Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004141.1 Kokia drynarioides strain JFW-HI SEQ_117339, 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: 6230
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33


Found at i:1679 original size:28 final size:28

Alignment explanation


    Indices: 1638--1692  Score: 92
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       1628 GATATCTGAT

                     *                  
       1638 TTACTCCCTGTTGACCCAAAGGTCATGC
          1 TTACTCCCTATTGACCCAAAGGTCATGC

                   *                   
       1666 TTACTCCTTATTGACCCAAAGGTCATG
          1 TTACTCCCTATTGACCCAAAGGTCATG

       1693 ATGCTCATTT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  28   25  1.00

ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31


Consensus pattern (28 bp):   
TTACTCCCTATTGACCCAAAGGTCATGC

Found at i:1726 original size:36 final size:36

Alignment explanation


    Indices: 1666--1764  Score: 139
    Period size: 36  Copynumber: 2.8  Consensus size: 36

       1656 AAGGTCATGC

                   *                             
       1666 TTACTCCTTATTG-ACCCAAAGGTCATGATGCTCATT
          1 TTACTCCCTA-TGAACCCAAAGGTCATGATGCTCATT

                      *                          
       1702 TTA-TCCCCTGTGAACCCAAAGGTCATGATGCTCATT
          1 TTACT-CCCTATGAACCCAAAGGTCATGATGCTCATT

                       *               
       1738 TTACTCCCTATTAACCCAAAGGTCATG
          1 TTACTCCCTATGAACCCAAAGGTCATG

       1765 CCTATTACCA


Statistics
Matches: 56,  Mismatches: 4, Indels: 6
        0.85            0.06        0.09

Matches are distributed among these distances:
  35    3  0.05
  36   52  0.93
  37    1  0.02

ACGTcount: A:0.26, C:0.27, G:0.14, T:0.32


Consensus pattern (36 bp):   
TTACTCCCTATGAACCCAAAGGTCATGATGCTCATT

Found at i:6065 original size:113 final size:113

Alignment explanation


    Indices: 5923--6149  Score: 393
    Period size: 113  Copynumber: 2.0  Consensus size: 113

       5913 ACTTAGCTAC

                                                                  *      *   
       5923 TAACTACTAAAAATGTAATAATTAATTATAAAATGCCTAGAAAACAATATCCTTGGGTGCGGAAA
          1 TAACTACTAAAAATGTAATAATTAATTATAAAATGCCTAGAAAACAATATCCTTAGGTGCGAAAA

                                         *                   
       5988 TATCCCAAAATAACTACTACATTTGACGTTAGGTT-AGACATCCCAAAA
         66 TATCCCAAAATAACTACTACATTTGACGTCA-GTTCAGACATCCCAAAA

                    *                                                        
       6036 TAACTACTGAAAATGTAATAATTAATTATAAAATGCCTAGAAAACAATATCCTTAGGTGCGAAAA
          1 TAACTACTAAAAATGTAATAATTAATTATAAAATGCCTAGAAAACAATATCCTTAGGTGCGAAAA

                                                        *   
       6101 TATCCCAAAATAACTACTACATTTGACGTCAGTTCAGACATCCCCAAA
         66 TATCCCAAAATAACTACTACATTTGACGTCAGTTCAGACATCCCAAAA

             
       6149 T
          1 T

       6150 GCAAAAGTGC


Statistics
Matches: 108,  Mismatches: 5, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
 112    3  0.03
 113  105  0.97

ACGTcount: A:0.43, C:0.18, G:0.11, T:0.27


Consensus pattern (113 bp):   
TAACTACTAAAAATGTAATAATTAATTATAAAATGCCTAGAAAACAATATCCTTAGGTGCGAAAA
TATCCCAAAATAACTACTACATTTGACGTCAGTTCAGACATCCCAAAA
Done.