Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005161.1 Kokia drynarioides strain JFW-HI SEQ_119009, 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: 7134
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:1283 original size:236 final size:236
Alignment explanation
Indices: 864--2262 Score: 2332
Period size: 236 Copynumber: 5.9 Consensus size: 236
854 GACTAATTAT
* * * *
864 AATACTACACATCGAGTTTACGTTTTATGTATATTTTAGGTTCGAGTAGAATAT-AGTCCGGAGT
1 AATACTACACATTGAGTTTACATTTTATGTATATTTCAGGTTCGAGTGGAAT-TCAGTCCGGAGT
* *
928 CATTAGTTGAAACTGAAGCAACTAATGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAATTT
65 CATTAGTTGAAACCGAAGTAACTAATGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAATTT
* **
993 ATAACTTCTTGTCCGGGTTTCGACAATGAGAACTTTATTGCTGACGACAATGAAGTGATCTCCAA
130 ATAACTTCTTGTCCGGTTTTCGACAATGAGAACTTTATTGCTGACGGGAATGAAGTGATCTCCAA
* *
1058 TCACCATTCACGAGTAAGAACACTTCTCTCGGAAATTTTTAA
195 TCACCAGTCACAAGTAAGAACACTTCTCTCGGAAATTTTTAA
*
1100 AATACTACACATAGAGTTTACATTTTATGTATATTTCAGGTTCGAGTGGAATTCAGTCCGGAGTC
1 AATACTACACATTGAGTTTACATTTTATGTATATTTCAGGTTCGAGTGGAATTCAGTCCGGAGTC
* *
1165 ATTAGTTGAAACCGAAGTAACTAATAAGTACGAGTGGACTCAAATTGAACAAACTAATGAATTTA
66 ATTAGTTGAAACCGAAGTAACTAATGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAATTTA
* *
1230 TAACTTCTTGTCCGGTTTTCAACAATGAGAACTTTCTTGCTGACGGGAATGAAGTGATCTCCAAT
131 TAACTTCTTGTCCGGTTTTCGACAATGAGAACTTTATTGCTGACGGGAATGAAGTGATCTCCAAT
*
1295 CACCAGTCACAAGTAAGAACACTTGTCTCGGAAATTTTTAA
196 CACCAGTCACAAGTAAGAACACTTCTCTCGGAAATTTTTAA
* * *
1336 AATACTACATATCGAGTTTACATTTTATGTATATTTCAGGTTCGAGTGGAATTCAGTCCGAAGTC
1 AATACTACACATTGAGTTTACATTTTATGTATATTTCAGGTTCGAGTGGAATTCAGTCCGGAGTC
*
1401 ATTAGTTGAAACCGAAGTAACTAATGAGTACGAGTGGACTCAAACTGAACAAACTAATGAATTTA
66 ATTAGTTGAAACCGAAGTAACTAATGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAATTTA
* * *
1466 TAACTTTTTGTCCGGGTTTCGACAATGAGAACTTTATTGTTGACGGGAATGAAGTGATCTCCAAT
131 TAACTTCTTGTCCGGTTTTCGACAATGAGAACTTTATTGCTGACGGGAATGAAGTGATCTCCAAT
1531 CACCAGTCACAAGTAAGAACACTTCTCTCGGAAATTTTTAA
196 CACCAGTCACAAGTAAGAACACTTCTCTCGGAAATTTTTAA
* * * *
1572 AATACTACACATTGAGTTTACATTTTATGTATATTTCAGGTTCGAGTGGAACTCGGTCTGAAGTC
1 AATACTACACATTGAGTTTACATTTTATGTATATTTCAGGTTCGAGTGGAATTCAGTCCGGAGTC
* *
1637 ATTAGTTGATACCGAAGTAACTAATAAGTACGAGTGGACTCAAAGTGAACAAACTAATGAATTTA
66 ATTAGTTGAAACCGAAGTAACTAATGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAATTTA
* * *
1702 TAACTTCTTGTCCGGTTTTCAACAATGAGAACTTTCTTGCTGATGGGAATGAAGTGATCTCCAAT
131 TAACTTCTTGTCCGGTTTTCGACAATGAGAACTTTATTGCTGACGGGAATGAAGTGATCTCCAAT
* *
1767 CACCAGTCACAAGTAAGAACACTTGTCTCGAAAATTTTTAA
