Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013800.1 Kokia drynarioides strain JFW-HI SEQ_128828, 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: 14931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:1371 original size:29 final size:28

Alignment explanation


    Indices: 1311--1371  Score: 68
    Period size: 29  Copynumber: 2.1  Consensus size: 28

       1301 CCCAAATCTT

                         *     **      *
       1311 TATTTTAAATTTATTTTAAGCTTAGAAT
          1 TATTTTAAATTTAATTTAAAATTAGAAA

                                    *    
       1339 TATTTTAAATTTAAATTTAAAATTTGAAA
          1 TATTTTAAATTT-AATTTAAAATTAGAAA

                
       1368 TATT
          1 TATT

       1372 GTTCAAGCTT


Statistics
Matches: 27,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  28   12  0.44
  29   15  0.56

ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52


Consensus pattern (28 bp):   
TATTTTAAATTTAATTTAAAATTAGAAA

Found at i:3513 original size:78 final size:78

Alignment explanation


    Indices: 3384--3539  Score: 312
    Period size: 78  Copynumber: 2.0  Consensus size: 78

       3374 GCGTTCCTCC

                                                                             
       3384 CAGTTTCTTGGGCCTCCCATTTTGGTGTACTGTTTGAATGTGTTTGGTCTTGGGTTCATATGTGA
          1 CAGTTTCTTGGGCCTCCCATTTTGGTGTACTGTTTGAATGTGTTTGGTCTTGGGTTCATATGTGA

                         
       3449 TGCTTGTTTTACG
         66 TGCTTGTTTTACG

                                                                             
       3462 CAGTTTCTTGGGCCTCCCATTTTGGTGTACTGTTTGAATGTGTTTGGTCTTGGGTTCATATGTGA
          1 CAGTTTCTTGGGCCTCCCATTTTGGTGTACTGTTTGAATGTGTTTGGTCTTGGGTTCATATGTGA

                         
       3527 TGCTTGTTTTACG
         66 TGCTTGTTTTACG

       3540 TATAATGTAA


Statistics
Matches: 78,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  78   78  1.00

ACGTcount: A:0.12, C:0.15, G:0.27, T:0.46


Consensus pattern (78 bp):   
CAGTTTCTTGGGCCTCCCATTTTGGTGTACTGTTTGAATGTGTTTGGTCTTGGGTTCATATGTGA
TGCTTGTTTTACG

Found at i:5243 original size:24 final size:24

Alignment explanation


    Indices: 5204--5250  Score: 67
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       5194 AACATCTATC

                       *     *      
       5204 AAAACGACGTAGTTTTATCTTTTA
          1 AAAACGACGTAATTTTACCTTTTA

                   *               
       5228 AAAACGATGTAATTTTACCTTTT
          1 AAAACGACGTAATTTTACCTTTT

       5251 CTTATTTGGA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43


Consensus pattern (24 bp):   
AAAACGACGTAATTTTACCTTTTA

Found at i:10285 original size:22 final size:22

Alignment explanation


    Indices: 10260--10306  Score: 94
    Period size: 22  Copynumber: 2.1  Consensus size: 22

      10250 TTACTATCAA

                                  
      10260 AAGCTTTCAAATTAAAAAGCCT
          1 AAGCTTTCAAATTAAAAAGCCT

                                  
      10282 AAGCTTTCAAATTAAAAAGCCT
          1 AAGCTTTCAAATTAAAAAGCCT

               
      10304 AAG
          1 AAG

      10307 GGCATCATTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   25  1.00

ACGTcount: A:0.47, C:0.17, G:0.11, T:0.26


Consensus pattern (22 bp):   
AAGCTTTCAAATTAAAAAGCCT
Done.