Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008801.1 Kokia drynarioides strain JFW-HI SEQ_123484, 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: 4092
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33


Found at i:2305 original size:15 final size:14

Alignment explanation


    Indices: 2270--2382  Score: 55
    Period size: 15  Copynumber: 7.6  Consensus size: 14

       2260 AAAATAATAC

                           
       2270 TAAAGTAAAACAAAA
          1 TAAA-TAAAACAAAA

                            
       2285 TAAAATAAAAGCAAAA
          1 T-AAATAAAA-CAAAA

                  **  *     
       2301 TAAATGGTAAGATAAA
          1 TAAAT-AAAACA-AAA

                      *    
       2317 TAAATAACAATAAAA
          1 TAAATAA-AACAAAA

            *     *   * *  
       2332 AAAATGCAAATATAA
          1 TAAAT-AAAACAAAA

                 **       
       2347 TAAATGCAACAAAA
          1 TAAATAAAACAAAA

             *       *    
       2361 TTAATAAAATAAAA
          1 TAAATAAAACAAAA

                    
       2375 TAAATAAA
          1 TAAATAAA

       2383 TAAATATATG


Statistics
Matches: 73,  Mismatches: 19, Indels: 13
        0.70            0.18        0.12

Matches are distributed among these distances:
  14   22  0.30
  15   28  0.38
  16   23  0.32

ACGTcount: A:0.69, C:0.05, G:0.06, T:0.19


Consensus pattern (14 bp):   
TAAATAAAACAAAA

Found at i:2590 original size:23 final size:23

Alignment explanation


    Indices: 2563--2619  Score: 114
    Period size: 23  Copynumber: 2.5  Consensus size: 23

       2553 ATTTAAAGTA

                                   
       2563 TAAATTAAAAAATGATAAAGGAT
          1 TAAATTAAAAAATGATAAAGGAT

                                   
       2586 TAAATTAAAAAATGATAAAGGAT
          1 TAAATTAAAAAATGATAAAGGAT

                       
       2609 TAAATTAAAAA
          1 TAAATTAAAAA

       2620 TAATAGAAAG


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   34  1.00

ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26


Consensus pattern (23 bp):   
TAAATTAAAAAATGATAAAGGAT

Found at i:2774 original size:19 final size:19

Alignment explanation


    Indices: 2745--2786  Score: 68
    Period size: 20  Copynumber: 2.2  Consensus size: 19

       2735 GGGTAAAATG

                               
       2745 AAAATAAATT-AAAAGATA
          1 AAAATAAATTAAAAAGATA

                                
       2763 AAAATAAAATTAAAAAGATA
          1 AAAAT-AAATTAAAAAGATA

                
       2783 AAAA
          1 AAAA

       2787 AGGCGTAAGG


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  18    5  0.23
  19    5  0.23
  20   12  0.55

ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19


Consensus pattern (19 bp):   
AAAATAAATTAAAAAGATA

Found at i:3554 original size:16 final size:17

Alignment explanation


    Indices: 3525--3564  Score: 50
    Period size: 16  Copynumber: 2.5  Consensus size: 17

       3515 ATTACAATTT

                             
       3525 TTTGTTTTACA-TTTTC
          1 TTTGTTTTACATTTTTC

                              
       3541 TTTGTTTT-CTATTTTTC
          1 TTTGTTTTAC-ATTTTTC

                    
       3558 TTT-TTTT
          1 TTTGTTTT

       3565 GTTTTGCAAG


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  15    1  0.05
  16   13  0.59
  17    8  0.36

ACGTcount: A:0.07, C:0.10, G:0.05, T:0.78


Consensus pattern (17 bp):   
TTTGTTTTACATTTTTC

Found at i:3761 original size:23 final size:25

Alignment explanation


    Indices: 3735--3781  Score: 62
    Period size: 23  Copynumber: 2.0  Consensus size: 25

       3725 TTTTGGGCTT

                                     
       3735 GTTAATTGGG-TATGGG-TATTTAG
          1 GTTAATTGGGCTATGGGTTATTTAG

                *       *           
       3758 GTTAGTTGGGCTTTGGGTTATTTA
          1 GTTAATTGGGCTATGGGTTATTTA

       3782 AGTAGTTGAG


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  23    9  0.45
  24    5  0.25
  25    6  0.30

ACGTcount: A:0.17, C:0.02, G:0.34, T:0.47


Consensus pattern (25 bp):   
GTTAATTGGGCTATGGGTTATTTAG
Done.