Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024021.1 Corchorus olitorius cultivar O-4 contig24054, 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: 7329
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Found at i:548 original size:124 final size:124
Alignment explanation
Indices: 336--591 Score: 390
Period size: 124 Copynumber: 2.1 Consensus size: 124
326 TGTCTTTGAA
* **
336 ACATTATTTTATTTTGCTTAGTGTTTAAAGAGATATTGTTGTTGATTAAAGGTATTAAAATTGGA
1 ACATTATTTTATTTTGCTTAATGTTTAAAGAGATATTGTTGTTGATTAAAGCCATTAAAATTGGA
* *
401 TTATAGCTCATCTTATATGGGGATTATGGTCTTGATCACTTAATTTTCCTTTCAATTTC
66 TTATAGCTCATCTTATATAGGGATTATGGTCTTGATCAATTAATTTTCCTTTCAATTTC
* *
460 ACATTATTTTATTTTGCTTAATGTTTAGATAGATATTGTTGTTGATT-AAGACCATTAAAATTGG
1 ACATTATTTTATTTTGCTTAATGTTTAAAGAGATATTGTTGTTGATTAAAG-CCATTAAAATTGG
* *
524 ATTATAGCTCAT-TTGGTATAGGGATTGTGGTCTTGATCAATTAATTTTCCTTTCAATTTC
65 ATTATAGCTCATCTT-ATATAGGGATTATGGTCTTGATCAATTAATTTTCCTTTCAATTTC
*
584 AAATTATT
1 ACATTATT
592 ATGTGTGCTA
Statistics
Matches: 120, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
123 5 0.04
124 115 0.96
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (124 bp):
ACATTATTTTATTTTGCTTAATGTTTAAAGAGATATTGTTGTTGATTAAAGCCATTAAAATTGGA
TTATAGCTCATCTTATATAGGGATTATGGTCTTGATCAATTAATTTTCCTTTCAATTTC
Found at i:797 original size:113 final size:112
Alignment explanation
Indices: 654--876 Score: 331
Period size: 113 Copynumber: 2.0 Consensus size: 112
644 TTGTTGATAA
** *
654 AAAGATAGATCATTTGATTTAGGAATGTTGGTGTTAGGTTCTTAATTTTACTTATAAATTATACT
1 AAAGATAGATCATTTGATTTAGGAATGTTGGTGTTAGGGCCTTAATTTTACTAATAAATTATACT
* *
719 TATTTGTATTTGTATTTAAGGGTGAGTTTGGGTTATAAATTATGCTTAC
66 TATTTATA-TT-TATTTAAGGGTGAGATTGGGTTATAAATTATGCTTAC
* * *
768 AAAGATGGATCGTTTGA-TTAGGAATGTTGGTGTTAGGGCCTTAATTTTACTAATAAATTATGCT
1 AAAGATAGATCATTTGATTTAGGAATGTTGGTGTTAGGGCCTTAATTTTACTAATAAATTATACT
* *
832 TATTTATATTTATTTAAGGGTGGGATTGGGTTATAGATTATGCTT
66 TATTTATATTTATTTAAGGGTGAGATTGGGTTATAAATTATGCTT
877 TAGGTGTTTA
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
111 32 0.32
112 2 0.02
113 50 0.51
114 15 0.15
ACGTcount: A:0.28, C:0.05, G:0.22, T:0.45
Consensus pattern (112 bp):
AAAGATAGATCATTTGATTTAGGAATGTTGGTGTTAGGGCCTTAATTTTACTAATAAATTATACT
TATTTATATTTATTTAAGGGTGAGATTGGGTTATAAATTATGCTTAC
Found at i:2892 original size:381 final size:382
Alignment explanation
Indices: 2367--3092 Score: 1355
Period size: 381 Copynumber: 1.9 Consensus size: 382
2357 CGTGATTGCT
2367 TAAGCATGTTTGTAACTATTATTTTTTTAATTGTGTCAGAAAGTTAGAGATTTTTTAGTAAAAAT
1 TAAGCATGTTTGTAACTATTATTTTTTTAATTGTGTCAGAAAGTTAGAGATTTTTTAGTAAAAAT
* *
2432 TGTAAATCTGATTGCATGAATTATATGAACAAAAAAGACAAATTGTTATTTGCAATCTCTTTCCT
66 TGTAAATCTGATTGCATGAATTATATGAACAAAAAAGACAAATTGTCAGTTGCAATCTCTTTCCT
2497 ATACATGTGTCTTTCCCATTTCTTAATTTAGTTTGATTTGTATAGTTTCTTTTGCTCATCATTTT
131 ATACATGTGTCTTTCCCATTTCTTAATTTAGTTTGATTTGTATAGTTTCTTTTGCTCATCATTTT
2562 AATAATTTAATTGGTTGAGAGATTTTGCAGGTCACTCATGTTGTACCATTTCTGCATCAAGACTT
196 AATAATTTAATTGGTTGAGAGATTTTGCAGGTCACTCATGTTGTACCATTTCTGCATCAAGACTT
* *
2627 GGTTGCTACATATAGTTTGGAGCAGCACATACTTTCTCGACACAGCCGTGA-GTATTCAATAAAT
