Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024688.1 Corchorus olitorius cultivar O-4 contig24721, 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: 14587
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Found at i:4284 original size:51 final size:51
Alignment explanation
Indices: 4211--4313 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 51
4201 GTTATTTCTG
* **
4211 AAAGAGAAACACGAATAAAGTGTTTTTATGTCCGGAGACAAGAT-TGAAACA
1 AAAGAAAAACACGAATAAAGTGTTTGGATGTCCGGAGACAAGATCT-AAACA
* * *
4262 AAAGAAAAACACTAA-AAGAGTGTTTGGGTGTCCTGAGACAAGATCTAAACA
1 AAAGAAAAACACGAATAA-AGTGTTTGGATGTCCGGAGACAAGATCTAAACA
4313 A
1 A
4314 GAAAAATATG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
50 2 0.05
51 41 0.93
52 1 0.02
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (51 bp):
AAAGAAAAACACGAATAAAGTGTTTGGATGTCCGGAGACAAGATCTAAACA
Found at i:4756 original size:37 final size:37
Alignment explanation
Indices: 4709--4780 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
4699 ACAATTCTTC
4709 CTTCTGCCTTTCACATTGCAGCAAGCTTTCGTTGCTT
1 CTTCTGCCTTTCACATTGCAGCAAGCTTTCGTTGCTT
4746 CTTCTGCCTTTCACATTGCAGCAAGCTTTCGTTGC
1 CTTCTGCCTTTCACATTGCAGCAAGCTTTCGTTGC
4781 CTCCTAGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.14, C:0.31, G:0.17, T:0.39
Consensus pattern (37 bp):
CTTCTGCCTTTCACATTGCAGCAAGCTTTCGTTGCTT
Found at i:6781 original size:26 final size:26
Alignment explanation
Indices: 6752--6930 Score: 182
Period size: 26 Copynumber: 6.9 Consensus size: 26
6742 GCTGAGATGT
* ** *
6752 CGAACTAAGGGCGACTGAAAAAATGG
1 CGAACTAGGGGCGACTGATGAAATGC
* * * *
6778 CGAACTAGGGGCGTCCGCTGAAATGG
1 CGAACTAGGGGCGACTGATGAAATGC
* * * *
6804 CGAACTAGGGGCGACTGAAGGACTGT
1 CGAACTAGGGGCGACTGATGAAATGC
6830 CGAACTAGGGGCGACT-ACTGAAATGC
1 CGAACTAGGGGCGACTGA-TGAAATGC
*
6856 CGAACTAGGGGCGACTGCTGAAATGC
1 CGAACTAGGGGCGACTGATGAAATGC
*
6882 CGAACTAGGGGCGACT-ACTGAGATGC
1 CGAACTAGGGGCGACTGA-TGAAATGC
* *
6908 CGAACTAGGGGCGATTGCTGAAA
1 CGAACTAGGGGCGACTGATGAAA
6931 GGTTTTGGAG
Statistics
Matches: 126, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
25 1 0.01
26 125 0.99
ACGTcount: A:0.30, C:0.21, G:0.35, T:0.15
Consensus pattern (26 bp):
CGAACTAGGGGCGACTGATGAAATGC
Found at i:6912 original size:78 final size:79
Alignment explanation
Indices: 6739--6930 Score: 232
Period size: 78 Copynumber: 2.5 Consensus size: 79
6729 TGAAATGACA
* ** * *
6739 ACTG-CTGAGATGTCGAACTAAGGGCGACTGA-AAAAATGGCGAACTAGGGGCGTCCGCTGAAAT
1 ACTGACTGAGATGTCGAACTAGGGGCGACT-ACTGAAATGCCGAACTAGGGGCGACCGCTGAAAT
*
6802 GGCGAACTAGGGGCG
65 GCCGAACTAGGGGCG
* *
6817 ACTGA-AG-GACTGTCGAACTAGGGGCGACTACTGAAATGCCGAACTAGGGGCGACTGCTGAAAT
1 ACTGACTGAGA-TGTCGAACTAGGGGCGACTACTGAAATGCCGAACTAGGGGCGACCGCTGAAAT
6880 GCCGAACTAGGGGCG
65 GCCGAACTAGGGGCG
* * *
6895 ACT-ACTGAGATGCCGAACTAGGGGCGATTGCTGAAA
1 ACTGACTGAGATGTCGAACTAGGGGCGACTACTGAAA
6931 GGTTTTGGAG
Statistics
Matches: 97, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
77 4 0.04
78 91 0.94
79 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.34, T:0.16
Consensus pattern (79 bp):
ACTGACTGAGATGTCGAACTAGGGGCGACTACTGAAATGCCGAACTAGGGGCGACCGCTGAAATG
CCGAACTAGGGGCG
Found at i:6930 original size:52 final size:52
Alignment explanation
Indices: 6743--6921 Score: 223
Period size: 52 Copynumber: 3.4 Consensus size: 52
6733 ATGACAACTG
* * * * * * **
6743 CTGAGATGTCGAACTAAGGGCGACTGAAAAAATGGCGAACTAGGGGCGTCCG
1 CTGAAATGCCGAACTAGGGGCGACTGAAGAAATGCCGAACTAGGGGCGACTA
* * * *
6795 CTGAAATGGCGAACTAGGGGCGACTGAAGGACTGTCGAACTAGGGGCGACTA
1 CTGAAATGCCGAACTAGGGGCGACTGAAGAAATGCCGAACTAGGGGCGACTA
**
6847 CTGAAATGCCGAACTAGGGGCGACTGCTGAAATGCCGAACTAGGGGCGACTA
1 CTGAAATGCCGAACTAGGGGCGACTGAAGAAATGCCGAACTAGGGGCGACTA
*
