Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006387.1 Kokia drynarioides strain JFW-HI SEQ_120964, 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: 8692
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3722 original size:67 final size:67
Alignment explanation
Indices: 3628--3760 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 67
3618 TTGTTTCATT
3628 TTGGTTTATTTTAATGAAGTAATACATCTCAAACATCATAAATCAGAAATTTAAATATTAATGCA
1 TTGGTTTATTTTAATGAAGTAATACATCTCAAACATCATAAATCAGAAATTTAAATATTAATGCA
3693 AA
66 AA
*
3695 TTGGTATT-TTTTAATGAAGTAATACATCTCAAACATCGTAAATCAGAAATTTAAATATTAATGC
1 TTGGT-TTATTTTAATGAAGTAATACATCTCAAACATCATAAATCAGAAATTTAAATATTAATGC
3759 AA
65 AA
3761 CTCAATAAAG
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 62 0.97
68 2 0.03
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.36
Consensus pattern (67 bp):
TTGGTTTATTTTAATGAAGTAATACATCTCAAACATCATAAATCAGAAATTTAAATATTAATGCA
AA
Found at i:4684 original size:27 final size:27
Alignment explanation
Indices: 4651--4710 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
4641 ACGAGCCAGA
* *
4651 CAGAATTATGCTCTTACCAACTAGAAT
1 CAGAATTACGCTATTACCAACTAGAAT
* *
4678 CAGAATTACGCTATTACGAGCTAGAAT
1 CAGAATTACGCTATTACCAACTAGAAT
4705 CAGAAT
1 CAGAAT
4711 ATCTTCATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (27 bp):
CAGAATTACGCTATTACCAACTAGAAT
Found at i:7986 original size:42 final size:42
Alignment explanation
Indices: 7927--8442 Score: 712
Period size: 42 Copynumber: 12.3 Consensus size: 42
7917 AAGGAAAGCA
* *
7927 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
**
7969 TTCATTACATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
** *
8011 TTCATTACATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
8053 TTCATCGCATTTAGAGGCCCATGTATGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
8095 TTCATCACATTTAGAGGCCTAGGTGTGGAGGTCCATTTAATT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
8137 TTCATCTCATTTAGAGGCCCATGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
8179 TTCATCGGATTTAGAGGCCCAAGTGTGGAGGTCCATATA-TT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
*
8220 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATATACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * * * *
8262 TTCATCACATTTAGAGGCCTAGGTGTGAAGGTCCATTCAGTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* *
8304 TTCATTGCATTTAGAGGCCT-AGTGTGGAGGTTCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
8345 TTCATCGCATTTAGAGGCCTAGGTGTGGATGTTCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
8387 TTCATCGCATTTAGAGGCCGAAGTATGAAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
*
8429 TTCATTGCATTTAG
1 TTCATCGCATTTAG
8443 CGTAATTGAG
Statistics
Matches: 426, Mismatches: 46, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
41 74 0.17
42 352 0.83
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (42 bp):
TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
Found at i:8288 original size:125 final size:126
Alignment explanation
Indices: 7927--8442 Score: 748
Period size: 125 Copynumber: 4.1 Consensus size: 126
7917 AAGGAAAGCA
* *
7927 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTACATTTAGAGGCCTAAG
1 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAAG
* *
7992 TGTGGAGGTCCATTTACTTTTCATTACATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
66 TGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAGGTGTGAAGGTCCATTTACTT
* * *
8053 TTCATCGCATTTAGAGGCCCATGTATGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAGG
1 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAAG
* * * * *
8118 TGTGGAGGTCCATTTAATTTTCATCTCATTTAGAGGCCCATGTGTGGAGGTCCATTTACTT
66 TGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAGGTGTGAAGGTCCATTTACTT
* * *
8179 TTCATCGGATTTAGAGGCCCAAGTGTGGAGGTCCATATA-TTTTCATCGCATTTAGAGGCCTAAG
1 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAAG
* * *
8243 TGTGGAGGTCCATATACTTTTCATCACATTTAGAGGCCTAGGTGTGAAGGTCCATTCAGTT
66 TGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAGGTGTGAAGGTCCATTTACTT
* * * * *
8304 TTCATTGCATTTAGAGG-CCTAGTGTGGAGGTTCATTTACTTTTCATCGCATTTAGAGGCCTAGG
1 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAAG
* * * * * *
8368 TGTGGATGTTCATTTACTTTTCATCGCATTTAGAGGCCGAAGTATGAAGGTCCATTTACTT
66 TGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAGGTGTGAAGGTCCATTTACTT
*
8429 TTCATTGCATTTAG
1 TTCATCGCATTTAG
8443 CGTAATTGAG
Statistics
Matches: 350, Mismatches: 39, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
124 18 0.05
125 181 0.52
126 151 0.43
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (126 bp):
TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAAG
TGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAGGTGTGAAGGTCCATTTACTT
Done.