Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007274.1 Kokia drynarioides strain JFW-HI SEQ_121890, 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: 15255
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:4616 original size:21 final size:22

Alignment explanation


    Indices: 4592--4644  Score: 72
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       4582 AGACTTCTAT

                                  
       4592 CGATACAAGTGAC-AGTCCTAC
          1 CGATACAAGTGACTAGTCCTAC

                          ** *    
       4613 CGATACAAGTGACTCTTTCTAC
          1 CGATACAAGTGACTAGTCCTAC

                      
       4635 CGATACAAGT
          1 CGATACAAGT

       4645 CTTACTTCTA


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  21   13  0.46
  22   15  0.54

ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25


Consensus pattern (22 bp):   
CGATACAAGTGACTAGTCCTAC

Found at i:4637 original size:22 final size:21

Alignment explanation


    Indices: 4586--4644  Score: 73
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       4576 TAGTGCAGAC

                 *               
       4586 TTCTATCGATACAAGTGACAG
          1 TTCTACCGATACAAGTGACAG

             *                  **
       4607 TCCTACCGATACAAGTGACTCT
          1 TTCTACCGATACAAGTGAC-AG

                            
       4629 TTCTACCGATACAAGT
          1 TTCTACCGATACAAGT

       4645 CTTACTTCTA


Statistics
Matches: 32,  Mismatches: 5, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  21   17  0.53
  22   15  0.47

ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29


Consensus pattern (21 bp):   
TTCTACCGATACAAGTGACAG

Found at i:12359 original size:12 final size:12

Alignment explanation


    Indices: 12342--12371  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

      12332 CATCATTGCC

                   *    
      12342 ATTATTAGTATT
          1 ATTATTACTATT

                        
      12354 ATTATTACTATT
          1 ATTATTACTATT

                  
      12366 ATTATT
          1 ATTATT

      12372 TGATCGATTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60


Consensus pattern (12 bp):   
ATTATTACTATT

Found at i:12751 original size:33 final size:33

Alignment explanation


    Indices: 12712--12776  Score: 121
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      12702 AGGACGACTT

                                 *           
      12712 AATTTTTTAACTTTTTTTTAAGTATAAAGATTC
          1 AATTTTTTAACTTTTTTTTAAATATAAAGATTC

                                            
      12745 AATTTTTTAACTTTTTTTTAAATATAAAGATT
          1 AATTTTTTAACTTTTTTTTAAATATAAAGATT

      12777 AAATCTTAAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   31  1.00

ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55


Consensus pattern (33 bp):   
AATTTTTTAACTTTTTTTTAAATATAAAGATTC

Found at i:13452 original size:60 final size:61

Alignment explanation


    Indices: 13388--13521  Score: 191
    Period size: 60  Copynumber: 2.2  Consensus size: 61

      13378 TTTTAATAGG

                                           *                     *        
      13388 ATTATTATTAAATGTAATTTAATAAAAATAATAATAAATAATTTAAT-CATT-TTAAATATA
          1 ATTATTATTAAATGTAATTTAATAAAAATAAAAATAAATAATTTAATACATTCGT-AATATA

                                    *           *                         
      13448 ATTATTATTAAATGTAATTTAATACAAATAAAAATATATAATTTAATAACATTCGTAATATA
          1 ATTATTATTAAATGTAATTTAATAAAAATAAAAATAAATAATTTAAT-ACATTCGTAATATA

            *           
      13510 TTTATTATTAAA
          1 ATTATTATTAAA

      13522 ATGCAATGCA


Statistics
Matches: 66,  Mismatches: 5, Indels: 4
        0.88            0.07        0.05

Matches are distributed among these distances:
  60   44  0.67
  62   21  0.32
  63    1  0.02

ACGTcount: A:0.51, C:0.03, G:0.02, T:0.43


Consensus pattern (61 bp):   
ATTATTATTAAATGTAATTTAATAAAAATAAAAATAAATAATTTAATACATTCGTAATATA
Done.