Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022701.1 Corchorus olitorius cultivar O-4 contig22734, 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: 7019
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Found at i:1673 original size:28 final size:29
Alignment explanation
Indices: 1637--1712 Score: 111
Period size: 28 Copynumber: 2.7 Consensus size: 29
1627 AAGTGAACCT
*
1637 AAAATGACCAAAATGCCCCTG-AACGTGC
1 AAAATGACCAAAATGCCCCTGAAACGTGA
*
1665 AAAATGACCAAAATGCCCC-GAAATGTGA
1 AAAATGACCAAAATGCCCCTGAAACGTGA
*
1693 AAAATGACAAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
1713 AGATTTTTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 1 0.02
28 42 0.98
ACGTcount: A:0.45, C:0.25, G:0.16, T:0.14
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGAAACGTGA
Found at i:2293 original size:98 final size:98
Alignment explanation
Indices: 2025--2312 Score: 409
Period size: 97 Copynumber: 2.9 Consensus size: 98
2015 AAGTACTCTC
* * * * * * *
2025 TTCTATAAATTAATTTTCTATTTCAACTTGGATACGGAATTTAACACAGAAAATGCATATCCGTG
1 TTCTATAAATAAATTTTTTATTTC-A-TTTGAAACGGAATTTAACACGGAAACTACATATCCGTG
* *
2090 TCTAAATCCGGTTCAAATTGATAATAATAAAATAA
64 TCTAAATCCGCTTCAAAATGATAATAATAAAATAA
2125 TTCTATAAATAAA--TTTTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATCCGTGT
1 TTCTATAAATAAATTTTTTATTTCATTT-GAAACGGAATTTAACACGGAAACTACATATCCGTGT
* * *
2188 CTAAATCCGCTTCTAACTGATAATAATAAAATTA
65 CTAAATCCGCTTCAAAATGATAATAATAAAATAA
*
2222 TTCTATAAATAAATTTTTTATTTCATTTGAAACGGAATTTAACACGGAAACTACATATCCATGTC
1 TTCTATAAATAAATTTTTTATTTCATTTGAAACGGAATTTAACACGGAAACTACATATCCGTGTC
*
2287 TAAATCCGCTTCCAAATGATAATAAT
66 TAAATCCGCTTCAAAATGATAATAAT
2313 TTTAATAAAT
Statistics
Matches: 171, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
96 2 0.01
97 76 0.44
98 68 0.40
99 13 0.08
100 12 0.07
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.35
Consensus pattern (98 bp):
TTCTATAAATAAATTTTTTATTTCATTTGAAACGGAATTTAACACGGAAACTACATATCCGTGTC
TAAATCCGCTTCAAAATGATAATAATAAAATAA
Found at i:4399 original size:16 final size:16
Alignment explanation
Indices: 4378--4409 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4368 TCAACTTTCA
*
4378 GTGAAAGTGATGAAGC
1 GTGAAAGCGATGAAGC
4394 GTGAAAGCGATGAAGC
1 GTGAAAGCGATGAAGC
4410 AAACGAAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.38, T:0.16
Consensus pattern (16 bp):
GTGAAAGCGATGAAGC
Found at i:4965 original size:99 final size:99
Alignment explanation
Indices: 4773--5175 Score: 493
Period size: 99 Copynumber: 4.1 Consensus size: 99
4763 AGATGAGTGC
* * *
4773 TAAATTCTATAAACAATTTTTTTTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATC
1 TAAATTCTATAAATAA-TTTTTCTATTTCATTTGGAAACGGAACTTAACACGGAAACTACATATC
* * ** *
4838 CGTGTCCAAATCCGCTTTCAAATTATAATATGTAA
65 CGTGTCTAAATCCGCTTCCAAACGATAATAAGTAA
* * * * * *
4873 TAAATTCCACAGATAAATTTTTC-ATTTCATTTGGAAACGAAATTTAACACGGAAACTACATATT
1 TAAATTCTATAAAT-AATTTTTCTATTTCATTTGGAAACGGAACTTAACACGGAAACTACATATC
* * * *
4937 CGTGTCTAAATCTGCTTCCAACCAATAATAAGTAC
65 CGTGTCTAAATCCGCTTCCAAACGATAATAAGTAA
* * *
4972 TAAATTCTATAAATGATTTTTCTACTTCATTTGGAAACGGAACTTAGCACGGAAACTACATATCC
1 TAAATTCTATAAATAATTTTTCTATTTCATTTGGAAACGGAACTTAACACGGAAACTACATATCC
* * **
5037 GTGTCTAAATCCGTTTCCAACCGATAATAAGTGC
66 GTGTCTAAATCCGCTTCCAAACGATAATAAGTAA
* * * *
5071 TAAATTCTATAAATAATTCTACTATTTCATTTGGAAACGGAACTTAGCATGGAAACTACATATCC
1 TAAATTCTATAAATAATTTTTCTATTTCATTTGGAAACGGAACTTAACACGGAAACTACATATCC
* * *
5136 ATGTCTAAATCCGCTTCCAAATGATAATATGTAA
66 GTGTCTAAATCCGCTTCCAAACGATAATAAGTAA
5170 TAAATT
1 TAAATT
5176 TTTATGGTAT
Statistics
Matches: 261, Mismatches: 40, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
98 7 0.03
99 237 0.91
100 15 0.06
101 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (99 bp):
TAAATTCTATAAATAATTTTTCTATTTCATTTGGAAACGGAACTTAACACGGAAACTACATATCC
GTGTCTAAATCCGCTTCCAAACGATAATAAGTAA
Found at i:5475 original size:97 final size:96
Alignment explanation
Indices: 5347--5628 Score: 381
Period size: 97 Copynumber: 2.9 Consensus size: 96
5337 TACTATCTTC
* * * *
5347 TATAAATTAATTTCTATTTCACTTGGAAACGGAATTTAACACGGAAACTGCATATCTGTGTCTAA
1 TATAAATAAATTT-TATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATCCGTGTCTAA
*
5412 ATCCGATTCAAATTGATAATGATAAAATAATTCA
65 ATCCGATTCAAA-TGATAATAATAAAATAATT-A
5446 -ATAAATAAATTTTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATCCGTGTCTAAA
1 TATAAATAAATTTTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATCCGTGTCTAAA
* *
5510 TCC-ACTTCTAACTGATAATAATAAAATTATTA
66 TCCGA-TTC-AAATGATAATAATAAAATAATTA
* *
5542 TATAAATAAATTTTTTATTTCATTT-GAAACGGAATATAACACGGAAACTACATATCCATGTCTA
1 TATAAATAAA--TTTTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATCCGTGTCTA
*
5606 AATCCGCTTCCAAATGATAATAA
64 AATCCGATT-CAAATGATAATAA
5629 ATTTAATAAA
Statistics
Matches: 165, Mismatches: 11, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
96 2 0.01
97 81 0.49
98 68 0.41
99 14 0.08
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (96 bp):
TATAAATAAATTTTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATCCGTGTCTAAA
TCCGATTCAAATGATAATAATAAAATAATTA
Done.