Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013560.1 Corchorus olitorius cultivar O-4 contig13593, 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: 5167
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Found at i:5024 original size:14 final size:13
Alignment explanation
Indices: 5005--5066 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
4995 AAATTCCAAA
5005 AAAAAACAAAGAAC
1 AAAAAACAAA-AAC
5019 AAAAAAATCAAAAATC
1 -AAAAAA-CAAAAA-C
*
5035 AAAAATA-AAAAAT
1 AAAAA-ACAAAAAC
*
5048 AAAAAATAAAAAC
1 AAAAAACAAAAAC
5061 AAAAAA
1 AAAAAA
5067 AATCAAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
12 1 0.02
13 16 0.39
14 5 0.12
15 13 0.32
16 6 0.15
ACGTcount: A:0.82, C:0.08, G:0.02, T:0.08
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:5038 original size:6 final size:7
Alignment explanation
Indices: 5021--5065 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
5011 CAAAGAACAA
5021 AAAAATC
1 AAAAATC
5028 AAAAATC
1 AAAAATC
*
5035 AAAAATA
1 AAAAATC
*
5042 AAAAATA
1 AAAAATC
5049 AAAAAT-
1 AAAAATC
5055 AAAAA-C
1 AAAAATC
5061 AAAAA
1 AAAAA
5066 AAATCAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
6 10 0.28
7 26 0.72
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAATC
Found at i:5044 original size:21 final size:22
Alignment explanation
Indices: 5006--5081 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
4996 AATTCCAAAA
*
5006 AAAAACAAAGAAC-AAAAAAATC
1 AAAAATAAA-AACAAAAAAAATC
* * *
5028 AAAAATCAAAA-ATAAAAAATA
1 AAAAATAAAAACAAAAAAAATC
5049 AAAAATAAAAACAAAAAAAATC
1 AAAAATAAAAACAAAAAAAATC
5071 AAATAA-AAAAA
1 AAA-AATAAAAA
5082 TCAATCACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
21 19 0.43
22 23 0.52
23 2 0.05
ACGTcount: A:0.82, C:0.08, G:0.01, T:0.09
Consensus pattern (22 bp):
AAAAATAAAAACAAAAAAAATC
Found at i:5045 original size:36 final size:35
Alignment explanation
Indices: 5002--5081 Score: 90
Period size: 36 Copynumber: 2.3 Consensus size: 35
4992 AATAAATTCC
* *
5002 AAAAAAAAACAAAGAACAAAAA-AATCAAAAATCAA
1 AAAAAAAAACAAAAAACAAAAACAA-AAAAAATCAA
* *
5037 AAATAAAAAATAAAAAATAAAAACAAAAAAAATCAA
1 AAA-AAAAAACAAAAAACAAAAACAAAAAAAATCAA
*
5073 ATAAAAAAA
1 AAAAAAAAA
5082 TCAATCACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
35 9 0.24
36 27 0.71
37 2 0.05
ACGTcount: A:0.82, C:0.07, G:0.01, T:0.09
Consensus pattern (35 bp):
AAAAAAAAACAAAAAACAAAAACAAAAAAAATCAA
Found at i:5067 original size:14 final size:14
Alignment explanation
Indices: 5004--5067 Score: 62
Period size: 14 Copynumber: 4.5 Consensus size: 14
4994 TAAATTCCAA
*
5004 AAAAAAACAAAGAAC
1 AAAAAAATAAA-AAC
5019 AAAAAAATCAAAAATC
1 AAAAAAAT-AAAAA-C
5035 --AAAAATAAAAA-
1 AAAAAAATAAAAAC
5046 ATAAAAAATAAAAAC
1 A-AAAAAATAAAAAC
5061 AAAAAAA
1 AAAAAAA
5068 ATCAAATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 5 0.12
14 23 0.55
15 10 0.24
16 4 0.10
ACGTcount: A:0.83, C:0.08, G:0.02, T:0.08
Consensus pattern (14 bp):
AAAAAAATAAAAAC
Found at i:5078 original size:13 final size:13
Alignment explanation
Indices: 5062--5109 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
5052 AATAAAAACA
5062 AAAAAAATCAAAT
1 AAAAAAATCAAAT
*
5075 AAAAAAATCAATCACA
1 AAAAAAATCAA--A-T
5091 AAAAAAATCAAAT
1 AAAAAAATCAAAT
5104 CAAAAA
1 -AAAAA
5110 CGAAGTCGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 11 0.38
14 6 0.21
15 1 0.03
16 11 0.38
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAATCAAAT
Found at i:5078 original size:14 final size:14
Alignment explanation
Indices: 5019--5109 Score: 71
Period size: 14 Copynumber: 6.3 Consensus size: 14
5009 AACAAAGAAC
5019 AAAAAAATCAAA-A
1 AAAAAAATCAAACA
* *
5032 ATCAAAAAT-AAAAA
1 A-AAAAAATCAAACA
*
5046 ATAAAAAATAAAAACA
1 A-AAAAAAT-CAAACA
*
5062 AAAAAAATCAAA-T
1 AAAAAAATCAAACA
5075 AAAAAAATCAATCACA
1 AAAAAAATCAA--ACA
5091 AAAAAAATCAAATCA
1 AAAAAAATCAAA-CA
5106 AAAA
1 AAAA
5110 CGAAGTCGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
13 15 0.23
14 19 0.30
15 14 0.22
16 16 0.25
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAAATCAAACA
Done.