6899 CTGAGATGCCGAACTAGGGGCGA
1 CTGAAATGCCGAACTAGGGGCGA
6922 TTGCTGAAAG
Statistics
Matches: 110, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 110 1.00
ACGTcount: A:0.29, C:0.21, G:0.35, T:0.15
Consensus pattern (52 bp):
CTGAAATGCCGAACTAGGGGCGACTGAAGAAATGCCGAACTAGGGGCGACTA
Found at i:7080 original size:10 final size:10
Alignment explanation
Indices: 7058--7101 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
7048 AGGATATGAT
7058 ATGATGC-AC
1 ATGATGCAAC
*
7067 ATGATGTAAC
1 ATGATGCAAC
7077 ATGATGCAA-
1 ATGATGCAAC
7086 AGTGATGCAAC
1 A-TGATGCAAC
7097 ATGAT
1 ATGAT
7102 TTCTTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 7 0.23
10 22 0.73
11 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.25
Consensus pattern (10 bp):
ATGATGCAAC
Found at i:7118 original size:16 final size:16
Alignment explanation
Indices: 7097--7129 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
7087 GTGATGCAAC
7097 ATGATTTCTTTGAAAG
1 ATGATTTCTTTGAAAG
7113 ATGATTTCTTTGAAAG
1 ATGATTTCTTTGAAAG
7129 A
1 A
7130 GTTGATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.42
Consensus pattern (16 bp):
ATGATTTCTTTGAAAG
Found at i:8173 original size:44 final size:44
Alignment explanation
Indices: 8110--8199 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
8100 ATTGGACTTG
8110 GAAACTCTTCCCCGTCCATTTCATGTAGAATCAGAGCTCCACCT
1 GAAACTCTTCCCCGTCCATTTCATGTAGAATCAGAGCTCCACCT
*
8154 GAAACTCTTCTCCGTCCATTTCATGTAGAATCAGAGCTCCACCT
1 GAAACTCTTCCCCGTCCATTTCATGTAGAATCAGAGCTCCACCT
8198 GA
1 GA
8200 GAAAGCTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (44 bp):
GAAACTCTTCCCCGTCCATTTCATGTAGAATCAGAGCTCCACCT
Found at i:12689 original size:29 final size:30
Alignment explanation
Indices: 12647--12705 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
12637 AAGGCCTCTG
12647 CATTTCAATCTTGGTTT-AGATCTTTACTT
1 CATTTCAATCTTGGTTTAAGATCTTTACTT
12676 CATTTCAATCTTGGTTTAAGATCTTTACTT
1 CATTTCAATCTTGGTTTAAGATCTTTACTT
12706 TATTAATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.22, C:0.17, G:0.10, T:0.51
Consensus pattern (30 bp):
CATTTCAATCTTGGTTTAAGATCTTTACTT
Found at i:12740 original size:33 final size:34
Alignment explanation
Indices: 12668--12743 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
12658 TGGTTTAGAT
* * * *
12668 CTTTACTTCATTTCAATCTTGGTTTAAGATCTTTA
1 CTTTA-TTAATTTCAATCCTGGCTTAAGATCATTA
*
12703 CTTTATTAATTTCAATCCT-GCTTAAGATCATTG
1 CTTTATTAATTTCAATCCTGGCTTAAGATCATTA
12736 CTTTATTA
1 CTTTATTA
12744 GTTAATTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
33 19 0.53
34 12 0.33
35 5 0.14
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (34 bp):
CTTTATTAATTTCAATCCTGGCTTAAGATCATTA
Found at i:12796 original size:39 final size:38
Alignment explanation
Indices: 12708--12828 Score: 138
Period size: 39 Copynumber: 3.2 Consensus size: 38
12698 CTTTACTTTA
* * * *
12708 TTAATTTCAATCCT-GCTTAAGATCATTGCTTTATTAG
1 TTAATTTCGATCCTGGTTTAGGATCATTGCTTTATCAG
* * *
12745 TTAATTTTGATCCTGGTTTAGGATTATTGCTTTATCGG
1 TTAATTTCGATCCTGGTTTAGGATCATTGCTTTATCAG
* *
12783 CTTAATTTCGATCCTGATTTAGGAGCATTGC-TTATCAG
1 -TTAATTTCGATCCTGGTTTAGGATCATTGCTTTATCAG
12821 TTAATTTC
1 TTAATTTC
12829 AAAATCATAT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
37 20 0.29
38 24 0.34
39 26 0.37
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.46
Consensus pattern (38 bp):
TTAATTTCGATCCTGGTTTAGGATCATTGCTTTATCAG
Found at i:14058 original size:6 final size:6
Alignment explanation
Indices: 14047--14071 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
14037 CAAATCAAAT
14047 AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA A
14072 CAATACACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Done.