Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015888.1 Corchorus capsularis cultivar CVL-1 contig15909, 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: 4670
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Found at i:1885 original size:49 final size:47
Alignment explanation
Indices: 1736--2192 Score: 201
Period size: 49 Copynumber: 9.4 Consensus size: 47
1726 TTCGTCCGGA
* * * * *
1736 AAGGGCATTTTAAGAAAAAGCGAGTAAAACT-AGCGCCTTCCATCCGGG
1 AAGGGCATTTT-GGGAAAAGCAAGTAAAA-TAAGCGTCTTCCATCCGAG
** * * * * * ** * *
1784 AAGGGTGTTTTAGAAAGAAGCAAGTAAAAATTAGTGCCTTCTGTCGGGG
1 AAGGGCATTTTGGGAA-AAGCAAGT-AAAATAAGCGTCTTCCATCCGAG
* ***
1833 AAGGGCACTTTGGGGAAAAGTGGGTAAAAATAAGCGTCTTCCATCCGAG
1 AAGGGCA-TTTTGGGAAAAGCAAGT-AAAATAAGCGTCTTCCATCCGAG
* * *
1882 AAGGGCATTTTTGGAAAATAGCAAGTAAAATAAGTGTCTTCCATCCGGG
1 AAGGGCA-TTTTGGGAAA-AGCAAGTAAAATAAGCGTCTTCCATCCGAG
* * * * *
1931 AAGGGCATTTTGGGAAAA-CAGGTAAAGATTAGTGCCTTCCGTCC-AGG
1 AAGGGCATTTTGGGAAAAGCAAGTAAA-ATAAGCGTCTTCCATCCGA-G
* * * * *
1978 AAGGGCGTTTTGGGAAATAGCAAGTAAAGATAAACGGCTTCCGTCCGGG
1 AAGGGCATTTTGGGAAA-AGCAAGTAAA-ATAAGCGTCTTCCATCCGAG
* * * * * *
2027 AAGGGCGTTTTGGGGAAATAGCAAGCAAAAGTAATG-GGCTTCCGTCTGGG
1 AAGGGCATTTT-GGGAAA-AGCAAGTAAAA-TAA-GCGTCTTCCATCCGAG
** * * *
2077 AAGGGCGCTTTGGGAAATAGCAAGTAAAGATGAATG-G-CTTCCGTCTGGG
1 AAGGGCATTTTGGGAAA-AGCAAGTAAA-AT-AA-GCGTCTTCCATCCGAG
* * * *
2126 AAGGGCGTTTTGGGAAATAGCAAGTAAAGATGAATG-G-CTTCCGTCTGGG
1 AAGGGCATTTTGGGAAA-AGCAAGTAAA-AT-AA-GCGTCTTCCATCCGAG
*
2175 AAGGGCGTTTTGGGAAAA
1 AAGGGCATTTTGGGAAAA
2193 AGTAGGTAAA
Statistics
Matches: 345, Mismatches: 49, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
46 7 0.02
47 37 0.11
48 28 0.08
49 215 0.62
50 58 0.17
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (47 bp):
AAGGGCATTTTGGGAAAAGCAAGTAAAATAAGCGTCTTCCATCCGAG
Found at i:1912 original size:98 final size:94
Alignment explanation
Indices: 1759--2044 Score: 254
Period size: 96 Copynumber: 3.0 Consensus size: 94
1749 GAAAAAGCGA
* * * *
1759 GTAAAACTAGCGCCTTCCATCCGGGAAGGG-TGTTTTAGAAAGA-AGCAAGTAAAAATTAGTGCC
1 GTAAAAATAGCGCCTTCCATCCGAGAAGGGCT-TTTTGGAAA-ATAGCAAGT-AAAATAAGTGCC
** * **
1822 TTCTGTCGGGGAAGGGCACTTTGGGGAAAAGTGG
63 TTCCATCCGGGAAGGGCA-TTTGGGGAAAA-CAG
* *
1856 GTAAAAATAAGCGTCTTCCATCCGAGAAGGGCATTTTTGGAAAATAGCAAGTAAAATAAGTGTCT
1 GTAAAAAT-AGCGCCTTCCATCCGAGAAGGGC-TTTTTGGAAAATAGCAAGTAAAATAAGTGCCT
*
1921 TCCATCCGGGAAGGGCATTTTGGGAAAACAG
64 TCCATCCGGGAAGGGCATTTGGGGAAAACAG
* * * * * ** *
1952 GTAAAGATTAGTGCCTTCCGTCC-AGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATAAACGGC
1 GTAAA-AATAGCGCCTTCCATCCGA-GAAGGGCTTTTTGGAAAATAGCAAGTAAA-ATAAGTGCC
* *
2016 TTCCGTCCGGGAAGGGCGTTTTGGGGAAA
63 TTCCATCCGGGAAGGGC-ATTTGGGGAAA
2045 TAGCAAGCAA
Statistics
Matches: 157, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
95 21 0.13
96 46 0.29
97 28 0.18
98 46 0.29
99 15 0.10
100 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (94 bp):
GTAAAAATAGCGCCTTCCATCCGAGAAGGGCTTTTTGGAAAATAGCAAGTAAAATAAGTGCCTTC
CATCCGGGAAGGGCATTTGGGGAAAACAG
Found at i:2091 original size:99 final size:96
Alignment explanation
Indices: 1881--2191 Score: 376
Period size: 99 Copynumber: 3.2 Consensus size: 96
1871 TTCCATCCGA
* * * * * *
1881 GAAGGGCATTTTTGGAAAATAGCAAGTAAA-ATAAGTGTCTTCCATCCGGGAAGGGCATTTTGGG
1 GAAGGGC-GTTTTGGGAAATAGCAAGTAAAGATAAATGGCTTCCGTCCGGGAAGGGCGTTTTGGG
* * * * **
1945 AAA-A-CAGGTAAAGATTAGTGCCTTCCGTCCAG
65 AAATAGCAAG-AAA-AGTAATGGCTTCCGTCTGG
*
1977 GAAGGGCGTTTTGGGAAATAGCAAGTAAAGATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGG
1 GAAGGGCGTTTTGGGAAATAGCAAGTAAAGATAAATGGCTTCCGTCCGGGAAGGGCGTTTT-GGG
2042 AAATAGCAAGCAAAAGTAATGGGCTTCCGTCTGG
