Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013200.1 Corchorus olitorius cultivar O-4 contig13233, 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: 3005
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Found at i:1334 original size:73 final size:73
Alignment explanation
Indices: 1245--1391 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
1235 TATCTCCCTA
1245 GATTTAGTTCCTAGTTTAAGTTAGATTTAGCTTTCTTGGGGCTTAATTCTAGGATTATATTCTAG
1 GATTTAGTTCCTAGTTTAAGTTAGATTTAGCTTTCTTGGGGCTTAATTCTAGGATTATATTCTAG
1310 TATAAAAG
66 TATAAAAG
1318 GATTTAGTTCCTAGTTTAAGTTAGATTTAGCTTTCTTGGGGCTTAATTCTAGGATTATATTCTAG
1 GATTTAGTTCCTAGTTTAAGTTAGATTTAGCTTTCTTGGGGCTTAATTCTAGGATTATATTCTAG
1383 TATAAAAG
66 TATAAAAG
1391 G
1 G
1392 CCTCTCATTG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.44
Consensus pattern (73 bp):
GATTTAGTTCCTAGTTTAAGTTAGATTTAGCTTTCTTGGGGCTTAATTCTAGGATTATATTCTAG
TATAAAAG
Found at i:1553 original size:4 final size:4
Alignment explanation
Indices: 1544--1578 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
1534 TAATGGGGTA
1544 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1579 CGTGTTTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2074 original size:13 final size:13
Alignment explanation
Indices: 2056--2112 Score: 71
Period size: 13 Copynumber: 4.4 Consensus size: 13
2046 CACGTCAGCA
*
2056 TTGACT-TTGATT
1 TTGACTGTTGACT
*
2068 GTTGACTGTTAACT
1 -TTGACTGTTGACT
*
2082 TTGATTGTTGACT
1 TTGACTGTTGACT
2095 TTGACTGTTGACT
1 TTGACTGTTGACT
2108 TTGAC
1 TTGAC
2113 CTCCGCGAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
13 34 0.89
14 4 0.11
ACGTcount: A:0.18, C:0.12, G:0.21, T:0.49
Consensus pattern (13 bp):
TTGACTGTTGACT
Found at i:2105 original size:20 final size:20
Alignment explanation
Indices: 2056--2105 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2046 CACGTCAGCA
2056 TTGACTTTGATTGTTGACTG
1 TTGACTTTGATTGTTGACTG
*
2076 TTAACTTTGATTGTTGACT-
1 TTGACTTTGATTGTTGACTG
2095 TTGACTGTTGA
1 TTGACT-TTGA
2106 CTTTGACCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.18, C:0.10, G:0.22, T:0.50
Consensus pattern (20 bp):
TTGACTTTGATTGTTGACTG
Found at i:2327 original size:27 final size:28
Alignment explanation
Indices: 2279--2331 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
2269 TGAATTTTGT
*
2279 CCTTGACCTATTTGGTCCCGTATTCTGC
1 CCTTGACCTATATGGTCCCGTATTCTGC
2307 CCTTGACCTA-ATGGTCCCGTATTCT
1 CCTTGACCTATATGGTCCCGTATTCT
2332 TGATGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.13, C:0.32, G:0.17, T:0.38
Consensus pattern (28 bp):
CCTTGACCTATATGGTCCCGTATTCTGC
Found at i:2359 original size:7 final size:7
Alignment explanation
Indices: 2344--2390 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
2334 ATGATTATGC
*
2344 TGTCCGT
1 TGTCTGT
2351 TGTCTGT
1 TGTCTGT
*
2358 TGTCCGT
1 TGTCTGT
*
2365 TGTCTGA
1 TGTCTGT
*
2372 T-TCCGT
1 TGTCTGT
2378 TGTCTGT
1 TGTCTGT
2385 TGTCTG
1 TGTCTG
2391 CTATCTGATT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
6 4 0.12
7 28 0.88
ACGTcount: A:0.02, C:0.21, G:0.28, T:0.49
Consensus pattern (7 bp):
TGTCTGT
Found at i:2363 original size:14 final size:14
Alignment explanation
Indices: 2344--2388 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
2334 ATGATTATGC
2344 TGTCCGTTGTCTGT
1 TGTCCGTTGTCTGT
*
2358 TGTCCGTTGTCTGA
1 TGTCCGTTGTCTGT
2372 T-TCCGTTGTCTGT
1 TGTCCGTTGTCTGT
2385 TGTC
1 TGTC
2389 TGCTATCTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.43
14 16 0.57
ACGTcount: A:0.02, C:0.22, G:0.27, T:0.49
Consensus pattern (14 bp):
TGTCCGTTGTCTGT
Found at i:2384 original size:27 final size:27
Alignment explanation
Indices: 2346--2408 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
2336 GATTATGCTG
* *
2346 TCCGTTGTCTGTTGTCCGTTGTCTGAT
1 TCCGTTGTCTGTTGTCCGCTATCTGAT
*
2373 TCCGTTGTCTGTTGTCTGCTATCTGAT
1 TCCGTTGTCTGTTGTCCGCTATCTGAT
*
2400 TCCGATGTC
1 TCCGTTGTC
2409 CGTGATCTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.06, C:0.24, G:0.24, T:0.46
Consensus pattern (27 bp):
TCCGTTGTCTGTTGTCCGCTATCTGAT
Done.