Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000396.1 Kokia drynarioides strain JFW-HI SEQ_111207, 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: 3727
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35


Found at i:502 original size:30 final size:29

Alignment explanation


    Indices: 406--520  Score: 176
    Period size: 29  Copynumber: 3.9  Consensus size: 29

        396 CCCAAGAGGT

                                      *  
        406 CCCGAAACTTCCAAAAATTCCATTTTAAC
          1 CCCGAAACTTCCAAAAATTCCATTTTTAC

              **                         
        435 CCTAAAACTTCCAAAAATTCCATTTTTAC
          1 CCCGAAACTTCCAAAAATTCCATTTTTAC

               *                          
        464 CCCCAAACTTCCAAAAATTCCATTTTTGAC
          1 CCCGAAACTTCCAAAAATTCCATTTTT-AC

                                       
        494 CCCGAAACTTCCAAAAATTACCATTTT
          1 CCCGAAACTTCCAAAAATT-CCATTTT

        521 GCCCCCGGAT


Statistics
Matches: 78,  Mismatches: 6, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  29   51  0.65
  30   20  0.26
  31    7  0.09

ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30


Consensus pattern (29 bp):   
CCCGAAACTTCCAAAAATTCCATTTTTAC

Found at i:548 original size:59 final size:59

Alignment explanation


    Indices: 410--570  Score: 168
    Period size: 59  Copynumber: 2.8  Consensus size: 59

        400 AGAGGTCCCG

                         *         *    *                              
        410 AAACTTCCAAAAATTCCATTTT-AACCCTAAAACTTCCAAAAATTCCATTTTTACCCCC
          1 AAACTTCCAAAAACTCCATTTTCGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC

                         *        *      *                        *     
        468 AAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACCA-TTTTGCCCCC
          1 AAACTTCCAAAAACTCCATTTTCGACCCCAAAACTTCCAAAAATT-CCATTTTTACCCCC

            **               *          *         *       
        527 GGA-TGTCCAAAAACTCTATTTTCGACCTCAAAAC-TCTAAAAATT
          1 AAACT-TCCAAAAACTCCATTTTCGACCCCAAAACTTCCAAAAATT

        571 TCCCTTTTAC


Statistics
Matches: 88,  Mismatches: 12, Indels: 6
        0.83            0.11        0.06

Matches are distributed among these distances:
  58   32  0.36
  59   53  0.60
  60    3  0.03

ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30


Consensus pattern (59 bp):   
AAACTTCCAAAAACTCCATTTTCGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC

Found at i:2152 original size:9 final size:9

Alignment explanation


    Indices: 2138--2168  Score: 53
    Period size: 9  Copynumber: 3.4  Consensus size: 9

       2128 GCAGCTGGAG

                   * 
       2138 AAGAAAGGA
          1 AAGAAAGAA

                     
       2147 AAGAAAGAA
          1 AAGAAAGAA

                     
       2156 AAGAAAGAA
          1 AAGAAAGAA

                
       2165 AAGA
          1 AAGA

       2169 GAAAATTTTG


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   9   21  1.00

ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00


Consensus pattern (9 bp):   
AAGAAAGAA

Found at i:3160 original size:24 final size:25

Alignment explanation


    Indices: 3115--3161  Score: 60
    Period size: 24  Copynumber: 1.9  Consensus size: 25

       3105 CAACAGTTGG

                      *              
       3115 TATTGAAAATTATAAAAATATAGAT
          1 TATTGAAAATGATAAAAATATAGAT

                         *   *     
       3140 TATT-AAAATGATGAAATTATAG
          1 TATTGAAAATGATAAAAATATAG

       3162 TCTTATTATC


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  24   15  0.79
  25    4  0.21

ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36


Consensus pattern (25 bp):   
TATTGAAAATGATAAAAATATAGAT
Done.