Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024526.1 Corchorus olitorius cultivar O-4 contig24559, 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: 2900
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:52 original size:35 final size:35
Alignment explanation
Indices: 1--272 Score: 384
Period size: 35 Copynumber: 7.8 Consensus size: 35
*
1 AAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTC
1 AAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTC
*** *
36 AAGAAGTTTCCAATGATCAGAGTTGATCTCGTTTC
1 AAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTC
* **
71 AAGAAGTTTTTTATGATCAGAGTTGATCTTATTTC
1 AAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTC
* *
106 AAGAAATTTTTGATGATCAGAGTTGATCTCGTTTC
1 AAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTC
*
141 AAGCAGTTTTTGATGATCAGAGTTGATCTCCTTTC
1 AAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTC
* * *
176 AAAAAGTTTTCGATGATC-GTAGTTGATCTCGTTTC
1 AAGAAGTTTTTGATGATCAG-AGTTGATCTCCTTTC
*
211 AAGAAATTTTTGATGATCAGAGTTGATCTCCTTTC
1 AAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTC
*
246 AAGAAGTTTTCGATGATCAGAGTTGAT
1 AAGAAGTTTTTGATGATCAGAGTTGAT
273 TTTCAATTTG
Statistics
Matches: 209, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
34 1 0.00
35 207 0.99
36 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (35 bp):
AAGAAGTTTTTGATGATCAGAGTTGATCTCCTTTC
Found at i:1991 original size:4 final size:4
Alignment explanation
Indices: 1963--2199 Score: 104
Period size: 4 Copynumber: 60.8 Consensus size: 4
1953 GACCAAAAAG
* * * * *
1963 ATTT TTTT A-TT ATTT ATTC A-CT ATTT ATTTT TTTT ATTT ATTT -TTA
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT
* * * *
2009 ACTATT ATCT ATTT ATTT A-CT ATTT ATTT -TTA ACTATT ATCT ATTT
1 A-T-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-T-TT ATTT ATTT
* * * *
2055 ATTT -GTT ATTT ATCTT -TTT ATTT ATTA ATTT AATT A-TT ATCT ATTT
1 ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * * * *
2101 ATTT A-CT ATTT ATCT ATTT ATTT ATTA ATTT AATT A-TT ATCT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * * ** *
2147 ATTT A-CT ATTT ATCTT -TTT CTTT ATTA ATTT AGCT A-TT ATCT ATTT
1 ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2193 ATTT ATT
1 ATTT ATT
2200 ATTATTATCT
Statistics
Matches: 169, Mismatches: 44, Indels: 40
0.67 0.17 0.16
Matches are distributed among these distances:
3 28 0.17
4 126 0.75
5 11 0.07
6 4 0.02
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (4 bp):
ATTT
Found at i:2000 original size:9 final size:10
Alignment explanation
Indices: 1986--2164 Score: 81
Period size: 11 Copynumber: 16.3 Consensus size: 10
1976 TTATTCACTA
1986 TTTATTT-TT
1 TTTATTTATT
1995 TTTATTTATT
1 TTTATTTATT
**
2005 TTTAACTATT
1 TTTATTTATT
*
2015 ATCTATTTATT
1 -TTTATTTATT
*
2026 TACTATTTATT
1 T-TTATTTATT
**
2037 TTTAACTATT
1 TTTATTTATT
*
2047 ATCTATTTATT
1 -TTTATTTATT
2058 TGTTATTTATCTT
1 T-TTATTTA--TT
2071 TTTATTTATT
1 TTTATTTATT
*
2081 AATTTAATTATT
1 --TTTATTTATT
*
2093 ATCTATTTATT
1 -TTTATTTATT
*
2104 TACTATTTATCT
1 T-TTATTTAT-T
2116 ATTTATTTATT
1 -TTTATTTATT
*
2127 AATTTAATTATT
1 --TTTATTTATT
*
2139 ATCTATTTATT
1 -TTTATTTATT
