Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013063.1 Corchorus olitorius cultivar O-4 contig13096, 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: 20605
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:2529 original size:68 final size:67
Alignment explanation
Indices: 2416--2551 Score: 186
Period size: 68 Copynumber: 2.0 Consensus size: 67
2406 TCAGTCTGGG
* * * *
2416 CTTTTGGGTTCAGATTGGTGTCGACATGTATATGGGCCGCTCAGTGGGCCTTGGTGCTG-AGACA
1 CTTTTGGGTTCAGATCGGTGTCGACATGTATATAGGCCACTCAGTGGGCCTTGATGC-GAAGACA
2480 GGA
65 GGA
*
2483 CTTTTGGGTTCCA-ATCGGTGTTCGACATGTGTATAGGCCACTCAGTGGGCCTTGATGCGAAGAC
1 CTTTTGGGTT-CAGATCGGTG-TCGACATGTATATAGGCCACTCAGTGGGCCTTGATGCGAAGAC
2547 AGGA
64 AGGA
2551 C
1 C
2552 CCGGGTTTCT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
67 17 0.28
68 44 0.72
ACGTcount: A:0.18, C:0.20, G:0.33, T:0.29
Consensus pattern (67 bp):
CTTTTGGGTTCAGATCGGTGTCGACATGTATATAGGCCACTCAGTGGGCCTTGATGCGAAGACAG
GA
Found at i:15329 original size:60 final size:59
Alignment explanation
Indices: 15230--15391 Score: 243
Period size: 60 Copynumber: 2.7 Consensus size: 59
15220 TTGCTGCCAG
**
15230 GCCCTTATTTGAGCATTTTGGCAAATATTAGGCCTTTATTTGGCCAAATTAAAAGATCGA
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCC-TTATTTGGCCAAATTAAAAGATCGA
** *
15290 GTTCTTATTTGAGCATTTTGGCAAACGTTAGGTCCTTATTTGGTCAAATTAAAAGATCGA
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGG-CCTTATTTGGCCAAATTAAAAGATCGA
*
15350 GCCCTCATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGG-CCTTATTTG
15392 AGCAATTATC
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 90 0.98
61 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (59 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCTTATTTGGCCAAATTAAAAGATCGA
Found at i:15331 original size:31 final size:31
Alignment explanation
Indices: 15293--15395 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
15283 AGATCGAGTT
*
15293 CTTATTTGAGCATTTTGGCAAACGTTAGGTC
1 CTTATTTGAGCATTTTGGCAAACGTTAGGCC
** * * *
15324 CTTATTTG-GTCAAATT---AAAAGATCGAGCC
1 CTTATTTGAG-CATTTTGGCAAACGTTAG-GCC
*
15353 CTCATTTGAGCATTTTGGCAAACGTTAGGCC
1 CTTATTTGAGCATTTTGGCAAACGTTAGGCC
15384 CTTATTTGAGCA
1 CTTATTTGAGCA
15396 ATTATCCAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
28 6 0.11
29 13 0.25
30 2 0.04
31 26 0.49
32 6 0.11
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (31 bp):
CTTATTTGAGCATTTTGGCAAACGTTAGGCC
Found at i:17103 original size:86 final size:86
Alignment explanation
Indices: 17011--17273 Score: 483
Period size: 86 Copynumber: 3.1 Consensus size: 86
17001 AAGAAGAAGT
*
17011 AAATTACTTATTAACAATTAAAACTTAATAAGTTTTGATGAAATAAAAATACATGTTTATCCTTC
1 AAATTACTTATTAATAATTAAAACTTAATAAGTTTTGATGAAATAAAAATACATGTTTATCCTTC
17076 AAAGGAATATTAAAATTTTTA
66 AAAGGAATATTAAAATTTTTA
17097 AAATTACTTATTAATAATTAAAACTTAATAAGTTTTGATGAAATAAAAATACATGTTTATCCTTC
1 AAATTACTTATTAATAATTAAAACTTAATAAGTTTTGATGAAATAAAAATACATGTTTATCCTTC
*
17162 AAAGGAATATTAAAATTTTAA
66 AAAGGAATATTAAAATTTTTA
* *
17183 AAATTACTTATAAATAATTAAAACTTAATAAGTTTTGATGAAATAAAAATACATGTTTATCCTTG
1 AAATTACTTATTAATAATTAAAACTTAATAAGTTTTGATGAAATAAAAATACATGTTTATCCTTC
17248 AAAGGAATATTAAAA-TTTTA
66 AAAGGAATATTAAAATTTTTA
17268 AAATTA
1 AAATTA
17274 AAAAGGATAA
Statistics
Matches: 172, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
85 10 0.06
86 162 0.94
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (86 bp):
AAATTACTTATTAATAATTAAAACTTAATAAGTTTTGATGAAATAAAAATACATGTTTATCCTTC
AAAGGAATATTAAAATTTTTA
Found at i:20361 original size:31 final size:29
Alignment explanation
Indices: 20314--20393 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
20304 GTTAAATACC
* * *
20314 CAAAAAAATCCTTTATGTTTTGTTTTTGAGA
1 CAAAATAATCCCTTATGTTTT-TTTTAG-GA
*
20345 CAAAATAATCTCTTATGTTTTTTTTAGGA
1 CAAAATAATCCCTTATGTTTTTTTTAGGA
* *
20374 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
20394 CAAAAATGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 19 0.45
30 5 0.12
31 18 0.43
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (29 bp):
CAAAATAATCCCTTATGTTTTTTTTAGGA
Found at i:20525 original size:30 final size:31
Alignment explanation
Indices: 20489--20552 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
20479 AAGGGACTGA
*
20489 TTTGTCCAAAAAGAAAAACATAAG-GGATTT
1 TTTGTCCAAAAAGAAAAACATAAGAGAATTT
* *
20519 TTTGTCCCAAAAGAAAAATATAAGAGAATTT
1 TTTGTCCAAAAAGAAAAACATAAGAGAATTT
20550 TTT
1 TTT
20553 TAGTATTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.31
Consensus pattern (31 bp):
TTTGTCCAAAAAGAAAAACATAAGAGAATTT
Done.