Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001490.1 Kokia drynarioides strain JFW-HI SEQ_113027, 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: 6753
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31


Found at i:347 original size:13 final size:13

Alignment explanation


    Indices: 329--355  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

        319 TTACTGGGTA

                         
        329 GGCGGCACTAGTG
          1 GGCGGCACTAGTG

                         
        342 GGCGGCACTAGTG
          1 GGCGGCACTAGTG

             
        355 G
          1 G

        356 CATCTTTGTC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.15, C:0.22, G:0.48, T:0.15


Consensus pattern (13 bp):   
GGCGGCACTAGTG

Found at i:3455 original size:53 final size:53

Alignment explanation


    Indices: 3386--3511  Score: 141
    Period size: 53  Copynumber: 2.4  Consensus size: 53

       3376 GTTTAGGATC

                  *                                  *     *       
       3386 TTAAGGATTTAGGGTTTAAAGTAATGAGTTTAGGGTTTAATTATTTTTAA-GGTT
          1 TTAAGGGTTTAGGGTTTAAAGTAATGAGTTTAGGGTTT-ATGATTTTCAATGG-T

                                  *  * *     *                   
       3440 TTAAGGGTTT-GGGTTTAAAGTGATTATTTTAGTGTTTATGATTTTCAATGGT
          1 TTAAGGGTTTAGGGTTTAAAGTAATGAGTTTAGGGTTTATGATTTTCAATGGT

                       *         
       3492 TT-AGGGTTTAAGGTTTAAAG
          1 TTAAGGGTTTAGGGTTTAAAG

       3512 GTTAAGTTTT


Statistics
Matches: 62,  Mismatches: 8, Indels: 6
        0.82            0.11        0.08

Matches are distributed among these distances:
  51    7  0.11
  52   21  0.34
  53   25  0.40
  54    9  0.15

ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47


Consensus pattern (53 bp):   
TTAAGGGTTTAGGGTTTAAAGTAATGAGTTTAGGGTTTATGATTTTCAATGGT

Found at i:3607 original size:8 final size:7

Alignment explanation


    Indices: 3489--3605  Score: 55
    Period size: 7  Copynumber: 16.7  Consensus size: 7

       3479 GATTTTCAAT

                  *
       3489 GGTTTAG
          1 GGTTTAA

                   
       3496 GGTTTAA
          1 GGTTTAA

                    
       3503 GGTTTAAA
          1 GGTTT-AA

                   
       3511 GG-TTAA
          1 GGTTTAA

             *   * 
       3517 GTTTTTA
          1 GGTTTAA

                     
       3524 GGTATTATA
          1 GGT-TTA-A

                  *
       3533 --TTTAG
          1 GGTTTAA

                   
       3538 GGTTTAA
          1 GGTTTAA

            *     *
       3545 TGTTTAG
          1 GGTTTAA

                    
       3552 GGTTTTAA
          1 GG-TTTAA

             ** *  
       3560 GCATCAA
          1 GGTTTAA

                   
       3567 -GTTTAA
          1 GGTTTAA

            *      
       3573 AGTTT-A
          1 GGTTTAA

              *    
       3579 GGGTTAA
          1 GGTTTAA

                    
       3586 GAGTTTAA
          1 G-GTTTAA

                   
       3594 GGTTTAA
          1 GGTTTAA

                 
       3601 GGTTT
          1 GGTTT

       3606 TAGTTTAGGG


Statistics
Matches: 80,  Mismatches: 20, Indels: 20
        0.67            0.17        0.17

Matches are distributed among these distances:
   6   13  0.16
   7   49  0.61
   8   17  0.21
   9    1  0.01

ACGTcount: A:0.27, C:0.02, G:0.26, T:0.44


Consensus pattern (7 bp):   
GGTTTAA
Done.