Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002993.1 Kokia drynarioides strain JFW-HI SEQ_115484, 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: 3865
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36


Found at i:3092 original size:17 final size:17

Alignment explanation


    Indices: 3067--3108  Score: 66
    Period size: 17  Copynumber: 2.5  Consensus size: 17

       3057 TATCGTGCAT

                *          * 
       3067 ATCATATAGCATAATTA
          1 ATCAAATAGCATAATCA

                             
       3084 ATCAAATAGCATAATCA
          1 ATCAAATAGCATAATCA

                    
       3101 ATCAAATA
          1 ATCAAATA

       3109 ATATTTACCA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  17   23  1.00

ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29


Consensus pattern (17 bp):   
ATCAAATAGCATAATCA

Found at i:3102 original size:62 final size:62

Alignment explanation


    Indices: 3035--3153  Score: 184
    Period size: 62  Copynumber: 1.9  Consensus size: 62

       3025 TGCATATCAT

                              *       *                    *              
       3035 ATCAATCAAATAATATTTGCCATATCGTGCATATCATATAGCATAATTAATCAAATAGCATA
          1 ATCAATCAAATAATATTTACCATATCATGCATATCATATAGCATAATCAATCAAATAGCATA

                                   *           *      *              
       3097 ATCAATCAAATAATATTTACCATTTCATGCATATCGTATAGCGTAATCAATCAAATA
          1 ATCAATCAAATAATATTTACCATATCATGCATATCATATAGCATAATCAATCAAATA

       3154 ATATTTACCA


Statistics
Matches: 51,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  62   51  1.00

ACGTcount: A:0.43, C:0.17, G:0.08, T:0.33


Consensus pattern (62 bp):   
ATCAATCAAATAATATTTACCATATCATGCATATCATATAGCATAATCAATCAAATAGCATA

Found at i:3153 original size:45 final size:45

Alignment explanation


    Indices: 3089--3865  Score: 856
    Period size: 45  Copynumber: 17.2  Consensus size: 45

       3079 AATTAATCAA

                                           *             
       3089 ATAGCATAATCAATCAAATAATATTTACCATTTCATGCATATCGT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

                 *                                *      
       3134 ATAGCGTAATCAATCAAATAATATTTACCATATCATGCGTATCGT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

                                       *                 
       3179 ATAGCATAATCAATCAAATAATATTTATCATATCATGCATATCGT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

                *  *     * *                           * 
       3224 ATAGAATGATCAACCGAATAATATTTACCATATCATGCATATCAT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

            *       *      *                      *      * 
       3269 GTAGCATACTCAATCGAATAATATTTACCATATCATGCGTATCATAT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATC--GT

               *    *   *  *       *                     
       3316 ATAACATAGTCAGTCGAATAATAATTACCATATCATGCATATCGT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

               *      *   **       *  *      *           
       3361 ATAACATAATGAATTGAATAATAATTGCCATATTATGCATATCGT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

            *            **      *                *      
       3406 GTAGCATAATCAAAAAAATAAAATTTACCATATCATGCGTATCGT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

               *      *                 *         **     
       3451 ATAACATAATTAATCAAATAATATTTACTATATCATGCGCATCGT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

                           *           * *               
       3496 ATAGCATAATCAATCGAATAATATTTAGCGTATCATGCATATCGT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

               *           *                    * *  *   
       3541 ATAACATAATCAATCGAATAATATTTACCATATCATACCTACCGT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

            *               * *        *               * 
       3586 TTAGCATAATCAATCAGAGAATATTTATCATATCATGCATATCAT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

                *                       *        **       
       3631 ATAGAATAATCAATCAAATAATATTTACTATATCATGTGTATCAG-
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATC-GT

                    *    * *       *            *        
       3676 ATAGCATAGTCAACCGAATAATAATTACCATATCATTCATATCGT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

               *             *      *              *    * 
       3721 ATAACATAA-CAAATCACATAATAATTACCATATCATGCTTATCAT
          1 ATAGCATAATC-AATCAAATAATATTTACCATATCATGCATATCGT

            *     *              *               **   *  
       3766 GTAGCACAATCAATCAAATAAAATTTACCATATCATGTGTATAGT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

               *           *         *                   
       3811 ATAACATAATCAATCGAATAATATTGACCATATCATGCATATCGT
          1 ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

                      
       3856 ATAGCATAAT
          1 ATAGCATAAT


Statistics
Matches: 606,  Mismatches: 120, Indels: 12
        0.82            0.16        0.02

Matches are distributed among these distances:
  44    2  0.00
  45  564  0.93
  46    1  0.00
  47   39  0.06

ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33


Consensus pattern (45 bp):   
ATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGT

Done.