Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014329.1 Corchorus olitorius cultivar O-4 contig14362, 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: 28764
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:6474 original size:32 final size:35
Alignment explanation
Indices: 6431--6500 Score: 101
Period size: 32 Copynumber: 2.1 Consensus size: 35
6421 TTAGTATTTA
*
6431 TTATTTGCAAAAGTTAAT-AA-A-TACAAAGCAAG
1 TTATTTACAAAAGTTAATAAATAGTACAAAGCAAG
*
6463 TTATTTACAAAAGTTGATAAATAGTACAAAGCAAG
1 TTATTTACAAAAGTTAATAAATAGTACAAAGCAAG
6498 TTA
1 TTA
6501 AATTCTCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 16 0.48
33 2 0.06
34 1 0.03
35 14 0.42
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.30
Consensus pattern (35 bp):
TTATTTACAAAAGTTAATAAATAGTACAAAGCAAG
Found at i:6520 original size:16 final size:16
Alignment explanation
Indices: 6499--6531 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6489 CAAAGCAAGT
6499 TAAATTCTCAAGTTAA
1 TAAATTCTCAAGTTAA
*
6515 TAAATTCTCATGTTAA
1 TAAATTCTCAAGTTAA
6531 T
1 T
6532 GATAATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (16 bp):
TAAATTCTCAAGTTAA
Found at i:7043 original size:38 final size:38
Alignment explanation
Indices: 6995--7069 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
6985 GGTGATTTAC
6995 TTTTAGTTCTAAGTATTTAAGTTGGGAAAAAAATAGAT
1 TTTTAGTTCTAAGTATTTAAGTTGGGAAAAAAATAGAT
* *
7033 TTTTTGTTCTAAGTATTTAAGTTGGGAAATAAATAGA
1 TTTTAGTTCTAAGTATTTAAGTTGGGAAAAAAATAGA
7070 GAATATAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.37, C:0.03, G:0.19, T:0.41
Consensus pattern (38 bp):
TTTTAGTTCTAAGTATTTAAGTTGGGAAAAAAATAGAT
Found at i:9570 original size:31 final size:33
Alignment explanation
Indices: 9508--9576 Score: 97
Period size: 31 Copynumber: 2.1 Consensus size: 33
9498 GTGAGAATTT
*
9508 ATCACCAGGCAGAGAGAGAAGGAAATGGGAAACG
1 ATCACCAGGCAGAGAGAGAACG-AATGGGAAACG
*
9542 ATCACCAGGCGGAGA-AGAACG-ATGGGAAACG
1 ATCACCAGGCAGAGAGAGAACGAATGGGAAACG
9573 ATCA
1 ATCA
9577 AAGTAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 14 0.42
33 5 0.15
34 14 0.42
ACGTcount: A:0.42, C:0.17, G:0.33, T:0.07
Consensus pattern (33 bp):
ATCACCAGGCAGAGAGAGAACGAATGGGAAACG
Found at i:11164 original size:30 final size:31
Alignment explanation
Indices: 11128--11185 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
11118 GTGTATTTTT
11128 TATTGGGCC-CTTTTGAGTG-GTTGTGAAGCA
1 TATTGGGCCACTTTTGAGTGTG-TGTGAAGCA
*
11158 TATTGGGCCACTTTTTAGTGTGTGTGAA
1 TATTGGGCCACTTTTGAGTGTGTGTGAA
11186 ATATGTTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 9 0.36
31 15 0.60
32 1 0.04
ACGTcount: A:0.17, C:0.12, G:0.31, T:0.40
Consensus pattern (31 bp):
TATTGGGCCACTTTTGAGTGTGTGTGAAGCA
Found at i:14985 original size:48 final size:48
Alignment explanation
Indices: 14887--14978 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
14877 CACCAATCTT
* *
14887 AAGCACCATTCTGCGGCAGAAGCCAATCACAATTTTACCGCAAAACTC
1 AAGCACCATTCTGCGGCAGAAGCCAACCACAATTCTACCGCAAAACTC
* *
14935 AAGCACCATTTTGCGGTAGAAGCCAACCACAATTCTACCGCAAA
1 AAGCACCATTCTGCGGCAGAAGCCAACCACAATTCTACCGCAAA
14979 GGTCAAGTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.36, C:0.30, G:0.15, T:0.18
Consensus pattern (48 bp):
AAGCACCATTCTGCGGCAGAAGCCAACCACAATTCTACCGCAAAACTC
Found at i:18224 original size:27 final size:27
Alignment explanation
Indices: 18193--18248 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
18183 AAATTTCCGC
*
18193 CAAAGTTCCCGCAGTAACCCAAAATTG
1 CAAAGTTCCCGCAGCAACCCAAAATTG
**
18220 CAAAGTTGTCGCAGCAACCCAAAATTG
1 CAAAGTTCCCGCAGCAACCCAAAATTG
18247 CA
1 CA
18249 GCAAGTACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.29, G:0.16, T:0.18
Consensus pattern (27 bp):
CAAAGTTCCCGCAGCAACCCAAAATTG
Found at i:26471 original size:24 final size:25
Alignment explanation
Indices: 26436--26486 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
26426 TTTGGTTGGT
*
26436 GTGTTTATGGTATA-CCTTTGATGG
1 GTGTTTAGGGTATACCCTTTGATGG
26460 GTGTTTAGGGTATACCCTTTGATGG
1 GTGTTTAGGGTATACCCTTTGATGG
26485 GT
1 GT
26487 ATACCCTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.16, C:0.10, G:0.31, T:0.43
Consensus pattern (25 bp):
GTGTTTAGGGTATACCCTTTGATGG
Found at i:26488 original size:16 final size:16
Alignment explanation
Indices: 26467--26500 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
26457 TGGGTGTTTA
26467 GGGTATACCCTTTGAT
1 GGGTATACCCTTTGAT
26483 GGGTATACCCTTTGAT
1 GGGTATACCCTTTGAT
26499 GG
1 GG
26501 ATATTCATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (16 bp):
GGGTATACCCTTTGAT
Found at i:26871 original size:17 final size:17
Alignment explanation
Indices: 26851--26885 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
26841 TGTGTGTGTA
*
26851 TTTTTTTT-TATGCTTC
1 TTTTTTTTGTTTGCTTC
26867 TTTTTTTTGTTTGCTTC
1 TTTTTTTTGTTTGCTTC
26884 TT
1 TT
26886 GGGAAACGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.03, C:0.11, G:0.09, T:0.77
Consensus pattern (17 bp):
TTTTTTTTGTTTGCTTC
Found at i:27473 original size:18 final size:18
Alignment explanation
Indices: 27450--27514 Score: 112
Period size: 18 Copynumber: 3.6 Consensus size: 18
27440 ATAGTTAGAC
*
27450 TTCTGCTCCAATTAGGAG
1 TTCTGCTCCAAGTAGGAG
27468 TTCTGCTCCAAGTAGGAG
1 TTCTGCTCCAAGTAGGAG
27486 TTCTGCTCCAAGTAGGAG
1 TTCTGCTCCAAGTAGGAG
*
27504 TTCTACTCCAA
1 TTCTGCTCCAA
27515 TTGGGTAAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.31
Consensus pattern (18 bp):
TTCTGCTCCAAGTAGGAG
Done.