Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021249.1 Corchorus olitorius cultivar O-4 contig21282, 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: 31031
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Found at i:6931 original size:20 final size:18
Alignment explanation
Indices: 6886--6933 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
6876 GAAAAAAAAA
6886 AAGCAGAGAGAACTGAAG
1 AAGCAGAGAGAACTGAAG
6904 AAGCAGAGAGAACTGAAG
1 AAGCAGAGAGAACTGAAG
*
6922 AGGCAGAGAGAA
1 AAGCAGAGAGAA
6934 ACAGAGTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.50, C:0.10, G:0.35, T:0.04
Consensus pattern (18 bp):
AAGCAGAGAGAACTGAAG
Found at i:6938 original size:28 final size:28
Alignment explanation
Indices: 6902--6957 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
6892 AGAGAACTGA
* *
6902 AGAAGCAGAG-AGAACTGAAGAGGCAGAG
1 AGAAACAGAGTAGAAAT-AAGAGGCAGAG
*
6930 AGAAACAGAGTATAAATAAGAGGCAGAG
1 AGAAACAGAGTAGAAATAAGAGGCAGAG
6958 GGAAGCGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.50, C:0.09, G:0.34, T:0.07
Consensus pattern (28 bp):
AGAAACAGAGTAGAAATAAGAGGCAGAG
Found at i:8139 original size:108 final size:109
Alignment explanation
Indices: 7946--8155 Score: 323
Period size: 108 Copynumber: 1.9 Consensus size: 109
7936 ACTTTCAAAT
* * *
7946 GATTAGGCTAACGGTATCGTCATGCCGCACTAACATGGGAATGTCACGTCAGACCAACTCGACCA
1 GATTAGGCTAACGGTATCGTCATGCCACACTAACATGGAAATGTCACGTCAGACCAACTCAACCA
* *
8011 ACATGGCATTATCACGTCGGACCAAATAGCTAACGTGACAATAC
66 ACATGGCATTATCACATCGGACCAAACAGCTAACGTGACAATAC
** *
8055 GATTAGGCTAACGGTA-CGTCATGCCATGCTAACGTGGAAATGTCACGTCAGACCAACTCAACCA
1 GATTAGGCTAACGGTATCGTCATGCCACACTAACATGGAAATGTCACGTCAGACCAACTCAACCA
* *
8119 ACTTGGCATTATCACATCGGACCAAACAGCTGACGTG
66 ACATGGCATTATCACATCGGACCAAACAGCTAACGTG
8156 GCATTACCAT
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
108 75 0.82
109 16 0.18
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (109 bp):
GATTAGGCTAACGGTATCGTCATGCCACACTAACATGGAAATGTCACGTCAGACCAACTCAACCA
ACATGGCATTATCACATCGGACCAAACAGCTAACGTGACAATAC
Found at i:17655 original size:6 final size:6
Alignment explanation
Indices: 17646--17713 Score: 54
Period size: 6 Copynumber: 11.5 Consensus size: 6
17636 TATTTTCTTT
*
17646 AAAAA- AAAAACC AAAAA- AAAACAA AAAAAC AAAAAC AAAAAC -AAAAC
1 AAAAAC AAAAA-C AAAAAC AAAA-AC AAAAAC AAAAAC AAAAAC AAAAAC
* *
17693 AAACAG AACAAAC -AAAAC AAA
1 AAAAAC AA-AAAC AAAAAC AAA
17714 CAAACAAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
5 18 0.35
6 22 0.43
7 11 0.22
ACGTcount: A:0.82, C:0.16, G:0.01, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:17661 original size:11 final size:10
Alignment explanation
Indices: 17647--17725 Score: 61
Period size: 11 Copynumber: 7.3 Consensus size: 10
17637 ATTTTCTTTA
17647 AAAAAAAAACC
1 AAAAAAAAA-C
17658 AAAAAAAAAC
1 AAAAAAAAAC
17668 AAAAAAACAA-
1 AAAAAAA-AAC
*
17678 AAACAAAAAC
1 AAAAAAAAAC
* *
