Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013512.1 Corchorus capsularis cultivar CVL-1 contig13533, 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: 12023
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Found at i:2004 original size:13 final size:13
Alignment explanation
Indices: 1986--2011 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1976 ACTCACCCTT
1986 CCACAGCTCATCA
1 CCACAGCTCATCA
1999 CCACAGCTCATCA
1 CCACAGCTCATCA
2012 TCCGCTCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.46, G:0.08, T:0.15
Consensus pattern (13 bp):
CCACAGCTCATCA
Found at i:3577 original size:40 final size:41
Alignment explanation
Indices: 3409--3593 Score: 282
Period size: 41 Copynumber: 4.5 Consensus size: 41
3399 AAGTAAAGTC
* *
3409 TTAATCCAGGGCGATTAAGAAGGTCAAACATAGTTAAGGTT
1 TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
* *
3450 TTAATCCAGGGCGATCATGAAAGTCAAACACAGTTAAGGTT
1 TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
3491 TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
1 TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
*** *
3532 TTAATCCAGGGCGATTAAGAAAGTC-AATTTAGTTAAAGTT
1 TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
*
3572 TTAATCCAGGGTGATTAAGAAA
1 TTAATCCAGGGCGATTAAGAAA
3594 AGAGCAGTTA
Statistics
Matches: 133, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
40 32 0.24
41 101 0.76
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (41 bp):
TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
Found at i:3661 original size:36 final size:38
Alignment explanation
Indices: 3572--3668 Score: 101
Period size: 36 Copynumber: 2.6 Consensus size: 38
3562 AGTTAAAGTT
* * * *
3572 TTAATCCAGGGTGATTAAGAAAAGAGCAGTTAAAGAAC
1 TTAATTCAGGGTAATTAAGTAAAGAGCAGTCAAAGAAC
* ** *
3610 TT-ACTCTTGGAAATTAAGTAAA-AGCAGTCAAAG-AC
1 TTAATTCAGGGTAATTAAGTAAAGAGCAGTCAAAGAAC
3645 TTAATTCAGGGTAATTAAGTAAAG
1 TTAATTCAGGGTAATTAAGTAAAG
3669 TAAGCACAGA
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
35 4 0.09
36 26 0.58
37 13 0.29
38 2 0.04
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (38 bp):
TTAATTCAGGGTAATTAAGTAAAGAGCAGTCAAAGAAC
Found at i:3721 original size:76 final size:76
Alignment explanation
Indices: 3641--4181 Score: 967
Period size: 76 Copynumber: 7.1 Consensus size: 76
3631 AAGCAGTCAA
3641 AGACTTAATTCAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTA
1 AGACTTAATTCAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTA
3706 AAGACAAGCAT
66 AAGACAAGCAT
* *
3717 AGACTTAATTTAGGGTAATTAAGTAAAGTAAGCACCGACTTAATTTCAAGGAAGGAAATTAGGTA
1 AGACTTAATTCAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTA
3782 AAGACAAGCAT
66 AAGACAAGCAT
*
3793 AGACTTAATTCAGGGTAATTAAGTAAAGTAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTA
1 AGACTTAATTCAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTA
3858 AAGACAAGCAT
66 AAGACAAGCAT
* *
3869 AGACTTAATTCGGGGTAATTAAGTAAAGTAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTA
1 AGACTTAATTCAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTA
3934 AAGACAAGCAT
66 AAGACAAGCAT
*
3945 AGACTTAATTCGGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTA
1 AGACTTAATTCAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTA
*
4010 AAGACAAACAT
66 AAGACAAGCAT
* * *
4021 AGACTTAATTCAGGGTAATTAAGTAAAGTAGGCACGGACTTAATTTCAAGGAAGGAATTTAGGTA
1 AGACTTAATTCAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTA
4086 AAGACAAGCAT
66 AAGACAAGCAT
*
4097 AGACTTAATTCGGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTC-AGTGAAGGAAATTAGGT
1 AGACTTAATTCAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAG-GAAGGAAATTAGGT
4161 AAAGACAAGCAT
