Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006185.1 Kokia drynarioides strain JFW-HI SEQ_120754, 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: 12418
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33


Found at i:7396 original size:21 final size:21

Alignment explanation


    Indices: 7360--7407  Score: 62
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       7350 ACATTTAGGT

                             *    
       7360 GTTAAGAGAATGATTAATTAAG
          1 GTTAAGAG-ATGATTAAGTAAG

                                  
       7382 GATTAAGAG-TGATTAAGTAAG
          1 G-TTAAGAGATGATTAAGTAAG

                 
       7403 GTTAA
          1 GTTAA

       7408 TGATGAAAGT


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  20    4  0.17
  21   12  0.50
  22    1  0.04
  23    7  0.29

ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31


Consensus pattern (21 bp):   
GTTAAGAGATGATTAAGTAAG

Found at i:7912 original size:13 final size:13

Alignment explanation


    Indices: 7894--7918  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       7884 ATGTAAGAGA

                         
       7894 ATGGTTATTTTGC
          1 ATGGTTATTTTGC

                        
       7907 ATGGTTATTTTG
          1 ATGGTTATTTTG

       7919 TAAAATTGTA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.16, C:0.04, G:0.24, T:0.56


Consensus pattern (13 bp):   
ATGGTTATTTTGC

Found at i:8349 original size:52 final size:52

Alignment explanation


    Indices: 8242--8373  Score: 169
    Period size: 52  Copynumber: 2.5  Consensus size: 52

       8232 AAGAGGTCCG

                   **                             *         *   
       8242 ATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGTTTCA
          1 ATGACTAAATGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGTCTCA

                   *               *                             
       8294 ATGACTATATGTCATCGTGAGTAAATGAATCCTTTACGAATTATGAGGTCT-A
          1 ATGACTAAATGTCATCGTGAGTATATGAATCCTTTACGAATTATGA-GTCTCA

                        *                
       8346 ATGAC-AAAGTGCCATCGTGAGTATATGA
          1 ATGACTAAA-TGTCATCGTGAGTATATGA

       8374 TTCGAAGATC


Statistics
Matches: 70,  Mismatches: 8, Indels: 4
        0.85            0.10        0.05

Matches are distributed among these distances:
  51    2  0.03
  52   65  0.93
  53    3  0.04

ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33


Consensus pattern (52 bp):   
ATGACTAAATGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGTCTCA

Found at i:9701 original size:19 final size:20

Alignment explanation


    Indices: 9657--9701  Score: 56
    Period size: 19  Copynumber: 2.3  Consensus size: 20

       9647 TCCCCAAAAA

                            * * 
       9657 CCCTCAAAACTCTTTATTTT
          1 CCCTCAAAACTCTTTACTCT

                                
       9677 CCCTCAAAACT-TTTACTCT
          1 CCCTCAAAACTCTTTACTCT

             *    
       9696 CTCTCA
          1 CCCTCA

       9702 TTTTCCCCTA


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  19   11  0.50
  20   11  0.50

ACGTcount: A:0.24, C:0.36, G:0.00, T:0.40


Consensus pattern (20 bp):   
CCCTCAAAACTCTTTACTCT

Found at i:12336 original size:24 final size:24

Alignment explanation


    Indices: 12305--12356  Score: 95
    Period size: 24  Copynumber: 2.2  Consensus size: 24

      12295 AAAAATAAAT

                                    
      12305 AGTTTAATTGAAACAAATAAACAA
          1 AGTTTAATTGAAACAAATAAACAA

                            *       
      12329 AGTTTAATTGAAACAATTAAACAA
          1 AGTTTAATTGAAACAAATAAACAA

                
      12353 AGTT
          1 AGTT

      12357 CAAGTCAAAG


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   27  1.00

ACGTcount: A:0.54, C:0.08, G:0.10, T:0.29


Consensus pattern (24 bp):   
AGTTTAATTGAAACAAATAAACAA
Done.