Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007421.1 Corchorus capsularis cultivar CVL-1 contig07442, 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: 37858
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:6233 original size:54 final size:54
Alignment explanation
Indices: 6158--6266 Score: 175
Period size: 54 Copynumber: 2.0 Consensus size: 54
6148 AAACTAAAGA
*
6158 TCACAACTATTCGGGATAAAC-ATTATTTGAGATGGTGAATGAAGATAAAAAGGG
1 TCACAACTATTCGGGAGAAACAATT-TTTGAGATGGTGAATGAAGATAAAAAGGG
* *
6212 TCACAACTATTCGGGAGAAACAATTTTTGAGATGGTGAATGAGGATAAGAAGGG
1 TCACAACTATTCGGGAGAAACAATTTTTGAGATGGTGAATGAAGATAAAAAGGG
6266 T
1 T
6267 TATCTTGAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 48 0.94
55 3 0.06
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.26
Consensus pattern (54 bp):
TCACAACTATTCGGGAGAAACAATTTTTGAGATGGTGAATGAAGATAAAAAGGG
Found at i:7930 original size:30 final size:30
Alignment explanation
Indices: 7882--7952 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
7872 CATGCTTACA
* *
7882 TGGAATTTT-TGGACCATGTTAGTGTCCACG
1 TGGAATTTTCAGG-CCATGTAAGTGTCCACG
*
7912 TGGATTTTTCAGGCCATGTAAGTGTCCACG
1 TGGAATTTTCAGGCCATGTAAGTGTCCACG
7942 TGGAATTTTCA
1 TGGAATTTTCA
7953 TATATAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 34 0.94
31 2 0.06
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (30 bp):
TGGAATTTTCAGGCCATGTAAGTGTCCACG
Found at i:13298 original size:2 final size:2
Alignment explanation
Indices: 13291--13318 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13281 TTTATGAATA
13291 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
13319 CGGTAGAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13641 original size:11 final size:11
Alignment explanation
Indices: 13621--13677 Score: 69
Period size: 11 Copynumber: 5.2 Consensus size: 11
13611 AAGTGATTAT
*
13621 GTGGACGCCAC
1 GTGGATGCCAC
13632 GTGGATGCCAC
1 GTGGATGCCAC
* *
13643 ATAGATGCCAC
1 GTGGATGCCAC
13654 GTGGATGCCAC
1 GTGGATGCCAC
* *
13665 ATAGATGCCAC
1 GTGGATGCCAC
13676 GT
1 GT
13678 AAGAAAATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 38 1.00
ACGTcount: A:0.25, C:0.28, G:0.30, T:0.18
Consensus pattern (11 bp):
GTGGATGCCAC
Found at i:13652 original size:22 final size:22
Alignment explanation
Indices: 13627--13677 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
13617 TTATGTGGAC
13627 GCCACGTGGATGCCACATAGAT
1 GCCACGTGGATGCCACATAGAT
13649 GCCACGTGGATGCCACATAGAT
1 GCCACGTGGATGCCACATAGAT
13671 GCCACGT
1 GCCACGT
13678 AAGAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.18
Consensus pattern (22 bp):
GCCACGTGGATGCCACATAGAT
Found at i:13766 original size:21 final size:21
Alignment explanation
Indices: 13723--13766 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13713 AAGAAAATAA
*
13723 AATAAATAAAAGAAATTAATT
1 AATAAATAAAAGAAATCAATT
13744 AATAAATAAAA-AAATCAACTT
1 AATAAATAAAAGAAATCAA-TT
13765 AA
1 AA
13767 ACTATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (21 bp):
AATAAATAAAAGAAATCAATT
Found at i:13971 original size:29 final size:30
Alignment explanation
Indices: 13933--13992 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
13923 GAATATGAAC
13933 AACCATCTTCTTCC-TCCAACAACTCACAA
1 AACCATCTTCTTCCTTCCAACAACTCACAA
13962 AACCATCTTCTTCCTTCCAACAACTCACAA
1 AACCATCTTCTTCCTTCCAACAACTCACAA
13992 A
1 A
13993 TGTTAATTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (30 bp):
AACCATCTTCTTCCTTCCAACAACTCACAA
Found at i:14953 original size:31 final size:29
Alignment explanation
Indices: 14875--14953 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
14865 CCTATTGGGT
* ** *
14875 AACGTTATATCCTGAAATGATCGTTCTCA
1 AACGTTATATCCTGAATTGATCGCACGCA
**
14904 AACGTTATATCCCAAATTGATCGGCACGGCA
1 AACGTTATATCCTGAATTGATC-GCAC-GCA
14935 AACGTTATATCCTGAATTG
1 AACGTTATATCCTGAATTG
14954 GTTATTTAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 19 0.47
30 2 0.05
31 19 0.47
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (29 bp):
AACGTTATATCCTGAATTGATCGCACGCA
Found at i:19420 original size:11 final size:11
Alignment explanation
Indices: 19404--19429 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19394 TTCTGGTCAA
19404 TTTTTTTATAT
1 TTTTTTTATAT
19415 TTTTTTTATAT
1 TTTTTTTATAT
19426 TTTT
1 TTTT
19430 CGATATAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTATAT
Found at i:20507 original size:30 final size:30
Alignment explanation
Indices: 20467--20524 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
20457 TGCTTCTCCT
* *
20467 TGCTATTTGAAGTAGGATTTGTGATTCCCA
1 TGCTACTTGAAGTAGGATTTGCGATTCCCA
* *
20497 TGCTACTTGAATTAGGGTTTGCGATTCC
1 TGCTACTTGAAGTAGGATTTGCGATTCC
20525 TCCTCCTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.40
Consensus pattern (30 bp):
TGCTACTTGAAGTAGGATTTGCGATTCCCA
Found at i:37580 original size:28 final size:28
Alignment explanation
Indices: 37540--37595 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
37530 GCAAAGGGAT
37540 AAGAATAAAAAAACTGGATTGCTAAACA
1 AAGAATAAAAAAACTGGATTGCTAAACA
37568 AAGAATAAAAAAACTGGATTGCTAAACA
1 AAGAATAAAAAAACTGGATTGCTAAACA
37596 CCGCCCCCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.18
Consensus pattern (28 bp):
AAGAATAAAAAAACTGGATTGCTAAACA
Found at i:37747 original size:26 final size:26
Alignment explanation
Indices: 37718--37785 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
37708 TTCCTTCATT
37718 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
37744 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
37770 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
37786 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Done.