Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008846.1 Kokia drynarioides strain JFW-HI SEQ_123532, 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, 721

Length: 1202
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25


Found at i:130 original size:78 final size:77

Alignment explanation


    Indices: 1--345  Score: 390
    Period size: 78  Copynumber: 4.5  Consensus size: 77

                                *     * **  *           *                    
          1 AGCCA-TCTGATCTTTTACCTCGAGCCTAAGGTAGATCACCATTAACCAATCTCTTACCCCGAGC
          1 AGCCATTC-GATCTTTTACCCCGAGCTTGGGGCAGATCACCA-TCACCAATCTCTTACCCCGAGC

                          
         65 CTGGGGCAGATTGC
         64 CTGGGGCAGATTGC

                                *          *                          **    *
         79 AGCCATTCGATCTTTTACCCTGAGCTTGGGGTAGATCACCATCACCCAATCTCTTACCTTGAGCT
          1 AGCCATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCA-CCAATCTCTTACCCCGAGCC

                 * *    *
        144 TGGGGTATATTGT
         65 TGGGGCAGATTGC

                                        *    *          *              *     
        157 AGCCATTCGATC--TTACCCCGAGCTTGAGGCAAATCACCATCAACAATCTCTTACCCCAAGCCT
          1 AGCCATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCACCAATCTCTTACCCCGAGCCT

                       *
        220 GGGGCAGATTGT
         66 GGGGCAGATTGC

                    *  *       * *   *                                      *
        232 AGCCATTCAATTTTTTACCTCAAGCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCT
          1 AGCCATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCA-CCAATCTCTTACCCCGAGCC

                         
        297 TGGGGCAGATTGC
         65 TGGGGCAGATTGC

                           *              *     
        310 AGCCATTCGATCTTTCACCCCGAGCTTGGGACAGAT
          1 AGCCATTCGATCTTTTACCCCGAGCTTGGGGCAGAT

        346 TGTAGCCATT


Statistics
Matches: 221,  Mismatches: 41, Indels: 10
        0.81            0.15        0.04

Matches are distributed among these distances:
  75   36  0.16
  76   26  0.12
  77   27  0.12
  78  130  0.59
  79    2  0.01

ACGTcount: A:0.24, C:0.30, G:0.20, T:0.27


Consensus pattern (77 bp):   
AGCCATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCACCAATCTCTTACCCCGAGCCT
GGGGCAGATTGC

Found at i:351 original size:117 final size:117

Alignment explanation


    Indices: 209--432  Score: 340
    Period size: 117  Copynumber: 1.9  Consensus size: 117

        199 ACAATCTCTT

                          *                   *       *        *             
        209 ACCCCAAGCCTGGGGCAGATTGTAGCCATTCAATTTTTTACCTCAAGCATGGGGCAGATCACCAT
          1 ACCCCAAGCCTGGGACAGATTGTAGCCATTCAATCTTTTACCCCAAGCATGAGGCAGATCACCAT

              *                   **          *                 
        274 CAGCCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTCGATCTTTC
         66 CAACCAATCTCTTACCCCGAGCCAGGGGCAGATTACAGCCATTCGATCTTTC

                 *   *                     *            *                    
        326 ACCCCGAGCTTGGGACAGATTGTAGCCATTCGATCTTTTACCCCGAGCATGAGGCAGATCACCAT
          1 ACCCCAAGCCTGGGACAGATTGTAGCCATTCAATCTTTTACCCCAAGCATGAGGCAGATCACCAT

                                                      
        391 CAACCAATCTCTTACCCCGAGCCAGGGGCAGATTACAGCCAT
         66 CAACCAATCTCTTACCCCGAGCCAGGGGCAGATTACAGCCAT

        433 CCAATATCTT


Statistics
Matches: 95,  Mismatches: 12, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
 117   95  1.00

ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23


Consensus pattern (117 bp):   
ACCCCAAGCCTGGGACAGATTGTAGCCATTCAATCTTTTACCCCAAGCATGAGGCAGATCACCAT
CAACCAATCTCTTACCCCGAGCCAGGGGCAGATTACAGCCATTCGATCTTTC

Found at i:437 original size:39 final size:39

Alignment explanation


    Indices: 46--445  Score: 236
    Period size: 39  Copynumber: 10.3  Consensus size: 39

         36 TCACCATTAA

                                                   
         46 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT
          1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT

            * *    *      *    *     *             
         85 TCGATCTTTTACCCTGAGCTTGGGGTAGA-T-CA-CCAT
          1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT

                            **    *     * *    *      
        121 CACCCAATCTCTTACCTTGAGCTTGGGGTATATTGTAGCCAT
          1 ---CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT

            * *                *  *      *         
        163 TCGA--TCTTACCCCGAGCTTGAGGCA-AAT-CA-CCAT
          1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT

                             *                *      
        197 CAACAATCTCTTACCCCAAGCCTGGGGCAGATTGTAGCCAT
          1 C--CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT

            *    * *     * *   *                   
        238 TCAATTTTTTACCTCAAGCATGGGGCAGA-T-CA-CCAT
          1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT

                                  *                   
        274 CAGCCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCAT
          1 ---CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT

            * *                 *    *       *      
        316 TCGATCT-TTCACCCCGAGCTTGGGACAGATTGTAGCCAT
          1 CCAATCTCTT-ACCCCGAGCCTGGGGCAGATTGCAGCCAT

            * *    *           *  *                
        355 TCGATCTTTTACCCCGAGCATGAGGCAGA-T-CA-CCAT
          1 CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT

                                   *          *       
        391 CAACCAATCTCTTACCCCGAGCCAGGGGCAGATTACAGCCAT
          1 ---CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT

                 *       
        433 CCAATATCTTACC
          1 CCAATCTCTTACC

        446 TAAAAAAAAT


Statistics
Matches: 280,  Mismatches: 54, Indels: 54
        0.72            0.14        0.14

Matches are distributed among these distances:
  34    4  0.01
  35    1  0.00
  36   16  0.06
  37   21  0.08
  38   23  0.08
  39  188  0.67
  40    6  0.02
  41    9  0.03
  42   12  0.04

ACGTcount: A:0.24, C:0.31, G:0.20, T:0.26


Consensus pattern (39 bp):   
CCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT
Done.