Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006208.1 Corchorus olitorius cultivar O-4 contig06233, 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: 5431
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Found at i:3402 original size:2 final size:2
Alignment explanation
Indices: 3364--3394 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3354 AAACTACTAA
3364 AT AT AT 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 AT AT AT A
3395 CTTATATAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3701 original size:31 final size:31
Alignment explanation
Indices: 3630--3701 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
3620 GTCTATCAGC
*
3630 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
3661 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
3691 GTTTTAATTTG
1 -TTTTAATTTG
3702 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:3928 original size:5 final size:5
Alignment explanation
Indices: 3913--3969 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
3903 TATTCAATCT
* *
3913 TTATA -TATA TTATA TTGATAA TAATG TTATA TTATA -T-TA TTATA TTATA
1 TTATA TTATA TTATA TT-AT-A TTATA TTATA TTATA TTATA TTATA TTATA
3962 -TATA TTAT
1 TTATA TTAT
3970 CAATATACTT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
3 2 0.05
4 10 0.24
5 24 0.57
6 4 0.10
7 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (5 bp):
TTATA
Found at i:3957 original size:13 final size:14
Alignment explanation
Indices: 3913--3969 Score: 71
Period size: 13 Copynumber: 3.9 Consensus size: 14
3903 TATTCAATCT
3913 TTATATATATTATA
1 TTATATATATTATA
*
3927 TTGATAATAATGTTATA
1 TT-AT-AT-ATATTATA
3944 TTATAT-TATTATA
1 TTATATATATTATA
3957 TTATATATATTAT
1 TTATATATATTAT
3970 CAATATACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 12 0.32
14 8 0.22
15 4 0.11
16 4 0.11
17 9 0.24
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (14 bp):
TTATATATATTATA
Found at i:3965 original size:22 final size:23
Alignment explanation
Indices: 3913--3969 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
3903 TATTCAATCT
3913 TTATATATATTATATTGATAATA
1 TTATATATATTATATTGATAATA
* * *
3936 ATGT-TATATTATATT-ATTATA
1 TTATATATATTATATTGATAATA
3957 TTATATATATTAT
1 TTATATATATTAT
3970 CAATATACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 7 0.25
22 19 0.68
23 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TTATATATATTATATTGATAATA
Found at i:3975 original size:9 final size:9
Alignment explanation
Indices: 3913--3969 Score: 57
Period size: 9 Copynumber: 6.4 Consensus size: 9
3903 TATTCAATCT
3913 TTATATATA
1 TTATATATA
3922 TTATAT-TGA
1 TTATATAT-A
* *
3931 TAATA-ATG
1 TTATATATA
3939 TTATATTATA
1 TTATA-TATA
3949 TTAT-TATA
1 TTATATATA
3957 TTATATATA
1 TTATATATA
3966 TTAT
1 TTAT
3970 CAATATACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
8 13 0.33
9 20 0.51
10 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (9 bp):
TTATATATA
Found at i:3985 original size:11 final size:10
Alignment explanation
Indices: 3914--3985 Score: 53
Period size: 11 Copynumber: 7.2 Consensus size: 10
3904 ATTCAATCTT
*
3914 TATA-TATAT
1 TATATTATAA
3923 TATATTGATAA
1 TATATT-ATAA
* *
3934 TAATGTTATAT
1 T-ATATTATAA
3945 TATATTAT--
1 TATATTATAA
3953 TATATTAT-A
1 TATATTATAA
3962 TATATTATCAA
1 TATATTAT-AA
3973 TATACTTATAA
1 TATA-TTATAA
3984 TA
1 TA
3986 CAAAAGATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
8 8 0.15
9 12 0.23
10 7 0.13
11 17 0.33
12 8 0.15
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (10 bp):
TATATTATAA
Found at i:4147 original size:16 final size:16
Alignment explanation
Indices: 4126--4183 Score: 82
Period size: 16 Copynumber: 3.6 Consensus size: 16
4116 CTACCCAAGA
4126 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
4142 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
*
4158 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
4174 CCGAACCCGA
1 CCGAACCCGA
4184 CTTAACCCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 3 0.08
16 30 0.83
17 3 0.08
ACGTcount: A:0.38, C:0.41, G:0.16, T:0.05
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:4172 original size:32 final size:32
Alignment explanation
Indices: 4126--4197 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
4116 CTACCCAAGA
4126 CCGAACCCGAAAATACCCGAACCCGACATAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
* *
4158 CCGAGCCCGAAAATACCCGAACCCGACTTAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
4190 CCGAACCC
1 CCGAACCC
4198 TCCCGAGCCC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.36, C:0.43, G:0.14, T:0.07
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCGAACCCGACATAAC
Found at i:4191 original size:16 final size:16
Alignment explanation
Indices: 4126--4197 Score: 76
Period size: 16 Copynumber: 4.5 Consensus size: 16
4116 CTACCCAAGA
*
4126 CCGAACCCGA-AAATAC
1 CCGAACCCGACATA-AC
4142 CCGAACCCGACATAAC
1 CCGAACCCGACATAAC
* *
4158 CCGAGCCCGA-AAATAC
1 CCGAACCCGACATA-AC
*
4174 CCGAACCCGACTTAAC
1 CCGAACCCGACATAAC
4190 CCGAACCC
1 CCGAACCC
4198 TCCCGAGCCC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
15 2 0.04
16 42 0.89
17 3 0.06
ACGTcount: A:0.36, C:0.43, G:0.14, T:0.07
Consensus pattern (16 bp):
CCGAACCCGACATAAC
Done.