Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007246.1 Kokia drynarioides strain JFW-HI SEQ_121861, 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: 5447
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35


Found at i:404 original size:15 final size:15

Alignment explanation


    Indices: 337--411  Score: 64
    Period size: 14  Copynumber: 5.1  Consensus size: 15

        327 TGCTAAGTCA

                          *
        337 ATTATGAACTC-ACA
          1 ATTATGAACTCAACG

                    *  *   
        351 ATTATGAAATCCA-G
          1 ATTATGAACTCAACG

            *             **
        365 GTTATGAACTCAAATA
          1 ATTATGAACTC-AACG

              *            
        381 ATGATGAACTCAACG
          1 ATTATGAACTCAACG

                           
        396 ATTATGAACTCAACG
          1 ATTATGAACTCAACG

             
        411 A
          1 A

        412 GTGGTTTCAG


Statistics
Matches: 47,  Mismatches: 11, Indels: 5
        0.75            0.17        0.08

Matches are distributed among these distances:
  14   19  0.40
  15   19  0.40
  16    9  0.19

ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27


Consensus pattern (15 bp):   
ATTATGAACTCAACG

Found at i:554 original size:24 final size:24

Alignment explanation


    Indices: 485--554  Score: 61
    Period size: 24  Copynumber: 3.0  Consensus size: 24

        475 TGGCATACTA

                  *         *     * 
        485 AAATCATATG-GGGTTTGCATACT
          1 AAATCACATGAGGGTTCGCATATT

              *    * *       **     
        508 AATTCACGTAAGGGTTCATATATT
          1 AAATCACATGAGGGTTCGCATATT

                                   
        532 AAATCACATGAGGGTTCGCATAT
          1 AAATCACATGAGGGTTCGCATAT

        555 GGGGTTCACA


Statistics
Matches: 33,  Mismatches: 13, Indels: 1
        0.70            0.28        0.02

Matches are distributed among these distances:
  23    6  0.18
  24   27  0.82

ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33


Consensus pattern (24 bp):   
AAATCACATGAGGGTTCGCATATT

Found at i:621 original size:23 final size:23

Alignment explanation


    Indices: 565--625  Score: 95
    Period size: 23  Copynumber: 2.7  Consensus size: 23

        555 GGGGTTCACA

                      **           
        565 CATAAGGGTTCACATACTGAATC
          1 CATAAGGGTTTGCATACTGAATC

                                   
        588 CATAAGGGTTTGCATACTGAATC
          1 CATAAGGGTTTGCATACTGAATC

             *             
        611 CTTAAGGGTTTGCAT
          1 CATAAGGGTTTGCAT

        626 TTAGGTTCGC


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  23   35  1.00

ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31


Consensus pattern (23 bp):   
CATAAGGGTTTGCATACTGAATC

Found at i:757 original size:16 final size:16

Alignment explanation


    Indices: 738--812  Score: 71
    Period size: 16  Copynumber: 4.7  Consensus size: 16

        728 GCATTCATAA

                 *          
        738 GGGTTGGCATACATGG
          1 GGGTTCGCATACATGG

                   *        
        754 GGGTTCGTATACAT-G
          1 GGGTTCGCATACATGG

                  *   *      
        769 GGGTTCACATTCATGAG
          1 GGGTTCGCATACATG-G

                     *     *
        786 GGGTTCGCACACATGC
          1 GGGTTCGCATACATGG

                 *     
        802 GGGTTTGCATA
          1 GGGTTCGCATA

        813 ACAGATTACC


Statistics
Matches: 46,  Mismatches: 11, Indels: 4
        0.75            0.18        0.07

Matches are distributed among these distances:
  15   12  0.26
  16   21  0.46
  17   13  0.28

ACGTcount: A:0.20, C:0.17, G:0.35, T:0.28


Consensus pattern (16 bp):   
GGGTTCGCATACATGG
Done.