Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017808.1 Corchorus olitorius cultivar O-4 contig17841, 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: 38541
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:5408 original size:11 final size:11
Alignment explanation
Indices: 5384--5418 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5374 GTGAAACTGG
*
5384 AAAAGTAAATA
1 AAAAGTAAAGA
*
5395 AAAAGAAAAGA
1 AAAAGTAAAGA
5406 AAAAGTAAAGA
1 AAAAGTAAAGA
5417 AA
1 AA
5419 GCAAACCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (11 bp):
AAAAGTAAAGA
Found at i:7974 original size:371 final size:371
Alignment explanation
Indices: 7291--7977 Score: 1268
Period size: 371 Copynumber: 1.9 Consensus size: 371
7281 CCTAATTTAG
*
7291 AACAATATTAAAGGAAACTGCTTCTGCATGATCTCCTATGCCATTTCCCTAGGTAGGGGCGGCAC
1 AACAATATTAAAGGAAACTGCTTCTGCATGATCTCCTATGCCACTTCCCTAGGTAGGGGCGGCAC
7356 AGAAGGAAATAATAATAATAATTATTCTGAAAAATAATTATTATTTAATAAATAATTAATAAATT
66 AGAAGGAAATAATAATAATAATTATTCTGAAAAATAATTATTATTTAATAAATAATTAATAAATT
7421 TCAGCCCTTATCAATTAATTACAAGATTTTCCTAATTCTATCAGAACTAGGGTGGTGCAGAAACC
131 TCAGCCCTTATCAATTAATTACAAGATTTTCCTAATTCTATCAGAACTAGGGTGGTGCAGAAACC
*
7486 AAGTTTCCTCAGGATTTTTGATTAAATCTTGACCACACATCTTAATAATATTTATGTGAAGACCA
196 AAGTTTCCTCAGGATTTTTAATTAAATCTTGACCACACATCTTAATAATATTTATGTGAAGACCA
* * *
7551 ATTTACCCTTAATTGTAGATTGAGGTATAAACAATATTATCATCGTTACTTTAAGGAAATATTAA
261 AATTACCCTCAATTGTAAATTGAGGTATAAACAATATTATCATCGTTACTTTAAGGAAATATTAA
7616 AGGAAACTCCTTCTGCATGATCTCCTATGCCACTTCCCTAGTTGAC
326 AGGAAACTCCTTCTGCATGATCTCCTATGCCACTTCCCTAGTTGAC
* *
7662 AACAATATTAAAGGAAACTGCTTTTGCATGATCTCCTATGCCACTTCCCTAGGTAGGGGCGGCAT
1 AACAATATTAAAGGAAACTGCTTCTGCATGATCTCCTATGCCACTTCCCTAGGTAGGGGCGGCAC
*
7727 AGAAGGAAATATTAATAATAATTATTCTGAAAAATAATTATTATTTAATAAATAATTAAT-AATT
66 AGAAGGAAATAATAATAATAATTATTCTGAAAAATAATTATTATTTAATAAATAATTAATAAATT
*
7791 TCCAGCCCTTATTAATTAATTACAAGATTTTCCTAATTCTATCAGAACTAGGGTGGTGCAGAAAC
131 T-CAGCCCTTATCAATTAATTACAAGATTTTCCTAATTCTATCAGAACTAGGGTGGTGCAGAAAC
*
7856 CAAGTTTCTTCAGGATTTTTAATTAAATCTTGACCACACATCTTAATAATATTTATGTGAAGACC
195 CAAGTTTCCTCAGGATTTTTAATTAAATCTTGACCACACATCTTAATAATATTTATGTGAAGACC
7921 AAATTACCCTCAATTGTAAATTGAGGTATAAACAATATTATCATCGTTACTTTAAGG
260 AAATTACCCTCAATTGTAAATTGAGGTATAAACAATATTATCATCGTTACTTTAAGG
7978 TTTAAAAGTT
Statistics
Matches: 305, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
370 5 0.02
371 300 0.98
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (371 bp):
AACAATATTAAAGGAAACTGCTTCTGCATGATCTCCTATGCCACTTCCCTAGGTAGGGGCGGCAC
AGAAGGAAATAATAATAATAATTATTCTGAAAAATAATTATTATTTAATAAATAATTAATAAATT
TCAGCCCTTATCAATTAATTACAAGATTTTCCTAATTCTATCAGAACTAGGGTGGTGCAGAAACC
AAGTTTCCTCAGGATTTTTAATTAAATCTTGACCACACATCTTAATAATATTTATGTGAAGACCA
AATTACCCTCAATTGTAAATTGAGGTATAAACAATATTATCATCGTTACTTTAAGGAAATATTAA
AGGAAACTCCTTCTGCATGATCTCCTATGCCACTTCCCTAGTTGAC
Found at i:8714 original size:41 final size:41
Alignment explanation
Indices: 8644--8800 Score: 192
Period size: 41 Copynumber: 3.9 Consensus size: 41
8634 GTTTGATTTG
* * *
8644 ATTTGATTCAAGGG--TCGAATGACTTGGTCTTGAATTGACA
1 ATTTAATTCAAGGGTCTCG-ATGACTTGATCTTGAATTGATA
* * * * *
8684 ATCTAATTCAAGGGTTTTGACGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
**
8725 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
*
8766 ATTTAATTCATGGGTCTCGATGACTTGATCTTGAA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
8801 CAAACGAAAA
Statistics
Matches: 100, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
40 12 0.12
41 86 0.86
42 2 0.02
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (41 bp):
ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
Found at i:32940 original size:25 final size:25
Alignment explanation
Indices: 32906--32954 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
32896 CCAAACAATC
32906 TTGAGCACTCTCGCTCGATCTCTAT
1 TTGAGCACTCTCGCTCGATCTCTAT
*
32931 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGATCTCTA
32955 CAAACAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.33, G:0.18, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGATCTCTAT
Found at i:34656 original size:25 final size:25
Alignment explanation
Indices: 34545--34658 Score: 156
Period size: 25 Copynumber: 4.6 Consensus size: 25
34535 CACTCGTGTT
* * *
34545 CTTGCGTTTGGAAAACGAACCTATG
1 CTTGCGTTTAGCAAACGAACCTGTG
*
34570 CTTGCGTTTAGAAAACGAACCTGTG
1 CTTGCGTTTAGCAAACGAACCTGTG
* * *
34595 CTTGCGTTTACCAAGCGAACCTGTA
1 CTTGCGTTTAGCAAACGAACCTGTG
*
34620 CTTGCATTTAGCAAACGAACCTGTG
1 CTTGCGTTTAGCAAACGAACCTGTG
34645 CTTGCGTTTAGCAA
1 CTTGCGTTTAGCAA
34659 GCGAGCCTTA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 78 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (25 bp):
CTTGCGTTTAGCAAACGAACCTGTG
Found at i:35698 original size:2 final size:2
Alignment explanation
Indices: 35693--35717 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35683 TTTTTTTTCA
35693 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35718 CTAATTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35842 original size:32 final size:32
Alignment explanation
Indices: 35789--35852 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
35779 ATAAATTACA
* * *
35789 TTAATTTGTAGTATATGACATAAAAAATATAT
1 TTAATTTATAGCATATAACATAAAAAATATAT
35821 TTAATTTATAGCATATAACATAAAAAATATAT
1 TTAATTTATAGCATATAACATAAAAAATATAT
35853 AATCTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.39
Consensus pattern (32 bp):
TTAATTTATAGCATATAACATAAAAAATATAT
Done.