196 CACCAGTCACAAGTAAGAACACTTCTCTCGGAAATTTTTAA
*
1808 AATACTACACATTGAGTTTACATTTTATGTATATTTCAGGTTCGAGTGGAATTCCGTCCGGAGTC
1 AATACTACACATTGAGTTTACATTTTATGTATATTTCAGGTTCGAGTGGAATTCAGTCCGGAGTC
1873 ATTAGTTGAAACCGAAGTAACTAATGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAATTTA
66 ATTAGTTGAAACCGAAGTAACTAATGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAATTTA
* * *
1938 TAACTTCTTGTCTGGTTGTCGACAATGAGAACTTTATTGCTGACGGGAATGAAGTGATCTCTAAT
131 TAACTTCTTGTCCGGTTTTCGACAATGAGAACTTTATTGCTGACGGGAATGAAGTGATCTCCAAT
2003 CACCAGTCACAAGTAAGAACACTTCTCTCGGAAATTTTTAA
196 CACCAGTCACAAGTAAGAACACTTCTCTCGGAAATTTTTAA
* * *
2044 AATACTACACATTGAGTTTACATTTTATGTATATTTCAAGTTCGAGTGGAACTCGGTCCGGAGTC
1 AATACTACACATTGAGTTTACATTTTATGTATATTTCAGGTTCGAGTGGAATTCAGTCCGGAGTC
*
2109 ATTAGTTGAAACCGAAGTAACTAATGAGTACGAGTGGACTCAAAGTGAACAAACTAATAAATTTA
66 ATTAGTTGAAACCGAAGTAACTAATGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAATTTA
* * * * * *
2174 TAACTCCCTGTCAGATTTTCGACAATGAGAATTTTATTGATGACGGGAATGAAGTGATCTCCAAT
131 TAACTTCTTGTCCGGTTTTCGACAATGAGAACTTTATTGCTGACGGGAATGAAGTGATCTCCAAT
*
2239 CACCCGTCACAAGTAAGAACACTT
196 CACCAGTCACAAGTAAGAACACTT
2263 TTCTTTAAAA
Statistics
Matches: 1092, Mismatches: 70, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
235 1 0.00
236 1091 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (236 bp):
AATACTACACATTGAGTTTACATTTTATGTATATTTCAGGTTCGAGTGGAATTCAGTCCGGAGTC
ATTAGTTGAAACCGAAGTAACTAATGAGTACGAGTGGACTCAAAGTGAACAAACTAATGAATTTA
TAACTTCTTGTCCGGTTTTCGACAATGAGAACTTTATTGCTGACGGGAATGAAGTGATCTCCAAT
CACCAGTCACAAGTAAGAACACTTCTCTCGGAAATTTTTAA
Found at i:4043 original size:23 final size:23
Alignment explanation
Indices: 4017--4063 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4007 TTAAGATGAT
*
4017 TTGACAACAACGTAAGTTTAAAA
1 TTGACAACAACGCAAGTTTAAAA
*
4040 TTGATAACAACGCAAGTTTAAAA
1 TTGACAACAACGCAAGTTTAAAA
4063 T
1 T
4064 GTAAAATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.28
Consensus pattern (23 bp):
TTGACAACAACGCAAGTTTAAAA
Found at i:4793 original size:22 final size:22
Alignment explanation
Indices: 4737--4799 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 22
4727 GTTTTGGTGC
*
4737 TTTTTTACTG-TTTG-GTTGAT
1 TTTTTTACTGTTTTGAGTTGTT
*
4757 TTTTTTGCTGTTTTTGAGTTGTT
1 TTTTTTACTG-TTTTGAGTTGTT
*
4780 TTTTTTATTGTTTTGA-TTGT
1 TTTTTTACTGTTTTGAGTTGT
4800 AATTTTCGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 9 0.25
21 4 0.11
22 10 0.28
23 13 0.36
ACGTcount: A:0.08, C:0.03, G:0.19, T:0.70
Consensus pattern (22 bp):
TTTTTTACTGTTTTGAGTTGTT
Found at i:4885 original size:12 final size:12
