Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001966.1 Kokia drynarioides strain JFW-HI SEQ_113804, 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: 17058
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35


Found at i:2871 original size:87 final size:87

Alignment explanation


    Indices: 2711--2871  Score: 186
    Period size: 87  Copynumber: 1.9  Consensus size: 87

       2701 AAAAGATTAT

                                *                    *     *     *         * 
       2711 GTACCAAATTAAGAAAAAGAGTTAAGTTCAGGTATCAAATTGGACCTCAAAAAGTTTAAGTACCA
          1 GTACCAAATTAAGAAAAAGAATTAAGTTCAGGTATCAAATTAGACCTAAAAAAATTTAAGTACAA

             * *                  
       2776 ATTTAAAAAGTGTCAAGTTTTG
         66 ACTAAAAAAGTGTCAAGTTTTG

                                          *                                  
       2798 GTACCAAATTAAGAAAAA-ATATTAAGTT-TGAGTATCAAATTAGA-CTAAAAAAATTT-AGATA
          1 GTACCAAATTAAGAAAAAGA-ATTAAGTTCAG-GTATCAAATTAGACCTAAAAAAATTTAAG-TA

                         
       2859 CTAAACTAAAAAA
         63 C-AAACTAAAAAA

       2872 AAATGTTAAG


Statistics
Matches: 62,  Mismatches: 8, Indels: 8
        0.79            0.10        0.10

Matches are distributed among these distances:
  85    2  0.03
  86   15  0.24
  87   45  0.73

ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28


Consensus pattern (87 bp):   
GTACCAAATTAAGAAAAAGAATTAAGTTCAGGTATCAAATTAGACCTAAAAAAATTTAAGTACAA
ACTAAAAAAGTGTCAAGTTTTG

Found at i:7357 original size:12 final size:12

Alignment explanation


    Indices: 7340--7435  Score: 76
    Period size: 12  Copynumber: 8.3  Consensus size: 12

       7330 ATAACATCCA

                        
       7340 AACAACAAAAAT
          1 AACAACAAAAAT

                        
       7352 AACAACAAAAAT
          1 AACAACAAAAAT

                *       
       7364 AACAGC---AA-
          1 AACAACAAAAAT

                    *    
       7372 AACAACATTAAA-
          1 AACAACA-AAAAT

                        
       7384 AACAACAAAAAT
          1 AACAACAAAAAT

             **     *  *
       7396 AGTAACAATAAC
          1 AACAACAAAAAT

                        
       7408 AACAACAAAAAT
          1 AACAACAAAAAT

                *      *
       7420 AACAGCAAAAAC
          1 AACAACAAAAAT

                
       7432 AACA
          1 AACA

       7436 CGAAAACAAG


Statistics
Matches: 66,  Mismatches: 13, Indels: 10
        0.74            0.15        0.11

Matches are distributed among these distances:
   8    5  0.08
   9    2  0.03
  11    3  0.05
  12   56  0.85

ACGTcount: A:0.70, C:0.19, G:0.03, T:0.08


Consensus pattern (12 bp):   
AACAACAAAAAT

Found at i:7363 original size:32 final size:32

Alignment explanation


    Indices: 7326--7396  Score: 99
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       7316 AAAAATGCAT

                      * *                    
       7326 AAAAATAACATCCAAACAACA-AAAATAACAAC
          1 AAAAATAACAGCAAAACAACATAAAA-AACAAC

                                  *         
       7358 AAAAATAACAGCAAAACAACATTAAAAACAAC
          1 AAAAATAACAGCAAAACAACATAAAAAACAAC

                   
       7390 AAAAATA
          1 AAAAATA

       7397 GTAACAATAA


Statistics
Matches: 35,  Mismatches: 3, Indels: 2
        0.88            0.08        0.05

Matches are distributed among these distances:
  32   32  0.91
  33    3  0.09

ACGTcount: A:0.70, C:0.18, G:0.01, T:0.10


Consensus pattern (32 bp):   
AAAAATAACAGCAAAACAACATAAAAAACAAC

Found at i:7441 original size:24 final size:23

Alignment explanation


    Indices: 7344--7441  Score: 76
    Period size: 23  Copynumber: 4.3  Consensus size: 23

       7334 CATCCAAACA

                               *   
       7344 ACAAAAATAACAACAAAAATAAC
          1 ACAAAAATAACAACAAAAACAAC

                    *    **         
       7367 AGC-AAAACAACATTAAAAAC-A-
          1 A-CAAAAATAACAACAAAAACAAC

                     **     *      
       7388 ACAAAAATAGTAACAATAACAAC
          1 ACAAAAATAACAACAAAAACAAC

                         *          
       7411 AACAAAAATAACAGCAAAAACAAC
          1 -ACAAAAATAACAACAAAAACAAC

              *    
       7435 ACGAAAA
          1 ACAAAAA

       7442 CAAGAATCAA


Statistics
Matches: 55,  Mismatches: 15, Indels: 10
        0.69            0.19        0.12

Matches are distributed among these distances:
  20    1  0.02
  21   12  0.22
  22    2  0.04
  23   20  0.36
  24   20  0.36

ACGTcount: A:0.69, C:0.18, G:0.04, T:0.08


Consensus pattern (23 bp):   
ACAAAAATAACAACAAAAACAAC
Done.