Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008515.1 Corchorus capsularis cultivar CVL-1 contig08536, 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: 35721
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:2060 original size:18 final size:17
Alignment explanation
Indices: 2025--2062 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2015 GCAGGTTACT
2025 AAAGACTAAGTAAAGAG
1 AAAGACTAAGTAAAGAG
2042 AAAGAC-AAGTCAGAAGAG
1 AAAGACTAAGT-A-AAGAG
2060 AAA
1 AAA
2063 AACCAACCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.21
17 7 0.37
18 8 0.42
ACGTcount: A:0.61, C:0.08, G:0.24, T:0.08
Consensus pattern (17 bp):
AAAGACTAAGTAAAGAG
Found at i:8690 original size:29 final size:29
Alignment explanation
Indices: 8615--8690 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
8605 CAAGTAACTT
8615 GAAAAATAAAAAG-TAAAGAAAAATTAAC
1 GAAAAATAAAAAGATAAAGAAAAATTAAC
* *
8643 -TAAACTAAAAATTGA-AAAGAAAAA-TAAC
1 GAAAAATAAAAA--GATAAAGAAAAATTAAC
8671 GAAAAATATAAAAGATAAAG
1 GAAAAATA-AAAAGATAAAG
8691 GTAAGAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
27 9 0.24
28 6 0.16
29 19 0.50
30 4 0.11
ACGTcount: A:0.70, C:0.04, G:0.11, T:0.16
Consensus pattern (29 bp):
GAAAAATAAAAAGATAAAGAAAAATTAAC
Found at i:19572 original size:15 final size:15
Alignment explanation
Indices: 19549--19578 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19539 TGATGTTTAC
19549 TTTGACGAAATCTTT
1 TTTGACGAAATCTTT
*
19564 TTTGGCGAAATCTTT
1 TTTGACGAAATCTTT
19579 AAAGCATGTG
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:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (15 bp):
TTTGACGAAATCTTT
Found at i:21207 original size:2 final size:2
Alignment explanation
Indices: 21202--21244 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
21192 TATATATATA
21202 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
21244 T
1 T
21245 ATTGACAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:22332 original size:50 final size:50
Alignment explanation
Indices: 22221--22365 Score: 231
Period size: 49 Copynumber: 2.9 Consensus size: 50
22211 CGTTTGTAAG
* *
22221 TTTCCGTTTTTAAATCCGTTTCTGACTTAAAGAAAT-AAAAAAAATTTCT
1 TTTCCGCTTTTAAATCCGTTTCTGACTTAAAGAAATAAAAAAAAAATTCT
* *
22270 TTTCCGCTTTTAAATCTGTTCCTGACTTAAAGAAATAAAAAAAAAATTCT
1 TTTCCGCTTTTAAATCCGTTTCTGACTTAAAGAAATAAAAAAAAAATTCT
22320 TTTCCGCTTTTAAATCCGTTTCTGA-TTAAAGAAATATAAAAAAAAA
1 TTTCCGCTTTTAAATCCGTTTCTGACTTAAAGAAATA-AAAAAAAAA
22366 AGTATTTTTC
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
49 44 0.50
50 44 0.50
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.37
Consensus pattern (50 bp):
TTTCCGCTTTTAAATCCGTTTCTGACTTAAAGAAATAAAAAAAAAATTCT
Found at i:27065 original size:2 final size:2
Alignment explanation
Indices: 27050--27088 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
27040 CTTTTGATTG
*
27050 TA TA TA -A TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27089 ATGTATAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:27233 original size:6 final size:6
Alignment explanation
Indices: 27212--27265 Score: 72
Period size: 6 Copynumber: 8.7 Consensus size: 6
27202 AAAAAGGCAA
* *
27212 ATTTAT ATCATTAT ATTTAT ATTTAT ATTTAT ATTTAT GTTTAT GTTTAT
1 ATTTAT AT--TTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
27262 ATTT
1 ATTT
27266 TTATAAATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 38 0.86
8 6 0.14
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (6 bp):
ATTTAT
Found at i:28251 original size:2 final size:2
Alignment explanation
Indices: 28244--28268 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28234 GCAAACAACC
28244 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28269 CTTTATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31900 original size:27 final size:27
Alignment explanation
Indices: 31848--31900 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
31838 CGACAATGAT
* *
31848 GATGATGATTGTGATGACAATGAGGAA
1 GATGATGATGGTGATGACAATAAGGAA
*
31875 GATGATGATGGTGATGACTATAAGGA
1 GATGATGATGGTGATGACAATAAGGA
31901 TGATTTTCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.34, T:0.26
Consensus pattern (27 bp):
GATGATGATGGTGATGACAATAAGGAA
Found at i:32821 original size:45 final size:45
Alignment explanation
Indices: 32770--32872 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
32760 AGGCAGCCTC
* * * *
32770 TTATTTTGTATA-TGTC-CTTAAATTGCCATTATCTAGAGGAGGCAT
1 TTATTTTGTATAGT-TCAC-TAAATTGCAATGATCTAGAAGAAGCAT
* *
32815 TTATTTTGTATAGTTCACTAACTTGCAATGATCTAGAAGAAGCCT
1 TTATTTTGTATAGTTCACTAAATTGCAATGATCTAGAAGAAGCAT
32860 TTATTTTGTATAG
1 TTATTTTGTATAG
32873 GTCAGGTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
45 48 0.96
46 2 0.04
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.43
Consensus pattern (45 bp):
TTATTTTGTATAGTTCACTAAATTGCAATGATCTAGAAGAAGCAT
Found at i:33063 original size:6 final size:6
Alignment explanation
Indices: 33052--33083 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
33042 CTTTTATTTT
33052 AATATA AATATA AATATA AATATA AAT-TA AAT
1 AATATA AATATA AATATA AATATA AATATA AAT
33084 GTATTATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Done.