Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013272.1 Corchorus olitorius cultivar O-4 contig13305, 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: 5724
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Found at i:818 original size:10 final size:10
Alignment explanation
Indices: 787--821 Score: 56
Period size: 9 Copynumber: 3.7 Consensus size: 10
777 GTAACACAAA
787 TCACATACC-
1 TCACATACCT
796 TCACATA-CT
1 TCACATACCT
805 TCACATACCT
1 TCACATACCT
815 TCACATA
1 TCACATA
822 ATTCTCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 1 0.04
9 14 0.58
10 9 0.38
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (10 bp):
TCACATACCT
Found at i:1639 original size:15 final size:16
Alignment explanation
Indices: 1606--1639 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1596 TTACTTTGCT
1606 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
1622 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
1637 TTG
1 TTG
1640 CGTTCTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:3925 original size:26 final size:26
Alignment explanation
Indices: 3896--3963 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
3886 TACTTCTTGA
3896 TTACTGATTACTATTTTTTACTATTT
1 TTACTGATTACTATTTTTTACTATTT
** *
3922 TTACTGATTACCGTTTTTTACTCTTT
1 TTACTGATTACTATTTTTTACTATTT
*
3948 TTGCTGATTACTATTT
1 TTACTGATTACTATTT
3964 CTCTCTTGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.19, C:0.15, G:0.07, T:0.59
Consensus pattern (26 bp):
TTACTGATTACTATTTTTTACTATTT
Found at i:4006 original size:21 final size:21
Alignment explanation
Indices: 3946--4012 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
3936 TTTTTACTCT
* *
3946 TTTTGCTGATTACTATTTCTC
1 TTTTGCTGATTACTATTACTA
* ** *
3967 TCTTGCTGACAACTCTTACTA
1 TTTTGCTGATTACTATTACTA
* *
3988 TTTTGCTGGTTACTATTACCA
1 TTTTGCTGATTACTATTACTA
4009 TTTT
1 TTTT
4013 TACTCTTTAC
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.18, C:0.21, G:0.10, T:0.51
Consensus pattern (21 bp):
TTTTGCTGATTACTATTACTA
Found at i:4019 original size:36 final size:35
Alignment explanation
Indices: 3978--4114 Score: 107
Period size: 36 Copynumber: 3.8 Consensus size: 35
3968 CTTGCTGACA
*
3978 ACTCTTACTATTTTGCTGGTTACTATTACCATTTTT
1 ACTCTTACT-TTTTGCTGATTACTATTACCATTTTT
* * * *
4014 ACTCTTTACTCTTTGCTCATTGCTATTACCA-TCTT
1 ACTC-TTACTTTTTGCTGATTACTATTACCATTTTT
* *
4049 ACTGTTTACTCTTTTACTGATTACTATTACTC-TTTTT
1 ACT-CTTACT-TTTTGCTGATTACTATTAC-CATTTTT
* * * *
4086 ACTCTTTACTCTTTACTGACTATTATTAC
1 ACTC-TTACTTTTTGCTGATTACTATTAC
4115 TCCTTTACTC
Statistics
Matches: 80, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
35 11 0.14
36 52 0.65
37 17 0.21
ACGTcount: A:0.20, C:0.23, G:0.06, T:0.52
Consensus pattern (35 bp):
ACTCTTACTTTTTGCTGATTACTATTACCATTTTT
Found at i:4023 original size:7 final size:7
Alignment explanation
Indices: 4011--4134 Score: 51
Period size: 7 Copynumber: 17.4 Consensus size: 7
4001 TATTACCATT
4011 TTTACTC
1 TTTACTC
4018 TTTACTC
1 TTTACTC
*
4025 TTTGCTC
1 TTTACTC
* *
4032 ATTGCT-
1 TTTACTC
*
4038 ATTAC-C
1 TTTACTC
*
4044 ATCTTACTG
1 -T-TTACTC
4053 TTTACTC
1 TTTACTC
*
4060 TTTTACTG
1 -TTTACTC
*
4068 ATTACT-
1 TTTACTC
*
4074 ATTACTC
1 TTTACTC
4081 TTTTTACTC
1 --TTTACTC
4090 TTTACTC
1 TTTACTC
*
4097 TTTACTG
1 TTTACTC
**
4104 ACTA-T-
1 TTTACTC
4109 TATTACTCC
1 T-TTACT-C
4118 TTTACTC
1 TTTACTC
4125 TTTACTC
1 TTTACTC
4132 TTT
1 TTT
4135 GCCATTGCCA
Statistics
Matches: 91, Mismatches: 14, Indels: 24
0.71 0.11 0.19
Matches are distributed among these distances:
6 13 0.14
7 55 0.60
8 16 0.18
9 7 0.08
ACGTcount: A:0.18, C:0.24, G:0.04, T:0.54
Consensus pattern (7 bp):
TTTACTC
Found at i:4072 original size:22 final size:22
Alignment explanation
Indices: 4047--4134 Score: 61
Period size: 22 Copynumber: 3.7 Consensus size: 22
4037 TATTACCATC
*
4047 TTACTGTTTACTC-TTTTACTGA
1 TTACT-TTTACTCTTTTTACTCA
* *
4069 TTACTATTACTCTTTTTACTCT
1 TTACTTTTACTCTTTTTACTCA
*
4091 TTACTCTTTACTGACTATTATTACTCCT