Alignment explanation
Indices: 4808--4885 Score: 56
Period size: 12 Copynumber: 6.8 Consensus size: 12
4798 GTAATTTTCG
4808 TGTTATTTTTAC
1 TGTTATTTTTAC
**
4820 TGTTATTTTTGT
1 TGTTATTTTTAC
* **
4832 TGCTATTTTTGT
1 TGTTATTTTTAC
4844 TGTTA-TTTT--
1 TGTTATTTTTAC
* *
4853 TGTTGTTTTTAA
1 TGTTATTTTTAC
*
4865 TGTT-GTTTTAC
1 TGTTATTTTTAC
4876 TGTTATTTTT
1 TGTTATTTTT
4886 GTTGTCGTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 13 0.24
12 33 0.61
ACGTcount: A:0.12, C:0.04, G:0.14, T:0.71
Consensus pattern (12 bp):
TGTTATTTTTAC
Found at i:4888 original size:20 final size:19
Alignment explanation
Indices: 4865--4927 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
4855 TTGTTTTTAA
*
4865 TGTTGTTTTACTGTTATTTT
1 TGTTGTTTGA-TGTTATTTT
*
4885 TGTTGTCGTTGGTTGTTATTTT
1 TGTTGT--TT-GATGTTATTTT
4907 TGTTGTTTGGATGTTATTTT
1 TGTTGTTT-GATGTTATTTT
4927 T
1 T
4928 TATGCGTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 20 0.54
22 17 0.46
ACGTcount: A:0.08, C:0.03, G:0.22, T:0.67
Consensus pattern (19 bp):
TGTTGTTTGATGTTATTTT
Found at i:4901 original size:22 final size:20
Alignment explanation
Indices: 4876--4927 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 20
4866 GTTGTTTTAC
*
4876 TGTTATTTTTGTTGTCGTTGGT
1 TGTTATTTTTGTTGT--TTGGA
4898 TGTTATTTTTGTTGTTTGGA
1 TGTTATTTTTGTTGTTTGGA
4918 TGTTATTTTT
1 TGTTATTTTT
4928 TATGCGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 14 0.48
22 15 0.52
ACGTcount: A:0.08, C:0.02, G:0.23, T:0.67
Consensus pattern (20 bp):
TGTTATTTTTGTTGTTTGGA
Found at i:4913 original size:12 final size:12
Alignment explanation
Indices: 4790--4859 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
4780 TTTTTTATTG
*
4790 TTTTGATTGTAAT
1 TTTTG-TTGTTAT
*
4803 TTTCG-TGTTAT
1 TTTTGTTGTTAT
**
4814 TTTTACTGTTAT
1 TTTTGTTGTTAT
*
4826 TTTTGTTGCTAT
1 TTTTGTTGTTAT
4838 TTTTGTTGTTAT
1 TTTTGTTGTTAT
4850 TTTTGTTGTT
1 TTTTGTTGTT
4860 TTTAATGTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
11 8 0.17
12 36 0.75
13 4 0.08
ACGTcount: A:0.11, C:0.04, G:0.16, T:0.69
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:5765 original size:30 final size:31
Alignment explanation
Indices: 5729--5791 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
5719 TGTCATTTAA
5729 TACTTAAATT-TAATTT-AGTATTCAATTTGG
1 TACTTAAATTGTAATTTAAG-ATTCAATTTGG
**
5759 TACTTAAATTGTGTTTTAAGATTCAATTTGG
1 TACTTAAATTGTAATTTAAGATTCAATTTGG
5790 TA
1 TA
5792 TTCATACCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 10 0.34
31 17 0.59
32 2 0.07
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (31 bp):
TACTTAAATTGTAATTTAAGATTCAATTTGG
Done.