Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007373.1 Kokia drynarioides strain JFW-HI SEQ_121989, 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: 2492
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37


Found at i:382 original size:28 final size:27

Alignment explanation


    Indices: 344--401  Score: 73
    Period size: 28  Copynumber: 2.1  Consensus size: 27

        334 TTTTATTATT

                                    *    
        344 TATAATATTTATTACATTTATA-ATTTTA
          1 TATAATATTTATT--ATTTATATAATTTA

                  *                    
        372 TATAATTTTTATTATTTATATAATTTA
          1 TATAATATTTATTATTTATATAATTTA

               
        399 TAT
          1 TAT

        402 TTAAATTATT


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

Matches are distributed among these distances:
  26    7  0.26
  27    8  0.30
  28   12  0.44

ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60


Consensus pattern (27 bp):   
TATAATATTTATTATTTATATAATTTA

Found at i:383 original size:11 final size:10

Alignment explanation


    Indices: 362--401  Score: 50
    Period size: 9  Copynumber: 4.3  Consensus size: 10

        352 TTATTACATT

                      
        362 TATAATTTTA
          1 TATAATTTTA

                      
        372 TATAATTTT-
          1 TATAATTTTA

               *      
        381 TATTA-TTTA
          1 TATAATTTTA

                      
        390 TATAA-TTTA
          1 TATAATTTTA

               
        399 TAT
          1 TAT

        402 TTAAATTATT


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

Matches are distributed among these distances:
   8    3  0.11
   9   15  0.56
  10    9  0.33

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (10 bp):   
TATAATTTTA

Found at i:387 original size:44 final size:43

Alignment explanation


    Indices: 316--399  Score: 125
    Period size: 44  Copynumber: 1.9  Consensus size: 43

        306 ACATTACTCA

                                                        
        316 ATTTACAATTTTAAATATTTTTATTATTTATA-ATATTTATTAC
          1 ATTTACAATTTTAAATATTTTTATTATTTATATA-ATTTATTAC

                 *       *                           
        359 ATTTATAATTTTATATAATTTTTATTATTTATATAATTTAT
          1 ATTTACAATTTTAAAT-ATTTTTATTATTTATATAATTTAT

        400 ATTTAAATTA


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  43   14  0.38
  44   22  0.59
  45    1  0.03

ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61


Consensus pattern (43 bp):   
ATTTACAATTTTAAATATTTTTATTATTTATATAATTTATTAC

Found at i:402 original size:18 final size:18

Alignment explanation


    Indices: 325--400  Score: 86
    Period size: 18  Copynumber: 4.3  Consensus size: 18

        315 AATTTACAAT

                        *   * 
        325 TTTA-AATATTTTTATTA
          1 TTTATAATATTTATATAA

                               
        342 TTTATAATATTTAT-TACA
          1 TTTATAATATTTATATA-A

                              
        360 TTTATAAT-TTTATATAA
          1 TTTATAATATTTATATAA

               *  *           
        377 TTTTTATTATTTATATAA
          1 TTTATAATATTTATATAA

                  
        395 TTTATA
          1 TTTATA

        401 TTTAAATTAT


Statistics
Matches: 50,  Mismatches: 5, Indels: 7
        0.81            0.08        0.11

Matches are distributed among these distances:
  17   17  0.34
  18   33  0.66

ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62


Consensus pattern (18 bp):   
TTTATAATATTTATATAA

Found at i:1064 original size:21 final size:22

Alignment explanation


    Indices: 1017--1057  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       1007 AATATGGTAC

                *       *         
       1017 AAATGTTTTAATTATGATTTGA
          1 AAATTTTTTAATAATGATTTGA

                                
       1039 AAATTTTTTAATAAT-ATTT
          1 AAATTTTTTAATAATGATTT

       1058 ATAAATTATT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    4  0.24
  22   13  0.76

ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54


Consensus pattern (22 bp):   
AAATTTTTTAATAATGATTTGA
Done.