Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008693.1 Kokia drynarioides strain JFW-HI SEQ_123375, 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: 7911
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35


Found at i:1167 original size:30 final size:30

Alignment explanation


    Indices: 1133--1215  Score: 125
    Period size: 30  Copynumber: 2.7  Consensus size: 30

       1123 TTAAAACCAA

                                          
       1133 GTCAAATTTGAATTTTTGAAAAGTTCAAGG
          1 GTCAAATTTGAATTTTTGAAAAGTTCAAGG

                                           
       1163 GTCAAATTTGAATTTTT-AGAAAGTTCAAGG
          1 GTCAAATTTGAATTTTTGA-AAAGTTCAAGG

                                    
       1193 GTCAAATTAT-AATTTTTGGAAAA
          1 GTCAAATT-TGAATTTTT-GAAAA

       1216 TTTGAGGGTA


Statistics
Matches: 49,  Mismatches: 0, Indels: 7
        0.88            0.00        0.12

Matches are distributed among these distances:
  29    1  0.02
  30   43  0.88
  31    4  0.08
  32    1  0.02

ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37


Consensus pattern (30 bp):   
GTCAAATTTGAATTTTTGAAAAGTTCAAGG

Found at i:2268 original size:16 final size:16

Alignment explanation


    Indices: 2247--2279  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       2237 ATTTATATTC

                             
       2247 ATAAAAT-AATAAATAA
          1 ATAAAATGAA-AAATAA

                            
       2263 ATAAAATGAAAAATAA
          1 ATAAAATGAAAAATAA

             
       2279 A
          1 A

       2280 ATTGGGTTTC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16   14  0.88
  17    2  0.12

ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21


Consensus pattern (16 bp):   
ATAAAATGAAAAATAA

Found at i:6451 original size:9 final size:9

Alignment explanation


    Indices: 6437--6471  Score: 61
    Period size: 9  Copynumber: 3.8  Consensus size: 9

       6427 AAACGAATTT

                     
       6437 AAATTTTTA
          1 AAATTTTTA

                     
       6446 AAATTTTTA
          1 AAATTTTTA

                      
       6455 AAATTTTTAA
          1 AAATTTTT-A

                   
       6465 AAATTTT
          1 AAATTTT

       6472 CAATTTTAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   9   17  0.68
  10    8  0.32

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (9 bp):   
AAATTTTTA
Done.