Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022626.1 Corchorus olitorius cultivar O-4 contig22659, 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: 9566
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Found at i:3850 original size:34 final size:34
Alignment explanation
Indices: 3812--3904 Score: 114
Period size: 34 Copynumber: 2.7 Consensus size: 34
3802 GGCCGTTCGG
3812 CACCTTTCCCATATTCTTGAAATTTGCCGCTCAA
1 CACCTTTCCCATATTCTTGAAATTTGCCGCTCAA
* * * * **
3846 CACCTATCCTATATACTTGAAATTTGTCGCTCGG
1 CACCTTTCCCATATTCTTGAAATTTGCCGCTCAA
* *
3880 CACCGTTCTCATATTCTTGAAATTT
1 CACCTTTCCCATATTCTTGAAATTT
3905 CAAATTGAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.24, C:0.28, G:0.11, T:0.38
Consensus pattern (34 bp):
CACCTTTCCCATATTCTTGAAATTTGCCGCTCAA
Found at i:4711 original size:122 final size:123
Alignment explanation
Indices: 4483--4784 Score: 356
Period size: 122 Copynumber: 2.5 Consensus size: 123
4473 CCAAGTTGAA
** ** * * * * *
4483 TGACCGAGTATGTAAAATGATGATGCCCTCAAGGGGCCCAACGCCAGCATGAGAGTGATCAGGCA
1 TGACCGAGTATGGGAAATGATGAAACCCCCAAGGGGCCCAACGCCAACAGGCGAGCGATCAGGCA
* * * *
4548 AGGCCGAGCTCGACCTAGTATGGCCCTCGACCGGCAGGCGATCGGCAAGAACCATCCC
66 AGGCCGAGCTCGACCTAATATGGCCATCCACCGGCAGGCGATCGACAAGAACCATCCC
* *
4606 TGACCGAGTATGGGAAATGAAGAAACCCCCAAGGGG-ACAACGCCAACAGGCGAGCGATCAGGCA
1 TGACCGAGTATGGGAAATGATGAAACCCCCAAGGGGCCCAACGCCAACAGGCGAGCGATCAGGCA
* ** * *
4670 AGGCCGAGCTCGACCTAATATGGTCATCCATTGAGTA-GCGATCGACATGAACCATCCC
66 AGGCCGAGCTCGACCTAATATGGCCATCCACCG-GCAGGCGATCGACAAGAACCATCCC
** * * *
4728 TGACTAAGTATGGGAAATGATGAAACCCCCAAGGGGTCCAACGCTAATAGGCGAGCG
1 TGACCGAGTATGGGAAATGATGAAACCCCCAAGGGGCCCAACGCCAACAGGCGAGCG
4785 TTCTCCAATG
Statistics
Matches: 151, Mismatches: 26, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
122 102 0.68
123 49 0.32
ACGTcount: A:0.30, C:0.27, G:0.28, T:0.15
Consensus pattern (123 bp):
TGACCGAGTATGGGAAATGATGAAACCCCCAAGGGGCCCAACGCCAACAGGCGAGCGATCAGGCA
AGGCCGAGCTCGACCTAATATGGCCATCCACCGGCAGGCGATCGACAAGAACCATCCC
Found at i:5067 original size:142 final size:142
Alignment explanation
Indices: 4806--5106 Score: 440
Period size: 142 Copynumber: 2.1 Consensus size: 142
4796 TCGAGATGGC
* * * *
4806 AAAAAAGATGACACCCGCAAGAAGCAAAGCGTGGGACGCTCCCCGAGCGCCAAAAGGAGAATGCT
1 AAAAAAGATGACGCTCGCAAGAAGCAAAGCGTGAGACGATCCCCGAGCGCCAAAAGGAGAATGCT
* *
4871 CCTTGAGAGCAAATTAAGAATGCCCAAGATGGCGAAAAAGATGACGATCGCCAAACGCGAAGCGT
66 CCTTGAGAGCAAATGAAGAATGCCCAAGATGGCGAAAAAGATGACGATCGCCAAACACGAAGCGT
*
4936 GGGACGTTCCCA
131 GGGACGCTCCCA
* * * * *
4948 AAAAAAGTTGACGCTCGCCAGAAGCGAAGCGTGAGACGATCGCCGAGCGCCAAATGGAGAATGCT
1 AAAAAAGATGACGCTCGCAAGAAGCAAAGCGTGAGACGATCCCCGAGCGCCAAAAGGAGAATGCT
** **
5013 CCTTGAGTTCAAATGAAGAATGCCCAAGATGGCGAAAAAGATGACGATTTCCAAACACGAAGCGT
66 CCTTGAGAGCAAATGAAGAATGCCCAAGATGGCGAAAAAGATGACGATCGCCAAACACGAAGCGT
5078 GGGACGCTCCCA
131 GGGACGCTCCCA
*
5090 AGAAAAAGATGATGCTC
1 A-AAAAAGATGACGCTC
5107 ACCGAATGCA
Statistics
Matches: 140, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
142 127 0.91
143 13 0.09
ACGTcount: A:0.36, C:0.23, G:0.27, T:0.13
Consensus pattern (142 bp):
AAAAAAGATGACGCTCGCAAGAAGCAAAGCGTGAGACGATCCCCGAGCGCCAAAAGGAGAATGCT
CCTTGAGAGCAAATGAAGAATGCCCAAGATGGCGAAAAAGATGACGATCGCCAAACACGAAGCGT
GGGACGCTCCCA
Found at i:5218 original size:25 final size:25
Alignment explanation
Indices: 5167--5219 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
5157 TCGCAAATGT
* * * *
