Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006934.1 Corchorus capsularis cultivar CVL-1 contig06955, 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: 12248
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:2985 original size:15 final size:15
Alignment explanation
Indices: 2965--2993 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2955 TTTATCAGCG
2965 AGAAAAAAGTGACTA
1 AGAAAAAAGTGACTA
2980 AGAAAAAAGTGACT
1 AGAAAAAAGTGACT
2994 GATTCAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.07, G:0.21, T:0.14
Consensus pattern (15 bp):
AGAAAAAAGTGACTA
Found at i:7448 original size:30 final size:31
Alignment explanation
Indices: 7412--7486 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 31
7402 GGCGAAAATG
7412 CAATTCAGGATACACAGTTATCAT-TTGTGT
1 CAATTCAGGATACACAGTTATCATCTTGTGT
* * **
7442 CAATTCAGGATATACCGTTATTGTCTTGTGT
1 CAATTCAGGATACACAGTTATCATCTTGTGT
7473 CAATTCAGGATACA
1 CAATTCAGGATACA
7487 GAGAAGTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 20 0.51
31 19 0.49
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (31 bp):
CAATTCAGGATACACAGTTATCATCTTGTGT
Found at i:10145 original size:35 final size:34
Alignment explanation
Indices: 10083--10167 Score: 111
Period size: 35 Copynumber: 2.5 Consensus size: 34
10073 ACGAGTAATT
10083 AATTCTTGAAAT-TTGA-TTTTTTTTTTTTGCCGA
1 AATTCTTG-AATCTTGATTTTTTTTTTTTTGCCGA
*
10116 AATTCTTGAATCTTGATTTTTTTTTTTTTTGCGGA
1 AATTCTTGAATCTTGA-TTTTTTTTTTTTTGCCGA
* *
10151 AATTCATGAGTCTTGAT
1 AATTCTTGAATCTTGAT
10168 GAATATATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
32 3 0.07
33 12 0.26
34 1 0.02
35 30 0.65
ACGTcount: A:0.21, C:0.09, G:0.14, T:0.55
Consensus pattern (34 bp):
AATTCTTGAATCTTGATTTTTTTTTTTTTGCCGA
Found at i:10729 original size:16 final size:16
Alignment explanation
Indices: 10692--10749 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
10682 TACCCAATTC
*
10692 AAATACTCACCTGAT-
1 AAATACTCACCTGGTG
10707 AAATACTCACCTGGTG
1 AAATACTCACCTGGTG
*
10723 CAATACTCACCTGGTG
1 AAATACTCACCTGGTG
* *
10739 AGATGCTCACC
1 AAATACTCACC
10750 ACACTCACCC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 14 0.38
16 23 0.62
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (16 bp):
AAATACTCACCTGGTG
Found at i:10785 original size:15 final size:15
Alignment explanation
Indices: 10765--10793 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10755 CACCCAGTAC
10765 AATACTCACCTGGTA
1 AATACTCACCTGGTA
10780 AATACTCACCTGGT
1 AATACTCACCTGGT
10794 GAGAAACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (15 bp):
AATACTCACCTGGTA
Found at i:10805 original size:16 final size:15
Alignment explanation
Indices: 10692--10793 Score: 72
Period size: 16 Copynumber: 7.0 Consensus size: 15
10682 TACCCAATTC
*
10692 AAATACTCACCTGAT
1 AAATACTCACCTGGT
10707 AAATACTCACCTGGT
1 AAATACTCACCTGGT
*
10722 GCAATACTCACCTGGT
1 -AAATACTCACCTGGT
* *
10738 GAGATGCTCACC----
1 -AAATACTCACCTGGT
* **
10750 --ACACTCACCCAGT
1 AAATACTCACCTGGT
10763 ACAATACTCACCTGGT
1 A-AATACTCACCTGGT
10779 AAATACTCACCTGGT
1 AAATACTCACCTGGT
10794 GAGAAACTCA
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
9 7 0.10
15 28 0.41
16 34 0.49
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (15 bp):
AAATACTCACCTGGT
Found at i:10809 original size:57 final size:57
Alignment explanation
Indices: 10708--10837 Score: 208
Period size: 57 Copynumber: 2.3 Consensus size: 57
10698 TCACCTGATA
* **
10708 AATACTCACCTGGTGCAATACTCACCTGGTGAGATGCTCACCACACTCACCCAGTAC
1 AATACTCACCTGGTGAAATACTCACCTGGTGAGAAACTCACCACACTCACCCAGTAC
10765 AATACTCACCTGGT-AAATACTCACCTGGTGAGAAACTCACCCACACTCACCCAGTAC
1 AATACTCACCTGGTGAAATACTCACCTGGTGAGAAACTCA-CCACACTCACCCAGTAC
*
10822 AATACTCACCTAGTGA
1 AATACTCACCTGGTGA
10838 GGCCATGCTC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
56 22 0.33
57 44 0.66
58 1 0.01
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.21
Consensus pattern (57 bp):
AATACTCACCTGGTGAAATACTCACCTGGTGAGAAACTCACCACACTCACCCAGTAC
Done.