Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013546.1 Kokia drynarioides strain JFW-HI SEQ_128572, 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: 14672
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:3538 original size:17 final size:17
Alignment explanation
Indices: 3490--3572 Score: 69
Period size: 17 Copynumber: 4.9 Consensus size: 17
3480 TCTGGGCCCA
* *
3490 ATAAACTTAAGTTTATT
1 ATAAATTTAAATTTATT
* * * *
3507 TTAAAATTGAGTTTATT
1 ATAAATTTAAATTTATT
*
3524 ATAAATTTAAATTTAGCT
1 ATAAATTTAAATTTA-TT
*
3542 -GAAATTTAAATTTATT
1 ATAAATTTAAATTTATT
*
3558 ATAAATTTAATTTTA
1 ATAAATTTAAATTTA
3573 AAATTTATTT
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
16 1 0.02
17 50 0.96
18 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (17 bp):
ATAAATTTAAATTTATT
Found at i:4392 original size:3 final size:3
Alignment explanation
Indices: 4386--4413 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4376 TAAATGTTTA
4386 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4414 TTTAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5551 original size:59 final size:59
Alignment explanation
Indices: 5424--5794 Score: 469
Period size: 59 Copynumber: 6.3 Consensus size: 59
5414 CCCTAGACTG
* ** * * *
5424 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT-TTATTTTTGACCTCGAAACT
1 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
* * * *
5482 TCAAAAAATTATCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAAACT
1 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
* * *
5541 TCCAAAAATTACAATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAACCCCAAAACT
1 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
* * * *
5600 TCTAAAAATTACCA-TTTACCCCCAAACTTCCAAAAATCCCAATTTTAACCTCGAAACT
1 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
** * * * *
5658 TCC-AAAATTACCATTTTACCCTTAAACTTCTAAAAATCTCATTTTTAACCTCAAAATT
1 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
* * * *
5716 TCCAAAAATTACCATTTTACCCTCAAACTTCTAAAAATCCCATTTTTGACCCCGAAACT
1 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
*
5775 TCCAAAAATTACTATTTTAC
1 TCCAAAAATTACCATTTTAC
5795 TCCCGGATGT
Statistics
Matches: 275, Mismatches: 35, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
57 10 0.04
58 116 0.42
59 149 0.54
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
Found at i:5630 original size:117 final size:118
Alignment explanation
Indices: 5424--5799 Score: 515
Period size: 117 Copynumber: 3.2 Consensus size: 118
5414 CCCTAGACTG
* * *
5424 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT-TTATTTTTGACCTCGAAACTTCAAAA
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCTCAAAACTTCAAAA
* * *
5488 AATTATCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAAACT
66 AATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* * * * *
5541 TCCAAAAATTACAATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAACCCCAAAACTTCTAAA
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCTCAAAACTTCAAAA
* * *
5606 AATTACCA-TTTACCCCCAAACTTCCAAAAATCCCAATTTTAACCTCGAAACT
66 AATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
*** * * *
5658 TCC-AAAATTACCATTTTACCCTTAAACTTCTAAAAATCTCATTTTTAACCTCAAAATTTCCAAA
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCTCAAAACTTCAAAA
* *
5722 AATTACCATTTTACCCTCAAACTTCTAAAAATCCCATTTTTGACCCCGAAACT
66 AATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* *
5775 TCCAAAAATTACTATTTTACTCCCG
1 TCCAAAAATTACCATTTTACCCCCG
5800 GATGTCCGAA
Statistics
Matches: 222, Mismatches: 34, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
116 59 0.27
117 120 0.54
118 43 0.19
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.31
Consensus pattern (118 bp):
TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCTCAAAACTTCAAAA
AATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
Found at i:5882 original size:175 final size:175
Alignment explanation
Indices: 5424--5791 Score: 495
Period size: 175 Copynumber: 2.1 Consensus size: 175
5414 CCCTAGACTG
* ** * ** *
5424 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT-TTATTTTTGACCTCGAAACTTCAAAA
1 TCCAAAAATTACCA-TTTACCCCCAAACTTCCAAAAATCCCAATTTCAACCTCGAAACTTC-CAA
* ** * * *
5488 AATTATCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAAACTTCCAAAAATTAC
64 AATTACCATTTTACCCTTAAACTTCTAAAAATCTCATTTTTAACCCCAAAATTTCCAAAAATTAC
* * *
5553 AATTTTACCCCCGAACTCCCAAAAATCCCATTTTTAACCCCAAAACT
129 CATTTTACCCTCAAACTCCCAAAAATCCCATTTTTAACCCCAAAACT
* *
5600 TCTAAAAATTACCATTTACCCCCAAACTTCCAAAAATCCCAATTTTAACCTCGAAACTTCCAAAA
1 TCCAAAAATTACCATTTACCCCCAAACTTCCAAAAATCCCAATTTCAACCTCGAAACTTCCAAAA
*
5665 TTACCATTTTACCCTTAAACTTCTAAAAATCTCATTTTTAACCTCAAAATTTCCAAAAATTACCA
66 TTACCATTTTACCCTTAAACTTCTAAAAATCTCATTTTTAACCCCAAAATTTCCAAAAATTACCA
* * * *
5730 TTTTACCCTCAAACTTCTAAAAATCCCATTTTTGACCCCGAAACT
131 TTTTACCCTCAAACTCCCAAAAATCCCATTTTTAACCCCAAAACT
*
5775 TCCAAAAATTACTATTT
1 TCCAAAAATTACCATTT
5792 TACTCCCGGA
Statistics
Matches: 168, Mismatches: 23, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
175 137 0.82
176 31 0.18
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (175 bp):
TCCAAAAATTACCATTTACCCCCAAACTTCCAAAAATCCCAATTTCAACCTCGAAACTTCCAAAA
TTACCATTTTACCCTTAAACTTCTAAAAATCTCATTTTTAACCCCAAAATTTCCAAAAATTACCA
TTTTACCCTCAAACTCCCAAAAATCCCATTTTTAACCCCAAAACT
Done.