Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001831.1 Kokia drynarioides strain JFW-HI SEQ_113575, 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, 875

Length: 1459
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:43 original size:29 final size:29

Alignment explanation


    Indices: 1--111  Score: 125
    Period size: 29  Copynumber: 3.8  Consensus size: 29

                                         
          1 AAAATTTAATTTTGGAAAAGTTTGGGGTC
          1 AAAATTTAATTTTGGAAAAGTTTGGGGTC

                 *                  *   *
         30 AAAATATAATTTTGGAAAAGTTTGAGGTT
          1 AAAATTTAATTTTGGAAAAGTTTGGGGTC

                                    *   * 
         59 AAAATTTAATTTTTGG-AAAGTTTAGGGAC
          1 AAAATTTAA-TTTTGGAAAAGTTTGGGGTC

                 **      **         
         88 AAAATGCAATTTTACAAAAGTTTG
          1 AAAATTTAATTTTGGAAAAGTTTG

        112 AGGACCTCTT


Statistics
Matches: 67,  Mismatches: 13, Indels: 4
        0.80            0.15        0.05

Matches are distributed among these distances:
  28    4  0.06
  29   57  0.85
  30    6  0.09

ACGTcount: A:0.40, C:0.04, G:0.20, T:0.37


Consensus pattern (29 bp):   
AAAATTTAATTTTGGAAAAGTTTGGGGTC

Found at i:91 original size:58 final size:58

Alignment explanation


    Indices: 1--114  Score: 158
    Period size: 58  Copynumber: 2.0  Consensus size: 58

                                   *   *       *      **              
          1 AAAATTTAATTTTGGAAAAGTTTGGGGTCAAAATATAATTTTGGAAAAGTTTGAGGTT
          1 AAAATTTAATTTTGGAAAAGTTTAGGGACAAAATACAATTTTACAAAAGTTTGAGGTT

                                               *                     
         59 AAAATTTAATTTTTGG-AAAGTTTAGGGACAAAATGCAATTTTACAAAAGTTTGAGG
          1 AAAATTTAA-TTTTGGAAAAGTTTAGGGACAAAATACAATTTTACAAAAGTTTGAGG

        115 ACCTCTTGAG


Statistics
Matches: 49,  Mismatches: 6, Indels: 2
        0.86            0.11        0.04

Matches are distributed among these distances:
  58   43  0.88
  59    6  0.12

ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36


Consensus pattern (58 bp):   
AAAATTTAATTTTGGAAAAGTTTAGGGACAAAATACAATTTTACAAAAGTTTGAGGTT

Found at i:1137 original size:22 final size:22

Alignment explanation


    Indices: 1090--1137  Score: 55
    Period size: 23  Copynumber: 2.1  Consensus size: 22

       1080 TAGATCTACC

                                   
       1090 TTTCAAATGCCCTTTTGATTGTT
          1 TTTCAAATGCCCTTTT-ATTGTT

                                    
       1113 TTTC-AATGCTCCTTTT-TTGTAT
          1 TTTCAAATGC-CCTTTTATTGT-T

               
       1135 TTT
          1 TTT

       1138 TCGTGGGTAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 5
        0.82            0.00        0.18

Matches are distributed among these distances:
  21    4  0.17
  22    9  0.39
  23   10  0.43

ACGTcount: A:0.15, C:0.17, G:0.10, T:0.58


Consensus pattern (22 bp):   
TTTCAAATGCCCTTTTATTGTT
Done.