Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020139.1 Corchorus olitorius cultivar O-4 contig20172, 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: 15854
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Found at i:1844 original size:47 final size:47
Alignment explanation
Indices: 1780--2121 Score: 535
Period size: 47 Copynumber: 7.3 Consensus size: 47
1770 AACCTCTTCT
*
1780 TTAGTTTAATCACCTAGAATTAAACTAATCT-TTCCTTCTTCTT-CTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTT-CTTCTT-TTACTAC
* * * * *
1827 TTAGTTTAATTATCTAGACTCAAACCAATCTCTTCTCCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
1874 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
*
1921 TTAGTTTAATTACCTAGCATTAAACTTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAAC-TAATCTCTTCTTCTTTTACTAC
* *
1969 TTAGTTTAATTGCCTAGAATTAAACTAATCTCTTCTCCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
2016 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
* *
2063 TTAGTTTAATTAACTAGAATTAAACTAATCTCTTCCTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
*
2110 TTAGTCTAATTA
1 TTAGTTTAATTA
2122 AACTTAATCT
Statistics
Matches: 272, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
46 2 0.01
47 223 0.82
48 47 0.17
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.46
Consensus pattern (47 bp):
TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
Found at i:2105 original size:189 final size:189
Alignment explanation
Indices: 1780--2121 Score: 553
Period size: 189 Copynumber: 1.8 Consensus size: 189
1770 AACCTCTTCT
* *
1780 TTAGTTTAATCACCTAGAATTAAACTAATCTTTCCTTCTTCTTCTACTTAGTTTAATTATCTAGA
1 TTAGTTTAATCACCTAGAATTAAACTAATCTTTCCTCCTTCTTCTACTTAGTTTAATTACCTAGA
* * *
1845 CTCAAACCAATCTCTTCTCCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTCTTCT
66 ATCAAACCAATCTCTTCTCCTTTTACTACTTAGTTTAATTAACTAGAATTAAACTAATCTCTTCC
*
1910 TCTTTTACTACTTAGTTTAATTACCTAGCATTAAACTTAATCTCTTCTTCTTTTACTAC
131 TCTTTTACTACTTAGTCTAATTACCTAGCATTAAACTTAATCTCTTCTTCTTTTACTAC
**
1969 TTAGTTTAATTGCCTAGAATTAAACTAATCTCTT-CTCCTT-TTACTACTTAGTTTAATTACCTA
1 TTAGTTTAATCACCTAGAATTAAACTAATCT-TTCCTCCTTCTT-CTACTTAGTTTAATTACCTA
* * *
2032 GAATTAAACTAATCTCTTCTTCTTTTACTACTTAGTTTAATTAACTAGAATTAAACTAATCTCTT
64 GAATCAAACCAATCTCTTCTCCTTTTACTACTTAGTTTAATTAACTAGAATTAAACTAATCTCTT
2097 CCTCTTTTACTACTTAGTCTAATTA
129 CCTCTTTTACTACTTAGTCTAATTA
2122 AACTTAATCT
Statistics
Matches: 140, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
188 2 0.01
189 136 0.97
190 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.46
Consensus pattern (189 bp):
TTAGTTTAATCACCTAGAATTAAACTAATCTTTCCTCCTTCTTCTACTTAGTTTAATTACCTAGA
ATCAAACCAATCTCTTCTCCTTTTACTACTTAGTTTAATTAACTAGAATTAAACTAATCTCTTCC
TCTTTTACTACTTAGTCTAATTACCTAGCATTAAACTTAATCTCTTCTTCTTTTACTAC
Found at i:2134 original size:38 final size:37
Alignment explanation
Indices: 2080--2151 Score: 126
Period size: 38 Copynumber: 1.9 Consensus size: 37
2070 AATTAACTAG
2080 AATTAAACTAATCTCTTCCTCTTTTACTACTTAGTCT
1 AATTAAACTAATCTCTTCCTCTTTTACTACTTAGTCT
*
2117 AATTAAACTTAATCTCTTCTTCTTTTACTACTTAG
1 AATTAAAC-TAATCTCTTCCTCTTTTACTACTTAG
2152 GAGGCGTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 8 0.24
38 25 0.76
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.47
Consensus pattern (37 bp):
AATTAAACTAATCTCTTCCTCTTTTACTACTTAGTCT
Found at i:2232 original size:17 final size:16
Alignment explanation
Indices: 2179--2228 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
2169 TCACCCCCCC
* *
2179 GATCACTAGCGATCTAA
1 GATCACCAGTGATC-AA
2196 GATCACCAGTGATGCAA
1 GATCACCAGTGAT-CAA
*
2213 GATCACCGGTGATCAA
1 GATCACCAGTGATCAA
