Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002560.1 Kokia drynarioides strain JFW-HI SEQ_114757, 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: 2190
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35


Found at i:163 original size:20 final size:19

Alignment explanation


    Indices: 134--171  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 19

        124 TTCACCTGTT

                      *        
        134 AAATATTATCGATACCAAC
          1 AAATATTATCAATACCAAC

                               
        153 AAATAATTATCAATACCAA
          1 AAAT-ATTATCAATACCAA

        172 AAGCTAGGTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19    4  0.24
  20   13  0.76

ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26


Consensus pattern (19 bp):   
AAATATTATCAATACCAAC

Found at i:761 original size:24 final size:24

Alignment explanation


    Indices: 729--956  Score: 143
    Period size: 24  Copynumber: 9.5  Consensus size: 24

        719 ATAGATTCAT

                    *               
        729 TACGTTTATGCTCGTCAGCTTATA
          1 TACGTTTACGCTCGTCAGCTTATA

                    *      *  *  ** 
        753 TACGTTTATGCTCGTTAGATTGCA
          1 TACGTTTACGCTCGTCAGCTTATA

            *                *   ** 
        777 CACGTTTACGCTCGTCATCTTGCA
          1 TACGTTTACGCTCGTCAGCTTATA

            *       *    * *       *
        801 CACGTTTATGCTCATTAGCTTATG
          1 TACGTTTACGCTCGTCAGCTTATA

                   *         *   ** 
        825 TACGTTTGCGCTCGTCATCTTGCA
          1 TACGTTTACGCTCGTCAGCTTATA

            * *      *   *         *
        849 GATGTTTACACTCATCAGCTTATG
          1 TACGTTTACGCTCGTCAGCTTATA

                   * *       *      
        873 TACGTTTGCACTCGTCATCTTATA
          1 TACGTTTACGCTCGTCAGCTTATA

               *           *     ** 
        897 TACATTTACGCTCGTTAGCTTGCA
          1 TACGTTTACGCTCGTCAGCTTATA

            *        *               
        921 CACGTTTACTCTCGTC-GACTTATA
          1 TACGTTTACGCTCGTCAG-CTTATA

                        
        945 TACGTTTACGCT
          1 TACGTTTACGCT

        957 TTTATTTATA


Statistics
Matches: 148,  Mismatches: 55, Indels: 2
        0.72            0.27        0.01

Matches are distributed among these distances:
  23    1  0.01
  24  147  0.99

ACGTcount: A:0.20, C:0.25, G:0.17, T:0.39


Consensus pattern (24 bp):   
TACGTTTACGCTCGTCAGCTTATA

Found at i:791 original size:48 final size:48

Alignment explanation


    Indices: 730--956  Score: 177
    Period size: 48  Copynumber: 4.7  Consensus size: 48

        720 TAGATTCATT

                   *        *              *    *    *  *   
        730 ACGTTTATGCTCGTCAGCTTATATACGTTTATGCTCGTTAGATTGCAC
          1 ACGTTTACGCTCGTCATCTTATATACGTTTACGCTCATTAGCTTACAC

                                ** *       *             ***
        778 ACGTTTACGCTCGTCATCTTGCACACGTTTATGCTCATTAGCTTATGT
          1 ACGTTTACGCTCGTCATCTTATATACGTTTACGCTCATTAGCTTACAC

                  *             ** * *      *     *      ***
        826 ACGTTTGCGCTCGTCATCTTGCAGATGTTTACACTCATCAGCTTATGT
          1 ACGTTTACGCTCGTCATCTTATATACGTTTACGCTCATTAGCTTACAC

                  * *                 *         *       *   
        874 ACGTTTGCACTCGTCATCTTATATACATTTACGCTCGTTAGCTTGCAC
          1 ACGTTTACGCTCGTCATCTTATATACGTTTACGCTCATTAGCTTACAC

                    *                           
        922 ACGTTTACTCTCGTCGA-CTTATATACGTTTACGCT
          1 ACGTTTACGCTCGTC-ATCTTATATACGTTTACGCT

        957 TTTATTTATA


Statistics
Matches: 145,  Mismatches: 33, Indels: 2
        0.81            0.18        0.01

Matches are distributed among these distances:
  48  144  0.99
  49    1  0.01

ACGTcount: A:0.20, C:0.25, G:0.17, T:0.39


Consensus pattern (48 bp):   
ACGTTTACGCTCGTCATCTTATATACGTTTACGCTCATTAGCTTACAC
Done.