Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001898.1 Kokia drynarioides strain JFW-HI SEQ_113682, 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: 10346
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:3120 original size:30 final size:29

Alignment explanation


    Indices: 3077--3134  Score: 89
    Period size: 30  Copynumber: 2.0  Consensus size: 29

       3067 ACGTTAACAA

                                         
       3077 GACACCCCCACATTTTAAAGTGGTTGTAG
          1 GACACCCCCACATTTTAAAGTGGTTGTAG

                             **          
       3106 GACACCCTCCACATTTTCTAGTGGTTGTA
          1 GACACCC-CCACATTTTAAAGTGGTTGTA

       3135 AGATTGCTTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  29    7  0.27
  30   19  0.73

ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31


Consensus pattern (29 bp):   
GACACCCCCACATTTTAAAGTGGTTGTAG

Found at i:6238 original size:84 final size:83

Alignment explanation


    Indices: 5935--6244  Score: 243
    Period size: 84  Copynumber: 3.7  Consensus size: 83

       5925 TAATTATTAT

                               *   *       *     *        *      *           
       5935 AAAATCTAAATATAGAATATAATTTGTT-AATTGACGAGAATAAATTCCGAAATAGATTTAGTTA
          1 AAAATC-AAATATAGAATAAAATCTGTTAAACTG-CGGGAATAAATCCCGAAACAGATTTA-TTA

                      *          
       5999 ACTTATTATTGTTTTGGAAAC
         63 ACTTATTATTATTTTGGAAAC

                      * *                         *  *     **              * 
       6020 AAAATCAAA-CTGGAATAAAATCTGTTAAA-TGGCAGGAAAAAAATCTAGAAACAGATTTATTTA
          1 AAAATCAAATATAGAATAAAATCTGTTAAACT-GC-GGGAATAAATCCCGAAACAGATTTATTAA

                               * 
       6083 CTTAATTATTA-TTTGGAACC
         64 CTT-ATTATTATTTTGGAAAC

                 *            *      *  *   * *         * *       *          
       6103 AAAAGCCAAATATAGAATTAAATCTTTTGAACGGTGGGAATAAAACTCGAAACAAATTTATTCAA
          1 AAAA-TCAAATATAGAATAAAATCTGTTAAACTGCGGGAATAAATCCCGAAACAGATTTATT-AA

                  * *          *
       6168 CTTATTCTCATTTTGGAAAT
         64 CTTATTATTATTTTGGAAAC

                                  *                             *     
       6188 AAAATCAAA-ATAGAATAAAATATGTTAAACTGCGGGAAATAAATCCCGAAATAGATT
          1 AAAATCAAATATAGAATAAAATCTGTTAAACTGCGGG-AATAAATCCCGAAACAGATT

       6245 ATTTTCCAAT


Statistics
Matches: 172,  Mismatches: 43, Indels: 21
        0.73            0.18        0.09

Matches are distributed among these distances:
  83   54  0.31
  84   81  0.47
  85   37  0.22

ACGTcount: A:0.45, C:0.10, G:0.13, T:0.31


Consensus pattern (83 bp):   
AAAATCAAATATAGAATAAAATCTGTTAAACTGCGGGAATAAATCCCGAAACAGATTTATTAACT
TATTATTATTTTGGAAAC
Done.