Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019326.1 Corchorus olitorius cultivar O-4 contig19359, 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: 4677
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Found at i:1886 original size:4 final size:4
Alignment explanation
Indices: 1874--2109 Score: 79
Period size: 4 Copynumber: 61.5 Consensus size: 4
1864 AAAGATTTTT
* * * *
1874 TTTA ATTA TTTA TTCA -TTA TTTA TCTA TTTA TTTA TTT- TTAA CTATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -T-TTA
* * * * * ** *
1922 TCTA TATA TTTA -CTA TTTA TCTA TTTA TTT- TTT- TTAA ACTA -TAA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * ** *
1966 TCTA TTTA TTTA -CTA TTTA TTTT TTTA TTTT TTTCA ACTA -TTA TCTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA
* * * *
2013 CTTA TTTA -CTA TTTA TCTT- TTTA TTTA -TT- TTTA ATTA -TTA TCTA
1 TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * **
2057 TTTA TTTA -CTA TTTA TTTTA TTTA TTTA TTAA TTTA GCTA -TTA TTTA
1 TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
2104 TTTA TT
1 TTTA TT
2110 CATTATTATT
Statistics
Matches: 164, Mismatches: 49, Indels: 38
0.65 0.20 0.15
Matches are distributed among these distances:
3 31 0.19
4 122 0.74
5 9 0.05
6 2 0.01
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:1902 original size:19 final size:18
Alignment explanation
Indices: 1880--1941 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
1870 TTTTTTTAAT
1880 TATTTATTCATTATTTATC
1 TATTTATTCATTATTTA-C
*
1899 TATTTATTTATT-TTTAAC
1 TATTTATTCATTATTT-AC
1917 TA-TTA-TCTATATATTTAC
1 TATTTATTC-AT-TATTTAC
1935 TATTTAT
1 TATTTAT
1942 CTATTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
16 1 0.03
17 5 0.14
18 11 0.31
19 18 0.51
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTATTCATTATTTAC
Found at i:1945 original size:44 final size:44
Alignment explanation
Indices: 1880--2109 Score: 293
Period size: 44 Copynumber: 5.2 Consensus size: 44
1870 TTTTTTTAAT
* *
1880 TATTTATTCATTATTTATCTATTTATTTATTTTTAACTATTATC
1 TATTTATTTACTATTTATCTATTTATTTATTTTTAACTATTATC
* *
1924 TATATATTTACTATTTATCTATTTATTT-TTTTTAAACTATAATC
1 TATTTATTTACTATTTATCTATTTATTTATTTTT-AACTATTATC
* * *
1968 TATTTATTTACTATTTATTTTTTTATTT-TTTTCAACTATTATC
1 TATTTATTTACTATTTATCTATTTATTTATTTTTAACTATTATC
* * *
2011 TACTTATTTACTATTTATCTTTTTATTTATTTTTAATTATTATC
1 TATTTATTTACTATTTATCTATTTATTTATTTTTAACTATTATC
* * *
2055 TATTTATTTACTATTTATTTTATTTATTTATTAATTTAGCTATTATT
1 TATTTATTTACTATTTA-TCTATTTATTTATT--TTTAACTATTATC
2102 TATTTATT
1 TATTTATT
2110 CATTATTATT
Statistics
Matches: 162, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
43 40 0.25
44 92 0.57
45 12 0.07
47 18 0.11
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (44 bp):
TATTTATTTACTATTTATCTATTTATTTATTTTTAACTATTATC
Found at i:2024 original size:87 final size:88
Alignment explanation
Indices: 1876--2086 Score: 295
Period size: 87 Copynumber: 2.4 Consensus size: 88
1866 AGATTTTTTT
* * * * *
1876 TAAT-TATTTATTCATTATTTATCTATTTATTTATTTTTAACTATTATCTATATATTTACTATTT
1 TAATCTATTTATTTACTATTTATTTTTTTATTTATTTTCAACTATTATCTATATATTTACTATTT
1940 ATCTATTTATTT-TTTTTAAACTA
66 ATCTATTTATTTATTTTT-AACTA
1963 TAATCTATTTATTTACTATTTATTTTTTTATTT-TTTTCAACTATTATCTACT-TATTTACTATT
