Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013125.1 Kokia drynarioides strain JFW-HI SEQ_128144, 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: 25781
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


Found at i:11122 original size:13 final size:13

Alignment explanation


    Indices: 11104--11128  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      11094 TAAGTTGGAA

                         
      11104 ATGCTAAAAATGC
          1 ATGCTAAAAATGC

                        
      11117 ATGCTAAAAATG
          1 ATGCTAAAAATG

      11129 ATAAAATGGG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24


Consensus pattern (13 bp):   
ATGCTAAAAATGC

Found at i:14664 original size:23 final size:24

Alignment explanation


    Indices: 14634--14710  Score: 99
    Period size: 23  Copynumber: 3.3  Consensus size: 24

      14624 ACATTAGCAC

                                    
      14634 GCTTACTG-TTCTGCACTGTGAGT
          1 GCTTACTGATTCTGCACTGTGAGT

                              *      
      14657 GCTTACTGATTC-GCACTAT-ATGT
          1 GCTTACTGATTCTGCACTGTGA-GT

                                 *  
      14680 GCTTACTGATT-TGCACTGTGTGT
          1 GCTTACTGATTCTGCACTGTGAGT

                    
      14703 GCTTACTG
          1 GCTTACTG

      14711 TTTCCCCAGC


Statistics
Matches: 47,  Mismatches: 3, Indels: 8
        0.81            0.05        0.14

Matches are distributed among these distances:
  22    1  0.02
  23   43  0.91
  24    3  0.06

ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40


Consensus pattern (24 bp):   
GCTTACTGATTCTGCACTGTGAGT

Found at i:16618 original size:138 final size:137

Alignment explanation


    Indices: 16461--17152  Score: 920
    Period size: 138  Copynumber: 5.0  Consensus size: 137

      16451 ACATGGAGAA

                                             *                               
      16461 AATTAATATATGAATTTGATTCATACAAAATATGAATTGTATATATTTTATCAAAATTATTAATA
          1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTA-CAAAATTATTAATA

                *       *          *                                      *  
      16526 TAAATAGTTATAATAATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTAGA
         65 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA

                    
      16591 AAGAATAT
        130 AAGAATAT

                          *          *                             *         
      16599 AATTAATATATGAAATTGATTCATAAAAAATATTAA-T-TATATATTTTACCAAATTTATTAATA
          1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTA-CAAAATTATTAATA

                            * *                       *                      
      16662 TAAACAGTTATATTAAATCATTTCGGTCAAAATATAAAAGACTTGAAAATTAATATTCTTTTGGA
         65 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA

              *  *  
      16727 AATAACAT
        130 AAGAATAT

                    *               *                          **            
      16735 AATTAATAAATGAATTTGATTCATGCAAAATATTAATTGTATATATTTTACCGAATTGATTAATA
          1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAAAATT-ATTAATA

                *             *     *              *       *               * 
      16800 TAAATAGTTATATTAATTCATTTCAGTCAAAATATAAAAAACATGAATATTAATATTCTTTTGAA
         65 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA

              *     
      16865 AATAATAT
        130 AAGAATAT

                                 **        *   **               *  *         
      16873 AATTAATATATGAATTTGATTTGTACAAAATGTTACCTGTATATATTTTACTGAATTTATTAATA
          1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAC-AAAATTATTAATA

                  *                  * *                                     
      16938 TAAACAATTATATTAATTAATTTCGTTTAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
         65 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA

                    
      17003 AAGAATAT
        130 AAGAATAT

                     *  *           *         *                **            
      17011 AATTAATATTTGCATTTGATTCATGCAAAATATTTATTGTATATATTTTACCGAATTGATTAATA
          1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAAAATT-ATTAATA

                * *       *         *      *                                 
      17076 TAAAAAATTATATTTATTAATTTCAGTCAAATTATAAAAGACATGAAAATTAATATTCTTTTGGA
         65 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA

                    
      17141 AAGAATAT
        130 AAGAATAT

                
      17149 AATT
          1 AATT

      17153 CATTTTTCTA


Statistics
Matches: 482,  Mismatches: 67, Indels: 10
        0.86            0.12        0.02

Matches are distributed among these distances:
 136  120  0.25
 137    9  0.02
 138  350  0.73
 139    3  0.01

ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41


Consensus pattern (137 bp):   
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAAAATTATTAATAT
AAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAA
AGAATAT

Found at i:20192 original size:15 final size:16

Alignment explanation


    Indices: 20172--20210  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      20162 TTTATTATTC

                            
      20172 TTCTTTTT-TCCTTTA
          1 TTCTTTTTCTCCTTTA

                            
      20187 TTCTTTTTCTCCTTT-
          1 TTCTTTTTCTCCTTTA

              *      
      20202 TTGTTTTTC
          1 TTCTTTTTC

      20211 AAGTGACTAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15   16  0.73
  16    6  0.27

ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74


Consensus pattern (16 bp):   
TTCTTTTTCTCCTTTA

Done.