Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012656.1 Corchorus olitorius cultivar O-4 contig12689, 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: 20800
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:14246 original size:33 final size:33
Alignment explanation
Indices: 14209--14271 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
14199 TGATCTTGTT
**
14209 TTTTAGTCGGTTTGCCTAACTTTACCTTGATGC
1 TTTTAGTCGGTTTAACTAACTTTACCTTGATGC
*
14242 TTTTAGTCTGTTTAACTAACTTTACCTTGA
1 TTTTAGTCGGTTTAACTAACTTTACCTTGA
14272 CAGCTACTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (33 bp):
TTTTAGTCGGTTTAACTAACTTTACCTTGATGC
Found at i:17347 original size:122 final size:122
Alignment explanation
Indices: 17123--17364 Score: 328
Period size: 122 Copynumber: 2.0 Consensus size: 122
17113 CATTGCATAG
* * * ** *
17123 ATTTGCTTTCTGTGATTTTCCTTTGTCTGCTCTAATGGTTTCTTGATAGTGTTTCTTCTCGTCTG
1 ATTTGCTTGCTGTGAGTTTCCTTTGTCTGCTCTAATGGTTTCTGGATAACGTTTCTTCTCCTCTG
** *
17188 CAGTTGTCTCCCCATTGGAGCTGAGTTTATCTCTGTGGCAGCTA-GGATTGCCTTCAA
66 CAGTTGTCTCCCCATTGGAGCTGAGCATATCTCTGTGGCAGCAACGG-TTGCCTTCAA
* * *
17245 ATTTGCTTGCTGTGAGTTTCCTTCT-TCTGTTTTGATGGTTTCTGGATAACGTTTCTTCTCCTCT
1 ATTTGCTTGCTGTGAGTTTCCTT-TGTCTGCTCTAATGGTTTCTGGATAACGTTTCTTCTCCTCT
17309 GCAGTTGTCTCCCCATTGGAGCTGAGCATATC-CTTGTGGCAGCAACGGTTGCCTTC
65 GCAGTTGTCTCCCCATTGGAGCTGAGCATATCTC-TGTGGCAGCAACGGTTGCCTTC
17365 CTGTCTTGAC
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
121 1 0.01
122 101 0.96
123 3 0.03
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.43
Consensus pattern (122 bp):
ATTTGCTTGCTGTGAGTTTCCTTTGTCTGCTCTAATGGTTTCTGGATAACGTTTCTTCTCCTCTG
CAGTTGTCTCCCCATTGGAGCTGAGCATATCTCTGTGGCAGCAACGGTTGCCTTCAA
Found at i:17472 original size:20 final size:20
Alignment explanation
Indices: 17427--17800 Score: 295
Period size: 20 Copynumber: 18.5 Consensus size: 20
17417 CATTGAGGGC
*
17427 CAATGTGAATTAAGGCAAGTT
1 CAATGTGAATT-AGGAAAGTT
*
17448 CAATGTGAATTGGGAAAGTT
1 CAATGTGAATTAGGAAAGTT
* * *
17468 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
17488 CAATGTGAATTAGGAAAGTT
1 CAATGTGAATTAGGAAAGTT
* * *
17508 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
17528 CAATGTGAATT-GGAAAGTT
1 CAATGTGAATTAGGAAAGTT
* * *
17547 GAATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-TAGGAAAGTT
* * * *
17568 CAATGTCATTTGGGAAATTT
1 CAATGTGAATTAGGAAAGTT
* * *
17588 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
* * *
17608 CAATGTCAATTGGGAATGTT
1 CAATGTGAATTAGGAAAGTT
* * *
17628 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
*
17648 CAATGTCAATT-GGTAAAGTT
1 CAATGTGAATTAGG-AAAGTT
* * *
17668 GAATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-TAGGAAAGTT
* *
17689 CAATGTCAATT-GGAAAATTT
1 CAATGTGAATTAGG-AAAGTT
* * *
17709 GAATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-TAGGAAAGTT
* *
17730 CAATGTCAATTGGGAAAGTT
1 CAATGTGAATTAGGAAAGTT
* * *
17750 GAATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-TAGGAAAGTT
* *
17771 CAATGTCAATTGGGAAAGTT
1 CAATGTGAATTAGGAAAGTT
*
17791 TAATGTGAAT
1 CAATGTGAAT
17801 GCGCCGCGTA
Statistics
Matches: 265, Mismatches: 79, Indels: 19
0.73 0.22 0.05
Matches are distributed among these distances:
19 20 0.08
20 176 0.66
21 65 0.25
22 4 0.02
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.29
Consensus pattern (20 bp):
CAATGTGAATTAGGAAAGTT
Found at i:17596 original size:41 final size:40
Alignment explanation
Indices: 17428--17800 Score: 595
Period size: 40 Copynumber: 9.2 Consensus size: 40
17418 ATTGAGGGCC
*
17428 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAA-TAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* *
17469 AATGTGAATAAGGCAAGTTCAATGTGAATTAGGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
