Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010739.1 Kokia drynarioides strain JFW-HI SEQ_125692, 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: 1948
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35


Found at i:896 original size:58 final size:59

Alignment explanation


    Indices: 805--957  Score: 177
    Period size: 58  Copynumber: 2.6  Consensus size: 59

        795 CTAAACTATC

                  *                                *          * *      
        805 CAAAAAATCCAATTTTAACCCCAAAACTTCCAAAAATCATATTTATACCCTCGAACTTT
          1 CAAAAATTCCAATTTTAACCCCAAAACTTCCAAAAATCACATTTATACCCCCAAACTTT

                                  *              *      *              
        864 CAAAAATTCC-ATTTTAACCCCGAAACTTCCAAAAATTACATTTTTACCCCCAAACTTT
          1 CAAAAATTCCAATTTTAACCCCAAAACTTCCAAAAATCACATTTATACCCCCAAACTTT

            *       * *     *                     
        922 TAAAAATTACTA-TTTCACCCCAAAA-TGTCCAAAAAT
          1 CAAAAATTCCAATTTTAACCCCAAAACT-TCCAAAAAT

        958 TCCATTTTGA


Statistics
Matches: 81,  Mismatches: 11, Indels: 5
        0.84            0.11        0.05

Matches are distributed among these distances:
  57    1  0.01
  58   70  0.86
  59   10  0.12

ACGTcount: A:0.42, C:0.27, G:0.02, T:0.29


Consensus pattern (59 bp):   
CAAAAATTCCAATTTTAACCCCAAAACTTCCAAAAATCACATTTATACCCCCAAACTTT

Found at i:984 original size:58 final size:59

Alignment explanation


    Indices: 922--1036  Score: 151
    Period size: 58  Copynumber: 2.0  Consensus size: 59

        912 CCCAAACTTT

                      *                                                
        922 TAAAAATTACTATTTCACCCCAAAATGTCCAAAAA-TTCCATTTTGATCCCGATTTTCC
          1 TAAAAATTACCATTTCACCCCAAAATGTCCAAAAATTTCCATTTTGATCCCGATTTTCC

                           *     ***               **         *      
        980 TAAAAATTACCATTTTACCCCCGGATGTCCAAAAATTTCGTTTTTGATCCTGATTTT
          1 TAAAAATTACCATTTCACCCCAAAATGTCCAAAAATTTCCATTTTGATCCCGATTTT

       1037 TTCAAAAGTT


Statistics
Matches: 48,  Mismatches: 8, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  58   30  0.62
  59   18  0.38

ACGTcount: A:0.31, C:0.23, G:0.08, T:0.37


Consensus pattern (59 bp):   
TAAAAATTACCATTTCACCCCAAAATGTCCAAAAATTTCCATTTTGATCCCGATTTTCC

Found at i:1016 original size:29 final size:29

Alignment explanation


    Indices: 797--1001  Score: 127
    Period size: 29  Copynumber: 7.0  Consensus size: 29

        787 GGAGGCCTCT

                          *                *
        797 AAACTATCCAAAAAAT-CCAATTTTAACCCCA
          1 AAACT-TCCAAAAATTACC-ATTTT-ACCCCC

                          *  *          * 
        828 AAACTTCCAAAAATCA-TATTTATACCCTC
          1 AAACTTCCAAAAATTACCATTT-TACCCCC

            *     *                      *
        857 GAACTTTCAAAAATT-CCATTTTAACCCCG
          1 AAACTTCCAAAAATTACCATTTT-ACCCCC

                                          
        886 AAACTTCCAAAAATTA-CATTTTTACCCCC
          1 AAACTTCCAAAAATTACCA-TTTTACCCCC

                  **         *    *      
        915 AAACTTTTAAAAATTACTATTTCA-CCCC
          1 AAACTTCCAAAAATTACCATTTTACCCCC

               *                       *   
        943 AAAATGTCCAAAAATT-CCATTTTGA-TCCC
          1 AAACT-TCCAAAAATTACCATTTT-ACCCCC

            * **                          
        972 GATTTTCCTAAAAATTACCATTTTACCCCC
          1 AAACTTCC-AAAAATTACCATTTTACCCCC

       1002 GGATGTCCAA


Statistics
Matches: 134,  Mismatches: 28, Indels: 25
        0.72            0.15        0.13

Matches are distributed among these distances:
  28   17  0.13
  29   88  0.66
  30   24  0.18
  31    5  0.04

ACGTcount: A:0.39, C:0.28, G:0.02, T:0.31


Consensus pattern (29 bp):   
AAACTTCCAAAAATTACCATTTTACCCCC

Found at i:1083 original size:59 final size:59

Alignment explanation


    Indices: 922--1083  Score: 168
    Period size: 59  Copynumber: 2.8  Consensus size: 59

        912 CCCAAACTTT

                      *    *     * *                                   
        922 TAAAAATTACTATTTCACCCCAAAATGTCCAAAAATTCCA-TTTTGATCCCGATTTTCC
          1 TAAAAATTACCATTTTACCCCCAGATGTCCAAAAATTCCATTTTTGATCCCGATTTTCC

                                  *              * *          *       *
        980 TAAAAATTACCATTTTACCCCCGGATGTCCAAAAATTTCGTTTTTGATCCTGATTTT-T
          1 TAAAAATTACCATTTTACCCCCAGATGTCCAAAAATTCCATTTTTGATCCCGATTTTCC

                  *   *                   **               
       1038 TCAAAAGTTATCATTTTACCCCCA-AGTGTTTAAAAATTCCATTTTT
          1 T-AAAAATTACCATTTTACCCCCAGA-TGTCCAAAAATTCCATTTTT

       1084 AACCCCAAAC


Statistics
Matches: 85,  Mismatches: 16, Indels: 5
        0.80            0.15        0.05

Matches are distributed among these distances:
  58   35  0.41
  59   50  0.59

ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39


Consensus pattern (59 bp):   
TAAAAATTACCATTTTACCCCCAGATGTCCAAAAATTCCATTTTTGATCCCGATTTTCC
Done.