Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023193.1 Corchorus olitorius cultivar O-4 contig23226, 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: 15491
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Found at i:1576 original size:21 final size:22
Alignment explanation
Indices: 1546--1586 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1536 GCATAATTTC
*
1546 TAAAATCAAGGGTCAAATTGAA
1 TAAAATCAAGGATCAAATTGAA
1568 TAAAA-CAAGGATCAAATTG
1 TAAAATCAAGGATCAAATTG
1587 CATTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.10, G:0.17, T:0.22
Consensus pattern (22 bp):
TAAAATCAAGGATCAAATTGAA
Found at i:4497 original size:27 final size:27
Alignment explanation
Indices: 4467--4572 Score: 167
Period size: 27 Copynumber: 3.9 Consensus size: 27
4457 TGTGAACTTA
*
4467 AAATGACCAAAATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTAGATGTGC
*
4494 AAATGACCAAAATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTAGATGTGC
*
4521 AAATGACCAAAATACCCCTAGATGTGC
1 AAATGACCAAAATGCCCCTAGATGTGC
*
4548 AAATGACTAAAATGCCTCCTAGATG
1 AAATGACCAAAATGCC-CCTAGATG
4573 ACCGTAATGC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
27 66 0.89
28 8 0.11
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTAGATGTGC
Found at i:4989 original size:69 final size:68
Alignment explanation
Indices: 4905--5663 Score: 1009
Period size: 69 Copynumber: 11.1 Consensus size: 68
4895 CTCATTAAAC
* * * * * * * *
4905 TTGGCTTATGGAAAAGCCTCTGCT-ATATGGATGGACCCAATGTTTAAACTGACTCGTATGGAAG
1 TTGGCTTGTGGAAAAGCCTATG-TGCT-TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
4969 CGAGT
64 CGAGT
* * * *
4974 TTGACTTATGGAAAAGTCTAATG-GCTTGGATGAAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCT-ATGTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
5038 GAGT
65 GAGT
* *
5042 TTGGCTTGTGGAAAAAGCCTATGTGGCTTGAATGGAA-C----C---AACTGACTCATATGGAAA
1 TTGGCTTGTGG-AAAAGCCTATGT-GCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
5099 CGAGT
64 CGAGT
* * *
5104 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAATGCTTGATCGGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGT-GCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
*
5169 AAGT
65 GAGT
* * *
5173 TTGGCTTGTGGAAAAGTCTATGTGGCTTGGATGAAACCAAGGCTTGAACCGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGT-GCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
5238 GAGT
65 GAGT
*
5242 TTGGCTTTTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGT-GCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
5307 GAGT
65 GAGT
* *
5311 TTGGCTTATGGAAATGCCTATGTGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGT-GCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
5376 GAGT
65 GAGT
* *
5380 TTGGCTTGTGGAAAAGGCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGT-GCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
5445 GAGT
65 GAGT
* * *
5449 TTGGCTTGTGGAAAAGCCTATATGGCTTGGGTGGAACCAAGGCTTGAACTAACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGT-GCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
5514 GAGT
65 GAGT
**
5518 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGC-TGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATG-TGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
5582 GAGT
65 GAGT
** *
5586 TTGGCTTGTGGAAAAGCCCCTGCTGCGTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATG-TGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
5651 GAGT
65 GAGT
5655 TTGGTCTTG
1 TTGG-CTTG
5664 GAAGACTGAA
Statistics
Matches: 626, Mismatches: 48, Indels: 31
0.89 0.07 0.04
Matches are distributed among these distances:
61 24 0.04
62 34 0.05
65 1 0.00
66 1 0.00
68 114 0.18
69 435 0.69
70 17 0.03
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (68 bp):
TTGGCTTGTGGAAAAGCCTATGTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACG
AGT
Found at i:6002 original size:91 final size:91
Alignment explanation
Indices: 5861--6087 Score: 393
Period size: 91 Copynumber: 2.5 Consensus size: 91
5851 ATACCTTTAG
*
5861 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAATA-GAACCAAT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAA-AGGAACCAAT
5925 GTGCGGTCAACTTGAAAAACAACTTGA
65 GTGCGGTCAACTTGAAAAACAACTTGA
* *
5952 AAAATAACTCTGAGTCTGATGTTGTAAGTGAAAACTTCTTGATTGATGATGAAAAGGGACCAATG
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAGGAACCAATG
*
6017 TGCGGTGAACTTGAAAAACAACTTGA
66 TGCGGTCAACTTGAAAAACAACTTGA
*
6043 AAAATAGCTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTG
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTG
6088 TTGCTTTGAA
Statistics
Matches: 129, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
90 1 0.01
91 128 0.99
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (91 bp):
AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAGGAACCAATG
TGCGGTCAACTTGAAAAACAACTTGA
Found at i:7728 original size:27 final size:27
Alignment explanation
Indices: 7683--7735 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
7673 ATTCCAAGTG
*
7683 TCTTTATTTTCATTTTTCTTTTTTTTT
1 TCTTTATTTTCATTTTTCTCTTTTTTT
*
7710 TCTTT-TTTTCTTTTCTTCTCTTTTTT
1 TCTTTATTTTCATTT-TTCTCTTTTTT
7736 ATTATTGGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (27 bp):
TCTTTATTTTCATTTTTCTCTTTTTTT
Found at i:7731 original size:18 final size:19
Alignment explanation
Indices: 7695--7735 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
7685 TTTATTTTCA
* *
7695 TTTTTCTTTTTTTTTTCTT
1 TTTTTCTTTTTCTTCTCTT
7714 TTTTTC-TTTTCTTCTCTT
1 TTTTTCTTTTTCTTCTCTT
7732 TTTT
1 TTTT
7736 ATTATTGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTCTTTTTCTTCTCTT
Found at i:9819 original size:21 final size:22
Alignment explanation
Indices: 9784--9825 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
9774 TGAAGGTTTA
9784 ATGGAATGCATGAATGAATGCC
1 ATGGAATGCATGAATGAATGCC
*
9806 ATGGCATG-ATGAATGAATGC
1 ATGGAATGCATGAATGAATGC
9826 ATGAGGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.24
Consensus pattern (22 bp):
ATGGAATGCATGAATGAATGCC
Found at i:14577 original size:27 final size:27
Alignment explanation
Indices: 14547--14652 Score: 158
Period size: 27 Copynumber: 3.9 Consensus size: 27
14537 TGTGAACTTA
*
14547 AAATGACCAAAATGCCCCTAAATGTGC
1 AAATGACCAAAATGCCCCTAGATGTGC
* *
14574 AAATGATCAAAATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTAGATGTGC
*
14601 AAATGACCAAAATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTAGATGTGC
*
14628 AAATGACTAAAATGCCTCCTAGATG
1 AAATGACCAAAATGCC-CCTAGATG
14653 ACCCTAATGC
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
27 65 0.90
28 7 0.10
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTAGATGTGC
Done.