Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011143.1 Kokia drynarioides strain JFW-HI SEQ_126116, 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: 2235
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36


Found at i:363 original size:4 final size:4

Alignment explanation


    Indices: 346--389  Score: 65
    Period size: 4  Copynumber: 11.5  Consensus size: 4

        336 AACGAAAATT

                    *                                                
        346 AAAG AAAA AAAG AAAG AAAG AAAG --AG AAAG AAAG AAAG AAAG AA
          1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA

        390 GGAAGAAGGG


Statistics
Matches: 36,  Mismatches: 2, Indels: 4
        0.86            0.05        0.10

Matches are distributed among these distances:
   2    2  0.06
   4   34  0.94

ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00


Consensus pattern (4 bp):   
AAAG

Found at i:373 original size:22 final size:22

Alignment explanation


    Indices: 348--389  Score: 75
    Period size: 22  Copynumber: 1.9  Consensus size: 22

        338 CGAAAATTAA

                                  
        348 AGAAAAAAAGAAAGAAAGAAAG
          1 AGAAAAAAAGAAAGAAAGAAAG

                 *              
        370 AGAAAGAAAGAAAGAAAGAA
          1 AGAAAAAAAGAAAGAAAGAA

        390 GGAAGAAGGG


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00


Consensus pattern (22 bp):   
AGAAAAAAAGAAAGAAAGAAAG

Found at i:375 original size:14 final size:14

Alignment explanation


    Indices: 346--384  Score: 64
    Period size: 14  Copynumber: 2.9  Consensus size: 14

        336 AACGAAAATT

                          
        346 AAAGAAA-AAA-AG
          1 AAAGAAAGAAAGAG

                          
        358 AAAGAAAGAAAGAG
          1 AAAGAAAGAAAGAG

                         
        372 AAAGAAAGAAAGA
          1 AAAGAAAGAAAGA

        385 AAGAAGGAAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  12    7  0.28
  13    3  0.12
  14   15  0.60

ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00


Consensus pattern (14 bp):   
AAAGAAAGAAAGAG

Found at i:404 original size:9 final size:9

Alignment explanation


    Indices: 391--423  Score: 57
    Period size: 9  Copynumber: 3.7  Consensus size: 9

        381 AAGAAAGAAG

                    *
        391 GAAGAAGGG
          1 GAAGAAGGA

                     
        400 GAAGAAGGA
          1 GAAGAAGGA

                     
        409 GAAGAAGGA
          1 GAAGAAGGA

                  
        418 GAAGAA
          1 GAAGAA

        424 AAAAAAAGGT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   9   23  1.00

ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00


Consensus pattern (9 bp):   
GAAGAAGGA

Found at i:614 original size:12 final size:12

Alignment explanation


    Indices: 597--621  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        587 TTAAGTATGG

                        
        597 TTAATTTTAAAA
          1 TTAATTTTAAAA

                        
        609 TTAATTTTAAAA
          1 TTAATTTTAAAA

             
        621 T
          1 T

        622 ATTTTAATTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (12 bp):   
TTAATTTTAAAA

Found at i:820 original size:20 final size:21

Alignment explanation


    Indices: 779--821  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        769 TAATTTACTT

                                 
        779 TAATTTAATTTTGCTAGTTAG
          1 TAATTTAATTTTGCTAGTTAG

                  *        *     
        800 TAATTTTATTTTG-TTGTTAG
          1 TAATTTAATTTTGCTAGTTAG

              
        820 TA
          1 TA

        822 GTAGTAAGTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20    8  0.40
  21   12  0.60

ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58


Consensus pattern (21 bp):   
TAATTTAATTTTGCTAGTTAG
Done.