Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024898.1 Corchorus olitorius cultivar O-4 contig24931, 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: 14279
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:528 original size:205 final size:202
Alignment explanation
Indices: 187--574 Score: 722
Period size: 205 Copynumber: 1.9 Consensus size: 202
177 GCTTAATAAC
187 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
252 GATACAACACATTATTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
317 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
382 CGATTTA
196 CGATTTA
*
389 TTTATCCATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
454 GATACAAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGG
66 GATAC-AACACATTACTATTATATATAT--AACTATACCAAAAAAAAGTAGTTGAACATTAGTGG
519 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAG
128 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAG
575 TTTAGACTTA
Statistics
Matches: 180, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
202 69 0.38
203 21 0.12
205 90 0.50
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (202 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
CGATTTA
Found at i:3468 original size:36 final size:36
Alignment explanation
Indices: 3406--3509 Score: 138
Period size: 36 Copynumber: 2.8 Consensus size: 36
3396 CCAAGCTTGG
*
3406 CCTAGGCGC-TGGGCCATGCGCTGGCCCATGCGCCTGA
1 CCTAGGCGCTTGGGCC--GCGCTGGCCCACGCGCCTGA
* *
3443 CCTAGGCGCTTGGGCCGCGCTGGCCCGCGCGCCTGG
1 CCTAGGCGCTTGGGCCGCGCTGGCCCACGCGCCTGA
*
3479 CCTAGGCGCTTGGGCCGCGCTTGCCCGACGC
1 CCTAGGCGCTTGGGCCGCGCTGGCCC-ACGC
3510 CTGGCCTAGC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
36 42 0.70
37 12 0.20
38 6 0.10
ACGTcount: A:0.07, C:0.40, G:0.38, T:0.15
Consensus pattern (36 bp):
CCTAGGCGCTTGGGCCGCGCTGGCCCACGCGCCTGA
Found at i:6132 original size:86 final size:86
Alignment explanation
Indices: 5997--6238 Score: 403
Period size: 86 Copynumber: 2.8 Consensus size: 86
5987 TAAAAAAATG
* *
5997 ATGTTTTACTCATGTCATGAATTTATATAACAATTATGTACTAAGTCAAATCTTCAATCTTTAAG
1 ATGTCTTACTCATGTCATGAATTCATATAACAATTATGTACTAAGTCAAATCTTCAATCTTTAAG
6062 AAAAAGTTATCGGTTAAAAAA
66 AAAAAGTTATCGGTTAAAAAA
*
6083 ATGTCTTACTCATGTCATTAATTCATATAACAATTATGTACTAAGTCAAATCTTCAATCTTTAAG
1 ATGTCTTACTCATGTCATGAATTCATATAACAATTATGTACTAAGTCAAATCTTCAATCTTTAAG
6148 AAAAAGTTATCGGTTAAAAAA
66 AAAAAGTTATCGGTTAAAAAA
* * * * *
6169 ATGTCTTACTCATATCATGAATTCATATAACAATTACGTATTAAGTCAAATCTCCTAATTTTTAA
1 ATGTCTTACTCATGTCATGAATTCATATAACAATTATGTACTAAGTCAAATCTTC-AATCTTTAA
6234 GAAAA
65 GAAAA
6239 TCCAAGCACA
Statistics
Matches: 146, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
86 133 0.91
87 13 0.09
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (86 bp):
ATGTCTTACTCATGTCATGAATTCATATAACAATTATGTACTAAGTCAAATCTTCAATCTTTAAG
AAAAAGTTATCGGTTAAAAAA
Found at i:6320 original size:14 final size:15
Alignment explanation
Indices: 6293--6325 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
6283 TGACTGAAAA
6293 TAATATTAATTAAAT
1 TAATATTAATTAAAT
*
6308 TAATATTCA-TAAAT
1 TAATATTAATTAAAT
6322 TAAT
1 TAAT
6326 TCTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATTAATTAAAT
Found at i:6766 original size:2 final size:2
Alignment explanation
Indices: 6759--6784 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6749 AGATAGTAAG
6759 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
6785 TACTATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10051 original size:21 final size:21
Alignment explanation
Indices: 10027--10093 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
10017 AATTCTCTGT
10027 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
10048 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
10069 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
10090 AAAT
1 AAAT
10094 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:10073 original size:42 final size:42
Alignment explanation
Indices: 10014--10094 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
10004 ACTAAGTCTT
10014 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
10056 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
10095 CTGATCCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:10752 original size:34 final size:34
Alignment explanation
Indices: 10709--10773 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
10699 GTAGTAAAAG
10709 TGGTGATCTTGGGTGGCGATCTCAGATCACCTGT
1 TGGTGATCTTGGGTGGCGATCTCAGATCACCTGT
*
10743 TGGTGATCTTGGGTGGTGATCTCAGATCACC
1 TGGTGATCTTGGGTGGCGATCTCAGATCACC
10774 CCGTTTGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.15, C:0.20, G:0.32, T:0.32
Consensus pattern (34 bp):
TGGTGATCTTGGGTGGCGATCTCAGATCACCTGT
Found at i:10889 original size:17 final size:16
Alignment explanation
Indices: 10867--10924 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 16
10857 CTAAACCCAG
10867 GTGATCTAAGATCACCA
1 GTGATCT-AGATCACCA
* *
10884 GTGATCTTGCATTACCA
1 GTGATCTAG-ATCACCA
10901 GTGATCTTAGATCACCA
1 GTGATC-TAGATCACCA
10918 GTGATCT
1 GTGATCT
10925 GGGGGGTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 2 0.06
17 31 0.89
18 2 0.06
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (16 bp):
GTGATCTAGATCACCA
Done.