Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007943.1 Kokia drynarioides strain JFW-HI SEQ_122591, 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, 921

Length: 1536
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.28


Found at i:1291 original size:26 final size:26

Alignment explanation


    Indices: 1261--1482  Score: 202
    Period size: 26  Copynumber: 8.7  Consensus size: 26

       1251 GTACATAGTA

                            *         
       1261 CTTGCTAAACATTCACTGGCTCAAAG
          1 CTTGCTAAACATTCACCGGCTCAAAG

                    *  *               
       1287 CTTGCTAATCAATCACCGGCT-AAAGG
          1 CTTGCTAAACATTCACCGGCTCAAA-G

             * *             *    *   
       1313 CCTACTAAACATTCACCAGCTCGAAG
          1 CTTGCTAAACATTCACCGGCTCAAAG

             *         *              
       1339 CCTGCTAAA-AGTCACCGGCTC-AAG
          1 CTTGCTAAACATTCACCGGCTCAAAG

              *               *        
       1363 ACCTGCTAAACATTCACCAGCTCAAAG
          1 -CTTGCTAAACATTCACCGGCTCAAAG

             *         *            * 
       1390 CCTGCTAAA-AGTCACCGGCTCAAGG
          1 CTTGCTAAACATTCACCGGCTCAAAG

                             **   *   
       1415 CTTGCTAAACATTCACCAACTCGAAG
          1 CTTGCTAAACATTCACCGGCTCAAAG

               *       *              
       1441 CTTTCTAAA-AGTCACCGGCTCAAAG
          1 CTTGCTAAACATTCACCGGCTCAAAG

            *  *             
       1466 TTTACTAAACATTCACC
          1 CTTGCTAAACATTCACC

       1483 TCACATTTCT


Statistics
Matches: 158,  Mismatches: 31, Indels: 14
        0.78            0.15        0.07

Matches are distributed among these distances:
  24    3  0.02
  25   62  0.39
  26   88  0.56
  27    5  0.03

ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22


Consensus pattern (26 bp):   
CTTGCTAAACATTCACCGGCTCAAAG

Found at i:1375 original size:51 final size:51

Alignment explanation


    Indices: 1263--1482  Score: 271
    Period size: 51  Copynumber: 4.3  Consensus size: 51

       1253 ACATAGTACT

                          **         *                    *      
       1263 TGCTAAACATTCACTGGCTCAAAGCTTGCTAATCAA-TCACCGGCTAAAGGCC
          1 TGCTAAACATTCACCAGCTCAAAGCCTGCTAA--AAGTCACCGGCTCAAGGCC

             *                  *                           *  
       1315 TACTAAACATTCACCAGCTCGAAGCCTGCTAAAAGTCACCGGCTCAAGACC
          1 TGCTAAACATTCACCAGCTCAAAGCCTGCTAAAAGTCACCGGCTCAAGGCC

                                                              *
       1366 TGCTAAACATTCACCAGCTCAAAGCCTGCTAAAAGTCACCGGCTCAAGGCT
          1 TGCTAAACATTCACCAGCTCAAAGCCTGCTAAAAGTCACCGGCTCAAGGCC

                            *   *    * *                   * **
       1417 TGCTAAACATTCACCAACTCGAAGCTTTCTAAAAGTCACCGGCTCAAAGTT
          1 TGCTAAACATTCACCAGCTCAAAGCCTGCTAAAAGTCACCGGCTCAAGGCC

             *             
       1468 TACTAAACATTCACC
          1 TGCTAAACATTCACC

       1483 TCACATTTCT


Statistics
Matches: 149,  Mismatches: 18, Indels: 3
        0.88            0.11        0.02

Matches are distributed among these distances:
  50    2  0.01
  51  120  0.81
  52   27  0.18

ACGTcount: A:0.33, C:0.30, G:0.15, T:0.22


Consensus pattern (51 bp):   
TGCTAAACATTCACCAGCTCAAAGCCTGCTAAAAGTCACCGGCTCAAGGCC

Found at i:1431 original size:77 final size:78

Alignment explanation


    Indices: 1261--1431  Score: 190
    Period size: 77  Copynumber: 2.2  Consensus size: 78

       1251 GTACATAGTA

                            *          *      *        *                   * 
       1261 CTTGCTAAACATTCACTGGCTCAAAGCTTGCTAATCAATCACCGGCTAAAGGCCTACTAAACATT
          1 CTTGCTAAACATTCACCGGCTCAAAGCCTGCTAAACAATCACCAGCTAAAGGCCTACTAAACAGT

                         
       1326 CACCAGCTCGAAG
         66 CACCAGCTCGAAG

             *         *                          *                  *       
       1339 CCTGCTAAA-AGTCACCGGCTC-AAGACCTGCTAAACATTCACCAGCTCAAA-GCCTGCTAAA-A
          1 CTTGCTAAACATTCACCGGCTCAAAG-CCTGCTAAACAATCACCAGCT-AAAGGCCTACTAAACA

                  *         
       1400 GTCACCGGCTC-AAGG
         64 GTCACCAGCTCGAA-G

                             
       1415 CTTGCTAAACATTCACC
          1 CTTGCTAAACATTCACC

       1432 AACTCGAAGC


Statistics
Matches: 77,  Mismatches: 12, Indels: 9
        0.79            0.12        0.09

Matches are distributed among these distances:
  75    2  0.03
  76   22  0.29
  77   42  0.55
  78   11  0.14

ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21


Consensus pattern (78 bp):   
CTTGCTAAACATTCACCGGCTCAAAGCCTGCTAAACAATCACCAGCTAAAGGCCTACTAAACAGT
CACCAGCTCGAAG

Done.