Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009523.1 Corchorus olitorius cultivar O-4 contig09555, 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: 2452
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Found at i:33 original size:19 final size:19
Alignment explanation
Indices: 7--141 Score: 71
Period size: 19 Copynumber: 7.5 Consensus size: 19
1 TTTTTA
7 ACTA-TTATCTATTTATTT
1 ACTATTTATCTATTTATTT
25 ACTATTTATCT-TTTCATTT
1 ACTATTTATCTATTT-ATTT
* *
44 ATTAATTTAAT-TA-TTATCT
1 ACT-ATTT-ATCTATTTATTT
63 ATCTATTTA-CTATTTA--T
1 A-CTATTTATCTATTTATTT
* * *
80 -CTTTTTATTTATTAATTT
1 ACTATTTATCTATTTATTT
98 AGCTA-TTATCTATTTATTT
1 A-CTATTTATCTATTTATTT
*
117 ATTA-TTAT-TA-TT-TTT
1 ACTATTTATCTATTTATTT
132 AGCTATTTAT
1 A-CTATTTAT
142 TTATCTATTA
Statistics
Matches: 91, Mismatches: 11, Indels: 31
0.68 0.08 0.23
Matches are distributed among these distances:
15 10 0.11
16 9 0.10
17 7 0.08
18 17 0.19
19 36 0.40
20 10 0.11
21 2 0.02
ACGTcount: A:0.27, C:0.09, G:0.01, T:0.62
Consensus pattern (19 bp):
ACTATTTATCTATTTATTT
Found at i:46 original size:27 final size:25
Alignment explanation
Indices: 11--120 Score: 81
Period size: 27 Copynumber: 4.4 Consensus size: 25
1 TTTTTAACTA
* *
11 TTATCTATTTATTTACTATTTATCTT
1 TTATTTATTAATTTACTA-TTATCTT
37 TTCATTTATTAATTTA--ATTA----
1 TT-ATTTATTAATTTACTATTATCTT
*
57 TTATCTATCT-ATTTACTATTTATCTTT
1 TTATTTAT-TAATTTACTA-TTATC-TT
84 TTATTTATTAATTTAGCTATTATCTAT
1 TTATTTATTAATTTA-CTATTATCT-T
111 TTATTTATTA
1 TTATTTATTA
121 TTATTATTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 25
0.70 0.04 0.26
Matches are distributed among these distances:
19 10 0.15
20 3 0.04
21 1 0.01
22 3 0.04
24 3 0.04
25 1 0.01
26 4 0.06
27 39 0.58
28 3 0.04
ACGTcount: A:0.27, C:0.09, G:0.01, T:0.63
Consensus pattern (25 bp):
TTATTTATTAATTTACTATTATCTT
Found at i:70 original size:46 final size:46
Alignment explanation
Indices: 3--122 Score: 195
Period size: 46 Copynumber: 2.6 Consensus size: 46
1 TT
3 TTTAACTATTATCTATTTATTTACTATTTATCTTTTCATTTATTAA
1 TTTAACTATTATCTATTTATTTACTATTTATCTTTTCATTTATTAA
* * *
49 TTTAATTATTATCTATCTATTTACTATTTATCTTTTTATTTATTAA
1 TTTAACTATTATCTATTTATTTACTATTTATCTTTTCATTTATTAA
* *
95 TTTAGCTATTATCTATTTATTTATTATT
1 TTTAACTATTATCTATTTATTTACTATT
123 ATTATTTTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.28, C:0.09, G:0.01, T:0.62
Consensus pattern (46 bp):
TTTAACTATTATCTATTTATTTACTATTTATCTTTTCATTTATTAA
Found at i:131 original size:46 final size:45
Alignment explanation
Indices: 3--152 Score: 176
Period size: 46 Copynumber: 3.3 Consensus size: 45
1 TT
3 TTTAACTATTATCTATTTATTTACTA-TTTATCTTTTCATTTATTAA
1 TTTAACTATTATCTATTTATTTACTATTTTAT-TTTT-ATTTATTAA
* * *
49 TTTAATTATTATCTATCTATTTACTATTTATCTTTTTATTTATTAA
1 TTTAACTATTATCTATTTATTTACTATTT-TATTTTTATTTATTAA
* * ** *
95 TTTAGCTATTATCTATTTATTTATTATTATTATTTTTAGCTATTTA
1 TTTAACTATTATCTATTTATTTACTATT-TTATTTTTATTTATTAA
*
141 TTTATCTATTAT
1 TTTAACTATTAT
153 TCTCTATTCC
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
46 80 0.90
47 7 0.08
48 2 0.02
ACGTcount: A:0.27, C:0.09, G:0.01, T:0.63
Consensus pattern (45 bp):
TTTAACTATTATCTATTTATTTACTATTTTATTTTTATTTATTAA
Found at i:165 original size:28 final size:27
Alignment explanation
Indices: 83--169 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
73 TATTTATCTT
* * *
83 TTTATTTATTAAT-TTAGCTATTATCTA
1 TTTATTTATTATTATTA-TTATTACCTA
* *
110 TTTATTTATTATTATTATTTTTAGCTA
1 TTTATTTATTATTATTATTATTACCTA
*
137 TTTATTTATCTATTATTCTCTATT-CCTA
1 TTTATTTAT-TATTATTAT-TATTACCTA
165 TTTAT
1 TTTAT
170 CTTTTTTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 28 0.56
28 19 0.38
29 3 0.06
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTATTTATTATTATTATTATTACCTA
Found at i:177 original size:92 final size:92
Alignment explanation
Indices: 3--179 Score: 222
Period size: 92 Copynumber: 2.0 Consensus size: 92
1 TT
**
3 TTTAACTATTATCTATTTATTTACTATTTATCTTTTCATTTATTAATTTAATTATTATCTATCTA
1 TTTAACTATTATCTATTTATTTACTATTTATCTTTTCAGCTATTAATTTAATTATTATCTATCTA
68 TTTACTATTTATCTTTTTATTTATTAA
66 TTTACTATTTATCTTTTTATTTATTAA
* * * *
95 TTTAGCTATTATCTATTTATTTATTATTATTAT-TTTT-AGCTATTTATTT-ATCTATTAT-TCT
1 TTTAACTATTATCTATTTATTTACTA-T-TTATCTTTTCAGCTATTAATTTAAT-TATTATCTAT
*
156 CTA-TTCCTATTTATCTTTTT-TTTA
63 CTATTTACTATTTATCTTTTTATTTA
180 AAACTTATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
89 4 0.05
90 16 0.21
91 7 0.09
92 39 0.52
93 5 0.07
94 4 0.05
ACGTcount: A:0.25, C:0.10, G:0.01, T:0.63
Consensus pattern (92 bp):
TTTAACTATTATCTATTTATTTACTATTTATCTTTTCAGCTATTAATTTAATTATTATCTATCTA
TTTACTATTTATCTTTTTATTTATTAA
Done.