261 GGTTGCTACATATAGTTTGGAGCAGCACATACTTTCTCGACACAACCGCGACGTATTCAATAAAT
2691 TGTCTCCTGTTATTCTCAAAAAGTTAGAGATTCTTTTAATTGTGTCTCCTGTTCATA
326 TGTCTCCTGTTATTCTCAAAAAGTTAGAGATTCTTTTAATTGTGTCTCCTGTTCATA
*
2748 TAAGCATGTTTGTAACTATTATTTTTTTAATTGTGTCAGAAAGTTAGAGATTTTTTATTAAAAAT
1 TAAGCATGTTTGTAACTATTATTTTTTTAATTGTGTCAGAAAGTTAGAGATTTTTTAGTAAAAAT
* *
2813 TGTAAATCTGATTGCATGAATTATATGAACAAAAGAGACAAATTGTCAGTTGCAGTCTCTTTCCT
66 TGTAAATCTGATTGCATGAATTATATGAACAAAAAAGACAAATTGTCAGTTGCAATCTCTTTCCT
*
2878 ATACATGTGTCTTTCCCTTTTCTTAATTTAGTTTGATTTGTATAGTTTCTTTTGCTCATCATTTT
131 ATACATGTGTCTTTCCCATTTCTTAATTTAGTTTGATTTGTATAGTTTCTTTTGCTCATCATTTT
2943 AATAATTTAATTGGTTGAGAGATTTTGCAGGTCACTCATGTTGTACCATTTCTGCATCAAGACTT
196 AATAATTTAATTGGTTGAGAGATTTTGCAGGTCACTCATGTTGTACCATTTCTGCATCAAGACTT
*
3008 GGTTGCTACATATAGTTTGGAGCAGCACATACTTTCTCGACACAACCGCGACTTATTCAATAAAT
261 GGTTGCTACATATAGTTTGGAGCAGCACATACTTTCTCGACACAACCGCGACGTATTCAATAAAT
*
3073 TGTCTCCTTTTATTCTCAAA
326 TGTCTCCTGTTATTCTCAAA
3093 TTTGAATGGT
Statistics
Matches: 334, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
381 303 0.91
382 31 0.09
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (382 bp):
TAAGCATGTTTGTAACTATTATTTTTTTAATTGTGTCAGAAAGTTAGAGATTTTTTAGTAAAAAT
TGTAAATCTGATTGCATGAATTATATGAACAAAAAAGACAAATTGTCAGTTGCAATCTCTTTCCT
ATACATGTGTCTTTCCCATTTCTTAATTTAGTTTGATTTGTATAGTTTCTTTTGCTCATCATTTT
AATAATTTAATTGGTTGAGAGATTTTGCAGGTCACTCATGTTGTACCATTTCTGCATCAAGACTT
GGTTGCTACATATAGTTTGGAGCAGCACATACTTTCTCGACACAACCGCGACGTATTCAATAAAT
TGTCTCCTGTTATTCTCAAAAAGTTAGAGATTCTTTTAATTGTGTCTCCTGTTCATA
Found at i:6314 original size:2 final size:2
Alignment explanation
Indices: 6307--6338 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6297 GATGAAAGTG
6307 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6339 GTGTCGAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6986 original size:25 final size:24
Alignment explanation
Indices: 6958--7014 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
6948 GTGGATTGTA
*
6958 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
6983 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
7007 AAA-AAATT
1 AAATAAATT
7015 CAAGGCTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:7176 original size:16 final size:15
Alignment explanation
Indices: 7132--7179 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
7122 CCCAGCAAAC
7132 CCGAAACCCGAATGA
1 CCGAAACCCGAATGA
**
7147 CCTG-AACCAAAATGA
1 CC-GAAACCCGAATGA
7162 GCCGAAACCCGAATGA
1 -CCGAAACCCGAATGA
7178 CC
1 CC
7180 CGAGAAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.40, C:0.33, G:0.19, T:0.08
Consensus pattern (15 bp):
CCGAAACCCGAATGA
Found at i:7182 original size:16 final size:16
Alignment explanation
Indices: 7130--7182 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
7120 AACCCAGCAA
7130 ACCCGAAACCCGAATG
1 ACCCGAAACCCGAATG
* **
7146 ACCTG-AACCAAAATG
1 ACCCGAAACCCGAATG
*
7161 AGCCGAAACCCGAATG
1 ACCCGAAACCCGAATG
7177 ACCCGA
1 ACCCGA
7183 GAAAATCACC
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.40, C:0.34, G:0.19, T:0.08
Consensus pattern (16 bp):
ACCCGAAACCCGAATG
Done.