Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001948.1 Kokia drynarioides strain JFW-HI SEQ_113771, 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: 2664
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37


Found at i:92 original size:10 final size:10

Alignment explanation


    Indices: 77--124  Score: 51
    Period size: 10  Copynumber: 4.4  Consensus size: 10

         67 CCTCAGTCAA

                      
         77 AAAAAAAAAG
          1 AAAAAAAAAG

                       
         87 AAAAAAAAAAG
          1 -AAAAAAAAAG

                         
         98 AAAAAGGGAAAAG
          1 AAAAA---AAAAG

                *     
        111 AAAAGAAAAG
          1 AAAAAAAAAG

                
        121 AAAA
          1 AAAA

        125 CAATATGTTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 7
        0.80            0.02        0.17

Matches are distributed among these distances:
  10   14  0.42
  11   10  0.30
  13    9  0.27

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (10 bp):   
AAAAAAAAAG

Found at i:101 original size:18 final size:18

Alignment explanation


    Indices: 75--119  Score: 56
    Period size: 18  Copynumber: 2.6  Consensus size: 18

         65 TCCCTCAGTC

                              
         75 AAAAA-AAAAAAGAAAAA
          1 AAAAAGAAAAAAGAAAAA

                       * *    
         92 AAAAAGAAAAAGGGAAAA
          1 AAAAAGAAAAAAGAAAAA

            *         
        110 GAAAAGAAAA
          1 AAAAAGAAAA

        120 GAAAACAATA


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  17    5  0.21
  18   19  0.79

ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00


Consensus pattern (18 bp):   
AAAAAGAAAAAAGAAAAA

Found at i:1343 original size:30 final size:31

Alignment explanation


    Indices: 1307--1381  Score: 98
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       1297 CCCCAAAAAA

                        *          * *     
       1307 TTTAAGTATCAACTTAA-AAAAAGTGTCAAG
          1 TTTAAGTATCAAATTAAGAAAAAATATCAAG

                    *                      
       1337 TTTAAGTACCAAATTAAGAAAAAATATCAAG
          1 TTTAAGTATCAAATTAAGAAAAAATATCAAG

              *           
       1368 TTCAAGTATCAAAT
          1 TTTAAGTATCAAAT

       1382 ATTATAGTAA


Statistics
Matches: 38,  Mismatches: 6, Indels: 1
        0.84            0.13        0.02

Matches are distributed among these distances:
  30   15  0.39
  31   23  0.61

ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29


Consensus pattern (31 bp):   
TTTAAGTATCAAATTAAGAAAAAATATCAAG

Found at i:2609 original size:10 final size:10

Alignment explanation


    Indices: 2594--2637  Score: 52
    Period size: 10  Copynumber: 4.4  Consensus size: 10

       2584 AAATAAAATT

                      
       2594 TTTATTTTTA
          1 TTTATTTTTA

                      
       2604 TTTATTTTTA
          1 TTTATTTTTA

             **  *    
       2614 TACATATTTA
          1 TTTATTTTTA

                    * 
       2624 TTTATTTTCA
          1 TTTATTTTTA

                
       2634 TTTA
          1 TTTA

       2638 CCTATGCATA


Statistics
Matches: 27,  Mismatches: 7, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  10   27  1.00

ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70


Consensus pattern (10 bp):   
TTTATTTTTA
Done.