATTAATTATGA
AATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTG
TATAATAATCTTATAAAAAAATTATACAATACACCATCAGTGAAATTTAGCAAACTGCACACGCA
GGG
Found at i:5256 original size:12 final size:12
Alignment explanation
Indices: 5224--5256 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
5214 TCAAAACCAA
5224 TCGGTTTT-GGG
1 TCGGTTTTCGGG
5235 TCGG-TTTCGGG
1 TCGGTTTTCGGG
5246 TCGGTTTTCGG
1 TCGGTTTTCGG
5257 TTTAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 3 0.15
11 11 0.55
12 6 0.30
ACGTcount: A:0.00, C:0.15, G:0.42, T:0.42
Consensus pattern (12 bp):
TCGGTTTTCGGG
Found at i:5297 original size:7 final size:7
Alignment explanation
Indices: 5277--5317 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
5267 TTACACACAC
5277 ATATA-T
1 ATATATT
5283 ATATATT
1 ATATATT
*
5290 ACATATT
1 ATATATT
*
5297 A-ATAAT
1 ATATATT
5303 ATATATT
1 ATATATT
5310 ATATATT
1 ATATATT
5317 A
1 A
5318 AAATAAGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
6 10 0.33
7 20 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (7 bp):
ATATATT
Found at i:5322 original size:22 final size:20
Alignment explanation
Indices: 5281--5398 Score: 74
Period size: 20 Copynumber: 6.2 Consensus size: 20
5271 ACACACATAT
5281 ATATATATTACATATTAATA
1 ATATATATTACATATTAATA
*
5301 ATATATATTATATATTAA-A
1 ATATATATTACATATTAATA
* *
5320 ATAAGATTCTTACATA-T-AT-
1 AT-ATA-TATTACATATTAATA
*
5339 ATATATATT-CTTATT--TA
1 ATATATATTACATATTAATA
*
5356 CATATATATT-CTTATTTAATA
1 -ATATATATTACATA-TTAATA
* *
5377 AAATATTTTACATATTAA-A
1 ATATATATTACATATTAATA
5396 ATA
1 ATA
5399 AAAATGATTT
Statistics
Matches: 77, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
16 4 0.05
17 4 0.05
18 15 0.19
19 11 0.14
20 31 0.40
21 12 0.16
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (20 bp):
ATATATATTACATATTAATA
Found at i:5362 original size:18 final size:18
Alignment explanation
Indices: 5339--5373 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5329 TTACATATAT
5339 ATATATATTCTTATTTAC
1 ATATATATTCTTATTTAC
5357 ATATATATTCTTATTTA
1 ATATATATTCTTATTTA
5374 ATAAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATATATTCTTATTTAC
Found at i:5382 original size:18 final size:18
Alignment explanation
Indices: 5343--5383 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5333 ATATATATAT
*
5343 ATATTCTTATTTACATAT
1 ATATTCTTATTTACATAA
5361 ATATTCTTATTTA-ATAAA
1 ATATTCTTATTTACAT-AA
5379 ATATT
1 ATATT
5384 TTACATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTCTTATTTACATAA
Found at i:7023 original size:27 final size:27
Alignment explanation
Indices: 6987--7041 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
6977 GAAGGTTTTT
*
6987 GGGAATTGAATTCCATTTCATTTTTGC
1 GGGAAATGAATTCCATTTCATTTTTGC
7014 GGGAAATGAATTCCATTTCATTTTTGC
1 GGGAAATGAATTCCATTTCATTTTTGC
7041 G
1 G
7042 TTCCTCCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (27 bp):
GGGAAATGAATTCCATTTCATTTTTGC
Found at i:9355 original size:2 final size:2
Alignment explanation
Indices: 9350--9410 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
9340 ACATATATCA
9350 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
9392 AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC A
9411 AAGCCTCAAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.