Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012573.1 Corchorus capsularis cultivar CVL-1 contig12594, 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: 8949
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1907 original size:21 final size:22
Alignment explanation
Indices: 1877--1927 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
1867 GTCTGTTTTG
* *
1877 AATTTGAAAACCTC-TGATTA-
1 AATTTTAAAAACTCTTGATTAC
1897 AATTTTAAAAACTCTTGATTATC
1 AATTTTAAAAACTCTTGATTA-C
1920 AATTTTAA
1 AATTTTAA
1928 TCTATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 12 0.46
21 6 0.23
23 8 0.31
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (22 bp):
AATTTTAAAAACTCTTGATTAC
Found at i:2090 original size:13 final size:14
Alignment explanation
Indices: 2067--2095 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2057 ACCTCTACTT
2067 AATGTATGAATGCA
1 AATGTATGAATGCA
2081 AATG-ATGAATGCA
1 AATGTATGAATGCA
2094 AA
1 AA
2096 GTCCAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (14 bp):
AATGTATGAATGCA
Found at i:5301 original size:26 final size:27
Alignment explanation
Indices: 5272--5329 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
5262 AAATTAAAAG
*
5272 TGAA-CTTGAAATGACCAAAATGCCCC
1 TGAATCTTAAAATGACCAAAATGCCCC
*
5298 TGAATGTTAAAATGACCAAAATGCCCC
1 TGAATCTTAAAATGACCAAAATGCCCC
5325 TGAAT
1 TGAAT
5330 GACCTTGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 4 0.14
27 25 0.86
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (27 bp):
TGAATCTTAAAATGACCAAAATGCCCC
Found at i:5574 original size:23 final size:23
Alignment explanation
Indices: 5544--5644 Score: 132
Period size: 23 Copynumber: 4.4 Consensus size: 23
5534 GGCTGTCTTA
5544 TTGCTGTTTTATTGCTGTTATTG
1 TTGCTGTTTTATTGCTGTTATTG
* *
5567 TTGTTGTTTTAGTGCTGTTATTG
1 TTGCTGTTTTATTGCTGTTATTG
* *
5590 TTGCTGTTATATTGCTGTTTTTG
1 TTGCTGTTTTATTGCTGTTATTG
* *
5613 TTGCTCTTTTATTGATGCTT-TTG
1 TTGCTGTTTTATTGCTG-TTATTG
5636 TTGCTGTTT
1 TTGCTGTTT
5645 AATGGATCAA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
23 65 0.97
24 2 0.03
ACGTcount: A:0.08, C:0.09, G:0.22, T:0.61
Consensus pattern (23 bp):
TTGCTGTTTTATTGCTGTTATTG
Found at i:5596 original size:12 final size:11
Alignment explanation
Indices: 5516--5644 Score: 98
Period size: 11 Copynumber: 11.3 Consensus size: 11
5506 TATTGTTGTT
*
5516 TTTTGTGGCTG
1 TTTTGTTGCTG
*
5527 TTTTTGTGGCTG
1 -TTTTGTTGCTG
* *
5539 TCTTATTGCTG
1 TTTTGTTGCTG
*
5550 TTTTATTGCTG
1 TTTTGTTGCTG
*
5561 TTATTGTTGTTG
1 TT-TTGTTGCTG
5573 TTTTAG-TGCTG
1 TTTT-GTTGCTG
5584 TTATTGTTGCTG
1 TT-TTGTTGCTG
* *
5596 TTATATTGCTG
1 TTTTGTTGCTG
*
5607 TTTTTGTTGCTC
1 -TTTTGTTGCTG
* *
5619 TTTTATTGATG
1 TTTTGTTGCTG
5630 CTTTTGTTGCTG
1 -TTTTGTTGCTG
5642 TTT
1 TTT
5645 AATGGATCAA
Statistics
Matches: 94, Mismatches: 17, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
11 47 0.50
12 47 0.50
ACGTcount: A:0.07, C:0.09, G:0.23, T:0.60
Consensus pattern (11 bp):
TTTTGTTGCTG
Found at i:5622 original size:11 final size:12
Alignment explanation
Indices: 5516--5641 Score: 61
Period size: 12 Copynumber: 10.9 Consensus size: 12
5506 TATTGTTGTT
* *
5516 TTTTGTGGCTGT
1 TTTTGTTGCTGC
*
5528 TTTTGTGGCTG-
1 TTTTGTTGCTGC
* *
5539 TCTTATTGCTG-
1 TTTTGTTGCTGC
*
5550 TTTTATTGCTG-
1 TTTTGTTGCTGC
*
5561 TTATTGTTGTTG-
1 TT-TTGTTGCTGC
5573 TTTTAG-TGCTG-
1 TTTT-GTTGCTGC
5584 TTATTGTTGCTG-
1 TT-TTGTTGCTGC
* * *
5596 TTATATTGCTGT
1 TTTTGTTGCTGC
5608 TTTTGTTGCT-C
1 TTTTGTTGCTGC
* *
5619 TTTTATTGATGC
1 TTTTGTTGCTGC
5631 TTTTGTTGCTG
1 TTTTGTTGCTG
5642 TTTAATGGAT
Statistics
Matches: 92, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
11 44 0.48
12 48 0.52
ACGTcount: A:0.07, C:0.10, G:0.24, T:0.60
Consensus pattern (12 bp):
TTTTGTTGCTGC
Found at i:5709 original size:23 final size:23
Alignment explanation
Indices: 5548--5709 Score: 116
Period size: 23 Copynumber: 7.0 Consensus size: 23
5538 GTCTTATTGC
*
5548 TGTTTTATTGCTGTTATTGTTGT
1 TGTTTTATTGCTGTTTTTGTTGT
* * *
5571 TGTTTTAGTGCTGTTATTGTTGC
1 TGTTTTATTGCTGTTTTTGTTGT
* *
5594 TGTTATATTGCTGTTTTTGTTGC
1 TGTTTTATTGCTGTTTTTGTTGT
* * * *
5617 TCTTTTATTGATGCTTTTGTTGC
1 TGTTTTATTGCTGTTTTTGTTGT
* * ** *
5640 TGTTTAATGGATCAACTTCTTGTTGT
1 TGTTTTATTG--C-TGTTTTTGTTGT
*
5666 T-TTTATATTG-T-TTTTT-ATGT
1 TGTTT-TATTGCTGTTTTTGTTGT
5686 TGTTTTATTGCTGTTTTTGTTGT
1 TGTTTTATTGCTGTTTTTGTTGT
5709 T
1 T
5710 AATTTACAAC
Statistics
Matches: 107, Mismatches: 24, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
20 9 0.08
21 8 0.07
22 5 0.05
23 71 0.66
25 3 0.03
26 11 0.10
ACGTcount: A:0.10, C:0.07, G:0.20, T:0.62
Consensus pattern (23 bp):
TGTTTTATTGCTGTTTTTGTTGT
Done.