Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012643.1 Kokia drynarioides strain JFW-HI SEQ_127653, 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: 42639
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32

Warning! 7 characters in sequence are not A, C, G, or T


Found at i:28111 original size:25 final size:25

Alignment explanation


    Indices: 28083--28237  Score: 152
    Period size: 25  Copynumber: 6.2  Consensus size: 25

      28073 TTAAAGCATG

                    **       *       
      28083 AGATAACATTGACTCAAGGCTTGAT
          1 AGATAACACCGACTCAAAGCTTGAT

                       *           * 
      28108 AGATAACACCGGCTCAAAGCTTGCT
          1 AGATAACACCGACTCAAAGCTTGAT

                       *               
      28133 AGATAA-ACACTAGCTCAAAGCTTGAT
          1 AGATAACAC-CGA-CTCAAAGCTTGAT

                       *        * *  
      28159 AGATAACACCGGCTCAAAGCCTAAT
          1 AGATAACACCGACTCAAAGCTTGAT

                      *    *          
      28184 AGATAACA-CTAGCTTAAAGCTTGAT
          1 AGATAACACCGA-CTCAAAGCTTGAT

                    *           *    
      28209 AGATAACATCGACTCAAAGCCTGAT
          1 AGATAACACCGACTCAAAGCTTGAT

                
      28234 AGAT
          1 AGAT

      28238 GGAACATCAC


Statistics
Matches: 105,  Mismatches: 20, Indels: 10
        0.78            0.15        0.07

Matches are distributed among these distances:
  24    3  0.03
  25   79  0.75
  26   21  0.20
  27    2  0.02

ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23


Consensus pattern (25 bp):   
AGATAACACCGACTCAAAGCTTGAT

Found at i:28213 original size:50 final size:51

Alignment explanation


    Indices: 28095--28237  Score: 216
    Period size: 50  Copynumber: 2.8  Consensus size: 51

      28085 ATAACATTGA

                 *                           *  *              
      28095 CTCAAGGCTTGATAGATAACACCGGCTCAAAGCTTGCTAGATAAACACTAG
          1 CTCAAAGCTTGATAGATAACACCGGCTCAAAGCCTGATAGATAAACACTAG

                                               *               
      28146 CTCAAAGCTTGATAGATAACACCGGCTCAAAGCCTAATAGAT-AACACTAG
          1 CTCAAAGCTTGATAGATAACACCGGCTCAAAGCCTGATAGATAAACACTAG

              *                  *  *                 
      28196 CTTAAAGCTTGATAGATAACATCGACTCAAAGCCTGATAGAT
          1 CTCAAAGCTTGATAGATAACACCGGCTCAAAGCCTGATAGAT

      28238 GGAACATCAC


Statistics
Matches: 84,  Mismatches: 8, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  50   46  0.55
  51   38  0.45

ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22


Consensus pattern (51 bp):   
CTCAAAGCTTGATAGATAACACCGGCTCAAAGCCTGATAGATAAACACTAG

Found at i:33474 original size:20 final size:20

Alignment explanation


    Indices: 33426--33474  Score: 53
    Period size: 20  Copynumber: 2.5  Consensus size: 20

      33416 TCAAGGTATC

                   *  *    *    
      33426 GGTAGAACTGTAGTTGTATA
          1 GGTAGAAGTGGAGTTCTATA

                *              *
      33446 GGTAAAAGTGGAGTTCTATT
          1 GGTAGAAGTGGAGTTCTATA

                     
      33466 GGTAGAAGT
          1 GGTAGAAGT

      33475 CTCACTGGAG


Statistics
Matches: 23,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.31, C:0.04, G:0.33, T:0.33


Consensus pattern (20 bp):   
GGTAGAAGTGGAGTTCTATA

Found at i:35795 original size:20 final size:20

Alignment explanation


    Indices: 35766--35803  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      35756 GGTTTTTCAA

                        *       
      35766 AAAAAATCAACGGTCAACCT
          1 AAAAAATCAACGATCAACCT

                 *            
      35786 AAAAAGTCAACGATCAAC
          1 AAAAAATCAACGATCAAC

      35804 GATCAACAAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.53, C:0.24, G:0.11, T:0.13


Consensus pattern (20 bp):   
AAAAAATCAACGATCAACCT

Found at i:35823 original size:14 final size:14

Alignment explanation


    Indices: 35791--35836  Score: 56
    Period size: 14  Copynumber: 3.3  Consensus size: 14

      35781 AACCTAAAAA

                        * 
      35791 GTCAACGATCAACG
          1 GTCAACGATCAATG

            *     *       
      35805 ATCAACAATCAATG
          1 GTCAACGATCAATG

                   *      
      35819 GTCAACGGTCAATG
          1 GTCAACGATCAATG

                
      35833 GTCA
          1 GTCA

      35837 GGTTCGATCA


Statistics
Matches: 26,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  14   26  1.00

ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20


Consensus pattern (14 bp):   
GTCAACGATCAATG

Found at i:42639 original size:20 final size:20

Alignment explanation


    Indices: 42560--42639  Score: 58
    Period size: 20  Copynumber: 4.0  Consensus size: 20

      42550 GGCCTAGAGC

                     *          *
      42560 TATTTTGACTTGTTTGAAAAA
          1 TATTTTGACATGTTT-AAAAT

            *                    
      42581 CATTTTGA-A-GTGTTAAAAT
          1 TATTTTGACATGT-TTAAAAT

            *        *      *    
      42600 GATTTTGACTTAG-TTCAAAT
          1 TATTTTGACAT-GTTTAAAAT

                                
      42620 TATTTTGACATGTTTAAAAT
          1 TATTTTGACATGTTTAAAAT


Statistics
Matches: 45,  Mismatches: 9, Indels: 11
        0.69            0.14        0.17

Matches are distributed among these distances:
  19   14  0.31
  20   23  0.51
  21    7  0.16
  22    1  0.02

ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46


Consensus pattern (20 bp):   
TATTTTGACATGTTTAAAAT
Done.