Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009248.1 Kokia drynarioides strain JFW-HI SEQ_123953, 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: 2380
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38


Found at i:724 original size:29 final size:28

Alignment explanation


    Indices: 686--933  Score: 183
    Period size: 29  Copynumber: 8.5  Consensus size: 28

        676 TTTAAAAGTC

                                         
        686 ACATTTTAACCCCAAACTTTCCTAAAATT
          1 ACATTTTAACCCCAAACTTTCC-AAAATT

                        *  *     **      
        715 ACATTTTAACCCTAATCTTTTTAAAAATT
          1 ACATTTTAACCCCAAAC-TTTCCAAAATT

             *          **   *           
        744 AAATTTTAAGCCTAAAATTTTCCAAAATT
          1 ACATTTTAA-CCCCAAACTTTCCAAAATT

            *      **                     
        773 GCATTTTGGCCCCTAAACTTTCCCAAAATT
          1 ACATTTTAACCCC-AAACTTT-CCAAAATT

                   *                 *   
        803 AC-TTTTGACCCCAAACTTTCCTAACATT
          1 ACATTTTAACCCCAAACTTTCC-AAAATT

             *          *       *        
        831 ATATTTTAACCCTAAACTTTTCAAAAGTT
          1 ACATTTTAACCCCAAACTTTCCAAAA-TT

                    *     *   *           
        860 ACATTTTAGCCCTTAAAATTTTCCAAAATT
          1 ACATTTTAACCC--CAAACTTTCCAAAATT

            *      *              *       
        890 GCATTTTGACCCTCAAACTCTTTCAAAATT
          1 ACATTTTAACCC-CAAACT-TTCCAAAATT

              *           
        920 ACGTTTTAACCCCA
          1 ACATTTTAACCCCA

        934 TATTCTTTGA


Statistics
Matches: 169,  Mismatches: 40, Indels: 20
        0.74            0.17        0.09

Matches are distributed among these distances:
  27    2  0.01
  28   18  0.11
  29   93  0.55
  30   45  0.27
  31   11  0.07

ACGTcount: A:0.35, C:0.24, G:0.04, T:0.38


Consensus pattern (28 bp):   
ACATTTTAACCCCAAACTTTCCAAAATT

Found at i:845 original size:87 final size:88

Alignment explanation


    Indices: 679--931  Score: 255
    Period size: 87  Copynumber: 2.9  Consensus size: 88

        669 TATTTTGTTT

                  *        *              *             *    *  *    *       
        679 AAAAGTCACATTTTAACCCC-AAACTTTCCTAAAATTACATTTTAACCCTAATCTTTTTAAAAAT
          1 AAAAGTTACATTTTAGCCCCTAAACTTTCCCAAAATTACATTTTGACCCCAAACTTTCTAAAAAT

                      *             
        743 TAAATTTTAAGCCTAAAATTTTCC
         66 TAAATTTTAACCCTAAAATTTT-C

                   *      *                                                * 
        767 AAAA-TTGCATTTTGGCCCCTAAACTTTCCCAAAATTAC-TTTTGACCCCAAACTTTCCT-AACA
          1 AAAAGTTACATTTTAGCCCCTAAACTTTCCCAAAATTACATTTTGACCCCAAACTTT-CTAAAAA

               *              *     
        829 TTATATTTTAACCCTAAACTTTTC
         65 TTAAATTTTAACCCTAAAATTTTC

                               *    *   *        *                       *   
        853 AAAAGTTACATTTTAGCCCTTAAAATTTTCCAAAATTGCATTTTGACCCTCAAACTCTT-TCAAA
          1 AAAAGTTACATTTTAGCCCCTAAACTTTCCCAAAATTACATTTTGACCC-CAAACT-TTCTAAAA

                **         
        917 ATTACGTTTTAACCC
         64 ATTAAATTTTAACCC

        932 CATATTCTTT


Statistics
Matches: 136,  Mismatches: 22, Indels: 13
        0.80            0.13        0.08

Matches are distributed among these distances:
  86    5  0.04
  87   76  0.56
  88   32  0.24
  89   21  0.15
  90    2  0.01

ACGTcount: A:0.35, C:0.23, G:0.04, T:0.37


Consensus pattern (88 bp):   
AAAAGTTACATTTTAGCCCCTAAACTTTCCCAAAATTACATTTTGACCCCAAACTTTCTAAAAAT
TAAATTTTAACCCTAAAATTTTC

Done.