17688 AAAACAAACAG
1 AAAA-AAAAAC
17699 AACAAACAAAAC
1 AA-AAA-AAAAC
17711 AAACAAACAAAC
1 AAA-AAA-AAAC
17723 AAA
1 AAA
17726 CAAACAAGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
9 2 0.04
10 17 0.31
11 20 0.36
12 16 0.29
ACGTcount: A:0.81, C:0.18, G:0.01, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:17696 original size:9 final size:9
Alignment explanation
Indices: 17663--17732 Score: 87
Period size: 8 Copynumber: 8.2 Consensus size: 9
17653 AAACCAAAAA
17663 AAAACAAA-
1 AAAACAAAC
17671 AAAACAAA-
1 AAAACAAAC
17679 AACAA-AAAC
1 AA-AACAAAC
17688 AAAACAAAC
1 AAAACAAAC
*
17697 AGAACAAAC
1 AAAACAAAC
17706 AAAACAAAC
1 AAAACAAAC
17715 -AAACAAAC
1 AAAACAAAC
17723 -AAACAAAC
1 AAAACAAAC
17731 AA
1 AA
17733 GTACAAGGAT
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
8 31 0.55
9 25 0.45
ACGTcount: A:0.79, C:0.20, G:0.01, T:0.00
Consensus pattern (9 bp):
AAAACAAAC
Found at i:17706 original size:4 final size:4
Alignment explanation
Indices: 17664--17732 Score: 77
Period size: 4 Copynumber: 16.5 Consensus size: 4
17654 AACCAAAAAA
* *
17664 AAAC AAAA AAAC AAA- AACAA AAAC AAAAC AAAC AGAAC AAAC AAAAC
1 AAAC AAAC AAAC AAAC AA-AC AAAC -AAAC AAAC A-AAC AAAC -AAAC
17711 AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AA
17733 GTACAAGGAT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
3 2 0.04
4 41 0.72
5 14 0.25
ACGTcount: A:0.78, C:0.20, G:0.01, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:18033 original size:83 final size:83
Alignment explanation
Indices: 17892--18059 Score: 291
Period size: 83 Copynumber: 2.0 Consensus size: 83
17882 TCATATTCTA
*
17892 TTGTGAAAAAGTGAGTACACACCAAGACAAAAGTTTAAAGCAACAGAACCATTAAATTTTTAAGC
1 TTGTGAAAAAGTGAGAACACACCAAGACAAAAGTTTAAAGCAACAGAACCATTAAATTTTTAAGC
17957 CAGGCTTCCATAACAAAC
66 CAGGCTTCCATAACAAAC
* * *
17975 TTGTGAGAAAGTGAGAACACACCAAGACAAAAGTTTAAAGCAACAGAACCATTGAATTTTTAAGT
1 TTGTGAAAAAGTGAGAACACACCAAGACAAAAGTTTAAAGCAACAGAACCATTAAATTTTTAAGC
*
18040 CAGGTTTCCATAACAAAC
66 CAGGCTTCCATAACAAAC
18058 TT
1 TT
18060 CTTTGTATGC
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.23
Consensus pattern (83 bp):
TTGTGAAAAAGTGAGAACACACCAAGACAAAAGTTTAAAGCAACAGAACCATTAAATTTTTAAGC
CAGGCTTCCATAACAAAC
Found at i:27181 original size:32 final size:32
Alignment explanation
Indices: 27145--27283 Score: 215
Period size: 32 Copynumber: 4.3 Consensus size: 32
27135 ACTATTTTAA
* *
27145 GGCGTTTTATTCAGTAGACGCCGCTAAGTAGG
1 GGCGTTTTCTTCAGTAGACGCCGCTAAATAGG
* * *
27177 GGCGTTTTCTTCAGTAGTCACCGCTAAATAAG
1 GGCGTTTTCTTCAGTAGACGCCGCTAAATAGG
27209 GGCGTTTTCTTCAGTAGACGCCGCTAAATAGG
1 GGCGTTTTCTTCAGTAGACGCCGCTAAATAGG
*
27241 GGCATTTTCTTCAGTAGACGCCGCTAAATAGG
1 GGCGTTTTCTTCAGTAGACGCCGCTAAATAGG
*
27273 GGCATTTTCTT
1 GGCGTTTTCTT
27284 TTCATAGATG
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 98 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (32 bp):
GGCGTTTTCTTCAGTAGACGCCGCTAAATAGG
Done.