Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007790.1 Kokia drynarioides strain JFW-HI SEQ_122424, 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, 835

Length: 1392
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36


Found at i:88 original size:49 final size:48

Alignment explanation


    Indices: 1--172  Score: 161
    Period size: 49  Copynumber: 3.5  Consensus size: 48

                 *       *                   *           *   
          1 GTTGCTACTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTTGTC
          1 GTTGCGACTTAAACCTTTCCCTTCATGCTTC-GTGGTACAAGGTTCGTC

                                  *    *            *       * 
         50 GTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTAC-TGGATTCGCC
          1 GTTGCGACTTAAACCTTTCCCTTCAT-GCTTCGTGGTACAAGG-TTCGTC

               *    *     *                            *       
         99 GTTAC-AGTTTAAATCTTTCCCTTCATGCTTC-TAAGGTACAATGTTCGTC
          1 GTTGCGA-CTTAAACCTTTCCCTTCATGCTTCGT--GGTACAAGGTTCGTC

                                     
        148 GTTGCGACTTAAACCTTTCCCTTCA
          1 GTTGCGACTTAAACCTTTCCCTTCA

        173 AATCTTTGTG


Statistics
Matches: 97,  Mismatches: 19, Indels: 14
        0.75            0.15        0.11

Matches are distributed among these distances:
  47    1  0.01
  48    7  0.07
  49   83  0.86
  50    6  0.06

ACGTcount: A:0.19, C:0.26, G:0.16, T:0.38


Consensus pattern (48 bp):   
GTTGCGACTTAAACCTTTCCCTTCATGCTTCGTGGTACAAGGTTCGTC

Found at i:178 original size:98 final size:98

Alignment explanation


    Indices: 7--215  Score: 312
    Period size: 98  Copynumber: 2.1  Consensus size: 98

          1 GTTGCT

                                      *            *                         
          7 ACTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTTGTCGTTGCGACTTAAACCTTTCCCT
          1 ACTTAAATCTTTCCCTTCATGCTTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCT

               *              *        *     
         72 CCATATCTTCGTGGTACTGGATTCGCCGTTAC-
         66 CCAAATCTTCGTGGTACTAGATTCGCCATTACG

              *                                 *                            
        104 AGTTTAAATCTTTCCCTTCATGCTTCTAAGGTACAATGTTCGTCGTTGCGACTTAAACCTTTCCC
          1 A-CTTAAATCTTTCCCTTCATGCTTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCC

             *        *      *                
        169 TTCAAATCTTTGTGGTATTAGATTCGCCATTACG
         65 TCCAAATCTTCGTGGTACTAGATTCGCCATTACG

                         
        203 ACTTAAATCTTTC
          1 ACTTAAATCTTTC

        216 TCATAATATC


Statistics
Matches: 99,  Mismatches: 11, Indels: 3
        0.88            0.10        0.03

Matches are distributed among these distances:
  97    1  0.01
  98   97  0.98
  99    1  0.01

ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39


Consensus pattern (98 bp):   
ACTTAAATCTTTCCCTTCATGCTTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCT
CCAAATCTTCGTGGTACTAGATTCGCCATTACG

Found at i:1352 original size:63 final size:63

Alignment explanation


    Indices: 1253--1378  Score: 243
    Period size: 63  Copynumber: 2.0  Consensus size: 63

       1243 AGGTTTTCAA

                                                                   *       
       1253 CTCAAATCTCCTTATGTTTCAAAGTGCCCTTTACGGGTTTTCACCTCGACCTCGACCTCTCCT
          1 CTCAAATCTCCTTATGTTTCAAAGTGCCCTTTACGGGTTTTCACCTCGACCTCGAACTCTCCT

                                                                           
       1316 CTCAAATCTCCTTATGTTTCAAAGTGCCCTTTACGGGTTTTCACCTCGACCTCGAACTCTCCT
          1 CTCAAATCTCCTTATGTTTCAAAGTGCCCTTTACGGGTTTTCACCTCGACCTCGAACTCTCCT

       1379 TTTTCTTTTT


Statistics
Matches: 62,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  63   62  1.00

ACGTcount: A:0.18, C:0.34, G:0.13, T:0.35


Consensus pattern (63 bp):   
CTCAAATCTCCTTATGTTTCAAAGTGCCCTTTACGGGTTTTCACCTCGACCTCGAACTCTCCT
Done.