*
2150 TACTATTTATCT
1 T-TTATTTAT-T
2162 TTT
1 TTT
2165 TCTTTATTAA
Statistics
Matches: 135, Mismatches: 20, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
9 7 0.05
10 22 0.16
11 66 0.49
12 36 0.27
13 4 0.03
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (10 bp):
TTTATTTATT
Found at i:2085 original size:27 final size:27
Alignment explanation
Indices: 1995--2151 Score: 126
Period size: 27 Copynumber: 6.3 Consensus size: 27
1985 ATTTATTTTT
*
1995 TTTATTTATT--TTTAACTATTATCTA
1 TTTATTTATTAATTTAATTATTATCTA
* * *
2020 TTTATTTACT-ATTT-ATTTTTAACTA
1 TTTATTTATTAATTTAATTATTATCTA
* * * *
2045 -TTATCTATTTATTT-GTTATTTATCTT
1 TTTATTTATTAATTTAATTA-TTATCTA
2071 TTTATTTATTAATTTAATTATTATCTA
1 TTTATTTATTAATTTAATTATTATCTA
*
2098 TTTA--T-TT-A-CT-A-T-TTATCTA
1 TTTATTTATTAATTTAATTATTATCTA
2117 TTTATTTATTAATTTAATTATTATCTA
1 TTTATTTATTAATTTAATTATTATCTA
2144 TTTATTTA
1 TTTATTTA
2152 CTATTTATCT
Statistics
Matches: 103, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
19 11 0.11
20 1 0.01
21 2 0.02
22 3 0.03
23 2 0.02
24 10 0.10
25 25 0.24
26 9 0.09
27 37 0.36
28 3 0.03
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (27 bp):
TTTATTTATTAATTTAATTATTATCTA
Found at i:2095 original size:46 final size:46
Alignment explanation
Indices: 2029--2212 Score: 264
Period size: 46 Copynumber: 4.0 Consensus size: 46
2019 ATTTATTTAC
**
2029 TATTTATT--TTTAACTATTATCTATTTATTTGTTATTTATCTTTT
1 TATTTATTAATTTAACTATTATCTATTTATTTACTATTTATCTTTT
* *
2073 TATTTATTAATTTAATTATTATCTATTTATTTACTATTTATCTATT
1 TATTTATTAATTTAACTATTATCTATTTATTTACTATTTATCTTTT
*
2119 TATTTATTAATTTAATTATTATCTATTTATTTACTATTTATCTTTT
1 TATTTATTAATTTAACTATTATCTATTTATTTACTATTTATCTTTT
* * *
2165 TCTTTATTAATTTAGCTATTATCTATTTATTTATTATTATTATCTTTT
1 TATTTATTAATTTAACTATTATCTATTTATTTACTA-T-TTATCTTTT
2213 CTTTAACTAC
Statistics
Matches: 127, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
44 8 0.06
46 109 0.86
47 1 0.01
48 9 0.07
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (46 bp):
TATTTATTAATTTAACTATTATCTATTTATTTACTATTTATCTTTT
Found at i:2102 original size:8 final size:8
Alignment explanation
Indices: 2100--2262 Score: 75
Period size: 8 Copynumber: 21.9 Consensus size: 8
2090 ATTATCTATT
2100 TATTTA-C
1 TATTTATC
2107 TATTTATC
1 TATTTATC
*
2115 TATTTATT
1 TATTTATC
* *
2123 TATTAATT
1 TATTTATC
*
2131 TAATTAT-
1 TATTTATC
* *
2138 TATCTATT
1 TATTTATC
2146 TATTTA-C
1 TATTTATC
2153 TATTTATC
1 TATTTATC
2161 T-TTT-TC
1 TATTTATC
2167 --TTTAT-
1 TATTTATC
*
2172 TAATTTAGC
1 T-ATTTATC
2181 TA-TTATC
1 TATTTATC
*
2188 TATTTATT
1 TATTTATC
2196 TA-TTAT-
1 TATTTATC
2202 TA-TTATC
1 TATTTATC
* *
2209 T-TTTCTT
1 TATTTATC
** *
2216 TAACTACC
1 TATTTATC
2224 TATTTATC
1 TATTTATC
2232 TA-TTATTC
1 TATTTA-TC
* *
2240 TCTGTATC
1 TATTTATC
2248 TATTTATC
1 TATTTATC
2256 TATTTAT
1 TATTTAT
2263 TTCTATACCT
Statistics
Matches: 117, Mismatches: 25, Indels: 27
0.69 0.15 0.16
Matches are distributed among these distances:
5 3 0.03
6 9 0.08
7 38 0.32
8 64 0.55
9 3 0.03
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.62
Consensus pattern (8 bp):
TATTTATC
Found at i:2140 original size:19 final size:19
Alignment explanation
