Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012350.1 Kokia drynarioides strain JFW-HI SEQ_127352, 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: 1945
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31


Found at i:1644 original size:59 final size:59

Alignment explanation


    Indices: 1474--1796  Score: 420
    Period size: 58  Copynumber: 5.5  Consensus size: 59

       1464 GGAGGTCCCT

                *                         *                      *     
       1474 AAACTTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTC
          1 AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTC

            *                           *                              
       1533 GAACCTTCTAAAAATTACCA-TTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCTC
          1 AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTC

                               *     *          **                   * 
       1591 AAACCTTCTAAAAATTACCTTTTTATCCCCAAACTTTGAAAAATCCCATTTTTGACCCC
          1 AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTC

            *                    *                                   * 
       1650 GAACCTTCTAAAAATTACCATATTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
          1 AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTC

            *                             *     *       **              
       1709 TAACCTTCT-AAAATTACCATTTTACCCCCTAACTTTCAAAAATATCATTTTTGA-CTCC
          1 AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCT-C

                 *        *         *      
       1767 AAACCCTC-AAAAACTACCATTTTGCCCCCA
          1 AAACCTTCTAAAAATTACCATTTTACCCCCA

       1797 TACATCCGAA


Statistics
Matches: 231,  Mismatches: 30, Indels: 7
        0.86            0.11        0.03

Matches are distributed among these distances:
  57    1  0.00
  58  118  0.51
  59  112  0.48

ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31


Consensus pattern (59 bp):   
AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTC

Found at i:1722 original size:117 final size:117

Alignment explanation


    Indices: 1470--1788  Score: 444
    Period size: 117  Copynumber: 2.7  Consensus size: 117

       1460 CCCCGGAGGT

                    *                         *     *                *   *   
       1470 CCCTAAACTTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGA
          1 CCCT-AACCTTCTAAAAATTACCATTTTACCCCCAAACTTTCAAAAATCCCATTTTTGACCCCGA

                                     *                           
       1535 ACCTTCTAAAAATTACCATTTACCCTCAAACTTCCAAAAATCCCATTTTTGAC
         65 ACCTTCTAAAAATTACCATTTACCCCCAAACTTCCAAAAATCCCATTTTTGAC

             * *                  *     *           *                        
       1588 CTCAAACCTTCTAAAAATTACCTTTTTATCCCCAAACTTTGAAAAATCCCATTTTTGACCCCGAA
          1 CCCTAACCTTCTAAAAATTACCATTTTACCCCCAAACTTTCAAAAATCCCATTTTTGACCCCGAA

                                                                 
       1653 CCTTCTAAAAATTACCATATTACCCCCAAACTTCCAAAAATCCCATTTTTGAC
         66 CCTTCTAAAAATTACCAT-TTACCCCCAAACTTCCAAAAATCCCATTTTTGAC

                                             *             **          *  *  
       1706 CCCTAACCTTCT-AAAATTACCATTTTACCCCCTAACTTTCAAAAATATCATTTTTGACTCCAAA
          1 CCCTAACCTTCTAAAAATTACCATTTTACCCCCAAACTTTCAAAAATCCCATTTTTGACCCCGAA

              *        *        
       1770 CCCTC-AAAAACTACCATTT
         66 CCTTCTAAAAATTACCATTT

       1789 TGCCCCCATA


Statistics
Matches: 177,  Mismatches: 23, Indels: 5
        0.86            0.11        0.02

Matches are distributed among these distances:
 115    2  0.01
 116   11  0.06
 117  119  0.67
 118   45  0.25

ACGTcount: A:0.35, C:0.31, G:0.03, T:0.32


Consensus pattern (117 bp):   
CCCTAACCTTCTAAAAATTACCATTTTACCCCCAAACTTTCAAAAATCCCATTTTTGACCCCGAA
CCTTCTAAAAATTACCATTTACCCCCAAACTTCCAAAAATCCCATTTTTGAC

Done.