Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008295.1 Kokia drynarioides strain JFW-HI SEQ_122960, 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: 17828
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31


Found at i:529 original size:52 final size:51

Alignment explanation


    Indices: 472--698  Score: 233
    Period size: 52  Copynumber: 4.4  Consensus size: 51

        462 ATGATTATGA

                                                     *           
        472 GTCATCGTGAGTATATGAATCCTTTACGGATTAAATGG-CTAGATGACTAAGT
          1 GTCATCGTGAGTATATGAATCCTTTACGGATTAAA-GGTC-CGATGACTAAGT

                        * *       *                             
        524 GTCATCGTGAGTGTCTGAATCCGTTACGGATTAAACGGTCCGATGACTAAGT
          1 GTCATCGTGAGTATATGAATCCTTTACGGATTAAA-GGTCCGATGACTAAGT

                 *           *          *                   **  
        576 GTCATAGTGAGTATATGGATCCTTTACGTATTAAGAGGTCCGATGACTTTGT
          1 GTCATCGTGAGTATATGAATCCTTTACGGATTAA-AGGTCCGATGACTAAGT

                           * *    *  *              * *  *   *  
        628 GTCATCGTGAGTATACGGATCCCTTGCGGATTATAAGGTCTGGTGGCTATGT
          1 GTCATCGTGAGTATATGAATCCTTTACGGATTA-AAGGTCCGATGACTAAGT

                  *             
        680 -TCATCATGAGTATATGAAT
          1 GTCATCGTGAGTATATGAAT

        699 GAAGTGAAAT


Statistics
Matches: 147,  Mismatches: 25, Indels: 7
        0.82            0.14        0.04

Matches are distributed among these distances:
  51   16  0.11
  52  128  0.87
  53    3  0.02

ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33


Consensus pattern (51 bp):   
GTCATCGTGAGTATATGAATCCTTTACGGATTAAAGGTCCGATGACTAAGT

Found at i:3511 original size:147 final size:147

Alignment explanation


    Indices: 3243--3542  Score: 494
    Period size: 147  Copynumber: 2.0  Consensus size: 147

       3233 GTCACAAACC

                                *       *                                *   
       3243 CATTGGGTCATAGTGTCATTGTTAATTTGGTATGTCGTAAATGTCCACTGAGAATTCGAGATTGT
          1 CATTGGGTCATAGTGTCATTATTAATTTAGTATGTCGTAAATGTCCACTGAGAATTCGAGACTGT

                                              *     *          *             
       3308 AAGTTCCCTACTGATTTGATGTTACTACCATATTTTGAGTTCAATGTAATTTTGGGAATGGACTG
         66 AAGTTCCCTACTGATTTGATGTTACTACCATATTCTGAGTCCAATGTAATTCTGGGAATGGACTG

                             
       3373 GCTAACTGAGCATGATG
        131 GCTAACTGAGCATGATG

                                                                      *      
       3390 CATTGGGTCATAGTGTCATTATTAATTTAGTATGTCGTAAATGTCCACTGAGAATTCGGGACTGT
          1 CATTGGGTCATAGTGTCATTATTAATTTAGTATGTCGTAAATGTCCACTGAGAATTCGAGACTGT

                     *                                                       
       3455 AAGTTCCCTGCTGATTTGATGTTACTACCAT-TTACTGAGTCCAATGTAATTCTGGGAATGGACT
         66 AAGTTCCCTACTGATTTGATGTTACTACCATATT-CTGAGTCCAATGTAATTCTGGGAATGGACT

              *     *         
       3519 GGTTAACTTAGCATGATG
        130 GGCTAACTGAGCATGATG

                  
       3537 CATTGG
          1 CATTGG

       3543 TTAATTGTAA


Statistics
Matches: 142,  Mismatches: 10, Indels: 2
        0.92            0.06        0.01

Matches are distributed among these distances:
 146    2  0.01
 147  140  0.99

ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37


Consensus pattern (147 bp):   
CATTGGGTCATAGTGTCATTATTAATTTAGTATGTCGTAAATGTCCACTGAGAATTCGAGACTGT
AAGTTCCCTACTGATTTGATGTTACTACCATATTCTGAGTCCAATGTAATTCTGGGAATGGACTG
GCTAACTGAGCATGATG

Found at i:6950 original size:52 final size:51

Alignment explanation


    Indices: 6887--7056  Score: 241
    Period size: 52  Copynumber: 3.3  Consensus size: 51

       6877 ATGATTATGA

                        *                           *           
       6887 GTCATCGTGAGTGTATGAATCCTTTACGGATTAAACGGTCTGATGACTAAGT
          1 GTCATCGTGAGTATATGAATCCTTTACGGATTAAA-GGTCCGATGACTAAGT

                  *                                       *     
       6939 GTCATCATGAGTATATGAATCCTTTACGGATTAAATGGTCCGATGAATAAGT
          1 GTCATCGTGAGTATATGAATCCTTTACGGATTAAA-GGTCCGATGACTAAGT

                             *        *                     **  
       6991 GTCATCGTGAGTATATGGATCCTTTATGGATTAAGAGGTCCGATGACTCTGT
          1 GTCATCGTGAGTATATGAATCCTTTACGGATTAA-AGGTCCGATGACTAAGT

                          
       7043 GTCATCGTGAGTAT
          1 GTCATCGTGAGTAT

       7057 CCTTGTGGAT


Statistics
Matches: 106,  Mismatches: 11, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  52  105  0.99
  53    1  0.01

ACGTcount: A:0.27, C:0.15, G:0.25, T:0.34


Consensus pattern (51 bp):   
GTCATCGTGAGTATATGAATCCTTTACGGATTAAAGGTCCGATGACTAAGT
Done.