Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012639.1 Kokia drynarioides strain JFW-HI SEQ_127649, 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, 824

Length: 1374
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30


Found at i:633 original size:163 final size:168

Alignment explanation


    Indices: 341--669  Score: 418
    Period size: 176  Copynumber: 1.9  Consensus size: 168

        331 AAATATGAAA

                      *        *       *               *                     
        341 TACAAAAAAAGCGAATCAATATTATGAGAAAATGACAGTATTATTTTAAAATACGAAGAAAATAG
          1 TACAAAAAAAACGAATCAAGATTATGAAAAAATGACAGTATTAATTTAAAATACGAAGAAAATAG

                *                                                            
        406 TTTAGTTTTATGTACAAAGAATCGAAGAAAAAGAAAATAAAAAAATGGGGTCGAAAAATGAAGTT
         66 TTTAATTTTATGTACAAAGAATC--AG--AAAG--AATAAAAAAA--GGGTCGAAAAATGAAGTT

                                                          
        471 TCGGAGGATTTGGGATCAAAATATAA-TTTGGAAAAGTTTGAGGGT
        123 TCGGAGGATTTGGGATCAAAATATAATTTTGGAAAAGTTTGAGGGT

                                                                     *       
        516 TACAAAAAAATACGAATCAAGATTATGAAAAAATGACAGTATTAATTTAAAATACGATGAAAATA
          1 TACAAAAAAA-ACGAATCAAGATTATGAAAAAATGACAGTATTAATTTAAAATACGAAGAAAATA

            *         *     *                           *                    
        581 TTTTAATTTTCTGTACGAAGAATC-G-AAG-A-AAAAAAA-GGTTGAAAAATGAAGTTTCGGAGG
         65 GTTTAATTTTATGTACAAAGAATCAGAAAGAATAAAAAAAGGGTCGAAAAATGAAGTTTCGGAGG

                   * *     *             
        641 ATTTGGGGTTAAAATGTAATTTTGGAAAA
        130 ATTTGGGATCAAAATATAATTTTGGAAAA

        670 ATTCAAGGGT


Statistics
Matches: 139,  Mismatches: 13, Indels: 15
        0.83            0.08        0.09

Matches are distributed among these distances:
 163   39  0.28
 164    9  0.06
 166    7  0.05
 167    1  0.01
 170    3  0.02
 173    1  0.01
 175   10  0.07
 176   69  0.50

ACGTcount: A:0.47, C:0.06, G:0.19, T:0.27


Consensus pattern (168 bp):   
TACAAAAAAAACGAATCAAGATTATGAAAAAATGACAGTATTAATTTAAAATACGAAGAAAATAG
TTTAATTTTATGTACAAAGAATCAGAAAGAATAAAAAAAGGGTCGAAAAATGAAGTTTCGGAGGA
TTTGGGATCAAAATATAATTTTGGAAAAGTTTGAGGGT

Found at i:713 original size:58 final size:60

Alignment explanation


    Indices: 642--781  Score: 164
    Period size: 58  Copynumber: 2.4  Consensus size: 60

        632 TTTCGGAGGA

                     *       *                                            
        642 TTTG-GGGTTAAAATGTAATTTTG-GAAAAATT-CAAGGGTCAAAATGTAATTGTAGAAAAG
          1 TTTGAGGGTCAAAATGTGATTTTGAGAAAAATTGCAA--GTCAAAATGTAATTGTAGAAAAG

                *                        **   *                *        
        701 -TT-CGGGTCAAAATGTGATTTTGAGAAAGTTTGGAAGTCAAAATGTAATTTTAGAAAAG
          1 TTTGAGGGTCAAAATGTGATTTTGAGAAAAATTGCAAGTCAAAATGTAATTGTAGAAAAG

                                   
        759 TTTGAGGGTCAAAATGTGATTTT
          1 TTTGAGGGTCAAAATGTGATTTT

        782 TTAGATAAAA


Statistics
Matches: 69,  Mismatches: 7, Indels: 9
        0.81            0.08        0.11

Matches are distributed among these distances:
  58   41  0.59
  59    8  0.12
  60   20  0.29

ACGTcount: A:0.37, C:0.04, G:0.24, T:0.34


Consensus pattern (60 bp):   
TTTGAGGGTCAAAATGTGATTTTGAGAAAAATTGCAAGTCAAAATGTAATTGTAGAAAAG

Found at i:728 original size:28 final size:28

Alignment explanation


    Indices: 646--781  Score: 130
    Period size: 30  Copynumber: 4.6  Consensus size: 28

        636 GGAGGATTTG

                *             *     *     
        646 GGGTTAAAATGTAATTTTGGAAAAATTCAA
          1 GGGTCAAAATGTAATTTTAGAAAAGTT--A

                            *          *
        676 GGGTCAAAATGTAATTGTAGAAAAGTTC
          1 GGGTCAAAATGTAATTTTAGAAAAGTTA

                        *               *
        704 GGGTCAAAATGTGATTTT-GAGAAAGTTT
          1 GGGTCAAAATGTAATTTTAGA-AAAGTTA

                                            
        732 GGAAGTCAAAATGTAATTTTAGAAAAGTTTGA
          1 GG--GTCAAAATGTAATTTTAGAAAAG-TT-A

                        *     
        764 GGGTCAAAATGTGATTTT
          1 GGGTCAAAATGTAATTTT

        782 TTAGATAAAA


Statistics
Matches: 89,  Mismatches: 11, Indels: 12
        0.79            0.10        0.11

Matches are distributed among these distances:
  27    2  0.02
  28   24  0.27
  30   57  0.64
  31    4  0.04
  32    2  0.02

ACGTcount: A:0.38, C:0.04, G:0.24, T:0.33


Consensus pattern (28 bp):   
GGGTCAAAATGTAATTTTAGAAAAGTTA
Done.