Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001292.1 Kokia drynarioides strain JFW-HI SEQ_112688, 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, 773

Length: 1289
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.37


Found at i:350 original size:32 final size:31

Alignment explanation


    Indices: 268--391  Score: 110
    Period size: 31  Copynumber: 4.0  Consensus size: 31

        258 AATTTGATAT

                                        *   
        268 TTAATTTTTTTTACTTAATTTGGTACCTGAAC
          1 TTAATTTTTTTT-CTTAATTTGGTACCTAAAC

                 *                         
        300 TTAATATTTTTTCTTAATTTGGTACCTAAAC
          1 TTAATTTTTTTTCTTAATTTGGTACCTAAAC

                *                  * *       *
        331 TTGGCATTTTTTTTC-TAATTTGATGCCTAAGAT
          1 TT--AATTTTTTTTCTTAATTTGGTACCTAA-AC

              *     **                    
        364 TTTATTTTGATTC--AATTTGGTACCTAAA
          1 TTAATTTTTTTTCTTAATTTGGTACCTAAA

        392 TTTATTAAAT


Statistics
Matches: 77,  Mismatches: 12, Indels: 9
        0.79            0.12        0.09

Matches are distributed among these distances:
  29    1  0.01
  30   12  0.16
  31   28  0.36
  32   24  0.31
  33   12  0.16

ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52


Consensus pattern (31 bp):   
TTAATTTTTTTTCTTAATTTGGTACCTAAAC

Found at i:582 original size:31 final size:31

Alignment explanation


    Indices: 541--710  Score: 86
    Period size: 31  Copynumber: 5.6  Consensus size: 31

        531 AAAAAAGATT

                 *                         
        541 AGGTATCAAATTAGAAAAAAGAGTCAAGTTC
          1 AGGTACCAAATTAGAAAAAAGAGTCAAGTTC

                           * ****   *  *  *
        572 AGGTACCAAATT-G-GACCCTA-TAAAATTT
          1 AGGTACCAAATTAGAAAAAAGAGTCAAGTTC

             *       *   *       *         
        600 AAGTACCAACTTAAAAAAAAGTGTCAAGTTC
          1 AGGTACCAAATTAGAAAAAAGAGTCAAGTTC

                          *      *         
        631 AGGTACCAAATTAGGAAAAAGTGTCAAGTT-
          1 AGGTACCAAATTAGAAAAAAGAGTCAAGTTC

            *  *         *          *        
        661 TGAATACCAAATTGGACAAAAA-AAT--A-TTC
          1 AG-GTACCAAATTAGA-AAAAAGAGTCAAGTTC

                                 
        690 AGGTACCAAATTAAGAAAAAA
          1 AGGTACCAAATT-AGAAAAAA

        711 TGTCAAATTC


Statistics
Matches: 98,  Mismatches: 34, Indels: 17
        0.66            0.23        0.11

Matches are distributed among these distances:
  28   31  0.32
  29    6  0.06
  30    3  0.03
  31   53  0.54
  32    5  0.05

ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23


Consensus pattern (31 bp):   
AGGTACCAAATTAGAAAAAAGAGTCAAGTTC

Found at i:696 original size:90 final size:89

Alignment explanation


    Indices: 541--731  Score: 217
    Period size: 90  Copynumber: 2.1  Consensus size: 89

        531 AAAAAAGATT

                                             *               * *             
        541 AGGTATCAAATTAGAAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCCTATAAAATTTAAGTAC
          1 AGGTATCAAATTAGAAAAAAGAGTCAAGTTCAGATACCAAATTGGA-CCAAAAAAATTTAAGTAC

               *                  *   
        606 CAACTTAA-AAAAAAGTGTCAAGTTC
         65 CAAATTAAGAAAAAA-TGTCAAATTC

                 *        *      *         *                              *  
        631 AGGTACCAAATTAGGAAAAAGTGTCAAGTT-TGAATACCAAATTGGA-CAAAAAAATATTCAGGT
          1 AGGTATCAAATTAGAAAAAAGAGTCAAGTTCAG-ATACCAAATTGGACCAAAAAAAT-TT-AAGT

                                       
        694 ACCAAATTAAGAAAAAATGTCAAATTC
         63 ACCAAATTAAGAAAAAATGTCAAATTC

             *         
        721 AAGTATCAAAT
          1 AGGTATCAAAT

        732 ATTGTACTAA


Statistics
Matches: 85,  Mismatches: 12, Indels: 8
        0.81            0.11        0.08

Matches are distributed among these distances:
  88    7  0.08
  89    3  0.04
  90   69  0.81
  91    6  0.07

ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24


Consensus pattern (89 bp):   
AGGTATCAAATTAGAAAAAAGAGTCAAGTTCAGATACCAAATTGGACCAAAAAAATTTAAGTACC
AAATTAAGAAAAAATGTCAAATTC
Done.