Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006060.1 Kokia drynarioides strain JFW-HI SEQ_120534, 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: 26590
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36

Warning! 22 characters in sequence are not A, C, G, or T


Found at i:3416 original size:11 final size:11

Alignment explanation


    Indices: 3400--3466  Score: 53
    Period size: 11  Copynumber: 6.1  Consensus size: 11

       3390 TGGTGTTTAC

                       
       3400 TACTATTTTGT
          1 TACTATTTTGT

                   *   
       3411 TACTATTATGT
          1 TACTATTTTGT

              * *      
       3422 TATTGTTTTGT
          1 TACTATTTTGT

               *    *  
       3433 TACCATTTCGT
          1 TACTATTTTGT

              *   *  * 
       3444 TATTATATTAT
          1 TACTATTTTGT

            *          
       3455 AACTATTTTGT
          1 TACTATTTTGT

             
       3466 T
          1 T

       3467 GTTATTGTTT


Statistics
Matches: 38,  Mismatches: 18, Indels: 0
        0.68            0.32        0.00

Matches are distributed among these distances:
  11   38  1.00

ACGTcount: A:0.22, C:0.09, G:0.09, T:0.60


Consensus pattern (11 bp):   
TACTATTTTGT

Found at i:3445 original size:22 final size:22

Alignment explanation


    Indices: 3405--3447  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       3395 TTTACTACTA

                     *            
       3405 TTTTGTTACTATTATGTTATTG
          1 TTTTGTTACCATTATGTTATTG

                                  
       3427 TTTTGTTACCATT-TCGTTATT
          1 TTTTGTTACCATTAT-GTTATT

       3448 ATATTATAAC


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  21    1  0.05
  22   18  0.95

ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63


Consensus pattern (22 bp):   
TTTTGTTACCATTATGTTATTG

Found at i:12578 original size:13 final size:15

Alignment explanation


    Indices: 12536--12578  Score: 54
    Period size: 13  Copynumber: 2.9  Consensus size: 15

      12526 ATGAAATAAA

                           
      12536 AATAAATTTTTAATT
          1 AATAAATTTTTAATT

                           
      12551 AATAAA--TTTAATT
          1 AATAAATTTTTAATT

                           
      12564 AATTAAAATTTTTAA
          1 AA-T-AAATTTTTAA

      12579 ATCATAAATC


Statistics
Matches: 24,  Mismatches: 0, Indels: 6
        0.80            0.00        0.20

Matches are distributed among these distances:
  13    9  0.38
  14    1  0.04
  15    9  0.38
  17    5  0.21

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (15 bp):   
AATAAATTTTTAATT

Found at i:13087 original size:15 final size:15

Alignment explanation


    Indices: 13067--13117  Score: 61
    Period size: 15  Copynumber: 3.5  Consensus size: 15

      13057 ACAAAATAAT

                           
      13067 AACATAAATGATTAA
          1 AACATAAATGATTAA

                          * 
      13082 AACATAACAT--TTCA
          1 AACATAA-ATGATTAA

                           
      13096 AACATAAATGATTAA
          1 AACATAAATGATTAA

              *    
      13111 AATATAA
          1 AACATAA

      13118 TCTAAGACAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 6
        0.77            0.08        0.15

Matches are distributed among these distances:
  13    2  0.07
  14   10  0.33
  15   16  0.53
  16    2  0.07

ACGTcount: A:0.59, C:0.10, G:0.04, T:0.27


Consensus pattern (15 bp):   
AACATAAATGATTAA

Found at i:21221 original size:22 final size:23

Alignment explanation


    Indices: 21178--21222  Score: 56
    Period size: 22  Copynumber: 2.0  Consensus size: 23

      21168 CCAACTGAAC

                             *     
      21178 TAAAATTTAATAATCAACTATTT
          1 TAAAATTTAATAATCAAATATTT

                     *    *        
      21201 TAAAATTT-TTAATTAAATATTT
          1 TAAAATTTAATAATCAAATATTT

      21223 AACCAAAAAT


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  22   11  0.58
  23    8  0.42

ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49


Consensus pattern (23 bp):   
TAAAATTTAATAATCAAATATTT
Done.