Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015105.1 Corchorus olitorius cultivar O-4 contig15138, 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: 23726
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Found at i:4905 original size:26 final size:23
Alignment explanation
Indices: 4875--4921 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
4865 CTTGAAAATT
4875 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
4901 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
4922 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Found at i:5431 original size:11 final size:11
Alignment explanation
Indices: 5380--5428 Score: 80
Period size: 11 Copynumber: 4.5 Consensus size: 11
5370 CTAAGGGTAA
5380 AGGAAAAAGCT
1 AGGAAAAAGCT
5391 AGGAAAAAGCT
1 AGGAAAAAGCT
5402 AGGAAAAAGCT
1 AGGAAAAAGCT
**
5413 AGGAAGGAGCT
1 AGGAAAAAGCT
5424 AGGAA
1 AGGAA
5429 GGACCCTACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.51, C:0.08, G:0.33, T:0.08
Consensus pattern (11 bp):
AGGAAAAAGCT
Found at i:6798 original size:27 final size:30
Alignment explanation
Indices: 6764--6818 Score: 80
Period size: 27 Copynumber: 1.9 Consensus size: 30
6754 CAATTCAATA
6764 TAATAATTT-AATT-CTTTAAT-TTTTTAT
1 TAATAATTTCAATTACTTTAATATTTTTAT
*
6791 TAATAATTTCAATTATTTTAATATTTTT
1 TAATAATTTCAATTACTTTAATATTTTT
6819 TTATTTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 9 0.38
28 4 0.17
29 6 0.25
30 5 0.21
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (30 bp):
TAATAATTTCAATTACTTTAATATTTTTAT
Found at i:6878 original size:2 final size:2
Alignment explanation
Indices: 6871--6905 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6861 AAGACTAGTT
6871 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6906 TTACACCTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9161 original size:24 final size:25
Alignment explanation
Indices: 9109--9169 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
9099 TTTTTATCTC
*
9109 AAAAAAAAC-TTAAAGCAAAACACT
1 AAAAAATACATTAAAGCAAAACACT
*
9133 AAAAAATACATTAAAGCAAAAGACT
1 AAAAAATACATTAAAGCAAAACACT
*
9158 AAAAAGTACATT
1 AAAAAATACATT
9170 TATAACTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 8 0.24
25 25 0.76
ACGTcount: A:0.64, C:0.13, G:0.07, T:0.16
Consensus pattern (25 bp):
AAAAAATACATTAAAGCAAAACACT
Found at i:9425 original size:31 final size:32
Alignment explanation
Indices: 9354--9435 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 32
9344 GTCTATCAGC
*
9354 TTTTAATTTATTTAATTTAAGGCTTTCAATTT
1 TTTTAATTTGTTTAATTTAAGGCTTTCAATTT
** *
9386 AATT-ATTTGTTTAATTTAATGC-TT-AATTT
1 TTTTAATTTGTTTAATTTAAGGCTTTCAATTT
*
9415 GTTTTAATTTGTAATAATTTA
1 -TTTTAATTTGT-TTAATTTA
9436 GAATTGATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
29 5 0.12
30 4 0.10
31 22 0.55
32 9 0.22
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (32 bp):
TTTTAATTTGTTTAATTTAAGGCTTTCAATTT
Found at i:9932 original size:16 final size:16
Alignment explanation
Indices: 9911--9987 Score: 86
Period size: 16 Copynumber: 4.8 Consensus size: 16
9901 CTACCTGAGA
*
9911 CCGAACCTGAAAATAC
1 CCGAACCCGAAAATAC
*
9927 CCGAACCCG-ATATAAC
1 CCGAACCCGAAAAT-AC
*
9943 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
*
9959 CCGAACCCGAATGA-AC
1 CCGAACCCGAA-AATAC
9975 CCGAACCCGAAAA
1 CCGAACCCGAAAA
9988 AAACCCGAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
15 4 0.08
16 43 0.84
17 4 0.08
ACGTcount: A:0.40, C:0.36, G:0.16, T:0.08
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:9960 original size:32 final size:32
Alignment explanation
Indices: 9911--9996 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
9901 CTACCTGAGA
*
9911 CCGAACCTGAAAATACCCGAACCCGATAT-AAC
1 CCGAACCCGAAAATACCCGAACCCGA-ATGAAC
*
9943 CCGAGCCCGAAAATACCCGAACCCGAATGAAC
1 CCGAACCCGAAAATACCCGAACCCGAATGAAC
*
9975 CCGAACCCGAAAAAAACCCGAA
1 CCGAACCCG-AAAATACCCGAA
9997 TCTAAACTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
31 2 0.04
32 35 0.73
33 11 0.23
ACGTcount: A:0.42, C:0.36, G:0.15, T:0.07
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCGAACCCGAATGAAC
Found at i:18864 original size:29 final size:25
Alignment explanation
Indices: 18806--18857 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
18796 AGGCTTCCAA
18806 CAAAATAAGACAGGAAGAAGAAATT
1 CAAAATAAGACAGGAAGAAGAAATT
18831 CAAAATAAGACAGGAAGAAGAAATT
1 CAAAATAAGACAGGAAGAAGAAATT
18856 CA
1 CA
18858 TTCAAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.60, C:0.10, G:0.19, T:0.12
Consensus pattern (25 bp):
CAAAATAAGACAGGAAGAAGAAATT
Found at i:18917 original size:19 final size:19
Alignment explanation
Indices: 18881--18917 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18871 AAATATAAAC
**
18881 TCAGGAAAGAGGTGATGAA
1 TCAGGAAAGAGGAAATGAA
18900 TCAGGAAAGAGGAAATGA
1 TCAGGAAAGAGGAAATGA
18918 GGGATTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.05, G:0.35, T:0.14
Consensus pattern (19 bp):
TCAGGAAAGAGGAAATGAA
Found at i:22988 original size:3 final size:3
Alignment explanation
Indices: 22982--23037 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
22972 AATAATAACA
22982 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
23030 ATT ATT AT
1 ATT ATT AT
23038 AAATGGGAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.