Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007789.1 Kokia drynarioides strain JFW-HI SEQ_122423, 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:0.27, C:0.19, G:0.18, T:0.36


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

Alignment explanation


    Indices: 1--215  Score: 177
    Period size: 49  Copynumber: 4.4  Consensus size: 48

                 *       *                                  * 
          1 GTTGCTACTTAAATCTTTCCCTTCATGCTTC-TAAGGTACAAGGTTCGTC
          1 GTTGCGACTTAAACCTTTCCCTTCATGCTTCGT--GGTACAAGGTTCGCC

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

               *    *     *                   *       *       
         99 GTTAC-AGTTTAAATCTTTCCCTTCATGCTTCTGAGGTACAATGTTCGCC
          1 GTTGCGA-CTTAAACCTTTCCCTTCATGCTTC-GTGGTACAAGGTTCGCC

                                                   **  *      
        148 GTTGCGACTTAAACCTTTCCCTTCAAAT-CTTCGTGGTATTAGATTCGCC
          1 GTTGCGACTTAAACCTTTCCCTTC--ATGCTTCGTGGTACAAGGTTCGCC

            *  *         *     
        197 ATTACGACTTAAATCTTTC
          1 GTTGCGACTTAAACCTTTC

        216 TCATAATATC


Statistics
Matches: 132,  Mismatches: 25, Indels: 18
        0.75            0.14        0.10

Matches are distributed among these distances:
  48    7  0.05
  49  112  0.85
  50   10  0.08
  51    3  0.02

ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38


Consensus pattern (48 bp):   
GTTGCGACTTAAACCTTTCCCTTCATGCTTCGTGGTACAAGGTTCGCC

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

Alignment explanation


    Indices: 7--215  Score: 321
    Period size: 98  Copynumber: 2.1  Consensus size: 98

          1 GTTGCT

                                                     *                       
          7 ACTTAAATCTTTCCCTTCATGCTTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCT
          1 ACTTAAATCTTTCCCTTCATGCTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT

               *              *        *     
         72 CCATATCTTCGTGGTACTGGATTCGCCGTTAC-
         66 CCAAATCTTCGTGGTACTAGATTCGCCATTACG

              *                        *        *                            
        104 AGTTTAAATCTTTCCCTTCATGCTTCTGAGGTACAATGTTCGCCGTTGCGACTTAAACCTTTCCC
          1 A-CTTAAATCTTTCCCTTCATGCTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCC

             *               *                
        169 TTCAAATCTTCGTGGTATTAGATTCGCCATTACG
         65 TCCAAATCTTCGTGGTACTAGATTCGCCATTACG

                         
        203 ACTTAAATCTTTC
          1 ACTTAAATCTTTC

        216 TCATAATATC


Statistics
Matches: 100,  Mismatches: 10, Indels: 3
        0.88            0.09        0.03

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

ACGTcount: A:0.21, C:0.26, G:0.15, T:0.37


Consensus pattern (98 bp):   
ACTTAAATCTTTCCCTTCATGCTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
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.