Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020256.1 Corchorus olitorius cultivar O-4 contig20289, 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: 31622
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1058 original size:31 final size:31
Alignment explanation
Indices: 1022--1080 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1012 GTTAATTAAA
*
1022 TCCCTAACGTTATAAATTCGACTCAAATATG
1 TCCCTAACGTTATAAAATCGACTCAAATATG
* *
1053 TCCCTAACGTTGTAAAATCGGCTCAAAT
1 TCCCTAACGTTATAAAATCGACTCAAAT
1081 CAGTGCCCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.31
Consensus pattern (31 bp):
TCCCTAACGTTATAAAATCGACTCAAATATG
Found at i:1542 original size:100 final size:99
Alignment explanation
Indices: 1358--1552 Score: 309
Period size: 100 Copynumber: 2.0 Consensus size: 99
1348 ATACAATACA
* * *
1358 CTATCAATGTAAATTTTGAACTCTACAAGCGGGTTAAGAAGTTGACAGACACACATTTTCTTGAT
1 CTATCAATGTAAATTTTGAACTCTACAAGCAGGTTAAAAAGTTGACACACACACATTTTCTTGAT
1423 TAATTTTGTTTTTAAAATTCAAAACTATTCCACT
66 TAATTTTGTTTTTAAAATTCAAAACTATTCCACT
* * *
1457 CTATCAAGTGTAAATTTTGGACTCTACAAGCAGGTTAAAAAGTTGATACATACACATTTTCTTGA
1 CTATCAA-TGTAAATTTTGAACTCTACAAGCAGGTTAAAAAGTTGACACACACACATTTTCTTGA
**
1522 TTAATTTTGTTTTTGTAATTCAAAACTATTC
65 TTAATTTTGTTTTTAAAATTCAAAACTATTC
1553 GCTAAAGGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
99 7 0.08
100 80 0.92
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (99 bp):
CTATCAATGTAAATTTTGAACTCTACAAGCAGGTTAAAAAGTTGACACACACACATTTTCTTGAT
TAATTTTGTTTTTAAAATTCAAAACTATTCCACT
Found at i:5864 original size:95 final size:95
Alignment explanation
Indices: 5744--5933 Score: 371
Period size: 95 Copynumber: 2.0 Consensus size: 95
5734 CTCAACTATT
*
5744 GAATTATTACTCAGTTTCCTTTTAAGTAGACCATAATTTTTGACAATAAATTTATATTGATGGGG
1 GAATTATTACTCAGTTTCCTTTTAAGTAGACCATAATTTCTGACAATAAATTTATATTGATGGGG
5809 TTATTAAATTAATTAGGATAAAAATTTGGA
66 TTATTAAATTAATTAGGATAAAAATTTGGA
5839 GAATTATTACTCAGTTTCCTTTTAAGTAGACCATAATTTCTGACAATAAATTTATATTGATGGGG
1 GAATTATTACTCAGTTTCCTTTTAAGTAGACCATAATTTCTGACAATAAATTTATATTGATGGGG
5904 TTATTAAATTAATTAGGATAAAAATTTGGA
66 TTATTAAATTAATTAGGATAAAAATTTGGA
5934 TTAAATCATG
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.41
Consensus pattern (95 bp):
GAATTATTACTCAGTTTCCTTTTAAGTAGACCATAATTTCTGACAATAAATTTATATTGATGGGG
TTATTAAATTAATTAGGATAAAAATTTGGA
Found at i:6115 original size:13 final size:13
Alignment explanation
Indices: 6097--6128 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
6087 TAATTTTGCA
6097 TTTTTTATAATTT
1 TTTTTTATAATTT
6110 TTTTTTATAATTT
1 TTTTTTATAATTT
6123 TTTTTT
1 TTTTTT
6129 TGCTACATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTATAATTT
Found at i:7474 original size:22 final size:22
Alignment explanation
Indices: 7446--7488 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
7436 ATGATGGATC
* *
7446 AAGTTAGAGGTGACGGTGTTAG
1 AAGTTAGAGGTAACAGTGTTAG
7468 AAGTTAGAGGTAACAGTGTTA
1 AAGTTAGAGGTAACAGTGTTA
7489 AGATTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.35, T:0.28
Consensus pattern (22 bp):
AAGTTAGAGGTAACAGTGTTAG
Found at i:20093 original size:12 final size:12
Alignment explanation
Indices: 20078--20112 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
20068 GAAAGAGAAA
20078 AAGAAGAAGGAC
1 AAGAAGAAGGAC
* *
20090 AAGAAGAAGAAG
1 AAGAAGAAGGAC
20102 AAGAAGAAGGA
1 AAGAAGAAGGA
20113 AAAGGCTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.63, C:0.03, G:0.34, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGGAC
Found at i:22805 original size:31 final size:32
Alignment explanation
Indices: 22767--22831 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
22757 GCACCTTGGT
22767 CGTGGCA-TTTTGGTCCAATGTGGCATTGCCA
1 CGTGGCATTTTTGGTCCAATGTGGCATTGCCA
* *
22798 CGTGGCATTTTTTTGTCCGATGTGGCATTGCCA
1 CGTGGCA-TTTTTGGTCCAATGTGGCATTGCCA
22831 C
1 C
22832 ATCAGCAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 7 0.23
33 23 0.77
ACGTcount: A:0.14, C:0.23, G:0.28, T:0.35
Consensus pattern (32 bp):
CGTGGCATTTTTGGTCCAATGTGGCATTGCCA
Done.