Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006158.1 Kokia drynarioides strain JFW-HI SEQ_120707, 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, 810

Length: 1350
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39


Found at i:731 original size:216 final size:216

Alignment explanation


    Indices: 2--775  Score: 837
    Period size: 216  Copynumber: 3.6  Consensus size: 216

          1 T

                         *  *                    *                    *      
          2 TATTTACGTGAGATTTATTTCTCTCTTGGTTCTCGGATGAACTTACGTACTAGTCAAACTTTTAC
          1 TATTTACGTGAGAATTGTTTCTCTCTTGGTTCTCGGACGAACTTACGTACTAGTCAAAATTTTAC

                                          *                  *               
         67 GAGTTCTTTTACAACTTTGGTTCCTTAAAGCACTCAAGACTATCCATTCATTTGAGCCATTTTTC
         66 GAGTTCTTTTACAACTTTGGTTCCTTAAAGTACTCAAGACTATCCATTCCTTTGAGCCATTTTTC

                           *                                          *      
        132 GAACATTCCATGCTCGAGAAATCGTATCATTTGGTCTAAATAGTTTGTCATTTTGTAAGCAACTT
        131 GAACATTCCATGCTCCAGAAATCGTATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTT

                                *
        197 TTGGTCTTTGAATTAAAAACT
        196 TTGGTCTTTGAATTAAAAACA

                                     **      *    *  *  **     *       *     
        218 TATTTACGTGAGAATTGTTTCTCTCACGGTTCTTGGACAAAATTTTGTACTTG-CGGAACA-TTT
          1 TATTTACGTGAGAATTGTTTCTCTCTTGGTTCTCGGACGAACTTACGTACTAGTC--AAAATTTT

             **  *      **     **      * **                                  
        281 AATAGCTCTTTTGTAACTTAAGTTCCTGAGTGTACTCAAGA-TGATCCATTCCTTTGA-CCAATT
         64 ACGAGTTCTTTTACAACTTTGGTTCCTTAAAGTACTCAAGACT-ATCCATTCCTTTGAGCC-ATT

                    *           * *            *    *   * *         *        
        344 TTTCGAACTTTCCATGCT-CGGGAATCGTATCATTCGGTCCAAAAACTTTGTCATTATGTAAACA
        127 TTTCGAACATTCCATGCTCCAGAAATCGTATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACA

                  *     *           *
        408 ACTTTTAGTCTTCGAATTAAAAACC
        192 ACTTTTGGTCTTTGAATTAAAAACA

                  *                           *             *       *  *     
        433 TATTTAAGTGAGAATTG-TTC-CTCTTGTGTTCTAGGACGAACTTACGAACTAGTCGAACTTTTA
          1 TATTTACGTGAGAATTGTTTCTCTCTTG-GTTCTCGGACGAACTTACGTACTAGTCAAAATTTTA

                     ** *             *     **                   **          
        496 CGAGTTCTTCGATAACTTTGGTTCCTCAAAGTGTTCAAGACTATCCATTCCTTAAAGCCA-TTTT
         65 CGAGTTCTTTTACAACTTTGGTTCCTTAAAGTACTCAAGACTATCCATTCCTTTGAGCCATTTTT

                               *           *                   *      *      
        560 CTGAACATTCCATGCTCCAAAAATC-TCATCTTTTGGTCTAAATAGTTTGTGATTTTGCAAACAA
        130 C-GAACATTCCATGCTCCAGAAATCGT-ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAA

            *           *           
        624 ATTTTGGTCTTTAAATTAAAAACA
        193 CTTTTGGTCTTTGAATTAAAAACA

                       *                         *         *      *          
        648 TATTTACGTGACAATTGTTTCTCTCTTGGTTCTCGGATGAACTTACGGACTAGTTAAAATTTTAC
          1 TATTTACGTGAGAATTGTTTCTCTCTTGGTTCTCGGACGAACTTACGTACTAGTCAAAATTTTAC

                 *                                           *     *       
        713 GAGTTGTTTTACAACTTTGGTTCCTTAAAGTACTCAAGACTATCCATTCATTTGATCCATTTT
         66 GAGTTCTTTTACAACTTTGGTTCCTTAAAGTACTCAAGACTATCCATTCCTTTGAGCCATTTT

        776 GTAAAAACCT


Statistics
Matches: 441,  Mismatches: 102, Indels: 29
        0.77            0.18        0.05

Matches are distributed among these distances:
 213   10  0.02
 214   79  0.18
 215  151  0.34
 216  190  0.43
 217   11  0.02

ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39


Consensus pattern (216 bp):   
TATTTACGTGAGAATTGTTTCTCTCTTGGTTCTCGGACGAACTTACGTACTAGTCAAAATTTTAC
GAGTTCTTTTACAACTTTGGTTCCTTAAAGTACTCAAGACTATCCATTCCTTTGAGCCATTTTTC
GAACATTCCATGCTCCAGAAATCGTATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTT
TTGGTCTTTGAATTAAAAACA
Done.