Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002686.1 Kokia drynarioides strain JFW-HI SEQ_114953, 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: 2725
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41


Found at i:1393 original size:39 final size:37

Alignment explanation


    Indices: 1305--1431  Score: 125
    Period size: 37  Copynumber: 3.3  Consensus size: 37

       1295 ACATGTGACA

                                                *  
       1305 AAAAACTAT-AAAAATATAAAAAATAT-TAAATTTTAAT
          1 AAAAA-TATAAAAAATATAAAAAAT-TGTAAATTTTTAT

                   *         *             *       
       1342 AAAAATACAAAAAATATTAAAAATTAG-AATTTTTTTAT
          1 AAAAATATAAAAAATATAAAAAATT-GTAA-ATTTTTAT

                                            *      
       1380 AAAAATCATAAAAAAATATAAAAAATTGTAAAATTTTAT
          1 AAAAAT-AT-AAAAAATATAAAAAATTGTAAATTTTTAT

                         
       1419 AAAAATTATAAAA
          1 AAAAA-TATAAAA

       1432 TGCATCAAAA


Statistics
Matches: 74,  Mismatches: 8, Indels: 15
        0.76            0.08        0.15

Matches are distributed among these distances:
  36    3  0.04
  37   21  0.28
  38   16  0.22
  39   15  0.20
  40   19  0.26

ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32


Consensus pattern (37 bp):   
AAAAATATAAAAAATATAAAAAATTGTAAATTTTTAT

Found at i:2055 original size:94 final size:92

Alignment explanation


    Indices: 1817--2056  Score: 255
    Period size: 94  Copynumber: 2.6  Consensus size: 92

       1807 AATAGGAGTG

                       *       *         * * *         *              ***    
       1817 GTTCAAGTACCCAATTGAGCGCAAAAAAATTAGTGGTTTAATTTCTTTTCTTTTTTTTTTTAAGT
          1 GTTCAAGTACCTAATTGAGTGCAAAAAAAATGGGGGTTTAATTGCTTTT-TTTTTTTTAAAAAGT

                 * *                    
       1882 TTGAGGGTCTTTTTGATGCATTTTGAAA
         65 TTGAGCGCCTTTTTGATGCATTTTGAAA

                      *                 *        **       *           *      
       1910 GTTCAAGTACTTAATTGAGTGCAAAAAAGATGTAGGGCCTTAATTGGTTTTTTTTTTTGAAAAAG
          1 GTTCAAGTACCTAATTGAGTGCAAAAAAAATG--GGGGTTTAATTGCTTTTTTTTTTTTAAAAAG

                           *          ** 
       1975 TTTGAGCGCCTTTTTTATGCATTTTGGTA
         64 TTTGAGCGCCTTTTTGATGCATTTTGAAA

                                  *                              
       2004 GTTCAAGTACCTAATTGAGTGAAAAAAAAAATGGGGGTTTAATTGCTTTTTTT
          1 GTTCAAGTACCTAATTGAGTG-CAAAAAAAATGGGGGTTTAATTGCTTTTTTT

       2057 GAAAAAGTTT


Statistics
Matches: 118,  Mismatches: 26, Indels: 6
        0.79            0.17        0.04

Matches are distributed among these distances:
  93   43  0.36
  94   54  0.46
  95   21  0.18

ACGTcount: A:0.28, C:0.10, G:0.20, T:0.43


Consensus pattern (92 bp):   
GTTCAAGTACCTAATTGAGTGCAAAAAAAATGGGGGTTTAATTGCTTTTTTTTTTTTAAAAAGTT
TGAGCGCCTTTTTGATGCATTTTGAAA
Done.