Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008593.1 Kokia drynarioides strain JFW-HI SEQ_123271, 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: 17733
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4078 original size:28 final size:27
Alignment explanation
Indices: 4038--4164 Score: 110
Period size: 28 Copynumber: 4.6 Consensus size: 27
4028 TGAAGCGAAA
* * *
4038 GGCTAGGATAGAGCAATGTTCTGATTTT
1 GGCTCGGATAGAGCAATATTCT-ATTCT
*
4066 GGCTCGGATAGAGCGATATTCTGATTCT
1 GGCTCGGATAGAGCAATATTCT-ATTCT
* * **
4094 AGCTTGGATAGAGTGATATTCTATATCT
1 GGCTCGGATAGAGCAATATTCTAT-TCT
* *
4122 GGCTCGGGTAGAGCATTATTCTATTTCT
1 GGCTCGGATAGAGCAATATTCTA-TTCT
* *
4150 GGTTCGGGTAGAGCA
1 GGCTCGGATAGAGCA
4165 TTACTTTGAA
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
27 2 0.02
28 80 0.96
29 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (27 bp):
GGCTCGGATAGAGCAATATTCTATTCT
Found at i:4162 original size:56 final size:56
Alignment explanation
Indices: 4102--4311 Score: 178
Period size: 56 Copynumber: 3.8 Consensus size: 56
4092 CTAGCTTGGA
*
4102 TAGAGTGATATTCTATATCTGGCTCGGGTAGAGCATTATTCTATTTCTGGTTCGGG
1 TAGAGCGATATTCTATATCTGGCTCGGGTAGAGCATTATTCTATTTCTGGTTCGGG
* * * * * *
4158 TAGAGC-ATTACTT-TGA-ATTTGGATCGAGTAGAGAATTATTCTATTTCT-ATCTCCGG
1 TAGAGCGA-TA-TTCT-ATATCTGGCTCGGGTAGAGCATTATTCTATTTCTGGT-TCGGG
* * * * *
4214 TAGAGCGTTACTCTAAATCTAGCTTGGGTAGAGCATTATTCTATTTCTGGCTT-GGG
1 TAGAGCGATATTCTATATCTGGCTCGGGTAGAGCATTATTCTATTTCTGG-TTCGGG
* * * * **
4270 TAGAGCGTTATTCTATTTTTGGCTTGGAAAGAGCATTATTCT
1 TAGAGCGATATTCTATATCTGGCTCGGGTAGAGCATTATTCT
4312 GTATCTAGGC
Statistics
Matches: 121, Mismatches: 24, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
55 4 0.03
56 112 0.93
57 4 0.03
58 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (56 bp):
TAGAGCGATATTCTATATCTGGCTCGGGTAGAGCATTATTCTATTTCTGGTTCGGG
Found at i:4165 original size:28 final size:28
Alignment explanation
Indices: 4110--4311 Score: 155
Period size: 28 Copynumber: 7.2 Consensus size: 28
4100 GATAGAGTGA
* *
4110 TATTCTATATCTGGCTCGGGTAGAGCAT
1 TATTCTATTTCTGGTTCGGGTAGAGCAT
4138 TATTCTATTTCTGGTTCGGGTAGAGCAT
1 TATTCTATTTCTGGTTCGGGTAGAGCAT
* * * *
4166 TACTT-TGAATT-TGGATCGAGTAGAGAAT
1 TA-TTCT-ATTTCTGGTTCGGGTAGAGCAT
* * *
4194 TATTCTATTTCT-ATCTCCGGTAGAGCGT
1 TATTCTATTTCTGGT-TCGGGTAGAGCAT
* ** *
4222 TACTCTAAATCTAGCTT-GGGTAGAGCAT
1 TATTCTATTTCT-GGTTCGGGTAGAGCAT
*
4250 TATTCTATTTCTGGCTT-GGGTAGAGCGT
1 TATTCTATTTCTGG-TTCGGGTAGAGCAT
* **
4278 TATTCTATTTTTGGCTT-GGAAAGAGCAT
1 TATTCTATTTCTGG-TTCGGGTAGAGCAT
4306 TATTCT
1 TATTCT
4312 GTATCTAGGC
Statistics
Matches: 138, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
27 6 0.04
28 125 0.91
29 6 0.04
30 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (28 bp):
TATTCTATTTCTGGTTCGGGTAGAGCAT
Found at i:6183 original size:25 final size:25
Alignment explanation
Indices: 6149--6199 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
6139 TCTTTAAGGC
6149 CGATTGAGGCCTAAAGGTTAGCTAA
1 CGATTGAGGCCTAAAGGTTAGCTAA
6174 CGATTGAGGCCTAAAGGTTAGCTAA
1 CGATTGAGGCCTAAAGGTTAGCTAA
6199 C
1 C
6200 ATACTTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (25 bp):
CGATTGAGGCCTAAAGGTTAGCTAA
Found at i:10598 original size:21 final size:21
Alignment explanation
Indices: 10566--10605 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
10556 AAAGTTAGAG
10566 TCCTCAATTGACCTTTCAAGT
1 TCCTCAATTGACCTTTCAAGT
10587 TCCT-AATATGACCTTTCAA
1 TCCTCAAT-TGACCTTTCAA
10606 AATTGGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.38
Consensus pattern (21 bp):
TCCTCAATTGACCTTTCAAGT
Found at i:11428 original size:51 final size:50
Alignment explanation
Indices: 11361--11484 Score: 178
Period size: 50 Copynumber: 2.5 Consensus size: 50
11351 TATGAAAATT
* * *
11361 AATTAC-TAATGCATGACTTTATTTAAGATGCAAACTTTAACTATCATGGG
1 AATTACATAATGCATGACATTATTTAAGATGCAAA-TTTAACTAACATGAG
* *
11411 AATTACATAATGCATGACATAATTTATGATGCAAATTTAACTAACATGAG
1 AATTACATAATGCATGACATTATTTAAGATGCAAATTTAACTAACATGAG
*
11461 AGTTACATAATGCATGACATTATT
1 AATTACATAATGCATGACATTATT
11485 AAATGTAGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 41 0.62
51 25 0.38
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (50 bp):
AATTACATAATGCATGACATTATTTAAGATGCAAATTTAACTAACATGAG
Found at i:15530 original size:3 final size:3
Alignment explanation
Indices: 15522--15561 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
15512 TGAAATATAG
15522 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
15562 TAAATGAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17575 original size:18 final size:15
Alignment explanation
Indices: 17543--17571 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17533 CTGCACAATG
17543 CTTCTTCTTCCTCCT
1 CTTCTTCTTCCTCCT
17558 CTTCTTC-TCCTCCT
1 CTTCTTCTTCCTCCT
17572 TCCTGCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (15 bp):
CTTCTTCTTCCTCCT
Done.