Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006078.1 Corchorus capsularis cultivar CVL-1 contig06096, 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: 16130
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Found at i:8538 original size:17 final size:17
Alignment explanation
Indices: 8516--8575 Score: 93
Period size: 17 Copynumber: 3.5 Consensus size: 17
8506 TCATAGTATC
8516 AGGTAGCATGAGGTACT
1 AGGTAGCATGAGGTACT
*
8533 AGGTAGCATGAGGTACC
1 AGGTAGCATGAGGTACT
*
8550 AGGTAGCATGAGGCACT
1 AGGTAGCATGAGGTACT
*
8567 AGGCAGCAT
1 AGGTAGCAT
8576 CTGTTGTATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.30, C:0.17, G:0.35, T:0.18
Consensus pattern (17 bp):
AGGTAGCATGAGGTACT
Found at i:12870 original size:75 final size:75
Alignment explanation
Indices: 12646--12913 Score: 432
Period size: 75 Copynumber: 3.6 Consensus size: 75
12636 TTAATATTTT
* * *
12646 CTAAATCTCCCACAATCTGGCAAGATTTAGGGAAATATTCTCATTCTTTATTATT-TATTTATTT
1 CTAAATCTCCCACAATTTGGCAAGATTTA-GAAAATATTCTCA-ACTTTATTATTAT-TTTATTT
12710 CTTAAAATATCTC
63 CTTAAAATATCTC
* * * *
12723 ATAAATCTTCCACAATTTGGCAAGATTTAG-AAATATTCTCAACTTTATTATTAGTTTATTTCCT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
12787 AAAATATCTC
66 AAAATATCTC
12797 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
12862 AAAATATCTC
66 AAAATATCTC
12872 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCA
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCA
12914 TTATTAATTC
Statistics
Matches: 179, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
74 57 0.32
75 95 0.53
76 1 0.01
77 26 0.15
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (75 bp):
CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
AAAATATCTC
Found at i:12928 original size:75 final size:74
Alignment explanation
Indices: 12646--13003 Score: 402
Period size: 75 Copynumber: 4.6 Consensus size: 74
12636 TTAATATTTT
* * * *
12646 CTAAATCTCCCACAATCTGGCAAGATTTAGGGAAATATTCTCATTCTTTATTATTTATTTATTTC
1 CTAAATCTCCCACAATTTGGCAAGATTTA-GAAAATATTCTCATT-ATTATT-TATATTTATTTC
12711 TTAAAATATCTC
63 TTAAAATATCTC
* * *
12723 ATAAATCTTCCACAATTTGGCAAGATTTAG-AAATATTCTCAACTTTATTA-TTA-GTTTATTTC
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTC-A--TTATTATTTATATTTATTTC
*
12785 CTAAAATATCTC
63 TTAAAATATCTC
12797 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTA-TTAT-TTTATTTC
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTC-A--TTATTATTTATATTTATTTC
12860 TTAAAATATCTC
63 TTAAAATATCTC
12872 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTAATTCTATTTTTAATTTA
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATT-ATT-TA----T-ATTTA
12937 TTTGTTTTCTTAAAATATCTC
59 -----TTTCTTAAAATATCTC
* *
12958 CTAAACCTTCCACAATTTGGCAAGATTTAGAAAATATTCTCATTAT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTAT
13004 GAATTTTGTT
Statistics
Matches: 250, Mismatches: 12, Indels: 29
0.86 0.04 0.10
Matches are distributed among these distances:
72 5 0.02
73 1 0.00
74 49 0.20
75 96 0.38
76 3 0.01
77 29 0.12
78 2 0.01
79 1 0.00
81 4 0.02
86 60 0.24
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (74 bp):
CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATTTATATTTATTTCTTA
AAATATCTC
Found at i:12938 original size:86 final size:86
Alignment explanation
Indices: 12848--13008 Score: 279
Period size: 86 Copynumber: 1.9 Consensus size: 86
12838 AACTTTATTA
*
12848 TTATTT-TATTTCTTAAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCT
1 TTATTTGT-TTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCT
*
12912 CATTATTAATTCTATTTTTAAT
65 CATTATGAATTCTATTTTTAAT
*
12934 TTATTTGTTTTCTTAAAATATCTCCTAAACCTTCCACAATTTGGCAAGATTTAGAAAATATTCTC
1 TTATTTGTTTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCTC
12999 ATTATGAATT
66 ATTATGAATT
13009 TTGTTAATCC
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
86 70 0.99
87 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.45
Consensus pattern (86 bp):
TTATTTGTTTTCTTAAAATATCTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCTC
ATTATGAATTCTATTTTTAAT
Found at i:13047 original size:86 final size:86
Alignment explanation
Indices: 12856--13028 Score: 229
Period size: 86 Copynumber: 2.0 Consensus size: 86
12846 TATTATTTTA
* * *
12856 TTTCTTAAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTAA
1 TTTCTTAAAATAACTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATGAA
** * *
12921 TTCTATTTTTAATTTATTTGT
66 TTCTATTAATAATTTAATTAT
* *
12942 TTTCTTAAAATATCTCCTAAACCTTCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATGAA
1 TTTCTTAAAATAACTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATGAA
* * **
13007 TTTTGTTAATCCTTTAATTAT
66 TTCTATTAATAATTTAATTAT
13028 T
1 T
13029 ATTTTTACAT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (86 bp):
TTTCTTAAAATAACTCCTAAACCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATGAA
TTCTATTAATAATTTAATTAT
Found at i:15493 original size:6 final size:6
Alignment explanation
Indices: 15482--15511 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
15472 TCCAAATAGA
15482 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
15512 GCATGCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
ACAAAT
Done.