Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014352.1 Corchorus olitorius cultivar O-4 contig14385, 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: 9295
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1488 original size:217 final size:217
Alignment explanation
Indices: 1113--1524 Score: 700
Period size: 217 Copynumber: 1.9 Consensus size: 217
1103 ATAGTTTTTT
* *
1113 ATGGCAAATTATACAATACACTAGCAGTGGAGTTTATCAAACTACACAAGCAGATCCTGAAGGGT
1 ATGGCAAATTATACAATACACCAGCAGTGGAGTTTAGCAAACTACACAAGCAGATCCTGAAGGGT
1178 GACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAAAGGACATG
66 GACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAAAGGACATG
** *
1243 TGTCAACTCCACAACCCGTTTGTGGAGTCCAAAATTTACACCGCCTG-TGTATCAAATAATTACC
131 TGTCAACTCCACAACCCACTTATGGAGTCCAAAATTTACACCGCC-GATGTATCAAATAATTACC
1307 CTTTTTTTATATGATTATTCAAG
195 CTTTTTTTATATGATTATTCAAG
* * * * * *
1330 ATGGCAAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACATAAGCGGGTCCTGAAGGGT
1 ATGGCAAATTATACAATACACCAGCAGTGGAGTTTAGCAAACTACACAAGCAGATCCTGAAGGGT
*
1395 GACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATG
66 GACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAAAGGACATG
1460 TGTCAACTCCACAACCCACTTATGGAGTCCAAAATTTACACCGCCGATGTATCAAATAATTACCC
131 TGTCAACTCCACAACCCACTTATGGAGTCCAAAATTTACACCGCCGATGTATCAAATAATTACCC
1525 ATTCAAGATT
Statistics
Matches: 182, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
216 1 0.01
217 181 0.99
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (217 bp):
ATGGCAAATTATACAATACACCAGCAGTGGAGTTTAGCAAACTACACAAGCAGATCCTGAAGGGT
GACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAAAGGACATG
TGTCAACTCCACAACCCACTTATGGAGTCCAAAATTTACACCGCCGATGTATCAAATAATTACCC
TTTTTTTATATGATTATTCAAG
Found at i:7694 original size:125 final size:125
Alignment explanation
Indices: 7525--8034 Score: 641
Period size: 125 Copynumber: 4.1 Consensus size: 125
7515 CAACCCTTGT
* * * ** * * *
7525 AAATGTCGGAACAAGTTGTTCACGTCATTTGATTTCGATGTATTCCGACTTTTGTAAGTGTTGGT
1 AAATGTCGGAACAAGTTCTTCACATCATTTAATTTCGACATATTCCGACATCTGTAAGCGTTGGT
** * * * *
7590 ATAGATATTATATCGTGACATTTATTAAACGTTGCAATAGAACACTATACCGACAATTAC
66 ATAGATATTATATCGTGACATTTATTAAACGTCACTATAAAAAACTATACCGACGATTAC
* *
7650 AAATGTCGGAACAAGTTCTTCACATCATTTAATTTTGACATATTCCGACATCTATAAGCGTTGGT
1 AAATGTCGGAACAAGTTCTTCACATCATTTAATTTCGACATATTCCGACATCTGTAAGCGTTGGT
* *
7715 ATAGATATTATATCGTGACATTTATTAGACGTCACTTTAAAAAA-TATACCGACGATTAC
66 ATAGATATTATATCGTGACATTTATTAAACGTCACTATAAAAAACTATACCGACGATTAC
* *
7774 AAATGTCGGAACAAGTTCTTCACATCA-TTACAATTCGACA-ATTCCGACATCTGTAAACGTTGG
1 AAATGTCGGAACAAGTTCTTCACATCATTTA-ATTTCGACATATTCCGACATCTGTAAGCGTTGG
* * *
