Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012851.1 Corchorus olitorius cultivar O-4 contig12884, 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: 47050
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:405 original size:51 final size:51
Alignment explanation
Indices: 350--453 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
340 AATAACTATT
350 ATATATACTATATATTATTTTTAGTGACTATGGAAATTACTTAAAAACCAA
1 ATATATACTATATATTATTTTTAGTGACTATGGAAATTACTTAAAAACCAA
*
401 ATATATACTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGACCAA
1 ATATATACTATATATTATTTTTAGTGACTATGGAAATTACTTAAAAACCAA
452 AT
1 AT
454 TGAGGATTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (51 bp):
ATATATACTATATATTATTTTTAGTGACTATGGAAATTACTTAAAAACCAA
Found at i:2299 original size:14 final size:14
Alignment explanation
Indices: 2278--2319 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2268 AAAAATTGTA
2278 AAATTTAAAAAATT
1 AAATTTAAAAAATT
** *
2292 TCATTTAAGAAA-T
1 AAATTTAAAAAATT
2305 AAATTTAAAAAATT
1 AAATTTAAAAAATT
2319 A
1 A
2320 TTATATATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (14 bp):
AAATTTAAAAAATT
Found at i:2523 original size:121 final size:127
Alignment explanation
Indices: 2307--2556 Score: 377
Period size: 121 Copynumber: 2.0 Consensus size: 127
2297 TAAGAAATAA
* *
2307 ATTTAAAAAATTATTATATATATAAGTTTTTTAATTAAAATATTAAAATGGTAAAAATAAAATAG
1 ATTTAAAAAATTACTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---ATA-
2372 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAGTA
62 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAGTA
2437 T
127 T
2438 ATTTAAAAAATT-CTA-ATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-
1 ATTTAAAAAATTACTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTAT
* * *
2498 AA-GATATTAGATTTAATTAATTAAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAAGT
66 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAGT
2557 TTAAACAATG
Statistics
Matches: 114, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
121 54 0.47
122 2 0.02
123 2 0.02
125 2 0.02
129 40 0.35
130 2 0.02
131 12 0.11
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.38
Consensus pattern (127 bp):
ATTTAAAAAATTACTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTAT
AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAGTAT
Found at i:4842 original size:24 final size:23
Alignment explanation
Indices: 4798--4843 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4788 TTCAATAAGA
*
4798 AAATTCAAGGATTCTAGAAAAAG
1 AAATTCAAGGATTCTACAAAAAG
*
4821 AAATTTAAGGATTCTACCAAAAA
1 AAATTCAAGGATTCTA-CAAAAA
4844 AAAAGGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.24
Consensus pattern (23 bp):
AAATTCAAGGATTCTACAAAAAG
Found at i:28200 original size:16 final size:17
Alignment explanation
Indices: 28179--28212 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
28169 GCTAGCAAGC
28179 TTTTCTTTTTCT-TTTT
1 TTTTCTTTTTCTGTTTT
28195 TTTTCTTTTTCTGTTTT
1 TTTTCTTTTTCTGTTTT
28212 T
1 T
28213 CACTTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTCTTTTTCTGTTTT
Found at i:31203 original size:31 final size:31
Alignment explanation
Indices: 31165--31264 Score: 122
Period size: 31 Copynumber: 3.4 Consensus size: 31
31155 CCAACATTTA
31165 ATAAGAATTTATGATTTTTTTTGGCATCAAT
1 ATAAGAATTTATGATTTTTTTTGGCATCAAT
* * **
31196 ATAAGAATTTATG---GTTTAT-G-ATTTA-
1 ATAAGAATTTATGATTTTTTTTGGCATCAAT
31221 ATAAGAATTTATGATTTTTTTTGGCATCAAT
1 ATAAGAATTTATGATTTTTTTTGGCATCAAT
31252 ATAAGAATTTATG
1 ATAAGAATTTATG
31265 GTTTATGATG
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
25 13 0.24
26 3 0.05
27 1 0.02
28 8 0.15
29 1 0.02
30 3 0.05
31 26 0.47
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (31 bp):
ATAAGAATTTATGATTTTTTTTGGCATCAAT
Found at i:31225 original size:56 final size:56
Alignment explanation
Indices: 31160--31273 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
31150 TTTTCCCAAC
31160 ATTTAATAAGAATTTATGATTTTTTTTGGCATCAATATAAGAATTTATGGTTTATG
1 ATTTAATAAGAATTTATGATTTTTTTTGGCATCAATATAAGAATTTATGGTTTATG
31216 ATTTAATAAGAATTTATGATTTTTTTTGGCATCAATATAAGAATTTATGGTTTATG
1 ATTTAATAAGAATTTATGATTTTTTTTGGCATCAATATAAGAATTTATGGTTTATG
31272 AT
1 AT
31274 GTATCTTTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.48
Consensus pattern (56 bp):
ATTTAATAAGAATTTATGATTTTTTTTGGCATCAATATAAGAATTTATGGTTTATG
Found at i:31291 original size:22 final size:22
Alignment explanation
Indices: 31263--31306 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31253 TAAGAATTTA
*
31263 TGGTTTATGATGTATCTTTTTT
1 TGGTTTATGATGTATATTTTTT
31285 TGGTTTATGATGTATATTTTTT
1 TGGTTTATGATGTATATTTTTT
31307 GTCATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.02, G:0.18, T:0.64
Consensus pattern (22 bp):
TGGTTTATGATGTATATTTTTT
Done.