Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022656.1 Corchorus olitorius cultivar O-4 contig22689, 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: 35817
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4755 original size:76 final size:76
Alignment explanation
Indices: 4618--4769 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
4608 ACAAGGACCC
* * * *
4618 CGACTCTACCTGGGTTCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
4683 GGGCAGTGTCA
66 GGGCAGTGTCA
* * **
4694 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGTGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
4756 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
4770 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.26
Consensus pattern (76 bp):
CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:8227 original size:17 final size:17
Alignment explanation
Indices: 8207--8249 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
8197 TTTAGTTGAC
8207 ATTATATATTAGTATAG
1 ATTATATATTAGTATAG
*
8224 ATTATATATTAGTATAT
1 ATTATATATTAGTATAG
8241 ATTACTATA
1 ATTA-TATA
8250 GACTAGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (17 bp):
ATTATATATTAGTATAG
Found at i:10181 original size:42 final size:42
Alignment explanation
Indices: 10126--10208 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
10116 TAAATTCTAG
* * *
10126 TACTCCATCTCTAGGTAATTCCTCAAAATAAAGCTAATATTC
1 TACTCCATCTCTAGATAATTCATCAAAACAAAGCTAATATTC
* *
10168 TACTTCATCTCTAGATAATTCATCAAAACAAATCTAATATT
1 TACTCCATCTCTAGATAATTCATCAAAACAAAGCTAATATT
10209 TATTGTTGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.35
Consensus pattern (42 bp):
TACTCCATCTCTAGATAATTCATCAAAACAAAGCTAATATTC
Found at i:11164 original size:2 final size:2
Alignment explanation
Indices: 11151--11183 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
11141 ATTAAAAATA
11151 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
11184 TAGGGAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13370 original size:11 final size:10
Alignment explanation
Indices: 13353--13397 Score: 54
Period size: 11 Copynumber: 4.2 Consensus size: 10
13343 TATATAAATC
13353 ATATATCTAT
1 ATATATCTAT
13363 ATATTATCTAT
1 ATA-TATCTAT
13374 ACTATATCTAT
1 A-TATATCTAT
*
13385 ATCTATACTAT
1 ATATAT-CTAT
13396 AT
1 AT
13398 TAAAAAGTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
10 7 0.23
11 22 0.71
12 2 0.06
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (10 bp):
ATATATCTAT
Found at i:13374 original size:17 final size:17
Alignment explanation
Indices: 13341--13397 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
13331 ATAAAATTAA
*
13341 TATATATAAATCATATATC
1 TATATATATATC-TATA-C
13360 TATATAT-TATCTATAC
1 TATATATATATCTATAC
*
13376 TATATCTATATCTATAC
1 TATATATATATCTATAC
13393 TATAT
1 TATAT
13398 TAAAAAGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 7 0.20
17 18 0.51
18 3 0.09
19 7 0.20
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATATATATCTATAC
Found at i:16401 original size:19 final size:18
Alignment explanation
Indices: 16368--16403 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16358 TTGAAATAGA
16368 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
16386 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
16404 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:22308 original size:19 final size:18
Alignment explanation
Indices: 22275--22310 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
22265 TTGAAATAGA
22275 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
22293 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
22311 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:27707 original size:21 final size:21
Alignment explanation
Indices: 27683--27735 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
27673 TCTGTGCCTT
*
27683 CCTCTGCGCCATCCGCGCTAC
1 CCTCCGCGCCATCCGCGCTAC
27704 CCTCCGCGCCATCCGCGCTAC
1 CCTCCGCGCCATCCGCGCTAC
27725 CCTCCGCGCCA
1 CCTCCGCGCCA
27736 CATGCCCGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.09, C:0.57, G:0.19, T:0.15
Consensus pattern (21 bp):
CCTCCGCGCCATCCGCGCTAC
Found at i:27711 original size:12 final size:12
Alignment explanation
Indices: 27694--27733 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
27684 CTCTGCGCCA
27694 TCCGCGCTACCC
1 TCCGCGCTACCC
*
27706 TCCGCG---CCA
1 TCCGCGCTACCC
27715 TCCGCGCTACCC
1 TCCGCGCTACCC
27727 TCCGCGC
1 TCCGCGC
27734 CACATGCCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
9 8 0.35
12 15 0.65
ACGTcount: A:0.07, C:0.57, G:0.20, T:0.15
Consensus pattern (12 bp):
TCCGCGCTACCC
Found at i:31538 original size:10 final size:10
Alignment explanation
Indices: 31523--31549 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
31513 TTTAGAAATA
31523 TATCTATATC
1 TATCTATATC
31533 TATCTATATC
1 TATCTATATC
31543 TATCTAT
1 TATCTAT
31550 CTATACTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.52
Consensus pattern (10 bp):
TATCTATATC
Found at i:31548 original size:14 final size:13
Alignment explanation
Indices: 31529--31558 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
31519 AATATATCTA
31529 TATCTATCTATATC
1 TATCTATCTATA-C
31543 TATCTATCTATAC
1 TATCTATCTATAC
31556 TAT
1 TAT
31559 ATATAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (13 bp):
TATCTATCTATAC
Found at i:31835 original size:26 final size:26
Alignment explanation
Indices: 31797--31850 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
31787 GTTATAAAAA
31797 TATTTTATGTAGAAAAATTCAATTTT
1 TATTTTATGTAGAAAAATTCAATTTT
*
31823 TATTTTATTTAGAAAAATTCAATTTT
1 TATTTTATGTAGAAAAATTCAATTTT
31849 TA
1 TA
31851 CAGTACCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.52
Consensus pattern (26 bp):
TATTTTATGTAGAAAAATTCAATTTT
Found at i:35307 original size:2 final size:2
Alignment explanation
Indices: 35300--35338 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
35290 TCCGATTTAT
35300 TA TA 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 TA TA T
35339 CTAAAAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.