Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009833.1 Corchorus capsularis cultivar CVL-1 contig09854, 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: 28385
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--31 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1 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 T
32 GGAGGAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:617 original size:2 final size:2
Alignment explanation
Indices: 612--636 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
602 ATAAAAAAAA
612 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
637 AATGGGTTCT
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:1479 original size:2 final size:2
Alignment explanation
Indices: 1472--1503 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1462 CAGATAATAC
1472 AT AT AT 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 AT AT AT
1504 TTGGAACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8354 original size:21 final size:22
Alignment explanation
Indices: 8312--8355 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
8302 TCAGAGCGGC
*
8312 AGAAAAACCCTAAAACAGAAGCA
1 AGAAAAACCCT-AAACAAAAGCA
8335 AGAAAAACCCT-AACAAAAGCA
1 AGAAAAACCCTAAACAAAAGCA
8356 GATAAAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
23 11 0.55
ACGTcount: A:0.61, C:0.23, G:0.11, T:0.05
Consensus pattern (22 bp):
AGAAAAACCCTAAACAAAAGCA
Found at i:8362 original size:21 final size:21
Alignment explanation
Indices: 8310--8362 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
8300 CCTCAGAGCG
*
8310 GCAGAAAAACCCTAAAACAGAA
1 GCAGAAAAACCCT-AAACAAAA
8332 GCAAGAAAAACCCT-AACAAAA
1 GC-AGAAAAACCCTAAACAAAA
8353 GCAGATAAAA
1 GCAGA-AAAA
8363 GGGTCCTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.11
21 12 0.43
22 2 0.07
23 11 0.39
ACGTcount: A:0.60, C:0.21, G:0.13, T:0.06
Consensus pattern (21 bp):
GCAGAAAAACCCTAAACAAAA
Found at i:8628 original size:2 final size:2
Alignment explanation
Indices: 8623--8663 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
8613 AGAAAATAAT
* * *
8623 AG AG AG GG AG AG AG AG AG AG AG AG AA AG AG AA AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
8664 AGGACAACAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12758 original size:37 final size:37
Alignment explanation
Indices: 12685--12760 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
12675 ATATGGTTCT
*
12685 TATGTAGACTATAGTTACTCTTTTGGCGCTTATTAGC
1 TATGTAGACTATAGTTACTCTTTTGGCACTTATTAGC
* *
12722 TATGTAGACTATAGTTACTCTTTTGGCATTTGTTAGC
1 TATGTAGACTATAGTTACTCTTTTGGCACTTATTAGC
12759 TA
1 TA
12761 GATGTTTCCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (37 bp):
TATGTAGACTATAGTTACTCTTTTGGCACTTATTAGC
Found at i:13737 original size:2 final size:2
Alignment explanation
Indices: 13730--13763 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
13720 GCCAATTCAT
*
13730 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13764 AATCTTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:20931 original size:15 final size:15
Alignment explanation
Indices: 20911--20940 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20901 TATATTTACA
20911 TTATTAGAGCAATAT
1 TTATTAGAGCAATAT
20926 TTATTAGAGCAATAT
1 TTATTAGAGCAATAT
20941 CTTCATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
TTATTAGAGCAATAT
Found at i:26999 original size:3 final size:3
Alignment explanation
Indices: 26991--27028 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
26981 AAGCAGAGCC
* *
26991 TCA TCA TCA TCC TCA TCA TCA TCC TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
27029 GCTAAACACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.26, C:0.39, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:27006 original size:12 final size:12
Alignment explanation
Indices: 26989--27025 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
26979 GCAAGCAGAG
26989 CCTCATCATCAT
1 CCTCATCATCAT
27001 CCTCATCATCAT
1 CCTCATCATCAT
27013 CCTCATCATCAT
1 CCTCATCATCAT
27025 C
1 C
27026 ATCGCTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.24, C:0.43, G:0.00, T:0.32
Consensus pattern (12 bp):
CCTCATCATCAT
Found at i:28333 original size:1 final size:1
Alignment explanation
Indices: 28327--28360 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
28317 CATTTATCGT
*
28327 AAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28361 CACACACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28365 original size:2 final size:2
Alignment explanation
Indices: 28360--28385 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28350 AAAAACAAAA
28360 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.