Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004587.1 Kokia drynarioides strain JFW-HI SEQ_118077, 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, 898

Length: 1498
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40


Found at i:322 original size:29 final size:29

Alignment explanation


    Indices: 279--466  Score: 175
    Period size: 30  Copynumber: 6.4  Consensus size: 29

        269 TTACTTATCC

                  *        *             
        279 AAAATTGCATTTTAAACCTAAAATTTTCT
          1 AAAATTACATTTTAACCCTAAAATTTTCT

                  *   *            *   *  
        308 AAAATTTCATCTTAACCCTTAAACTTTCCT
          1 AAAATTACATTTTAACCC-TAAAATTTTCT

                 *             *   *      
        338 AAAATCACATTTTAACCC-CAAACTTTCTT
          1 AAAATTACATTTTAACCCTAAAATTTTC-T

                 *                *     *
        367 AAAATCACATTTTAACCCTAAACTTTTCC
          1 AAAATTACATTTTAACCCTAAAATTTTCT

                                   *    * 
        396 AAAATTACATTTTAACCCCTAAACTTTTTT
          1 AAAATTACATTTTAA-CCCTAAAATTTTCT

                          *          *   
        426 AAAATTACATTTTACCCCT-AAATTCTCT
          1 AAAATTACATTTTAACCCTAAAATTTTCT

                          
        454 AAAACTT-CATTTT
          1 AAAA-TTACATTTT

        467 TTAACTCTTT


Statistics
Matches: 131,  Mismatches: 23, Indels: 11
        0.79            0.14        0.07

Matches are distributed among these distances:
  28   21  0.16
  29   54  0.41
  30   56  0.43

ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39


Consensus pattern (29 bp):   
AAAATTACATTTTAACCCTAAAATTTTCT

Found at i:342 original size:59 final size:57

Alignment explanation


    Indices: 271--447  Score: 176
    Period size: 59  Copynumber: 3.0  Consensus size: 57

        261 TAGCCCTCTT

                          *                            *               
        271 ACTTATCCAAAATTGCATTTTAAACCTAAAATTTTCTAAAATTTCATCTTAACCCTTAA
          1 ACTT-TCCAAAATTACATTTTAAACCTAAAATTTTCTAAAATTACATCTTAACCC-TAA

                         *            **   *           *    *          
        330 ACTTTCCTAAAATCACATTTT-AACCCCAAACTTTCTTAAAATCACATTTTAACCCTAA
          1 ACTTTCC-AAAATTACATTTTAAACCTAAAATTTTC-TAAAATTACATCTTAACCCTAA

                                    *      *    *           *   *      
        388 ACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTTTAAAATTACATTTTACCCCTAA
          1 AC-TTTCCAAAATTACATTTTAA-ACCTAAAATTTTCTAAAATTACATCTTAACCCTAA

             
        447 A
          1 A

        448 TTCTCTAAAA


Statistics
Matches: 96,  Mismatches: 17, Indels: 10
        0.78            0.14        0.08

Matches are distributed among these distances:
  58   31  0.32
  59   58  0.60
  60    7  0.07

ACGTcount: A:0.38, C:0.24, G:0.01, T:0.38


Consensus pattern (57 bp):   
ACTTTCCAAAATTACATTTTAAACCTAAAATTTTCTAAAATTACATCTTAACCCTAA

Found at i:432 original size:30 final size:30

Alignment explanation


    Indices: 249--466  Score: 209
    Period size: 29  Copynumber: 7.4  Consensus size: 30

        239 TTTTATTTTG

                          *       *    *  *
        249 AAAATTACATTTTAGCCCTCT-TACTTATCC
          1 AAAATTACATTTTAACCC-CTAAACTTTTCT

                  *         *      *      
        279 AAAATTGCATTTTAA-ACCTAAAATTTTCT
          1 AAAATTACATTTTAACCCCTAAACTTTTCT

                  *   *       *        *  
        308 AAAATTTCATCTTAACCCTTAAACTTTCCT
          1 AAAATTACATTTTAACCCCTAAACTTTTCT

                 *                         
        338 AAAATCACATTTTAACCCC-AAAC-TTTCTT
          1 AAAATTACATTTTAACCCCTAAACTTTTC-T

                 *                       *
        367 AAAATCACATTTTAA-CCCTAAACTTTTCC
          1 AAAATTACATTTTAACCCCTAAACTTTTCT

                                        * 
        396 AAAATTACATTTTAACCCCTAAACTTTTTT
          1 AAAATTACATTTTAACCCCTAAACTTTTCT

                                      *   
        426 AAAATTACATTTT-ACCCCTAAA-TTCTCT
          1 AAAATTACATTTTAACCCCTAAACTTTTCT

                          
        454 AAAACTT-CATTTT
          1 AAAA-TTACATTTT

        467 TTAACTCTTT


Statistics
Matches: 157,  Mismatches: 24, Indels: 16
        0.80            0.12        0.08

Matches are distributed among these distances:
  28   22  0.14
  29   68  0.43
  30   67  0.43

ACGTcount: A:0.36, C:0.23, G:0.01, T:0.39


Consensus pattern (30 bp):   
AAAATTACATTTTAACCCCTAAACTTTTCT

Done.