Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003505.1 Kokia drynarioides strain JFW-HI SEQ_116341, 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: 2067
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1229 original size:29 final size:29

Alignment explanation


    Indices: 1211--1266  Score: 94
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       1201 TGAGAATTTC

                    *    *               
       1211 GAGGCAAAGATGTGATTTTGGAGAAGTCT
          1 GAGGCAAAAATGTAATTTTGGAGAAGTCT

                                       
       1240 GAGGCAAAAATGTAATTTTGGAGAAGT
          1 GAGGCAAAAATGTAATTTTGGAGAAGT

       1267 TTGGGGGTCA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   25  1.00

ACGTcount: A:0.36, C:0.05, G:0.32, T:0.27


Consensus pattern (29 bp):   
GAGGCAAAAATGTAATTTTGGAGAAGTCT

Found at i:1282 original size:30 final size:30

Alignment explanation


    Indices: 1246--1390  Score: 161
    Period size: 30  Copynumber: 4.8  Consensus size: 30

       1236 GTCTGAGGCA

                          * *      * *    
       1246 AAAATGTAATTTTGGAGAAGTTTGGGGGTC
          1 AAAATGTAATTTTGAAAAAGTTTAGAGGTC

                        **            *   
       1276 AAAATGTAATTTCAAAAAAGTTTAGATGTC
          1 AAAATGTAATTTTGAAAAAGTTTAGAGGTC

                  *                        
       1306 AAAATGCAATTTTGAAAAAGTTT-GAGGGTC
          1 AAAATGTAATTTTGAAAAAGTTTAGA-GGTC

                                            
       1336 AAAATGTAATTTT-AGAAAAGTTTA-ACGGTC
          1 AAAATGTAATTTTGA-AAAAGTTTAGA-GGTC

                            *        
       1366 AAAATGTAATTTTGAAGAAGTTTAG
          1 AAAATGTAATTTTGAAAAAGTTTAG

       1391 GGACCCTTGG


Statistics
Matches: 96,  Mismatches: 14, Indels: 9
        0.81            0.12        0.08

Matches are distributed among these distances:
  29    3  0.03
  30   92  0.96
  31    1  0.01

ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33


Consensus pattern (30 bp):   
AAAATGTAATTTTGAAAAAGTTTAGAGGTC

Found at i:1310 original size:60 final size:60

Alignment explanation


    Indices: 1246--1392  Score: 208
    Period size: 60  Copynumber: 2.5  Consensus size: 60

       1236 GTCTGAGGCA

                          *         *                                *   
       1246 AAAATGTAATTTTGGAGAAGTTTGGGGGTCAAAATGTAATTTCAAAAAAGTTTAGA-TGTC
          1 AAAATGTAATTTTGAAGAAGTTTGAGGGTCAAAATGTAATTTCAAAAAAGTTTA-ACGGTC

                  *         *                         * *               
       1306 AAAATGCAATTTTGAAAAAGTTTGAGGGTCAAAATGTAATTTTAGAAAAGTTTAACGGTC
          1 AAAATGTAATTTTGAAGAAGTTTGAGGGTCAAAATGTAATTTCAAAAAAGTTTAACGGTC

                                        
       1366 AAAATGTAATTTTGAAGAAGTTT-AGGG
          1 AAAATGTAATTTTGAAGAAGTTTGAGGG

       1393 ACCCTTGGGC


Statistics
Matches: 77,  Mismatches: 9, Indels: 3
        0.87            0.10        0.03

Matches are distributed among these distances:
  59    5  0.06
  60   72  0.94

ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33


Consensus pattern (60 bp):   
AAAATGTAATTTTGAAGAAGTTTGAGGGTCAAAATGTAATTTCAAAAAAGTTTAACGGTC
Done.