1 TAATCTATTTATTTACTATTTATTTTTTTATTTATTTTCAACTATTATCTA-TATATTTACTATT
* *
2026 TATCTTTTTATTTATTTTTAATTA
65 TATCTATTTATTTATTTTTAACTA
*
2050 TTATCTATTTATTTACTATTTATTTTATTTATTTATT
1 TAATCTATTTATTTACTATTTATTTT-TTTATTTATT
2087 AATTTAGCTA
Statistics
Matches: 111, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
87 72 0.65
88 37 0.33
89 2 0.02
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (88 bp):
TAATCTATTTATTTACTATTTATTTTTTTATTTATTTTCAACTATTATCTATATATTTACTATTT
ATCTATTTATTTATTTTTAACTA
Found at i:2045 original size:25 final size:24
Alignment explanation
Indices: 2017--2109 Score: 63
Period size: 27 Copynumber: 3.8 Consensus size: 24
2007 TATCTACTTA
2017 TTTACTATTTATCTTTTTATTTATT
1 TTTACTATTTAT-TTTTTATTTATT
* *
2042 TTTA--A-TTATTATCTATTTA--
1 TTTACTATTTATTTTTTATTTATT
2061 TTTACTATTTATTTTATTTATTTATT
1 TTTACTATTTA-TTT-TTTATTTATT
2087 AATTTAGCTA-TTATTTATTTATT
1 --TTTA-CTATTTATTT-TTTATT
2110 CATTATTATT
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
19 4 0.07
21 9 0.17
22 7 0.13
23 3 0.06
24 7 0.13
25 4 0.07
27 10 0.19
28 7 0.13
29 3 0.06
ACGTcount: A:0.26, C:0.05, G:0.01, T:0.68
Consensus pattern (24 bp):
TTTACTATTTATTTTTTATTTATT
Found at i:2075 original size:32 final size:32
Alignment explanation
Indices: 2034--2120 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 32
2024 TTTATCTTTT
**
2034 TATTTATTTTTAATTATTATCT-ATTTATTTAC
1 TATTTATTTTTAATTATTAT-TAATTTAGCTAC
* *
2066 TATTTA-TTTTATTTATTTATTAATTTAGCTAT
1 TATTTATTTTTAATTA-TTATTAATTTAGCTAC
*
2098 TATTTATTTATTCATTATTATTA
1 TATTTATTT-TTAATTATTATTA
2121 TCCTTTTTAG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
31 9 0.20
32 23 0.51
33 8 0.18
34 5 0.11
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.66
Consensus pattern (32 bp):
TATTTATTTTTAATTATTATTAATTTAGCTAC
Found at i:2162 original size:24 final size:24
Alignment explanation
Indices: 2132--2190 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
2122 CCTTTTTAGC
*
2132 TACCTATTTATCTA-TTATTCTCTG
1 TACCTATTTATCTATTTA-TCTCTA
*
2156 TATCTATTTATCTATTTATCTCTA
1 TACCTATTTATCTATTTATCTCTA
2180 TACCTATTTAT
1 TACCTATTTAT
2191 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.24, C:0.19, G:0.02, T:0.56
Consensus pattern (24 bp):
TACCTATTTATCTATTTATCTCTA
Found at i:2169 original size:8 final size:8
Alignment explanation
Indices: 2135--2190 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
2125 TTTTAGCTAC
2135 CTATTTAT
1 CTATTTAT
2143 CTA-TTATT
1 CTATTTA-T
* *
2151 CTCTGTAT
1 CTATTTAT
2159 CTATTTAT
1 CTATTTAT
2167 CTATTTAT
1 CTATTTAT
* * *
2175 CTCTATAC
1 CTATTTAT
2183 CTATTTAT
1 CTATTTAT
2191 TTTTTTAAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
7 3 0.08
8 31 0.86
9 2 0.06
ACGTcount: A:0.23, C:0.18, G:0.02, T:0.57
Consensus pattern (8 bp):
CTATTTAT
Found at i:2197 original size:24 final size:25
Alignment explanation
Indices: 2132--2197 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 25
2122 CCTTTTTAGC
* * *
2132 TACCTATTTA-TCTATTATTCTCTG
1 TACCTATTTATTTTTTTATTCTCTA
* * *
2156 TATCTATTTATCTATTTA-TCTCTA
1 TACCTATTTATTTTTTTATTCTCTA
2180 TACCTATTTATTTTTTTA
1 TACCTATTTATTTTTTTA
2198 AAACTTATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.23, C:0.17, G:0.02, T:0.59
Consensus pattern (25 bp):
TACCTATTTATTTTTTTATTCTCTA
Done.