Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013708.1 Kokia drynarioides strain JFW-HI SEQ_128736, 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: 34387
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32

Warning! 69 characters in sequence are not A, C, G, or T


Found at i:13565 original size:21 final size:21

Alignment explanation


    Indices: 13522--13566  Score: 56
    Period size: 20  Copynumber: 2.1  Consensus size: 21

      13512 GCTTCTATTC

                            *     
      13522 AAAACTTACGTTTTAATGGCTA
          1 AAAACTTAC-TTTTAAAGGCTA

                                  
      13544 AAAACTTA-TTTTAAAGGACTA
          1 AAAACTTACTTTTAAAGG-CTA

              
      13565 AA
          1 AA

      13567 TATCATTTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  20    8  0.38
  21    5  0.24
  22    8  0.38

ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33


Consensus pattern (21 bp):   
AAAACTTACTTTTAAAGGCTA

Found at i:28899 original size:30 final size:30

Alignment explanation


    Indices: 28865--29071  Score: 197
    Period size: 30  Copynumber: 6.9  Consensus size: 30

      28855 ATTTTATTTA

                 *                        
      28865 AAAATTACATTTTAACCCTTAAACTTTTCC
          1 AAAATCACATTTTAACCCTTAAACTTTTCC

                                 * *    *  
      28895 AAAATCACATTTTAACTCC-TGAGCTTTCCC
          1 AAAATCACATTTTAAC-CCTTAAACTTTTCC

                         *        *    *  
      28925 AAAATCACATTTTGACCCTTAATCTTTCCC
          1 AAAATCACATTTTAACCCTTAAACTTTTCC

                              *   *       *
      28955 AAAATCACATTTTAACCCCTAATC-TTTCAT
          1 AAAATCACATTTTAACCCTTAAACTTTTC-C

                   *           *       *  
      28985 AAAATCAAATTTTAACCCTCAAACTTTCCC
          1 AAAATCACATTTTAACCCTTAAACTTTTCC

                           *    *          
      29015 AAAATCACATTTTGACCCCTCAAAC-TTTCC
          1 AAAATCACATTTT-AACCCTTAAACTTTTCC

                    *     *             
      29045 TAAAATCATATTTTTACCC-TAAACTTT
          1 -AAAATCACATTTTAACCCTTAAACTTT

      29072 CTAAAAATTA


Statistics
Matches: 146,  Mismatches: 24, Indels: 14
        0.79            0.13        0.08

Matches are distributed among these distances:
  29    9  0.06
  30  110  0.75
  31   27  0.18

ACGTcount: A:0.35, C:0.28, G:0.02, T:0.36


Consensus pattern (30 bp):   
AAAATCACATTTTAACCCTTAAACTTTTCC

Found at i:28943 original size:60 final size:60

Alignment explanation


    Indices: 28865--29087  Score: 268
    Period size: 60  Copynumber: 3.7  Consensus size: 60

      28855 ATTTTATTTA

                 *                     *                  *   * *      *
      28865 AAAATTACATTTTAACCCTTAAACTTTTCCAAAATCACATTTTAACTCCTGAGCTTTCCC
          1 AAAATCACATTTTAACCCTTAAACTTTCCCAAAATCACATTTTAACCCCTAAACTTTCCT

                         *        *                             *     * 
      28925 AAAATCACATTTTGACCCTTAATCTTTCCCAAAATCACATTTTAACCCCTAATCTTTCAT
          1 AAAATCACATTTTAACCCTTAAACTTTCCCAAAATCACATTTTAACCCCTAAACTTTCCT

                   *           *                       *                 
      28985 AAAATCAAATTTTAACCCTCAAACTTTCCCAAAATCACATTTTGACCCCTCAAACTTTCCT
          1 AAAATCACATTTTAACCCTTAAACTTTCCCAAAATCACATTTTAACCCCT-AAACTTTCCT

                   *     *              **     *       
      29046 AAAATCATATTTTTACCC-TAAACTTTCTAAAAATTACATTTT
          1 AAAATCACATTTTAACCCTTAAACTTTCCCAAAATCACATTTT

      29088 GACCAGATAA


Statistics
Matches: 140,  Mismatches: 22, Indels: 2
        0.85            0.13        0.01

Matches are distributed among these distances:
  60  116  0.83
  61   24  0.17

ACGTcount: A:0.35, C:0.26, G:0.02, T:0.36


Consensus pattern (60 bp):   
AAAATCACATTTTAACCCTTAAACTTTCCCAAAATCACATTTTAACCCCTAAACTTTCCT

Found at i:29018 original size:90 final size:90

Alignment explanation


    Indices: 28865--29077  Score: 270
    Period size: 90  Copynumber: 2.4  Consensus size: 90

      28855 ATTTTATTTA

                 *            *          *       *            * *            
      28865 AAAATTACATTTTAACCCTTAAACTTTTCCAAAATCACATTTTAACTCCTGAGCTTTCCCAAAAT
          1 AAAATCACATTTTAACCCCTAAAC-TTTCTAAAATCAAATTTTAACTCCTAAACTTTCCCAAAAT

                           *  *       
      28930 CACATTTTGA-CCCTTAATCTTTCCC
         65 CACATTTTGACCCCTCAAACTTTCCC

                                  *                                          
      28955 AAAATCACATTTTAACCCCTAATCTTTCATAAAATCAAATTTTAAC-CCTCAAACTTTCCCAAAA
          1 AAAATCACATTTTAACCCCTAAACTTTC-TAAAATCAAATTTTAACTCCT-AAACTTTCCCAAAA

                                      *
      29019 TCACATTTTGACCCCTCAAACTTTCCT
         64 TCACATTTTGACCCCTCAAACTTTCCC

                   *     *                   
      29046 AAAATCATATTTTTA-CCCTAAACTTTCTAAAA
          1 AAAATCACATTTTAACCCCTAAACTTTCTAAAA

      29078 ATTACATTTT


Statistics
Matches: 107,  Mismatches: 13, Indels: 7
        0.84            0.10        0.06

Matches are distributed among these distances:
  89   12  0.11
  90   70  0.65
  91   25  0.23

ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35


Consensus pattern (90 bp):   
AAAATCACATTTTAACCCCTAAACTTTCTAAAATCAAATTTTAACTCCTAAACTTTCCCAAAATC
ACATTTTGACCCCTCAAACTTTCCC

Done.