Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014778.1 Corchorus capsularis cultivar CVL-1 contig14799, 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: 9453
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:6659 original size:15 final size:16
Alignment explanation
Indices: 6641--6692 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
6631 TGCAGCAGCA
6641 AATGGTG-CCACACCC
1 AATGGTGACCACACCC
*
6656 AATGGCTGCACCATACCC
1 AATGG-TG-ACCACACCC
6674 AATGGTCGTACCACACCC
1 AATGGT-G-ACCACACCC
6692 A
1 A
6693 GTGGCCGCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 5 0.17
16 2 0.07
17 1 0.03
18 22 0.73
ACGTcount: A:0.29, C:0.38, G:0.17, T:0.15
Consensus pattern (16 bp):
AATGGTGACCACACCC
Found at i:6712 original size:18 final size:18
Alignment explanation
Indices: 6648--6710 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
6638 GCAAATGGTG
* *
6648 CCACACCCAATGGCTGCA
1 CCACACCCAATGGCCGCT
* *
6666 CCATACCCAATGGTCG-T
1 CCACACCCAATGGCCGCT
*
6683 ACCACACCCAGTGGCCGCT
1 -CCACACCCAATGGCCGCT
6702 CCACACCCA
1 CCACACCCA
6711 GTTCTCGCAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
18 35 0.97
19 1 0.03
ACGTcount: A:0.25, C:0.46, G:0.16, T:0.13
Consensus pattern (18 bp):
CCACACCCAATGGCCGCT
Found at i:6732 original size:36 final size:36
Alignment explanation
Indices: 6651--6762 Score: 100
Period size: 36 Copynumber: 3.1 Consensus size: 36
6641 AATGGTGCCA
* * * * * *
6651 CACCCAATGGCTGCACCATACCCAA-TGGTCGTACCA
1 CACCCAGTGGCCGCACCACA-CCAAGTGCTCGCACCG
* * *
6687 CACCCAGTGGCCGCTCCACACCCAGTTCTCGCACCG
1 CACCCAGTGGCCGCACCACACCAAGTGCTCGCACCG
* * *
6723 CACCTAGTGGCCGCACCATACCAAGTGGTCGCACCG
1 CACCCAGTGGCCGCACCACACCAAGTGCTCGCACCG
6759 CACC
1 CACC
6763 AAGTTGCCAC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
35 3 0.05
36 57 0.95
ACGTcount: A:0.22, C:0.44, G:0.20, T:0.14
Consensus pattern (36 bp):
CACCCAGTGGCCGCACCACACCAAGTGCTCGCACCG
Found at i:6737 original size:18 final size:18
Alignment explanation
Indices: 6716--6766 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
6706 ACCCAGTTCT
*
6716 CGCACCGCACCTAGTGGC
1 CGCACCGCACCAAGTGGC
** *
6734 CGCACCATACCAAGTGGT
1 CGCACCGCACCAAGTGGC
6752 CGCACCGCACCAAGT
1 CGCACCGCACCAAGT
6767 TGCCACACTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.41, G:0.24, T:0.12
Consensus pattern (18 bp):
CGCACCGCACCAAGTGGC
Found at i:8059 original size:15 final size:15
Alignment explanation
Indices: 8041--8195 Score: 79
Period size: 15 Copynumber: 10.3 Consensus size: 15
8031 AAAATCAACT
8041 GCACCCAAGATGATG
1 GCACCCAAGATGATG
* *
8056 GCACCTC-AGGTGACG
1 GCACC-CAAGATGATG
*
8071 GCACTCTAA-ATGATG
1 GCAC-CCAAGATGATG
* *
8086 GCA-CCAAAATCAACT-
1 GCACCCAAGAT-GA-TG
8101 GCACCCAAGATGATG
1 GCACCCAAGATGATG
* *
8116 GCACCTC-AGGTGACG
1 GCACC-CAAGATGATG
* * *
8131 GCACTCTAGGTGATG
1 GCACCCAAGATGATG
* *
8146 GCACCGAA-ATTGACG
1 GCACCCAAGA-TGATG
*
8161 GCACCAAAGATGATG
1 GCACCCAAGATGATG
* *
8176 GCACCCAAGGTGATT
1 GCACCCAAGATGATG
8191 GCACC
1 GCACC
8196 GAAAGTGTTT
Statistics
Matches: 105, Mismatches: 23, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
13 3 0.03
14 4 0.04
15 86 0.82
16 12 0.11
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (15 bp):
GCACCCAAGATGATG
Found at i:8096 original size:60 final size:60
Alignment explanation
Indices: 8003--8188 Score: 293
Period size: 60 Copynumber: 3.1 Consensus size: 60
7993 CCATAAAGGA
8003 AGGTGACGGCACTCTAAATGATGGCACCAAAATCAACTGCACCCAAGATGATGGCACCTC
1 AGGTGACGGCACTCTAAATGATGGCACCAAAATCAACTGCACCCAAGATGATGGCACCTC
8063 AGGTGACGGCACTCTAAATGATGGCACCAAAATCAACTGCACCCAAGATGATGGCACCTC
1 AGGTGACGGCACTCTAAATGATGGCACCAAAATCAACTGCACCCAAGATGATGGCACCTC
** * ** * *
8123 AGGTGACGGCACTCTAGGTGATGGCACCGAAATTGACGGCACCAAAGATGATGGCACC-C
1 AGGTGACGGCACTCTAAATGATGGCACCAAAATCAACTGCACCCAAGATGATGGCACCTC
8182 AAGGTGA
1 -AGGTGA
8189 TTGCACCGAA
Statistics
Matches: 118, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
59 1 0.01
60 117 0.99
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.16
Consensus pattern (60 bp):
AGGTGACGGCACTCTAAATGATGGCACCAAAATCAACTGCACCCAAGATGATGGCACCTC
Found at i:8160 original size:30 final size:30
Alignment explanation
Indices: 8006--8180 Score: 127
Period size: 30 Copynumber: 5.8 Consensus size: 30
7996 TAAAGGAAGG
*
8006 TGACGGCACTCTAAATGATGGCACCAAAAT
1 TGACGGCACTCTAGATGATGGCACCAAAAT
** * * * ** **
8036 CAACTGCACCCAAGATGATGGCACCTCAGG
1 TGACGGCACTCTAGATGATGGCACCAAAAT
*
8066 TGACGGCACTCTAAATGATGGCACCAAAAT
1 TGACGGCACTCTAGATGATGGCACCAAAAT
** * * * ** **
8096 CAACTGCACCCAAGATGATGGCACCTCAGG
1 TGACGGCACTCTAGATGATGGCACCAAAAT
* *
8126 TGACGGCACTCTAGGTGATGGCACCGAAAT
1 TGACGGCACTCTAGATGATGGCACCAAAAT
*
8156 TGACGGCAC-CAAAGATGATGGCACC
1 TGACGGCACTC-TAGATGATGGCACC
8181 CAAGGTGATT
Statistics
Matches: 102, Mismatches: 42, Indels: 2
0.70 0.29 0.01
Matches are distributed among these distances:
29 1 0.01
30 101 0.99
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (30 bp):
TGACGGCACTCTAGATGATGGCACCAAAAT
Done.