65 AAATAGCAAG-AAAAGTAAT-GGCTTCCGTCTGG
* * *
2076 GAAGGGCGCTTTGGGAAATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGA
1 GAAGGGCGTTTTGGGAAATAGCAAGTAAAGATAAATGGCTTCCGTCCGGGAAGGGCGTTTTGGGA
*
2141 AATAGCAAGTAAAGATGAATGGCTTCCGTCTGG
66 AATAGCAAGAAAAG-T-AATGGCTTCCGTCTGG
2174 GAAGGGCGTTTTGGGAAA
1 GAAGGGCGTTTTGGGAAA
2192 AAGTAGGTAA
Statistics
Matches: 188, Mismatches: 20, Indels: 12
0.85 0.09 0.05
Matches are distributed among these distances:
95 20 0.11
96 33 0.18
97 10 0.05
98 49 0.26
99 76 0.40
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (96 bp):
GAAGGGCGTTTTGGGAAATAGCAAGTAAAGATAAATGGCTTCCGTCCGGGAAGGGCGTTTTGGGA
AATAGCAAGAAAAGTAATGGCTTCCGTCTGG
Found at i:2136 original size:148 final size:145
Alignment explanation
Indices: 1856--2192 Score: 424
Period size: 148 Copynumber: 2.3 Consensus size: 145
1846 GGAAAAGTGG
* * * * * * * * *
1856 GTAAAAATAAGCGTCTTCCATCCGAGAAGGGCATTTTTGGAAAATAGCAAGTAAAATAAGTGTCT
1 GTAAAGATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAAATAGCAAGCAAAATAAGTGGCT
* * * *
1921 TCCATCCGGGAAGGGCATTTTGGGAAAACAGGTAAAGATTAGTGCCTTCCGTCCAGGAAGGGCGT
66 TCCATCCGGGAAGGGCACTTTGGGAAAACAAGTAAAGATGAATGCCTTCCGTCCAGGAAGGGCGT
1986 TTTGGGAAATAGCAA
131 TTTGGGAAATAGCAA
*
2001 GTAAAGATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAAATAGCAAGCAAAAGTAA-TGGG
1 GTAAAGATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAAATAGCAAGCAAAA-TAAGT-GG
* * * * **
2065 CTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAGG
64 CTTCCATCCGGGAAGGGCACTTTGGGAAA-A-CAAGTAAAGATGAATGCCTTCCGTCCAGGAAGG
2130 GCGTTTTGGGAAATAGCAA
127 GCGTTTTGGGAAATAGCAA
* * *
2149 GTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAAA
1 GTAAAGATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAAA
2193 AGTAGGTAAA
Statistics
Matches: 164, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
145 48 0.29
146 29 0.18
147 1 0.01
148 86 0.52
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (145 bp):
GTAAAGATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAAATAGCAAGCAAAATAAGTGGCT
TCCATCCGGGAAGGGCACTTTGGGAAAACAAGTAAAGATGAATGCCTTCCGTCCAGGAAGGGCGT
TTTGGGAAATAGCAA
Found at i:2202 original size:49 final size:49
Alignment explanation
Indices: 1870--2209 Score: 386
Period size: 49 Copynumber: 6.9 Consensus size: 49
1860 AAATAAGCGT
* * * * *
1870 CTTCCATCCGAGAAGGGCATTTTTGGAAAATAGCAAGTAAA-AT-AAGTGT
1 CTTCCGTCCGGGAAGGGC-GTTTTGGGAAATAGCAAGTAAAGATGAA-TGG
* * * * * *
1919 CTTCCATCCGGGAAGGGCATTTTGGGAAA-A-CAGGTAAAGATTAGTGC
1 CTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATGAATGG
* * *
1966 CTTCCGTCCAGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATAAACGG
1 CTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATGAATGG
*
2015 CTTCCGTCCGGGAAGGGCGTTTTGGGGAAATAGCAAGCAAA-A-GTAATGGG
1 CTTCCGTCCGGGAAGGGCGTTTT-GGGAAATAGCAAGTAAAGATG-AAT-GG
* *
2065 CTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAGATGAATGG
1 CTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATGAATGG
*
2114 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATGAATGG
1 CTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATGAATGG
* * * *
2163 CTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGTAGGTAAAGACTGAA
1 CTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGA-TGAA
2210 AGCTGAAATG
Statistics
Matches: 256, Mismatches: 25, Indels: 19
0.85 0.08 0.06
Matches are distributed among these distances:
46 7 0.03
47 31 0.12
48 11 0.04
49 159 0.62
50 47 0.18
51 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.23
Consensus pattern (49 bp):
CTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATGAATGG
Done.