Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006943.1 Kokia drynarioides strain JFW-HI SEQ_121547, 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: 23531
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:3893 original size:3 final size:3

Alignment explanation


    Indices: 3873--3910  Score: 58
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       3863 ATAGTTGACT

                     *       *                                
       3873 TTA TTA TCA TTA TCA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

       3911 CTGGTGATAA


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63


Consensus pattern (3 bp):   
TTA

Found at i:5536 original size:48 final size:48

Alignment explanation


    Indices: 5465--5558  Score: 188
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       5455 GGTGAGAAAG

                                                            
       5465 ACCTATAAACTAATTTCTCCTAATTCGTAGTAATAGTTACACACAATC
          1 ACCTATAAACTAATTTCTCCTAATTCGTAGTAATAGTTACACACAATC

                                                          
       5513 ACCTATAAACTAATTTCTCCTAATTCGTAGTAATAGTTACACACAA
          1 ACCTATAAACTAATTTCTCCTAATTCGTAGTAATAGTTACACACAA

       5559 CCACTTAATG


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  48   46  1.00

ACGTcount: A:0.38, C:0.22, G:0.06, T:0.33


Consensus pattern (48 bp):   
ACCTATAAACTAATTTCTCCTAATTCGTAGTAATAGTTACACACAATC

Found at i:6599 original size:14 final size:14

Alignment explanation


    Indices: 6569--6607  Score: 53
    Period size: 14  Copynumber: 2.9  Consensus size: 14

       6559 GTTCTATTAT

                          
       6569 TATTAAAT-ATACA
          1 TATTAAATAATACA

                       *  
       6582 TATTAAATAATTCA
          1 TATTAAATAATACA

                *       
       6596 TATTCAATAATA
          1 TATTAAATAATA

       6608 TAATATTATT


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  13    8  0.36
  14   14  0.64

ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41


Consensus pattern (14 bp):   
TATTAAATAATACA

Found at i:13856 original size:41 final size:41

Alignment explanation


    Indices: 13804--13920  Score: 139
    Period size: 41  Copynumber: 2.9  Consensus size: 41

      13794 AAATACCGTA

                              *                       
      13804 AAAGGT-AAAGCAATAGCAGCGCTTATG-GAAAAGCGCCGCT
          1 AAAGGTCAAAGCAATAGCGGCGCTTATGTG-AAAGCGCCGCT

                                *    *    *    *     
      13844 AAAGGTCAAAGCAATAGCGGTGCTTTTGTGCAAGCTCCGCT
          1 AAAGGTCAAAGCAATAGCGGCGCTTATGTGAAAGCGCCGCT

                    *                *    *     
      13885 AAAGGTCAGAGCAATAGCGGCGCTTTTGTGCAAGCG
          1 AAAGGTCAAAGCAATAGCGGCGCTTATGTGAAAGCG

      13921 TGTTCTATTT


Statistics
Matches: 67,  Mismatches: 8, Indels: 3
        0.86            0.10        0.04

Matches are distributed among these distances:
  40    6  0.09
  41   60  0.90
  42    1  0.01

ACGTcount: A:0.31, C:0.21, G:0.29, T:0.20


Consensus pattern (41 bp):   
AAAGGTCAAAGCAATAGCGGCGCTTATGTGAAAGCGCCGCT

Found at i:17892 original size:18 final size:18

Alignment explanation


    Indices: 17869--17907  Score: 78
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      17859 CTTGTTGGGT

                              
      17869 TCAATTTTAATTGTGGAA
          1 TCAATTTTAATTGTGGAA

                              
      17887 TCAATTTTAATTGTGGAA
          1 TCAATTTTAATTGTGGAA

               
      17905 TCA
          1 TCA

      17908 TATAATAATA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44


Consensus pattern (18 bp):   
TCAATTTTAATTGTGGAA

Found at i:21080 original size:27 final size:28

Alignment explanation


    Indices: 21022--21080  Score: 82
    Period size: 30  Copynumber: 2.0  Consensus size: 28

      21012 ATGATAATAT

                               *          
      21022 CCCACCACATGTCGAATATTCCTTATGCCC
          1 CCCACCACATGTCGAATATGCCTTA--CCC

                             *          
      21052 CCCACCACATGTCGAATCTGCCTTACCC
          1 CCCACCACATGTCGAATATGCCTTACCC

             
      21080 C
          1 C

      21081 AAAATGCTGA


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  28    4  0.15
  30   23  0.85

ACGTcount: A:0.22, C:0.44, G:0.10, T:0.24


Consensus pattern (28 bp):   
CCCACCACATGTCGAATATGCCTTACCC
Done.