Indices: 2072--2151 Score: 54
Period size: 23 Copynumber: 3.8 Consensus size: 19
2062 ATTTATCTTT
2072 TTATTTATTAATTTAATTATTA
1 TTATTTATTAATTT-A--ATTA
2094 TCTATTTATTTACTATTT-ATCTA
1 T-TATTTA-TTA--ATTTAAT-TA
2117 TTTATTTATTAATTTAATTA
1 -TTATTTATTAATTTAATTA
* *
2137 TTATCTATTTATTTA
1 TTATTTATTAATTTA
2152 CTATTTATCT
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
19 13 0.27
20 6 0.12
21 2 0.04
22 6 0.12
23 14 0.29
24 4 0.08
26 4 0.08
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTATTAATTTAATTA
Found at i:2159 original size:19 final size:19
Alignment explanation
Indices: 1983--2184 Score: 96
Period size: 19 Copynumber: 11.3 Consensus size: 19
1973 TATTTATTCA
*
1983 CTATTTATTT--TTTTTAT
1 CTATTTATTTACTATTTAT
* *
2000 TTATTT-TTAACTA-TTAT
1 CTATTTATTTACTATTTAT
2017 CTATTTATTTACTATTTAT
1 CTATTTATTTACTATTTAT
2036 -T-TTTA---ACTA-TTAT
1 CTATTTATTTACTATTTAT
**
2049 CTATTTATTTGTTATTTAT
1 CTATTTATTTACTATTTAT
* *
2068 CTTTTTATTTATTAATTTA-
1 CTATTTATTTACT-ATTTAT
2087 --A-TTA-TTATCTATTTAT
1 CTATTTATTTA-CTATTTAT
* *
2103 TTA-CTATTTATCTATTTAT
1 CTATTTATTTA-CTATTTAT
* * *
2122 TTATTAATTTAAT-TATTAT
1 CTATTTATTTACTAT-TTAT
2141 CTATTTATTTACTATTTAT
1 CTATTTATTTACTATTTAT
* * * *
2160 CTTTTTCTTTATTAATTTAG
1 CTATTTATTTACT-ATTTAT
2180 CTATT
1 CTATT
2185 ATCTATTTAT
Statistics
Matches: 142, Mismatches: 23, Indels: 37
0.70 0.11 0.18
Matches are distributed among these distances:
13 4 0.03
14 5 0.04
15 12 0.08
16 6 0.04
17 18 0.13
18 14 0.10
19 63 0.44
20 20 0.14
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.65
Consensus pattern (19 bp):
CTATTTATTTACTATTTAT
Found at i:2172 original size:27 final size:27
Alignment explanation
Indices: 2137--2200 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
2127 AATTTAATTA
* * *
2137 TTATCTATTTATTTA-CTATTTATCTTT
1 TTATTTATTAATTTAGCTA-TTATCTAT
*
2164 TTCTTTATTAATTTAGCTATTATCTAT
1 TTATTTATTAATTTAGCTATTATCTAT
2191 TTATTTATTA
1 TTATTTATTA
2201 TTATTATCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 28 0.90
28 3 0.10
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (27 bp):
TTATTTATTAATTTAGCTATTATCTAT
Found at i:2254 original size:24 final size:24
Alignment explanation
Indices: 2220--2276 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
2210 TTTCTTTAAC
*
2220 TACCTATTTATCTA-TTATTCTCTG
1 TACCTATTTATCTATTTATT-TCTA
*
2244 TATCTATTTATCTATTTATTTCTA
1 TACCTATTTATCTATTTATTTCTA
2268 TACCTATTT
1 TACCTATTT
2277 TTTTTAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.23, C:0.18, G:0.02, T:0.58
Consensus pattern (24 bp):
TACCTATTTATCTATTTATTTCTA
Found at i:2264 original size:36 final size:32
Alignment explanation
Indices: 2183--2264 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 32
2173 AATTTAGCTA
*
2183 TTATCTATTTATTTATTATTATTATCTTTTCT
1 TTATCTATTTATTTATTATTATTATCTTTTAT
* ** *
2215 TTAACTACCTATTTATCTATTATTCTCTGTATCTAT
1 TTATCTATTTATTTAT-TATTATTATCT-T-T-TAT
2251 TTATCTATTTATTT
1 TTATCTATTTATTT
2265 CTATACCTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
32 13 0.34
33 10 0.26
34 1 0.03
35 1 0.03
36 13 0.34
ACGTcount: A:0.23, C:0.13, G:0.01, T:0.62
Consensus pattern (32 bp):
TTATCTATTTATTTATTATTATTATCTTTTAT
Done.