Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013348.1 Corchorus olitorius cultivar O-4 contig13381, 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: 7099
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Found at i:431 original size:64 final size:63
Alignment explanation
Indices: 342--642 Score: 358
Period size: 64 Copynumber: 4.7 Consensus size: 63
332 GTGTGAAAAG
* * *
342 AAAACGCACTTATTTAGCGGTGTCTACAAAACAAAACGCC-CTTATTTAGCGGCGTCTATAGA-A
1 AAAACGCCCTTATTTAGCGGCGTCTACAAAACGAAACGCCAC-TATTTAGCGGCGTCT-TA-ACA
405 C
63 C
*
406 AAAACGCCCTTATTTGGCGGCGTCTA-AAGAACGAAACGCCACTATTTAGCGGCGTCTTCAACAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAA-AACGAAACGCCACTATTTAGCGGCGTCTT-AACAC
* * * *
470 GAAACACCGTTATTTGGCGGCGTCTA-AAGAACGAAACGCCACTATTTAGCGGCGTCTTTAACAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAA-AACGAAACGCCACTATTTAGCGGCGTC-TTAACAC
* * * *
534 GAAACGCCGTTATTTAGCGGCGTCTACAGAACGAAACGCCACTATTTAGCGGCGTCTTAAAACC
1 AAAACGCCCTTATTTAGCGGCGTCTACAAAACGAAACGCCACTATTTAGCGGCGTCTTAACA-C
* * * *
598 AAAACGCCCTTATTTAGCGGCGTCTTCAGAACAAAACGCCGCTAT
1 AAAACGCCCTTATTTAGCGGCGTCTACAAAACGAAACGCCACTAT
643 ATTTAACTGC
Statistics
Matches: 214, Mismatches: 16, Indels: 14
0.88 0.07 0.06
Matches are distributed among these distances:
63 9 0.04
64 201 0.94
65 4 0.02
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (63 bp):
AAAACGCCCTTATTTAGCGGCGTCTACAAAACGAAACGCCACTATTTAGCGGCGTCTTAACAC
Found at i:483 original size:96 final size:95
Alignment explanation
Indices: 343--642 Score: 338
Period size: 96 Copynumber: 3.1 Consensus size: 95
333 TGTGAAAAGA
* * *
343 AAACG-CACTTATTTAGCGGTGTCTACAAAACAAAACGCCCTTATTTAGCGGCGTCTATAGAACA
1 AAACGCCAC-TATTTAGCGGCGTCTAC-AAACGAAACGCCATTATTTAGCGGCGTCTATAGAACA
* *
407 AAACGCCCTTATTTGGCGGCGTCTAAAGAACG
64 AAACGCCCTTATTTAGCGGCGTCTTAAGAACG
* * * * * *
439 AAACGCCACTATTTAGCGGCGTCTTCAACACGAAACACCGTTATTTGGCGGCGTCTAAAGAACGA
1 AAACGCCACTATTTAGCGGCGTCTACAA-ACGAAACGCCATTATTTAGCGGCGTCTATAGAACAA
*
504 AACGCCAC-TATTTAGCGGCGTCTTTAA-CACG
65 AACGCC-CTTATTTAGCGGCGTC-TTAAGAACG
** * *
535 AAACGCCGTTATTTAGCGGCGTCTACAGAACGAAACGCCACTATTTAGCGGCGTCT-TAAAACCA
1 AAACGCCACTATTTAGCGGCGTCTACA-AACGAAACGCCATTATTTAGCGGCGTCTATAGAA-CA
* *
599 AAACGCCCTTATTTAGCGGCGTCTTCAGAACA
64 AAACGCCCTTATTTAGCGGCGTCTTAAGAACG
*
631 AAACGCCGCTAT
1 AAACGCCACTAT
643 ATTTAACTGC
Statistics
Matches: 171, Mismatches: 25, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
95 9 0.05
96 154 0.90
97 8 0.05
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (95 bp):
AAACGCCACTATTTAGCGGCGTCTACAAACGAAACGCCATTATTTAGCGGCGTCTATAGAACAAA
ACGCCCTTATTTAGCGGCGTCTTAAGAACG
Found at i:637 original size:32 final size:32
Alignment explanation
Indices: 342--647 Score: 293
Period size: 32 Copynumber: 9.5 Consensus size: 32
332 GTGTGAAAAG
* * * *
342 AAAACGCACTTATTTAGCGGTGTCTACAAAAC
1 AAAACGCCCTTATTTAGCGGCGTCTTCAGAAC
374 AAAACGCCCTTATTTAGCGGCGTCTAT-AGAAC
1 AAAACGCCCTTATTTAGCGGCGTCT-TCAGAAC
* **
406 AAAACGCCCTTATTTGGCGGCGTCTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTTCAGAAC
*
438 GAAACGCCAC-TATTTAGCGGCGTCTTCA-ACAC
1 AAAACGCC-CTTATTTAGCGGCGTCTTCAGA-AC
* * * * **
470 GAAACACCGTTATTTGGCGGCGTCTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTTCAGAAC
* *
502 GAAACGCCAC-TATTTAGCGGCGTCTTTA-ACAC
1 AAAACGCC-CTTATTTAGCGGCGTCTTCAGA-AC
* * *
534 GAAACGCCGTTATTTAGCGGCGTCTACAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTTCAGAAC
* *
566 GAAACGCCAC-TATTTAGCGGCGTCTT-AAAACC
1 AAAACGCC-CTTATTTAGCGGCGTCTTCAGAA-C
598 AAAACGCCCTTATTTAGCGGCGTCTTCAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTTCAGAAC
630 AAAACGCCGCTATATTTA
1 AAAACGCC-CT-TATTTA
648 ACTGCTTCAA
Statistics
Matches: 230, Mismatches: 28, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
31 6 0.03
32 210 0.91
33 8 0.03
34 6 0.03
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTTCAGAAC
Found at i:2177 original size:73 final size:77
Alignment explanation
Indices: 1994--2200 Score: 314
Period size: 73 Copynumber: 2.7 Consensus size: 77
1984 AATTCATTTG
* *
1994 ATTATAGTGGTCTTTGGAACTTAATTTATTCTTATTAATTTTAAATTATTTTGTGTCCTAATTAT
1 ATTATA-TGATCTTAGGAACTTAATTTATTCTTATTAATTTTAAATTATTTTGTGTCCTAA-TAT
2059 AGATTGAGTTATAT
64 AGATTGAGTTATAT
* * *
2073 ATTATATGATCTTAGGAACTTTATTTTTTCTTATTAATTTTAAATTTTTTTGTGTCCT-A-A-A-
1 ATTATATGATCTTAGGAACTTAATTTATTCTTATTAATTTTAAATTATTTTGTGTCCTAATATAG
2134 ATTGAGTTATAT
66 ATTGAGTTATAT
*
2146 ATTATATGATCTTAGGAACTTAATTTCTTCTTATTAATTTTAAATTATTTTGTGT
1 ATTATATGATCTTAGGAACTTAATTTATTCTTATTAATTTTAAATTATTTTGTGT
2201 ATGGCCTTTA
Statistics
Matches: 120, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
73 64 0.53
74 1 0.01
75 1 0.01
77 1 0.01
78 47 0.39
79 6 0.05
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.54
Consensus pattern (77 bp):
ATTATATGATCTTAGGAACTTAATTTATTCTTATTAATTTTAAATTATTTTGTGTCCTAATATAG
ATTGAGTTATAT
Done.