Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002561.1 Kokia drynarioides strain JFW-HI SEQ_114758, 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: 161
    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 TACGTTTACGCTCGTCATCTTGCA
          1 TACGTTTACGCTCGTCAGCTTATA

            * *      *   *         *
        849 CATGTTTACACTCATCAGCTTATG
          1 TACGTTTACGCTCGTCAGCTTATA

                   * *       *      
        873 TACGTTTGCACTCGTCATCTTATA
          1 TACGTTTACGCTCGTCAGCTTATA

               *                 ** 
        897 TACATTTACGCTCGTCAGCTTGCA
          1 TACGTTTACGCTCGTCAGCTTATA

            *        *               
        921 CACGTTTACTCTCGTC-GACTTATA
          1 TACGTTTACGCTCGTCAG-CTTATA

                        
        945 TACGTTTACGCT
          1 TACGTTTACGCT

        957 TTTATTTATA


Statistics
Matches: 152,  Mismatches: 51, Indels: 2
        0.74            0.25        0.01

Matches are distributed among these distances:
  23    1  0.01
  24  151  0.99

ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39


Consensus pattern (24 bp):   
TACGTTTACGCTCGTCAGCTTATA

Found at i:943 original size:72 final size:72

Alignment explanation


    Indices: 729--953  Score: 227
    Period size: 72  Copynumber: 3.1  Consensus size: 72

        719 ATAGATTCAT

                    **                      *      *  *              *       
        729 TACGTTTATGCTCGTCAGCTTATATACGTTTATGCTCGTTAGATTGCACACGTTTACGCTCGTCA
          1 TACGTTTACACTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACGTTTACACTCGTCA

            *   ** 
        794 TCTTGCA
         66 GCTTATA

            *       **   * *       *                 *        *          *   
        801 CACGTTTATGCTCATTAGCTTATGTACGTTTACGCTCGTCATCTTGCACATGTTTACACTCATCA
          1 TACGTTTACACTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACGTTTACACTCGTCA

                  *
        866 GCTTATG
         66 GCTTATA

                   *         *         *                             *       
        873 TACGTTTGCACTCGTCATCTTATATACATTTACGCTCGTCAGCTTGCACACGTTTACTCTCGTC-
          1 TACGTTTACACTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACGTTTACACTCGTCA

                    
        937 GACTTATA
         66 G-CTTATA

                     
        945 TACGTTTAC
          1 TACGTTTAC

        954 GCTTTTATTT


Statistics
Matches: 122,  Mismatches: 30, Indels: 2
        0.79            0.19        0.01

Matches are distributed among these distances:
  71    1  0.01
  72  121  0.99

ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39


Consensus pattern (72 bp):   
TACGTTTACACTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACGTTTACACTCGTCA
GCTTATA
Done.