Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023668.1 Corchorus olitorius cultivar O-4 contig23701, 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: 18501
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:11265 original size:55 final size:55
Alignment explanation
Indices: 11204--11313 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
11194 ACAAGATTGA
11204 AACAAGAAAATATTGAAGAACGAGTAAGAACTCGTGATGAACAAGATGAAATCGC
1 AACAAGAAAATATTGAAGAACGAGTAAGAACTCGTGATGAACAAGATGAAATCGC
11259 AACAAGAAAATATTGAAGAACGAGTAAGAACTCGTGATGAACAAGATGAAATCGC
1 AACAAGAAAATATTGAAGAACGAGTAAGAACTCGTGATGAACAAGATGAAATCGC
11314 GGAGATTTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.49, C:0.13, G:0.22, T:0.16
Consensus pattern (55 bp):
AACAAGAAAATATTGAAGAACGAGTAAGAACTCGTGATGAACAAGATGAAATCGC
Found at i:17204 original size:18 final size:15
Alignment explanation
Indices: 17159--17210 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
17149 TGCTAGGGTG
17159 AACGGTGCAAACAAC
1 AACGGTGCAAACAAC
17174 AACGGTGCAAACAAC
1 AACGGTGCAAACAAC
*
17189 AACGGTGCAAATAAC
1 AACGGTGCAAACAAC
*
17204 AATGGTG
1 AACGGTG
17211 TGAATAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (15 bp):
AACGGTGCAAACAAC
Found at i:18235 original size:40 final size:40
Alignment explanation
Indices: 18192--18501 Score: 458
Period size: 40 Copynumber: 7.7 Consensus size: 40
18182 AGGAATAGGA
* * * * *
18192 ACAACACCTCCCGATGAGGAAGGGCAAACTGGGAACTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG
* *
18232 ACAACACTTTCCGGTGGGGAAAGGCAAACTGGGAATTTTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAA-TTTAG
18273 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG
* *
18313 ACAACACCTTCCGGTGGGGATGGGCAAACTGGGAACTTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG
*
18353 ACAACACCTTCCGGTGGGGAAGGGCAAAATGGGTAATTTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGG-AATTTAG
* *
18394 ACAACACCTTCCGGTGGGGAAGGGCAGACTGGGAACTTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG
* * * *
18434 ACAATACCTTCCGGTGGGGAAGGACAAACTGGGTATTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG
18474 ACAACACCTTCCGGTGGGGAAGGGCAAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAA
Statistics
Matches: 243, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
40 170 0.70
41 73 0.30
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.17
Consensus pattern (40 bp):
ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG
Found at i:18327 original size:81 final size:80
Alignment explanation
Indices: 18192--18501 Score: 467
Period size: 81 Copynumber: 3.9 Consensus size: 80
18182 AGGAATAGGA
* * * * * *
18192 ACAACACCTCCCGATGAGGAAGGGCAAACTGGGAACTTAAACAACACTTTCCGGTGGGGAAAGGC
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGC
*
18257 AAACTGGGAATTTTAG
66 AAACTGGGAA-CTTAG
* *
18273 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAGACAACACCTTCCGGTGGGGATGGGC
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGC
18338 AAACTGGGAACTTAG
66 AAACTGGGAACTTAG
* *
18353 ACAACACCTTCCGGTGGGGAAGGGCAAAATGGGTAATTTAGACAACACCTTCCGGTGGGGAAGGG
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGG-AATTTAAACAACACCTTCCGGTGGGGAAGGG
*
18418 CAGACTGGGAACTTAG
65 CAAACTGGGAACTTAG
* * *
18434 ACAATACCTTCCGGTGGGGAAGGACAAACTGGGTATTTAAACAACACCTTCCGGTGGGGAAGGGC
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGC
18499 AAA
66 AAA
Statistics
Matches: 210, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
80 68 0.32
81 142 0.68
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.17
Consensus pattern (80 bp):
ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGC
AAACTGGGAACTTAG
Found at i:18397 original size:121 final size:121
Alignment explanation
Indices: 18192--18501 Score: 478
Period size: 121 Copynumber: 2.6 Consensus size: 121
18182 AGGAATAGGA
* * * * *
18192 ACAACACCTCCCGATGAGGAAGGGCAAACTGGGAACTTAAACAACACTTTCCGGTGGGGAAAGGC
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAGGGC
* *
18257 AAACTGGGAATTTTAGACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG
66 AAAATGGGAATTTTAGACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAACTTAG
* *
18313 ACAACACCTTCCGGTGGGGATGGGCAAACTGGGAACTTAGACAACACCTTCCGGTGGGGAAGGGC
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAGGGC
*
18378 AAAATGGGTAA-TTTAGACAACACCTTCCGGTGGGGAAGGGCAGACTGGGAACTTAG
66 AAAATGGG-AATTTTAGACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAACTTAG
* * * *
18434 ACAATACCTTCCGGTGGGGAAGGACAAACTGGGTATTTAAACAACACCTTCCGGTGGGGAAGGGC
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAGGGC
18499 AAA
66 AAA
Statistics
Matches: 172, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
121 170 0.99
122 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.17
Consensus pattern (121 bp):
ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAGGGC
AAAATGGGAATTTTAGACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAACTTAG
Done.