Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006320.1 Corchorus capsularis cultivar CVL-1 contig06341, 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: 29290
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--36 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37 CTTTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:132 original size:20 final size:18
Alignment explanation
Indices: 107--151 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
97 TCACACATGT
107 TACTAATAAATAATAATATA
1 TACTAATAAAT-A-AATATA
* *
127 TACTAACAAATAAATATT
1 TACTAATAAATAAATATA
145 TACTAAT
1 TACTAAT
152 TTTGCTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
TACTAATAAATAAATATA
Found at i:289 original size:30 final size:30
Alignment explanation
Indices: 220--292 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
210 CCCACGAGGA
*
220 CGGGGATGGAGACTACATTCCATTCCCCGC
1 CGGGGATGGGGACTACATTCCATTCCCCGC
* *
250 CGGGGATGGGGACTACATTTCATTCCTCGC
1 CGGGGATGGGGACTACATTCCATTCCCCGC
280 CGGGGATGGGGAC
1 CGGGGATGGGGAC
293 GGGGACGGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.18, C:0.27, G:0.34, T:0.21
Consensus pattern (30 bp):
CGGGGATGGGGACTACATTCCATTCCCCGC
Found at i:432 original size:7 final size:7
Alignment explanation
Indices: 422--446 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
412 AAAAAATGAA
422 AAAAATG
1 AAAAATG
429 AAAAATG
1 AAAAATG
436 AAAAATG
1 AAAAATG
443 AAAA
1 AAAA
447 GAAGAAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:11756 original size:34 final size:35
Alignment explanation
Indices: 11718--11794 Score: 111
Period size: 34 Copynumber: 2.2 Consensus size: 35
11708 TTTTTTAATG
* *
11718 ATGGCTGCCCCTGGTCTTTGGATGATA-CCTAGTT
1 ATGGCTACCCCTGGTCTTTGGATGATACCCTAGCT
* *
11752 ATGGCTACCCGTGGTGTTTGGATGATACCCTAGCT
1 ATGGCTACCCCTGGTCTTTGGATGATACCCTAGCT
11787 ATGGCTAC
1 ATGGCTAC
11795 TTGCTATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
34 24 0.63
35 14 0.37
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.32
Consensus pattern (35 bp):
ATGGCTACCCCTGGTCTTTGGATGATACCCTAGCT
Found at i:15551 original size:1 final size:1
Alignment explanation
Indices: 15545--15572 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
15535 TTACTTACCC
15545 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
15573 CTCTTCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18128 original size:43 final size:43
Alignment explanation
Indices: 18080--18169 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
18070 GAAATTTACA
18080 TGCTCAATTTAATTTGCTGAATTGCTAAACACCGCCCTATTTT
1 TGCTCAATTTAATTTGCTGAATTGCTAAACACCGCCCTATTTT
18123 TGCTCAATTTAATTTGCTGAATTGCTAAACACCGCCCTATTTT
1 TGCTCAATTTAATTTGCTGAATTGCTAAACACCGCCCTATTTT
18166 TGCT
1 TGCT
18170 ATTCACCGCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.40
Consensus pattern (43 bp):
TGCTCAATTTAATTTGCTGAATTGCTAAACACCGCCCTATTTT
Found at i:18426 original size:33 final size:32
Alignment explanation
Indices: 18398--18491 Score: 88
Period size: 33 Copynumber: 2.9 Consensus size: 32
18388 AGCGGCTGAG
18398 CCATGGCCAAGCCGCC-CTCCTGGGGCGGCACTA
1 CCATGGCCAAGCCGCCTC-CCTGGGGCGG-ACTA
*
18431 CCATGGCCAGGCCGCCTCCCTGGGGC-GACCCTA
1 CCATGGCCAAGCCGCCTCCCTGGGGCGGA--CTA
*
18464 CCATGG--ATAGACCGCCCCCCTGGGGCGG
1 CCATGGCCA-AG-CCGCCTCCCTGGGGCGG
18492 CACCGGTACT
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
31 2 0.04
32 2 0.04
33 46 0.88
34 2 0.04
ACGTcount: A:0.14, C:0.43, G:0.32, T:0.12
Consensus pattern (32 bp):
CCATGGCCAAGCCGCCTCCCTGGGGCGGACTA
Found at i:18710 original size:32 final size:32
Alignment explanation
Indices: 18559--18706 Score: 228
Period size: 32 Copynumber: 4.6 Consensus size: 32
18549 AAAATGACTT
* *
18559 GCCGCCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
18591 GCCGTCCTAGT-GGGACGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGA-GGCTAGCCGTGGCAGA
*
18623 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
*
18655 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCT-AGCCGTGGCAGA
18688 GCCGTCCTAGT-GGGAGGCT
1 GCCGTCCTAGTGGGGAGGCT
18707 CCGCGTGGCT
Statistics
Matches: 108, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
31 3 0.03
32 80 0.74
33 25 0.23
ACGTcount: A:0.13, C:0.29, G:0.43, T:0.16
Consensus pattern (32 bp):
GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
Found at i:20206 original size:21 final size:21
Alignment explanation
Indices: 20180--20226 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
20170 CTGATTATAT
*
20180 TCTCATCTGTACAGTATCTAA
1 TCTCATCTGTACAGTAACTAA
*
20201 TCTCATCTGTACGGTAACTAA
1 TCTCATCTGTACAGTAACTAA
20222 TCTCA
1 TCTCA
20227 CCATTTCAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.36
Consensus pattern (21 bp):
TCTCATCTGTACAGTAACTAA
Found at i:28668 original size:27 final size:27
Alignment explanation
Indices: 28625--28677 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28615 GAAAAGACTT
* *
28625 CAAAGAAGAAAGGTTTGGAGAAGCCTA
1 CAAAGAAGAAAGGTTTGAACAAGCCTA
28652 CAAAGAA-AAAGGATTTGAACAAGCCT
1 CAAAGAAGAAAGG-TTTGAACAAGCCT
28678 GCCAGGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.47, C:0.13, G:0.25, T:0.15
Consensus pattern (27 bp):
CAAAGAAGAAAGGTTTGAACAAGCCTA
Done.