2229 AGATTACATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (16 bp):
GATCACCAGTGATCAA
Found at i:2557 original size:94 final size:94
Alignment explanation
Indices: 2396--2678 Score: 487
Period size: 94 Copynumber: 3.0 Consensus size: 94
2386 AAACGGCCTT
2396 TTAGTTTAATTACCTAGAATTAAA-TCAATCTCTTCTTCTTTTACTACTTAGTTTAATTACCTAG
1 TTAGTTTAATTACCTAGAATTAAACT-AATCTCTTCTTCTTTTACTACTTAGTTTAATTACCTAG
2460 AATTAAACTAATCTCCTCCTCTTTTACTAC
65 AATTAAACTAATCTCCTCCTCTTTTACTAC
* *
2490 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCCTTTACTACTTAGTTTAATTACTTAGA
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGA
*
2555 ATTAAACTAATCTCCTCCTCTTTTAATAC
66 ATTAAACTAATCTCCTCCTCTTTTACTAC
* * *
2584 TTAGTCTAATTACCTAGGATGAAACTAATCTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGA
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGA
*
2649 ATTAAACTAATCTCCTCCTCTTTTTCTAC
66 ATTAAACTAATCTCCTCCTCTTTTACTAC
2678 T
1 T
2679 CATTTTAAAA
Statistics
Matches: 178, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
94 177 0.99
95 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (94 bp):
TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTACTTAGTTTAATTACCTAGA
ATTAAACTAATCTCCTCCTCTTTTACTAC
Found at i:2686 original size:47 final size:47
Alignment explanation
Indices: 2396--2678 Score: 433
Period size: 47 Copynumber: 6.0 Consensus size: 47
2386 AAACGGCCTT
* *
2396 TTAGTTTAATTACCTAGAATTAAA-TCAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACT-AATCTCCTCCTCTTTTACTAC
2443 TTAGTTTAATTACCTAGAATTAAACTAATCTCCTCCTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCCTCCTCTTTTACTAC
* * *
2490 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCCTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCCTCCTCTTTTACTAC
* *
2537 TTAGTTTAATTACTTAGAATTAAACTAATCTCCTCCTCTTTTAATAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCCTCCTCTTTTACTAC
* * * * *
2584 TTAGTCTAATTACCTAGGATGAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCCTCCTCTTTTACTAC
*
2631 TTAGTTTAATTACCTAGAATTAAACTAATCTCCTCCTCTTTTTCTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCCTCCTCTTTTACTAC
2678 T
1 T
2679 CATTTTAAAA
Statistics
Matches: 212, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
47 211 1.00
48 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (47 bp):
TTAGTTTAATTACCTAGAATTAAACTAATCTCCTCCTCTTTTACTAC
Found at i:5922 original size:16 final size:17
Alignment explanation
Indices: 5883--5925 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
5873 TTTTGGGTAT
*
5883 CCGAACCCGAAAATGAG
1 CCGAACCCGAAAATGAC
*
5900 CCAAACCC-AAAATGAC
1 CCGAACCCGAAAATGAC
5916 CCGAACCCGA
1 CCGAACCCGA
5926 TCAACTCGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.42, C:0.37, G:0.16, T:0.05
Consensus pattern (17 bp):
CCGAACCCGAAAATGAC
Found at i:7469 original size:15 final size:15
Alignment explanation
Indices: 7415--7471 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
7405 TCCGAATCGT
*
7415 ATGACCCGAAACCGAAA
1 ATGACCCG-AACC-CAA
*
7432 ACGACCC-AACCCAGA
1 ATGACCCGAACCCA-A
7447 ATTGACCCGAACCCAA
1 A-TGACCCGAACCCAA
7463 ATGACCCGA
1 ATGACCCGA
7472 CATTTGAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 14 0.41
16 7 0.21
17 12 0.35
ACGTcount: A:0.40, C:0.37, G:0.16, T:0.07
Consensus pattern (15 bp):
ATGACCCGAACCCAA
Found at i:8522 original size:25 final size:25
Alignment explanation
Indices: 8488--8536 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
8478 TAGTTGATTA
8488 AATTAGATTTGAGCTACATGAATGG
1 AATTAGATTTGAGCTACATGAATGG
8513 AATTAGATTTGAGCTACATGAATG
1 AATTAGATTTGAGCTACATGAATG
8537 CAAAATACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (25 bp):
AATTAGATTTGAGCTACATGAATGG
Done.