1 TTACT-TTTACT--CT-TT-TTACT-CA
4119 TTACTCTTTACTCTTT
1 TTACT-TTTACTCTTT
4135 GCCATTGCCA
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
21 6 0.11
22 17 0.31
23 5 0.09
25 4 0.07
26 4 0.07
27 5 0.09
28 14 0.25
ACGTcount: A:0.18, C:0.23, G:0.03, T:0.56
Consensus pattern (22 bp):
TTACTTTTACTCTTTTTACTCA
Found at i:4079 original size:21 final size:21
Alignment explanation
Indices: 4054--4123 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
4044 ATCTTACTGT
*
4054 TTACTCTTTTACTGATTACTA
1 TTACTCTTTTACTGACTACTA
4075 TTACTCTTTT--T-ACT-CT-
1 TTACTCTTTTACTGACTACTA
*
4091 TTACTC-TTTACTGACTATTA
1 TTACTCTTTTACTGACTACTA
*
4111 TTACTCCTTTACT
1 TTACTCTTTTACT
4124 CTTTACTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
15 3 0.07
16 6 0.15
17 3 0.07
18 5 0.12
19 2 0.05
20 6 0.15
21 16 0.39
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.54
Consensus pattern (21 bp):
TTACTCTTTTACTGACTACTA
Found at i:4113 original size:72 final size:72
Alignment explanation
Indices: 3978--4134 Score: 185
Period size: 72 Copynumber: 2.2 Consensus size: 72
3968 CTTGCTGACA
* * * * * *
3978 ACTC-TTACTATTTTGCTGGTTACTATTACCATTTTTACTCTTTACTCTTTGCTCATTGCTATTA
1 ACTCTTTACTCTTTTACTGATTACTATTACCATTTTTACTCTTTACTCTTTACTCACTACTATTA
4042 C-CATCTT
66 CTCAT-TT
* * *
4049 ACTGTTTACTCTTTTACTGATTACTATTACTC-TTTTTACTCTTTACTCTTTACTGACTATTATT
1 ACTCTTTACTCTTTTACTGATTACTATTAC-CATTTTTACTCTTTACTCTTTACTCACTACTATT
*
4113 ACTCCTTT
65 ACTCATTT
4121 ACTCTTTACTCTTT
1 ACTCTTTACTCTTT
4135 GCCATTGCCA
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
71 3 0.04
72 66 0.92
73 3 0.04
ACGTcount: A:0.18, C:0.24, G:0.05, T:0.53
Consensus pattern (72 bp):
ACTCTTTACTCTTTTACTGATTACTATTACCATTTTTACTCTTTACTCTTTACTCACTACTATTA
CTCATTT
Found at i:4115 original size:36 final size:35
Alignment explanation
Indices: 3997--4134 Score: 152
Period size: 36 Copynumber: 3.9 Consensus size: 35
3987 ATTTTGCTGG
* *
3997 TTACTATTACCATTTTTACTCTTTACTCTTTGCTCA
1 TTACTATTACC-TTTTTACTCTTTACTCTTTACTGA
* * * *
4033 TTGCTATTACCATCTTACTGTTTACTCTTTTACTGA
1 TTACTATTACCTTTTTACTCTTTACTC-TTTACTGA
4069 TTACTATTACTCTTTTTACTCTTTACTCTTTACTGA
1 TTACTATTAC-CTTTTTACTCTTTACTCTTTACTGA
* * *
4105 CTATTATTA-CTCCTTTACTCTTTACTCTTT
1 TTACTATTACCT-TTTTACTCTTTACTCTTT
4135 GCCATTGCCA
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
34 2 0.02
35 30 0.35
36 40 0.47
37 14 0.16
ACGTcount: A:0.19, C:0.24, G:0.04, T:0.54
Consensus pattern (35 bp):
TTACTATTACCTTTTTACTCTTTACTCTTTACTGA
Found at i:4284 original size:32 final size:32
Alignment explanation
Indices: 4236--4388 Score: 173
Period size: 32 Copynumber: 4.7 Consensus size: 32
4226 TTATCCTTAG
** *
4236 TTACTAACCACCATTTTA-CTCTTTAAATTTGA
1 TTACTAATTACCATTTTACCT-TTTGAATTTGA
* *
4268 TTGCTAATTACTATTTTACCTTTTGAATTTGA
1 TTACTAATTACCATTTTACCTTTTGAATTTGA
* * * *
4300 TTGCTAACTACTATTTTACCCTTTTGAACTTGA
1 TTACTAATTACCATTTTA-CCTTTTGAATTTGA
*
4333 TTACTAATTACCATTTTACCATTTGAATTTGA
1 TTACTAATTACCATTTTACCTTTTGAATTTGA
*
4365 TTACTAGTTACCATTTTACTCTTT
1 TTACTAATTACCATTTTAC-CTTT
4389 ACTGACTGAC
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
32 71 0.68
33 33 0.32
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (32 bp):
TTACTAATTACCATTTTACCTTTTGAATTTGA
Found at i:4381 original size:65 final size:65
Alignment explanation
Indices: 4236--4388 Score: 200
Period size: 65 Copynumber: 2.4 Consensus size: 65
4226 TTATCCTTAG
* * * * *
4236 TTACTAACCACCATTTTACTC-TTTAAATTTGATTGCTAATTACTATTTTACCTTTTGAATTTGA
1 TTACTAACTACCATTTTACTCTTTTAAACTTGATTACTAATTACCATTTTACCATTTGAATTTGA
* * * *
4300 TTGCTAACTACTATTTTACCCTTTTGAACTTGATTACTAATTACCATTTTACCATTTGAATTTGA
1 TTACTAACTACCATTTTACTCTTTTAAACTTGATTACTAATTACCATTTTACCATTTGAATTTGA
**
4365 TTACTAGTTACCATTTTACTCTTT
1 TTACTAACTACCATTTTACTCTTT
4389 ACTGACTGAC
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
64 17 0.23
65 57 0.77
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (65 bp):
TTACTAACTACCATTTTACTCTTTTAAACTTGATTACTAATTACCATTTTACCATTTGAATTTGA
Done.