17509 AATGTGAATAAGGCAAGTTCAATGTGAATT-GGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* *
17548 AATGTGAATCAAGGCAAGTTCAATGTCATTTGGGAAATTTG
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
17589 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAATGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
17629 AATGTGAATAAGGCAAGTTCAATGTCAATTGGTAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* *
17669 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGAAAATTTG
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
17710 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
17751 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGGAAAGTTT
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
17792 AATGTGAAT
1 AATGTGAAT
17801 GCGCCGCGTA
Statistics
Matches: 315, Mismatches: 14, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
39 18 0.06
40 155 0.49
41 142 0.45
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.29
Consensus pattern (40 bp):
AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
Found at i:20717 original size:335 final size:331
Alignment explanation
Indices: 19979--20799 Score: 992
Period size: 335 Copynumber: 2.5 Consensus size: 331
19969 AGATATGACT
* *
19979 TCAAATCCAATGTGGCTGAGATTTGATT-A-GAATATAGATATTTTAACGACTCTCGATACCAAA
1 TCAAATCCAATGTGGCTGAGATTTGGTTGATGAATATAGATATTTTAACGACTCTCGGTACCAAA
* * *
20042 AATCATGTAAAACTGAGCCGATGCCCCTAAACACGCGTTTTTAGCTAAAAACCGTGATGGTAATA
66 AATCATGCAAAACTGAG-CGAT-CCCCTAAACACGCGTTTTTAGCCAAAAACCGTGATGGTTA-A
* * * *
20107 TACACGATTTCGGTTAAAATATTGCAAAATTTGACCCGAAATATTTTTCCTCAATTTTTGGCCAA
128 TACACGATTTCGGCTAAAATTTTGCAAAAATTAACCCGAAATATTTTTCCTCAATTTTTGGCCAA
* *
20172 AATACTCAGAAAAAAAAATATATAATTCAACGCAAAAAAGTTTGAAGTCGTTTAATGTTTCTAAA
193 AATACTC--AAAAAAAAATATATAATTCAAAGCAAAAAAGTTTGAAGTCGTTTAACGTTTCTAAA
* * * *
20237 ATTGTTTTCCAATTTTTCCCTAAATTAATTTCTGATTGAATTGAAACCAGATATTGATGCTCATA
256 ATTGTTTTCCAATTTTTCCCTAAATTAATTTCTGATTAAATGGAAACAAGATATTGAGGCTCATA
20302 AAAACTAATCA
321 AAAACTAATCA
* *
20313 TCAAATCCAATGTGGCTGAGATTTGGTTGGATGAATATAGATATTTTAACGACTCTTGGTACTAA
1 TCAAATCCAATGTGGCTGAGATTTGGTT-GATGAATATAGATATTTTAACGACTCTCGGTACCAA
* **
20378 AAATCATGCAAAACTGAGCAGATACCCCTAAACACTCGTTTTTAGCCAAAAACCAAGATGGTTAA
65 AAATCATGCAAAACTGAGC-GAT-CCCCTAAACACGCGTTTTTAGCCAAAAACCGTGATGGTTAA
* * *
20443 TACAAGATTTCGGCTAAAATTTTTCAAAAATTAACCCGAAATATTTTTTCTCAATTTTTGGCCAA
128 TACACGATTTCGGCTAAAATTTTGCAAAAATTAACCCGAAATATTTTTCCTCAATTTTTGGCCAA
* * * * * * *
20508 GATACTC-ATAAAAAA-ATATAATTCAAATCCAAAAAGTTTGAAGTGCTTTTGACGTTTCTAATA
193 AATACTCAAAAAAAAATATATAATTCAAAGCAAAAAAGTTTGAAGT-CGTTTAACGTTTCTAAAA
* *
20571 TCGTTTTTTCCAATTTTTTCCTAAATTAATTTCTGATTAAATCGGAAA-AAGAT-TTAGAGGCTC
257 T--TGTTTTCCAATTTTTCCCTAAATTAATTTCTGATTAAAT-GGAAACAAGATATT-GAGGCTC
* *
20634 GTAAAAA-TAAATCC
318 ATAAAAACT-AATCA
* * * * * * **
20648 TCAAATCCAATCTGTCTGAGATTTGGTTAGATGAATAAAGGTATATTAAAGACTCTCGGCGCCAA
1 TCAAATCCAATGTGGCTGAGATTTGGTT-GATGAATATAGATATTTTAACGACTCTCGGTACCAA
* * * ** * * *
20713 AAATCATGCAAAACTGTGTCGGTGCCCTGGA-ACGCATTTTTAGCCAAAAATCGTGATGGTTAGT
65 AAATCATGCAAAACTGAG-CGATCCCCTAAACACGCGTTTTTAGCCAAAAACCGTGATGGTTAAT
20777 ACACGATTTCGGCTAAAATTTTG
129 ACACGATTTCGGCTAAAATTTTG
20800 T
Statistics
Matches: 417, Mismatches: 59, Indels: 23
0.84 0.12 0.05
Matches are distributed among these distances:
332 26 0.06
333 70 0.17
334 35 0.08
335 129 0.31
336 72 0.17
337 85 0.20
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (331 bp):
TCAAATCCAATGTGGCTGAGATTTGGTTGATGAATATAGATATTTTAACGACTCTCGGTACCAAA
AATCATGCAAAACTGAGCGATCCCCTAAACACGCGTTTTTAGCCAAAAACCGTGATGGTTAATAC
ACGATTTCGGCTAAAATTTTGCAAAAATTAACCCGAAATATTTTTCCTCAATTTTTGGCCAAAAT
ACTCAAAAAAAAATATATAATTCAAAGCAAAAAAGTTTGAAGTCGTTTAACGTTTCTAAAATTGT
TTTCCAATTTTTCCCTAAATTAATTTCTGATTAAATGGAAACAAGATATTGAGGCTCATAAAAAC
TAATCA
Done.