Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011930.1 Kokia drynarioides strain JFW-HI SEQ_126928, 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: 2002
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.30

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:499 original size:31 final size:31

Alignment explanation


    Indices: 463--529  Score: 100
    Period size: 30  Copynumber: 2.2  Consensus size: 31

        453 GAAACAGTAA

                                       *   
        463 TTTTGGGAAAATTTGGGGTCAAAAATGGGAT
          1 TTTTGGGAAAATTTGGGGTCAAAAATGAGAT

                   *  *                    
        494 TTTT-GGTAATTTTGGGGTCAAAAATGAGAT
          1 TTTTGGGAAAATTTGGGGTCAAAAATGAGAT

                  
        524 TTTTGG
          1 TTTTGG

        530 AGGTTCGGGG


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  30   27  0.84
  31    5  0.16

ACGTcount: A:0.28, C:0.03, G:0.30, T:0.39


Consensus pattern (31 bp):   
TTTTGGGAAAATTTGGGGTCAAAAATGAGAT

Found at i:539 original size:29 final size:29

Alignment explanation


    Indices: 477--582  Score: 131
    Period size: 29  Copynumber: 3.6  Consensus size: 29

        467 GGGAAAATTT

                                      *  *
        477 GGGGTCAAAAATGGGATTTTTGGTAATTTT
          1 GGGGTCAAAAATGGGATTTTTGG-AAGTTC

                         *          *    
        507 GGGGTCAAAAATGAGATTTTTGGAGGTTC
          1 GGGGTCAAAAATGGGATTTTTGGAAGTTC

                **                       
        536 GGGGGAAAAAATGGGATTTTTGGAAGTTC
          1 GGGGTCAAAAATGGGATTTTTGGAAGTTC

            *    *            
        565 AGGGTTAAAAATGGGATT
          1 GGGGTCAAAAATGGGATT

        583 GTTGAACAAT


Statistics
Matches: 65,  Mismatches: 11, Indels: 1
        0.84            0.14        0.01

Matches are distributed among these distances:
  29   43  0.66
  30   22  0.34

ACGTcount: A:0.30, C:0.04, G:0.34, T:0.32


Consensus pattern (29 bp):   
GGGGTCAAAAATGGGATTTTTGGAAGTTC

Found at i:1377 original size:78 final size:78

Alignment explanation


    Indices: 1238--1395  Score: 185
    Period size: 78  Copynumber: 2.0  Consensus size: 78

       1228 CCAGTCGCGA

                *                *               *   *                       
       1238 GTCCGTAGCCACGCGCCGTTGTGCGCTTCCGCCAAGGTAACGTCCGACCGTCCACGCGCCCCACA
          1 GTCCATAGCCACGCGCCGTTGCGCGCTTCCGCCAAGGCAACATCCGACCGTCCACGCGCCCCACA

                *        
       1303 TCTCTAGTCACCG
         66 TCTCCAGTCACCG

                                                         *   *     *  *     *
       1316 GTCCATAGCCACGCGCCGTTGCGCG-TCTCCGCCATA-GCAACATTCGATCGTCCCCGTGCCCCG
          1 GTCCATAGCCACGCGCCGTTGCGCGCT-TCCGCCA-AGGCAACATCCGACCGTCCACGCGCCCCA

                   *       
       1379 CATCTCCGGTCACCG
         64 CATCTCCAGTCACCG

              
       1394 GT
          1 GT

       1396 AAGTTGAAAA


Statistics
Matches: 67,  Mismatches: 11, Indels: 4
        0.82            0.13        0.05

Matches are distributed among these distances:
  77    1  0.01
  78   65  0.97
  79    1  0.01

ACGTcount: A:0.15, C:0.42, G:0.24, T:0.19


Consensus pattern (78 bp):   
GTCCATAGCCACGCGCCGTTGCGCGCTTCCGCCAAGGCAACATCCGACCGTCCACGCGCCCCACA
TCTCCAGTCACCG

Found at i:1802 original size:17 final size:17

Alignment explanation


    Indices: 1780--1813  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       1770 CTAATTTTAG

                             
       1780 TTTAAAATAAACTCAAA
          1 TTTAAAATAAACTCAAA

                  *          
       1797 TTTAAATTAAACTCAAA
          1 TTTAAAATAAACTCAAA

       1814 CTCATAATTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32


Consensus pattern (17 bp):   
TTTAAAATAAACTCAAA
Done.