Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009593.1 Kokia drynarioides strain JFW-HI SEQ_124309, 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: 3985
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34


Found at i:650 original size:25 final size:23

Alignment explanation


    Indices: 535--708  Score: 115
    Period size: 23  Copynumber: 7.5  Consensus size: 23

        525 ACACTAGCGC

                              *  *  
        535 GCTCTCTGTTTAGCACATCT-CGT
          1 GCTCTCTGTTTAGCAC-TTTGTGT

                               *     
        558 GCTCTCTGTTATTAGCACTATGTGT
          1 GCTCTCTG-T-TTAGCACTTTGTGT

                    *   *          
        583 GCTCTCTGATTATCACTTTGTGT
          1 GCTCTCTGTTTAGCACTTTGTGT

                    *    *         
        606 GCTCTCTGATTAGTACTTTGTGT
          1 GCTCTCTGTTTAGCACTTTGTGT

            *                *      
        629 ACTCTCTGTTTAGCACAGTT-TGT
          1 GCTCTCTGTTTAGCAC-TTTGTGT

                 *       * *      *   
        652 GCTCTTTGTTGCCCAACAC-TTATGT
          1 GCTCTCTGTT---TAGCACTTTGTGT

                         *         
        677 GCTCTCTG-TTAGTACTTTG-GT
          1 GCTCTCTGTTTAGCACTTTGTGT

            *          
        698 ACTCTCTGTTT
          1 GCTCTCTGTTT

        709 GTTCCGTATA


Statistics
Matches: 120,  Mismatches: 21, Indels: 21
        0.74            0.13        0.13

Matches are distributed among these distances:
  21   12  0.10
  22    4  0.03
  23   65  0.54
  24    8  0.07
  25   27  0.22
  26    4  0.03

ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45


Consensus pattern (23 bp):   
GCTCTCTGTTTAGCACTTTGTGT

Found at i:653 original size:46 final size:46

Alignment explanation


    Indices: 536--656  Score: 136
    Period size: 46  Copynumber: 2.6  Consensus size: 46

        526 CACTAGCGCG

                               *                           *
        536 CTCTCTGTTTAGCACATCTCGTGCTCTCTGTTATTAGCACTATGTGTG
          1 CTCTCTGTTTAGCACAT-TTGTGCTCTCTG-TATTAGCACTATGTGTA

                   *   *   *                    *   *      
        584 CTCTCTGATTATCACTTTGTGTGCTCTCTG-ATTAGTACTTTGTGTA
          1 CTCTCTGTTTAGCACATT-TGTGCTCTCTGTATTAGCACTATGTGTA

                                       
        630 CTCTCTGTTTAGCACAGTTTGTGCTCT
          1 CTCTCTGTTTAGCACA-TTTGTGCTCT

        657 TTGTTGCCCA


Statistics
Matches: 61,  Mismatches: 10, Indels: 6
        0.79            0.13        0.08

Matches are distributed among these distances:
  46   34  0.56
  47    3  0.05
  48   24  0.39

ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45


Consensus pattern (46 bp):   
CTCTCTGTTTAGCACATTTGTGCTCTCTGTATTAGCACTATGTGTA

Found at i:2425 original size:22 final size:22

Alignment explanation


    Indices: 2382--2426  Score: 56
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2372 ACCCATATTT

                *            *    
       2382 ATTTTAATTTATTTAGTTTTGA
          1 ATTTCAATTTATTTAGTGTTGA

                                   
       2404 ATTTCAATTTCATTTAG-GTTGA
          1 ATTTCAATTT-ATTTAGTGTTGA

             
       2426 A
          1 A

       2427 AATTAATAAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  22   14  0.70
  23    6  0.30

ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56


Consensus pattern (22 bp):   
ATTTCAATTTATTTAGTGTTGA
Done.