Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016276.1 Corchorus capsularis cultivar CVL-1 contig16297, 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: 13268
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Found at i:1823 original size:33 final size:33
Alignment explanation
Indices: 1777--1861 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 33
1767 AGCACTAGTG
* *
1777 ACCGACCATGCGACTTGGAGAAGCCCGACCAAC
1 ACCGGCCACGCGACTTGGAGAAGCCCGACCAAC
* * * *
1810 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGAAGCCCGACCAAC
*
1843 ACCGGCCACGCGACATGGA
1 ACCGGCCACGCGACTTGGA
1862 CATGTCCGGC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.25, C:0.39, G:0.28, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGAAGCCCGACCAAC
Found at i:1871 original size:33 final size:32
Alignment explanation
Indices: 1799--1883 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 32
1789 ACTTGGAGAA
* *
1799 GCCCGACCAACACCGGCCACGCGACTCGGAGAT
1 GCCCGGCC-ACACCGGCCACGCGACTCGGACAT
1832 GCCCGGCCATCACCGGCCACGCGACAT-GGACAT
1 GCCCGGCCA-CACCGGCCACGCGAC-TCGGACAT
*
1865 GTCCGGCCACAACCGGCCA
1 GCCCGGCCAC-ACCGGCCA
1884 TCGCTTGGCG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
32 2 0.04
33 43 0.93
34 1 0.02
ACGTcount: A:0.22, C:0.44, G:0.27, T:0.07
Consensus pattern (32 bp):
GCCCGGCCACACCGGCCACGCGACTCGGACAT
Found at i:2556 original size:8 final size:8
Alignment explanation
Indices: 2537--2572 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
2527 ACTTAGTTGT
2537 TTGTGAATC
1 TTGTG-ATC
2546 TTGTGATC
1 TTGTGATC
2554 TTGTGATC
1 TTGTGATC
2562 TTGTGATC
1 TTGTGATC
2570 TTG
1 TTG
2573 AGAATTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 22 0.81
9 5 0.19
ACGTcount: A:0.14, C:0.11, G:0.25, T:0.50
Consensus pattern (8 bp):
TTGTGATC
Found at i:2564 original size:16 final size:17
Alignment explanation
Indices: 2537--2577 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
2527 ACTTAGTTGT
2537 TTGTGAATCTTGTGATC
1 TTGTGAATCTTGTGATC
2554 TTGTG-ATCTTGTGATC
1 TTGTGAATCTTGTGATC
*
2570 TTGAGAAT
1 TTGTGAAT
2578 TCAATTGCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.46
Consensus pattern (17 bp):
TTGTGAATCTTGTGATC
Found at i:4117 original size:10 final size:10
Alignment explanation
Indices: 4102--4126 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4092 GTTCCTGCAC
4102 AATTCCAGAA
1 AATTCCAGAA
4112 AATTCCAGAA
1 AATTCCAGAA
4122 AATTC
1 AATTC
4127 TAAAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:10084 original size:33 final size:33
Alignment explanation
Indices: 10042--10106 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
10032 CCTGCCATGC
*
10042 GACTTGGAGAAGCCCGGCCAACACCGGCCACGT
1 GACTCGGAGAAGCCCGGCCAACACCGGCCACGT
*
10075 GACTCGGAGATGCCCGGCCAACACCGGCCACG
1 GACTCGGAGAAGCCCGGCCAACACCGGCCACG
10107 CGACATGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (33 bp):
GACTCGGAGAAGCCCGGCCAACACCGGCCACGT
Found at i:10127 original size:33 final size:33
Alignment explanation
Indices: 10035--10137 Score: 102
Period size: 33 Copynumber: 3.1 Consensus size: 33
10025 CTAGTGACCT
* * * *
10035 GCCATGCGACTTGGAGAAGCCCGGCCAACACCG
1 GCCACGCGACTCGGACATGCCCGGCCAACACCG
* *
10068 GCCACGTGACTCGGAGATGCCCGGCCAACACCG
1 GCCACGCGACTCGGACATGCCCGGCCAACACCG
* *
10101 GCCACGCGACAT-GGACATGTCTGGCC-ACAACCG
1 GCCACGCGAC-TCGGACATGCCCGGCCAAC-ACCG
10134 GCCA
1 GCCA
10138 TAGCTTGGCG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.03
33 57 0.95
34 1 0.02
ACGTcount: A:0.23, C:0.38, G:0.29, T:0.10
Consensus pattern (33 bp):
GCCACGCGACTCGGACATGCCCGGCCAACACCG
Found at i:12700 original size:33 final size:33
Alignment explanation
Indices: 12612--12707 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 33
12602 GTGTTTCAGA
* * ** *
12612 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
1 TGTTGTTTGCAATGATACTAAATCTGTTTTAAG
* *
12645 TATTGTTTGCAATGACACTAAATCTGTTTTAAG
1 TGTTGTTTGCAATGATACTAAATCTGTTTTAAG
*
12678 TGTTGTTTGTAATGATACTAAATCTGTTTT
1 TGTTGTTTGCAATGATACTAAATCTGTTTT
12708 GGATGCTAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (33 bp):
TGTTGTTTGCAATGATACTAAATCTGTTTTAAG
Found at i:12807 original size:33 final size:33
Alignment explanation
Indices: 12735--12838 Score: 124
Period size: 33 Copynumber: 3.2 Consensus size: 33
12725 AAAACAAATA
* **
12735 TGTTTTGGTTGATCATAGCATTAAAAATAATTT
1 TGTTTTGGTTGATCATAGCATTGAAAATAATCC
*
12768 TGTTTTGGTTGATCATAGCATTGCAAATAATCC
1 TGTTTTGGTTGATCATAGCATTGAAAATAATCC
* * *
12801 TATTTTGGTAGAT-A-A-CATTGAAAATAAACC
1 TGTTTTGGTTGATCATAGCATTGAAAATAATCC
12831 TGTTTTGG
1 TGTTTTGG
12839 GTGACGAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
30 20 0.32
31 1 0.02
32 1 0.02
33 40 0.65
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTTTTGGTTGATCATAGCATTGAAAATAATCC
Done.