65 AAAGACAAGCAT
4173 AGACTTAAT
1 AGACTTAAT
4182 ATCAAGGAAA
Statistics
Matches: 446, Mismatches: 18, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
75 2 0.00
76 444 1.00
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.25
Consensus pattern (76 bp):
AGACTTAATTCAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTA
AAGACAAGCAT
Found at i:4306 original size:36 final size:36
Alignment explanation
Indices: 4230--4328 Score: 105
Period size: 36 Copynumber: 2.8 Consensus size: 36
4220 AATTCAAGGT
* *
4230 AATTAAGT-AAATTAGCAAAGACTTAATTTCATAAG
1 AATTAAGTAAAATCAGCAAAGACTTAATTCCATAAG
*
4265 AATTAAGTAAAATCATCAAAGACTTAA-TCCA-AAG
1 AATTAAGTAAAATCAGCAAAGACTTAATTCCATAAG
* *
4299 ATGATTAAGTAAGATCAGACAAAAACTTAA
1 A--ATTAAGTAAAATCAG-CAAAGACTTAA
4329 CCTTCGGGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
34 4 0.07
35 11 0.20
36 29 0.54
37 10 0.19
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (36 bp):
AATTAAGTAAAATCAGCAAAGACTTAATTCCATAAG
Found at i:4391 original size:37 final size:37
Alignment explanation
Indices: 4338--4566 Score: 314
Period size: 37 Copynumber: 6.2 Consensus size: 37
4328 ACCTTCGGGG
* * *
4338 ATTAAGTAAAGAAAAGGACTTGGTTCCAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
* *
4375 ATTAAGTAGAGCAAAGGACTTGATTCCAAGGAAGGGT
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
* *
4412 ATTAAGTAGAGTAAAGAACTTGATTCCAAGGAAGGAA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
*
4449 ATTAAGTAGAGTAAGGGACTTGATTCCAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
* *
4486 ATTAAGTAGAGTAGAGGACTTGATTCCAAGAAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
* * * * * *
4523 ATTAACTAGAGTAGAGGAGTTAATTTCAAGGAAGGAA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
4560 ATTAAGT
1 ATTAAGT
4567 CAAGTCAGAG
Statistics
Matches: 171, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 171 1.00
ACGTcount: A:0.41, C:0.08, G:0.28, T:0.22
Consensus pattern (37 bp):
ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
Found at i:4666 original size:36 final size:36
Alignment explanation
Indices: 4575--4728 Score: 220
Period size: 36 Copynumber: 4.2 Consensus size: 36
4565 GTCAAGTCAG
*
4575 AGGCTTAATTCGGGGTAATTAAGTAGCGTCAATAAA
1 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
* *
4611 GGGACTTTATTCAGGGTAATTAAGTAGCGTCAATAAA
1 AGG-CTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
**
4648 AGGCTTAATTCAGGGTAATTAAGTAATGTCAATAAA
1 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
* *
4684 AGGCTTAATTCAGGGTAATTAAGTGGAGTCAAT-AA
1 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
4719 AGAGCTTAAT
1 AG-GCTTAAT
4729 CTAAGAAGAG
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
35 4 0.04
36 69 0.65
37 33 0.31
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (36 bp):
AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
Found at i:4728 original size:72 final size:73
Alignment explanation
Indices: 4575--4728 Score: 222
Period size: 73 Copynumber: 2.1 Consensus size: 73
4565 GTCAAGTCAG
* * * * *
4575 AGGCTTAATTCGGGGTAATTAAGTAGCGTCAATAAAGGGACTTTATTCAGGGTAATTAAGTAGCG
1 AGGCTTAATTCAGGGTAATTAAGTAACGTCAATAAAAGGACTTAATTCAGGGTAATTAAGTAGAG
4640 TCAATAAA
66 TCAATAAA
* *
4648 AGGCTTAATTCAGGGTAATTAAGTAATGTCAATAAAAGG-CTTAATTCAGGGTAATTAAGTGGAG
1 AGGCTTAATTCAGGGTAATTAAGTAACGTCAATAAAAGGACTTAATTCAGGGTAATTAAGTAGAG
4712 TCAAT-AA
66 TCAATAAA
4719 AGAGCTTAAT
1 AG-GCTTAAT
4729 CTAAGAAGAG
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
71 4 0.05
72 34 0.47
73 35 0.48
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (73 bp):
AGGCTTAATTCAGGGTAATTAAGTAACGTCAATAAAAGGACTTAATTCAGGGTAATTAAGTAGAG
TCAATAAA
Done.