Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012073.1 Kokia drynarioides strain JFW-HI SEQ_127071, 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: 2985
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Found at i:159 original size:30 final size:29
Alignment explanation
Indices: 125--483 Score: 290
Period size: 30 Copynumber: 12.1 Consensus size: 29
115 GGAGGTCCTT
125 GAACTCTCCAAAAATTACCATTTTACCCTC
1 GAACT-TCCAAAAATTACCATTTTACCCTC
* *
155 GAACTTCCAAAACTT-CCATTTTTGACTCT-
1 GAACTTCCAAAAATTACCA-TTTT-ACCCTC
*
184 GAACTTTCCAAAAATTACCATTTTACCCCC
1 GAAC-TTCCAAAAATTACCATTTTACCCTC
* * *
214 GAACTTCCAAAAA-TCCCATTTTTAACCAC
1 GAACTTCCAAAAATTACCA-TTTTACCCTC
* *
243 GAACCTTCTAAAAATTACCATTTTACCCCC
1 GAA-CTTCCAAAAATTACCATTTTACCCTC
* * *
273 AAACTTCCAAAAA-TCCCATTTTTGA-CCTT
1 GAACTTCCAAAAATTACCA-TTTT-ACCCTC
*
302 GAACTTTCTAAAAATTACCATTTTACCCTC
1 GAAC-TTCCAAAAATTACCATTTTACCCTC
* * *
332 TAATTTCCAAAAA-TCCCATCTTTGACCC-C
1 GAACTTCCAAAAATTACCAT-TTT-ACCCTC
*
361 GAACTTTCCAAAAATT-CCAATTTTA-ACTCC
1 GAAC-TTCCAAAAATTACC-ATTTTACCCT-C
391 GAAACCTTCCAAAAATTACCATTTTACCCTC
1 G-AA-CTTCCAAAAATTACCATTTTACCCTC
* *
422 GAACTTCCAAAAA-TCCCATTTTTGA-CTTC
1 GAACTTCCAAAAATTACCA-TTTT-ACCCTC
* *
451 GAACCTTCCAAAAATTACCCTTTTACCCCC
1 GAA-CTTCCAAAAATTACCATTTTACCCTC
481 GAA
1 GAA
484 TGTTTAAAAT
Statistics
Matches: 265, Mismatches: 35, Indels: 58
0.74 0.10 0.16
Matches are distributed among these distances:
28 21 0.08
29 95 0.36
30 106 0.40
31 38 0.14
32 5 0.02
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.31
Consensus pattern (29 bp):
GAACTTCCAAAAATTACCATTTTACCCTC
Found at i:217 original size:59 final size:58
Alignment explanation
Indices: 124--443 Score: 344
Period size: 59 Copynumber: 5.4 Consensus size: 58
114 CGGAGGTCCT
* * * *
124 TGAACTCTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAACTTCCATTTTTGACTC
1 TGAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGAC-C
*
183 TGAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACC
1 TGAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACC
* * * *
241 ACGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACC
1 -TGAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACC
* * * * *
300 TTGAACTTTCTAAAAATTACCATTTTACCCTCTAATTTCCAAAAATCCCATCTTTGACCC
1 -TGAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CC
* * * *
360 CGAACTTTCCAAAAATT-CCAATTTTAACTCCGAAACCTTCCAAAAATTACCA-TTTT-ACCC
1 TGAACTTTCCAAAAATTACC-ATTTTACCCCCG-AA-CTTCCAAAAA-TCCCATTTTTGA-CC
*
420 TCGAAC-TTCCAAAAA-TCCCATTTT
1 T-GAACTTTCCAAAAATTACCATTTT
444 TGACTTCGAA
Statistics
Matches: 226, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
58 3 0.01
59 184 0.81
60 19 0.08
61 16 0.07
62 4 0.02
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (58 bp):
TGAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACC
Found at i:417 original size:149 final size:147
Alignment explanation
Indices: 153--478 Score: 421
Period size: 149 Copynumber: 2.2 Consensus size: 147
143 CATTTTACCC
* ***
153 TCGAA-CTTCCAAAACTT-CCATTTTTGACTCTGAACTTTCCAAAAATTACCATTTTACCCCCGA
1 TCGAACCTTCCAAAAATTACCATTTTACCCTCT-AA-TTTCCAAAAATTACCATTTTACCCCCGA
* *
216 ACTTCCAAAAATCCCATTTTTAACCACGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCC
64 ACTTCCAAAAATCCCAATTTTAACCACGAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCC
281 AAAAATCCCATTTTTGACCT
129 AAAAATCCCATTTTTGA-CT
* * *
301 T-GAACTTTCTAAAAATTACCATTTTACCCTCTAATTTCCAAAAA-TCCCATCTTTGA-CCCCGA
1 TCGAACCTTCCAAAAATTACCATTTTACCCTCTAATTTCCAAAAATTACCAT-TTT-ACCCCCGA
* * *
363 ACTTTCCAAAAATTCCAATTTTAACTC-CGAAACCTTCCAAAAATTACCATTTTACCCTCGAACT
64 AC-TTCCAAAAATCCCAATTTTAAC-CACG-AACCTTCCAAAAATTACCATTTTACCCCCAAACT
427 TCCAAAAATCCCATTTTTGACT
126 TCCAAAAATCCCATTTTTGACT
*
449 TCGAACCTTCCAAAAATTACCCTTTTACCC
1 TCGAACCTTCCAAAAATTACCATTTTACCC
479 CCGAATGTTT
Statistics
Matches: 155, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
146 5 0.03
147 24 0.15
148 38 0.25
149 88 0.57
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (147 bp):
TCGAACCTTCCAAAAATTACCATTTTACCCTCTAATTTCCAAAAATTACCATTTTACCCCCGAAC
TTCCAAAAATCCCAATTTTAACCACGAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAA
AAATCCCATTTTTGACT
Found at i:463 original size:59 final size:60
Alignment explanation
Indices: 336--479 Score: 186
Period size: 59 Copynumber: 2.4 Consensus size: 60
326 ACCCTCTAAT
* *
336 TTCCAAAAA-TCCCATCTTTGACCCCGAACTTTCCAAAAATTCCAATTTTAACTCCGAAACC
1 TTCCAAAAATTACCAT-TTT-ACCCCGAACTTTCCAAAAATCCCAATTTTAACTCCGAAACC
* * *
397 TTCCAAAAATTACCATTTTACCCTCGAAC-TTCCAAAAATCCCATTTTTGACTTCG-AACC
1 TTCCAAAAATTACCATTTTACCC-CGAACTTTCCAAAAATCCCAATTTTAACTCCGAAACC
*
456 TTCCAAAAATTACCCTTTTACCCC
1 TTCCAAAAATTACCATTTTACCCC
480 CGAATGTTTA
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
58 1 0.01
59 26 0.35
60 26 0.35
61 17 0.23
62 5 0.07
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.31
Consensus pattern (60 bp):
TTCCAAAAATTACCATTTTACCCCGAACTTTCCAAAAATCCCAATTTTAACTCCGAAACC
Done.