7837 TATAGATATTATATCGTGACCTTGATTAAACGTCACTATAAAAAAC-ATACCGACGATTAT
65 TATAGATATTATATCGTGACATTTATTAAACGTCACTATAAAAAACTATACCGACGATTAC
* * * * * * * * *
7897 AAATGTCGAAACAAGTTGTACAAATTATTTGAGTTCGACATATTCCGACATTTGTAAGCGTTGTT
1 AAATGTCGGAACAAGTTCTTCACATCATTTAATTTCGACATATTCCGACATCTGTAAGCGTTGGT
* * * * * *
7962 ATAAATATTATATCGTGACATTTATTAAATGTCGCTATAAAATAGTATACCGACGCTTAC
66 ATAGATATTATATCGTGACATTTATTAAACGTCACTATAAAAAACTATACCGACGATTAC
8022 AAATGTCGGAACA
1 AAATGTCGGAACA
8035 CTTTATTCGC
Statistics
Matches: 333, Mismatches: 47, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
123 108 0.32
124 109 0.33
125 116 0.35
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (125 bp):
AAATGTCGGAACAAGTTCTTCACATCATTTAATTTCGACATATTCCGACATCTGTAAGCGTTGGT
ATAGATATTATATCGTGACATTTATTAAACGTCACTATAAAAAACTATACCGACGATTAC
Found at i:8060 original size:247 final size:248
Alignment explanation
Indices: 7525--8050 Score: 631
Period size: 247 Copynumber: 2.1 Consensus size: 248
7515 CAACCCTTGT
* * * ** * ** * * **
7525 AAATGTCGGAACAAGTTGTTCACGTCATTTGATTTCGATGTATTCCGACTTTTGTAAGTGTTGGT
1 AAATGTCGGAACAAGTTATTCACATCAATACAATTCGA-CAATTCCGACATCTGTAAACGTTGGT
* ** * *
7590 ATAGATATTATATCGTGACATTTATTAAACGTTGCAATAGAACACTATACCGACAATTACAAATG
65 ATAGATATTATATCGTGACATTGATTAAACGTCACAATAAAAAACTATACCGACAATTACAAATG
* * * * * *
7655 TCGGAACAAGTTCTTCACATCATTTAATTTTGACATATTCCGACATCTATAAGCGTTGGTATAGA
130 TCGAAACAAGTTCTACAAATCATTTAAGTTCGACATATTCCGACATCTATAAGCGTTGGTATAAA
* *
7720 TATTATATCGTGACATTTATTAGACGTCACTTTAAAAAATATACCGACGATTAC
195 TATTATATCGTGACATTTATTAAACGTCACTATAAAAAATATACCGACGATTAC
* *
7774 AAATGTCGGAACAAGTTCTTCACATCATTACAATTCGACAATTCCGACATCTGTAAACGTTGGTA
1 AAATGTCGGAACAAGTTATTCACATCAATACAATTCGACAATTCCGACATCTGTAAACGTTGGTA
* * * *
7839 TAGATATTATATCGTGACCTTGATTAAACGTCACTATAAAAAAC-ATACCGACGATTATAAATGT
66 TAGATATTATATCGTGACATTGATTAAACGTCACAATAAAAAACTATACCGACAATTACAAATGT
* * * * * *
7903 CGAAACAAGTTGTACAAATTATTTGAGTTCGACATATTCCGACATTTGTAAGCGTTGTTATAAAT
131 CGAAACAAGTTCTACAAATCATTTAAGTTCGACATATTCCGACATCTATAAGCGTTGGTATAAAT
* * * *
7968 ATTATATCGTGACATTTATTAAATGTCGCTATAAAATAGTATACCGACGCTTAC
196 ATTATATCGTGACATTTATTAAACGTCACTATAAAA-AATATACCGACGATTAC
** *
8022 AAATGTCGGAACACTTTATTCGCATCAAT
1 AAATGTCGGAACAAGTTATTCACATCAAT
8051 GGATTCGACA
Statistics
Matches: 233, Mismatches: 43, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
247 103 0.44
248 97 0.42
249 33 0.14
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (248 bp):
AAATGTCGGAACAAGTTATTCACATCAATACAATTCGACAATTCCGACATCTGTAAACGTTGGTA
TAGATATTATATCGTGACATTGATTAAACGTCACAATAAAAAACTATACCGACAATTACAAATGT
CGAAACAAGTTCTACAAATCATTTAAGTTCGACATATTCCGACATCTATAAGCGTTGGTATAAAT
ATTATATCGTGACATTTATTAAACGTCACTATAAAAAATATACCGACGATTAC
Done.