Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006388.1 Kokia drynarioides strain JFW-HI SEQ_120965, 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: 8685
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3713 original size:67 final size:67
Alignment explanation
Indices: 3635--3760 Score: 243
Period size: 67 Copynumber: 1.9 Consensus size: 67
3625 ATTTTGGTTA
3635 ATTTTAATGAAGTAATACATCTCAAACATCATAAATCAGAAATTTAAATATTAATGCAAATTGGT
1 ATTTTAATGAAGTAATACATCTCAAACATCATAAATCAGAAATTTAAATATTAATGCAAATTGGT
3700 AT
66 AT
*
3702 ATTTTAATGAAGTAATACATCTCAAACATCGTAAATCAGAAATTTAAATATTAATGCAA
1 ATTTTAATGAAGTAATACATCTCAAACATCATAAATCAGAAATTTAAATATTAATGCAA
3761 CTCAATAAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (67 bp):
ATTTTAATGAAGTAATACATCTCAAACATCATAAATCAGAAATTTAAATATTAATGCAAATTGGT
AT
Found at i:4159 original size:15 final size:16
Alignment explanation
Indices: 4139--4170 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
4129 TGTTTCAACT
4139 TTTCATAACAA-TACA
1 TTTCATAACAATTACA
4154 TTTCATAACAATTACA
1 TTTCATAACAATTACA
4170 T
1 T
4171 GACATTCGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
TTTCATAACAATTACA
Found at i:4657 original size:25 final size:26
Alignment explanation
Indices: 4602--4660 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
4592 ACAGAGTTTA
*
4602 GCTCTTACGAGCCTAAATAAAATATC
1 GCTCTTACGAGCCTAAACAAAATATC
* *
4628 ACTCTTACGAGCC-AGACAAAATTAT-
1 GCTCTTACGAGCCTAAACAAAA-TATC
4653 GCTCTTAC
1 GCTCTTAC
4661 CAACTAGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 13 0.46
26 15 0.54
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (26 bp):
GCTCTTACGAGCCTAAACAAAATATC
Found at i:4687 original size:27 final size:27
Alignment explanation
Indices: 4647--4703 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
4637 AGCCAGACAA
* *
4647 AATTATGCTCTTACCAACTAGAATCAG
1 AATTACGCTATTACCAACTAGAATCAG
* *
4674 AATTACGCTATTACGAGCTAGAATCAG
1 AATTACGCTATTACCAACTAGAATCAG
4701 AAT
1 AAT
4704 ATCTTCATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (27 bp):
AATTACGCTATTACCAACTAGAATCAG
Found at i:7979 original size:42 final size:42
Alignment explanation
Indices: 7920--8435 Score: 712
Period size: 42 Copynumber: 12.3 Consensus size: 42
7910 AAGGAAAGCA
* *
7920 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
**
7962 TTCATTACATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
** *
8004 TTCATTACATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
8046 TTCATCGCATTTAGAGGCCCATGTATGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
8088 TTCATCACATTTAGAGGCCTAGGTGTGGAGGTCCATTTAATT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
8130 TTCATCTCATTTAGAGGCCCATGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
8172 TTCATCGGATTTAGAGGCCCAAGTGTGGAGGTCCATATA-TT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
*
8213 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATATACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * * * *
8255 TTCATCACATTTAGAGGCCTAGGTGTGAAGGTCCATTCAGTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* *
8297 TTCATTGCATTTAGAGGCCT-AGTGTGGAGGTTCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
8338 TTCATCGCATTTAGAGGCCTAGGTGTGGATGTTCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
* * *
8380 TTCATCGCATTTAGAGGCCGAAGTATGAAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
*
8422 TTCATTGCATTTAG
1 TTCATCGCATTTAG
8436 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:8281 original size:125 final size:126
Alignment explanation
Indices: 7920--8435 Score: 748
Period size: 125 Copynumber: 4.1 Consensus size: 126
7910 AAGGAAAGCA
* *
7920 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTACATTTAGAGGCCTAAG
1 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAAG
* *
7985 TGTGGAGGTCCATTTACTTTTCATTACATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
66 TGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAGGTGTGAAGGTCCATTTACTT
* * *
8046 TTCATCGCATTTAGAGGCCCATGTATGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAGG
1 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAAG
* * * * *
8111 TGTGGAGGTCCATTTAATTTTCATCTCATTTAGAGGCCCATGTGTGGAGGTCCATTTACTT
66 TGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAGGTGTGAAGGTCCATTTACTT
* * *
8172 TTCATCGGATTTAGAGGCCCAAGTGTGGAGGTCCATATA-TTTTCATCGCATTTAGAGGCCTAAG
1 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAAG
* * *
8236 TGTGGAGGTCCATATACTTTTCATCACATTTAGAGGCCTAGGTGTGAAGGTCCATTCAGTT
66 TGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAGGTGTGAAGGTCCATTTACTT
* * * * *
8297 TTCATTGCATTTAGAGG-CCTAGTGTGGAGGTTCATTTACTTTTCATCGCATTTAGAGGCCTAGG
1 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAAG
* * * * * *
8361 TGTGGATGTTCATTTACTTTTCATCGCATTTAGAGGCCGAAGTATGAAGGTCCATTTACTT
66 TGTGGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTAGGTGTGAAGGTCCATTTACTT
*
8422 TTCATTGCATTTAG
1 TTCATCGCATTTAG
8436 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.