Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003668.1 Kokia drynarioides strain JFW-HI SEQ_116585, 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: 6214
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32


Found at i:525 original size:24 final size:24

Alignment explanation


    Indices: 493--542  Score: 100
    Period size: 24  Copynumber: 2.1  Consensus size: 24

        483 TATACTAGTT

                                    
        493 TTAGTGTAATAAGGTCAGAGTAGA
          1 TTAGTGTAATAAGGTCAGAGTAGA

                                    
        517 TTAGTGTAATAAGGTCAGAGTAGA
          1 TTAGTGTAATAAGGTCAGAGTAGA

              
        541 TT
          1 TT

        543 CAAGTTCCCC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32


Consensus pattern (24 bp):   
TTAGTGTAATAAGGTCAGAGTAGA

Found at i:1118 original size:24 final size:26

Alignment explanation


    Indices: 1091--1138  Score: 66
    Period size: 24  Copynumber: 1.9  Consensus size: 26

       1081 AGAGAAATGT

                                       
       1091 AAATG-TGATATATGA-A-ATTATGAG
          1 AAATGATGA-ATATGAGAGATTATGAG

                                    
       1115 AAATGATGAATATGAGAGATTATG
          1 AAATGATGAATATGAGAGATTATG

       1139 CCCATGTAGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24   11  0.52
  25    4  0.19
  26    6  0.29

ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31


Consensus pattern (26 bp):   
AAATGATGAATATGAGAGATTATGAG

Found at i:1268 original size:23 final size:23

Alignment explanation


    Indices: 1242--1322  Score: 67
    Period size: 23  Copynumber: 3.6  Consensus size: 23

       1232 TTTCGTACTT

                               *   
       1242 TGTGTGCCTACTGATTTGCGTTA
          1 TGTGTGCCTACTGATTTGCATTA

                **                *
       1265 TGTGCACCTACTGA-TTGCATTG
          1 TGTGTGCCTACTGATTTGCATTA

                   *             * *
       1287 TGTGTGCTTACTAGA-TTGCACTG
          1 TGTGTGCCTACT-GATTTGCATTA

                   *     
       1310 TGTGTGCTTACTG
          1 TGTGTGCCTACTG

       1323 TTTCCCAGCA


Statistics
Matches: 49,  Mismatches: 8, Indels: 3
        0.82            0.13        0.05

Matches are distributed among these distances:
  22   16  0.33
  23   33  0.67

ACGTcount: A:0.15, C:0.19, G:0.26, T:0.41


Consensus pattern (23 bp):   
TGTGTGCCTACTGATTTGCATTA
Done.