Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005059.1 Kokia drynarioides strain JFW-HI SEQ_118852, 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: 26720
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34


Found at i:4983 original size:23 final size:24

Alignment explanation


    Indices: 4948--4992  Score: 65
    Period size: 23  Copynumber: 1.9  Consensus size: 24

       4938 TTAATCCCTA

                          *         
       4948 TATTCTAATTTGTTTAATTTTAGT
          1 TATTCTAATTTGTTGAATTTTAGT

                *                 
       4972 TATTGTAA-TTGTTGAATTTTA
          1 TATTCTAATTTGTTGAATTTTA

       4993 AAATTTCAAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  23   12  0.63
  24    7  0.37

ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60


Consensus pattern (24 bp):   
TATTCTAATTTGTTGAATTTTAGT

Found at i:5336 original size:15 final size:15

Alignment explanation


    Indices: 5313--5352  Score: 53
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       5303 GACTAAATTT

                *          
       5313 TAAATTTAAAAAATA
          1 TAAAATTAAAAAATA

                        *  
       5328 TAAAATTAAAAACTA
          1 TAAAATTAAAAAATA

             *        
       5343 TCAAATTAAA
          1 TAAAATTAAA

       5353 TTAGAAATAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  15   22  1.00

ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30


Consensus pattern (15 bp):   
TAAAATTAAAAAATA

Found at i:8085 original size:25 final size:24

Alignment explanation


    Indices: 8030--8085  Score: 78
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       8020 GAAGAGCACA

                                    
       8030 ATGATTATTTTTATTAAAAAATTT
          1 ATGATTATTTTTATTAAAAAATTT

                                       
       8054 ATCGATT-TTTTTATTAAAAAACTTTT
          1 AT-GATTATTTTTATTAAAAAA--TTT

                  
       8080 ATGATT
          1 ATGATT

       8086 GAAAGAATAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
  24   16  0.55
  25    8  0.28
  26    5  0.17

ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54


Consensus pattern (24 bp):   
ATGATTATTTTTATTAAAAAATTT

Found at i:9897 original size:31 final size:31

Alignment explanation


    Indices: 9860--9922  Score: 81
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       9850 TTTCTTTAAA

                                             
       9860 TATATATGATTAAATAAAAATTAAAATTTCATG
          1 TATATAT--TTAAATAAAAATTAAAATTTCATG

                     *   * *              
       9893 TATATATTTGAATCACAATTAAAATTTCAT
          1 TATATATTTAAATAAAAATTAAAATTTCAT

       9923 TACAATATAT


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  31   20  0.74
  33    7  0.26

ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41


Consensus pattern (31 bp):   
TATATATTTAAATAAAAATTAAAATTTCATG
Done.