Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023725.1 Corchorus olitorius cultivar O-4 contig23758, 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: 59905
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2255 original size:33 final size:33
Alignment explanation
Indices: 2218--2315 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
2208 AAAGCCCAAC
2218 TAGCGGCGTTTCTTGTACGGAAACGCCACTATA
1 TAGCGGCGTTTCTTGTACGGAAACGCCACTATA
*
2251 TAGCGGCGTTTCTTGTACGGAAACGCCACTAAA
1 TAGCGGCGTTTCTTGTACGGAAACGCCACTATA
* *
2284 TAGCGGCATTTCTTGTACGGAAACGCCGCTAT
1 TAGCGGCGTTTCTTGTACGGAAACGCCACTAT
2316 TCCTAAATCC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (33 bp):
TAGCGGCGTTTCTTGTACGGAAACGCCACTATA
Found at i:3210 original size:21 final size:21
Alignment explanation
Indices: 3172--3216 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3162 GGCGCCCACA
* *
3172 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGTCTGAACACCCAGG
*
3193 TGGTTTGTCTGATCACCCAGG
1 TGGTTTGTCTGAACACCCAGG
3214 TGG
1 TGG
3217 CCAATGTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (21 bp):
TGGTTTGTCTGAACACCCAGG
Found at i:4617 original size:14 final size:15
Alignment explanation
Indices: 4598--4627 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4588 AACTAGGAAA
4598 AATAAATAA-CAAGG
1 AATAAATAAGCAAGG
4612 AATAAATAAGCAAGG
1 AATAAATAAGCAAGG
4627 A
1 A
4628 TTGGATTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAAATAAGCAAGG
Found at i:8584 original size:7 final size:7
Alignment explanation
Indices: 8572--8619 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
8562 TAAGTTAGAT
8572 AAAATTA
1 AAAATTA
8579 AAAATTA
1 AAAATTA
*
8586 AGAATTA
1 AAAATTA
8593 AAAATTA
1 AAAATTA
* *
8600 AGAATTT
1 AAAATTA
8607 AAAATTA
1 AAAATTA
*
8614 AGAATT
1 AAAATT
8620 GGGTTGCCTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (7 bp):
AAAATTA
Found at i:8593 original size:14 final size:14
Alignment explanation
Indices: 8574--8619 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
8564 AGTTAGATAA
8574 AATTAAAAATTAAG
1 AATTAAAAATTAAG
8588 AATTAAAAATTAAG
1 AATTAAAAATTAAG
*
8602 AATTTAAAATTAAG
1 AATTAAAAATTAAG
8616 AATT
1 AATT
8620 GGGTTGCCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
AATTAAAAATTAAG
Found at i:19882 original size:15 final size:15
Alignment explanation
Indices: 19858--19887 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19848 TTACTAACCC
*
19858 TTAATTTTTCTTTCT
1 TTAATCTTTCTTTCT
19873 TTAATCTTTCTTTCT
1 TTAATCTTTCTTTCT
19888 CTTTTTAGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TTAATCTTTCTTTCT
Found at i:25359 original size:22 final size:21
Alignment explanation
Indices: 25331--25384 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
25321 AAAGTTCGTG
25331 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
25353 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
25372 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
25385 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:35846 original size:41 final size:41
Alignment explanation
Indices: 35760--35854 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
35750 AAATAAAATC
* * * *
35760 CTAAATCAGGGGCGAAATTGAATCAATAAATAAATATTACT
1 CTAAATCAGGGACGAAATTGAATCAATAAACAAATATAACA
*
35801 CTAAATCAGGGAC-AATATTGAATCAATTAACAAATGA-AACA
1 CTAAATCAGGGACGAA-ATTGAATCAATAAACAAAT-ATAACA
35842 CTAAATCAGGGAC
1 CTAAATCAGGGAC
35855 CCAAAAGAGC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 2 0.04
41 44 0.94
42 1 0.02
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (41 bp):
CTAAATCAGGGACGAAATTGAATCAATAAACAAATATAACA
Found at i:40134 original size:27 final size:27
Alignment explanation
Indices: 40104--40178 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
40094 TGGACTAAAG
*
40104 TGACCAAAATGCCCCTGGATGTGCAAA
1 TGACCAAAATGCCCCTAGATGTGCAAA
* * * **
40131 TGACCAAAACGCCCTTATACATGCAAA
1 TGACCAAAATGCCCCTAGATGTGCAAA
40158 TGACCAAAATGCCCCTAGATG
1 TGACCAAAATGCCCCTAGATG
40179 ATCCTAGTGC
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (27 bp):
TGACCAAAATGCCCCTAGATGTGCAAA
Found at i:42060 original size:12 final size:12
Alignment explanation
Indices: 42031--42064 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
42021 GAAGTTTGTC
*
42031 TTTGAAGACTCA
1 TTTGAAGACTTA
42043 -TTGAAGACTTA
1 TTTGAAGACTTA
42054 TTTGAAGACTT
1 TTTGAAGACTT
42065 GAAGATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTTA
Found at i:58844 original size:50 final size:53
Alignment explanation
Indices: 58744--58844 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 53
58734 ACACTAGTTT
*
58744 ATGTATAAACTAAACTAAGTCATATTTTATTGACACTAATCATGATAACACTAGC
1 ATGTATAAACTAAACTAAGTCATACTTTATTGACACTAATCA--ATAACACTAGC
*
58799 ATGTATAAACTAAACT-AGTCATACTTTATTGACA-TAGTC-ATAACAC
1 ATGTATAAACTAAACTAAGTCATACTTTATTGACACTAATCAATAACAC
58845 CGACAAACAC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
50 7 0.16
53 4 0.09
54 17 0.39
55 16 0.36
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.33
Consensus pattern (53 bp):
ATGTATAAACTAAACTAAGTCATACTTTATTGACACTAATCAATAACACTAGC
Found at i:59542 original size:42 final size:43
Alignment explanation
Indices: 59495--59580 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 43
59485 TTTTATCTTA
*
59495 ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAAC
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAC
59537 ATTCTACTGCTCCATCTCTAGATAATTCATCAAAATAAAGCTAA
1 ATTCTAC--CTCCATCTCTAGATAATTCATCAAAATAAAGCTAA
59581 TATTAATTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 6 0.15
45 34 0.85
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.31
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAC
Done.