Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022569.1 Corchorus olitorius cultivar O-4 contig22602, 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: 26051
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--39 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1 C
2 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40 GTTGTGTCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5744 original size:15 final size:15
Alignment explanation
Indices: 5667--5760 Score: 62
Period size: 16 Copynumber: 6.0 Consensus size: 15
5657 GGCCTGCCTA
*
5667 GCAGGCCTGGCGCGC
1 GCAGGCCTGGTGCGC
*
5682 GCAGCCCTGGTGCGC
1 GCAGGCCTGGTGCGC
* * *
5697 GCTGGACCAGCTGCGC
1 GCAGG-CCTGGTGCGC
* * *
5713 GCTGGGCCAGCTGGCGC
1 GC-AGGCCTGGT-GCGC
5730 GCAGGCCTGGTGCGC
1 GCAGGCCTGGTGCGC
* *
5745 GCTGGGCCTGGCGCGC
1 GC-AGGCCTGGTGCGC
5761 CTTGGTCCAG
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
15 22 0.35
16 33 0.52
17 8 0.13
ACGTcount: A:0.06, C:0.37, G:0.45, T:0.12
Consensus pattern (15 bp):
GCAGGCCTGGTGCGC
Found at i:5752 original size:16 final size:16
Alignment explanation
Indices: 5687--5760 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 16
5677 CGCGCGCAGC
*
5687 CCTGGTGCGCGCTGGA
1 CCTGGTGCGCGCTGGG
* *
5703 CCAGCTGCGCGCTGGG
1 CCTGGTGCGCGCTGGG
* * *
5719 CCAGCTGGCGCGC-AGG
1 CCTGGT-GCGCGCTGGG
5735 CCTGGTGCGCGCTGGG
1 CCTGGTGCGCGCTGGG
*
5751 CCTGGCGCGC
1 CCTGGTGCGC
5761 CTTGGTCCAG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
15 6 0.12
16 36 0.75
17 6 0.12
ACGTcount: A:0.05, C:0.36, G:0.45, T:0.14
Consensus pattern (16 bp):
CCTGGTGCGCGCTGGG
Found at i:5826 original size:12 final size:13
Alignment explanation
Indices: 5809--5838 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
5799 CTTGGGCCCA
5809 AATAAAAAAA-AT
1 AATAAAAAAACAT
5821 AATAAAAAAACAT
1 AATAAAAAAACAT
5834 AATAA
1 AATAA
5839 TAAAGTGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (13 bp):
AATAAAAAAACAT
Found at i:5913 original size:18 final size:17
Alignment explanation
Indices: 5881--5922 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
5871 AAAGAGACAT
5881 AAGGAAAGAAAAAGAGA
1 AAGGAAAGAAAAAGAGA
*
5898 AAGGAAGAGGAAAAGAGA
1 AAGGAA-AGAAAAAGAGA
*
5916 AAAGAAA
1 AAGGAAA
5923 AAGAGAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AAGGAAAGAAAAAGAGA
Found at i:7284 original size:13 final size:12
Alignment explanation
Indices: 7266--7310 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
7256 ATTTTATTAC
7266 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
7279 TGTTTTATAAAT
1 TGTTTTATAAAT
*
7291 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
7305 TGTTTT
1 TGTTTT
7311 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:9384 original size:6 final size:6
Alignment explanation
Indices: 9368--9414 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
9358 ACAGTACAAC
*
9368 AAAAC- AAAACG AAAACG -AAAC- AAAACA AAAACAG AAAACG AAAACG
1 AAAACG AAAACG AAAACG AAAACG AAAACG AAAAC-G AAAACG AAAACG
9414 A
1 A
9415 TGTCAAACAG
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
5 13 0.35
6 19 0.51
7 5 0.14
ACGTcount: A:0.72, C:0.17, G:0.11, T:0.00
Consensus pattern (6 bp):
AAAACG
Found at i:11331 original size:178 final size:178
Alignment explanation
Indices: 11019--11356 Score: 459
Period size: 178 Copynumber: 1.9 Consensus size: 178
11009 TTCCACCATA
* * * * *
11019 AGCACAAATTATGTAATATTAACTAGACCGTCTATTTCCTTTAACTGAAACAACTAATTCTTTGG
1 AGCACAAATTATATAATATTAACTAGACCGTCTATTACCGTTAACCGAAACAACAAATTCTTTGG
* *
11084 AAGCAATTTTTATATCTCGAACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAGATCAT
66 AAACAATTTTTATATCTCGAACATTAAATTTAGTTTTCGAGCCATTCATGAAAGTTGTAGATCAT
*
11149 GGAACAACCTTTCAAGAGACACTTGAATCATCTCAATTACACATCTGG
131 GGAACAACCTTTCAAGAGACACTTAAATCATCTCAATTACACATCTGG
* * *
11197 AGCA-AAAGTTATATAATATTAAGTGGACTGTCTATTACCGTTAACCGAAACAACAAATT-TTTC
1 AGCACAAA-TTATATAATATTAACTAGACCGTCTATTACCGTTAACCGAAACAACAAATTCTTT-
* *
11260 GGAAAC-ATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCATTCATGAAAGTTGTAGA
64 GGAAACAATTTTT-ATATCTCG-AACATTAAATTTAGTTTTCGAGCCATTCATGAAAGTTGTAGA
* * * *
11323 TGATGGAACAATCTTTTAATAGACACTTAAATCA
127 TCATGGAACAACCTTTCAAGAGACACTTAAATCA
11357 CCTTAATCGG
Statistics
Matches: 139, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
177 15 0.11
178 124 0.89
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (178 bp):
AGCACAAATTATATAATATTAACTAGACCGTCTATTACCGTTAACCGAAACAACAAATTCTTTGG
AAACAATTTTTATATCTCGAACATTAAATTTAGTTTTCGAGCCATTCATGAAAGTTGTAGATCAT
GGAACAACCTTTCAAGAGACACTTAAATCATCTCAATTACACATCTGG
Found at i:11391 original size:178 final size:178
Alignment explanation
Indices: 11032--11401 Score: 424
Period size: 178 Copynumber: 2.1 Consensus size: 178
11022 ACAAATTATG
* * * * *
11032 TAATATTAACTAGACCGTCTATTTCCTTTAACTGAAACAACTAATTCTTTGGAAGCAATTTTTAT
1 TAATATTAACTAGACCGTCTATTACCGTTAACCGAAACAACAAATTCTTTGGAAACAATTTTTAT
*
11097 ATCTCGAACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAGATCATGGAACAACCTTTC
66 ATCTCGAACATTAAATTTAGTTTTCGAGCCATTCATGAAAGTTGTAGATCATGGAACAACCTTTC
* * * * * * *
11162 AAGAGACACTTGAATCATCTCAATTACACATCTGGAGCAAAAGTTATA
131 AAGAGACACTTAAATCACCTCAATCACACAACCGGAGCAAAAATAATA
* * *
11210 TAATATTAAGTGGACTGTCTATTACCGTTAACCGAAACAACAAATT-TTTCGGAAAC-ATTTTTG
1 TAATATTAACTAGACCGTCTATTACCGTTAACCGAAACAACAAATTCTTT-GGAAACAATTTTT-
* * * *
11273 ATA-CTTGAAACATTAAATTTAGTTTTCGAGTCATTCATGAAAGTTGTAGATGATGGAACAATCT
64 ATATCTCG-AACATTAAATTTAGTTTTCGAGCCATTCATGAAAGTTGTAGATCATGGAACAACCT
* * * ** *
11337 TTTAATAGACACTTAAATCACCTTAATCGGATAACCGGAG-AGAAAATAATA
128 TTCAAGAGACACTTAAATCACCTCAATCACACAACCGGAGCA-AAAATAATA
* *
11388 TAATGTTAAATAGA
1 TAATATTAACTAGA
11402 TGATTTAGTC
Statistics
Matches: 159, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
177 13 0.08
178 146 0.92
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (178 bp):
TAATATTAACTAGACCGTCTATTACCGTTAACCGAAACAACAAATTCTTTGGAAACAATTTTTAT
ATCTCGAACATTAAATTTAGTTTTCGAGCCATTCATGAAAGTTGTAGATCATGGAACAACCTTTC
AAGAGACACTTAAATCACCTCAATCACACAACCGGAGCAAAAATAATA
Found at i:16300 original size:17 final size:17
Alignment explanation
Indices: 16278--16313 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
16268 CCGAATTTAG
16278 TAAATAATTATTATAAT
1 TAAATAATTATTATAAT
*
16295 TAAATAATTATTATTAT
1 TAAATAATTATTATAAT
16312 TA
1 TA
16314 TCAAGTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATAATTATTATAAT
Found at i:18516 original size:58 final size:58
Alignment explanation
Indices: 18428--18550 Score: 158
Period size: 58 Copynumber: 2.1 Consensus size: 58
18418 TTTTTTGAAC
* * * *
18428 GAATTATAAAGATTTTCTATAGTATCAGTAAAATAAAGATTTTAA-ATTATTTTTCTAT
1 GAATTATAAAGATTTTATATAATATCAGTAAAATAAAGA-TTTAATAATACTTTTCTAT
* * *
18486 GAATTATAAGGATTTTATGTAATATGAGTAAAATAAAGATTTAATAATACTTTTCTAT
1 GAATTATAAAGATTTTATATAATATCAGTAAAATAAAGATTTAATAATACTTTTCTAT
*
18544 AAATTAT
1 GAATTAT
18551 TTTCCAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
57 5 0.09
58 51 0.91
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (58 bp):
GAATTATAAAGATTTTATATAATATCAGTAAAATAAAGATTTAATAATACTTTTCTAT
Found at i:19701 original size:51 final size:52
Alignment explanation
Indices: 19608--19706 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 52
19598 TAATTTTAGG
* * *
19608 AAAAAGAAGTTAAATACAACTATATAAATTCAACTTAATTAAAACACTACTC
1 AAAAAGAACTTAAATACAACCATATAAATTCAACTGAATTAAAACACTACTC
* * **
19660 AAAAA-AACTTAAATACAACCATCTAAGTTCAACTGGCTTAAAACACT
1 AAAAAGAACTTAAATACAACCATATAAATTCAACTGAATTAAAACACT
19707 CTTTTTTCTC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
51 35 0.88
52 5 0.12
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (52 bp):
AAAAAGAACTTAAATACAACCATATAAATTCAACTGAATTAAAACACTACTC
Found at i:25221 original size:13 final size:13
Alignment explanation
Indices: 25205--25239 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
25195 GTGCATCTTA
25205 TCATAGCATCATG
1 TCATAGCATCATG
25218 TCATAGCATCATG
1 TCATAGCATCATG
25231 TCATAGCAT
1 TCATAGCAT
25240 ACTTGTACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (13 bp):
TCATAGCATCATG
Done.