5167 AGAACGCTCGCCGAATGCGAAGTGG
1 AGAACACTCGCCGAACGCAAAGCGG
*
5192 AGAACACTCGCCGAGCGCAAAGCGG
1 AGAACACTCGCCGAACGCAAAGCGG
5217 AGA
1 AGA
5220 TCCCTAAAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.26, G:0.34, T:0.08
Consensus pattern (25 bp):
AGAACACTCGCCGAACGCAAAGCGG
Found at i:5287 original size:91 final size:91
Alignment explanation
Indices: 5138--5306 Score: 205
Period size: 91 Copynumber: 1.9 Consensus size: 91
5128 ACTCCCCATT
* * ** * * *
5138 AGAGGAGGACGATCGTCGATCGCAAATGTAGAACGCTCGCCGAATGCGAAGTGGAGAACACTCGC
1 AGAGGAGGACGATCGCCGATCGCAAATGTAGAACGCTCACCGAACACCAAGCGGAGAACAATCGC
*
5203 CGAGCGCAAAGCGGAGATCCCTAAAG
66 CGAACGCAAAGCGGAGATCCCTAAAG
* * * *
5229 AGAGGAGGACGATCGCCGATCGTAAATGTAGAATGC-CTACCGAGCACCAAGCGTAGAACAATCG
1 AGAGGAGGACGATCGCCGATCGCAAATGTAGAACGCTC-ACCGAACACCAAGCGGAGAACAATCG
*
5293 CCGAACGCCAAGCG
65 CCGAACGCAAAGCG
5307 CAGAACGCCC
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
90 1 0.02
91 63 0.98
ACGTcount: A:0.33, C:0.25, G:0.30, T:0.12
Consensus pattern (91 bp):
AGAGGAGGACGATCGCCGATCGCAAATGTAGAACGCTCACCGAACACCAAGCGGAGAACAATCGC
CGAACGCAAAGCGGAGATCCCTAAAG
Found at i:5395 original size:26 final size:26
Alignment explanation
Indices: 5366--5423 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
5356 CCCAAACACG
* *
5366 AAGCGTAGAATGCTTGCCAAGCGCTA
1 AAGCGTAGAATGCTCGCCAAGCGCCA
*
5392 AAGCAG-AGAATGCTCGCCGAGCGCCA
1 AAGC-GTAGAATGCTCGCCAAGCGCCA
5418 AA-CGTA
1 AAGCGTA
5424 AATCCCCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 1 0.04
25 2 0.07
26 23 0.85
27 1 0.04
ACGTcount: A:0.33, C:0.26, G:0.28, T:0.14
Consensus pattern (26 bp):
AAGCGTAGAATGCTCGCCAAGCGCCA
Found at i:5468 original size:25 final size:25
Alignment explanation
Indices: 5438--5486 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5428 CCCAAGGAGA
** *
5438 GGAGAACGCTTGCCGAGTGCCAAGG
1 GGAGAACGCCCGCCGAGCGCCAAGG
*
5463 GGAGAAGGCCCGCCGAGCGCCAAG
1 GGAGAACGCCCGCCGAGCGCCAAG
5487 CGTAGATCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.24, C:0.29, G:0.41, T:0.06
Consensus pattern (25 bp):
GGAGAACGCCCGCCGAGCGCCAAGG
Found at i:6670 original size:28 final size:27
Alignment explanation
Indices: 6634--6705 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
6624 AGTGGACTTA
* *
6634 AAATTACCAAAATGCCCCCTGAATGTAC
1 AAATGACCAAAATGCCCCCTG-ATGCAC
** *
6662 AAATGACCAAAATGCCCTTTGGTGCAC
1 AAATGACCAAAATGCCCCCTGATGCAC
6689 AAATGACCAAAATGCCC
1 AAATGACCAAAATGCCC
6706 ATGGGTGACC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.39, C:0.28, G:0.14, T:0.19
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCCTGATGCAC
Found at i:6726 original size:27 final size:27
Alignment explanation
Indices: 6660--6712 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
6650 CCCTGAATGT
* *
6660 ACAAATGACCAAAATGCCCTTTGGTGC
1 ACAAATGACCAAAATGCCCATGGGTGC
6687 ACAAATGACCAAAATGCCCATGGGTG
1 ACAAATGACCAAAATGCCCATGGGTG
6713 ACCCTAATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19
Consensus pattern (27 bp):
ACAAATGACCAAAATGCCCATGGGTGC
Found at i:7144 original size:24 final size:24
Alignment explanation
Indices: 7093--7144 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
7083 ATGCCCAAAC
* *
7093 ATTTACTTATAGTTTAGTGTCATA
1 ATTTACTTATAGTTTAGTCTAATA
*
7117 ATTTACTTATAGTTT-GATCTAATT
1 ATTTACTTATAGTTTAG-TCTAATA
7141 ATTT
1 ATTT
7145 GCATTTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.54
Consensus pattern (24 bp):
ATTTACTTATAGTTTAGTCTAATA
Done.