Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008809.1 Kokia drynarioides strain JFW-HI SEQ_123492, 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: 10962
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2487 original size:14 final size:14

Alignment explanation


    Indices: 2448--2502  Score: 58
    Period size: 14  Copynumber: 3.9  Consensus size: 14

       2438 AAACCCAAAA

                          
       2448 AGTCAACGGTCAAC
          1 AGTCAACGGTCAAC

                *   *      
       2462 -GNTTAACTGTCAAC
          1 AG-TCAACGGTCAAC

                          
       2476 AGTCAACGGTCAAC
          1 AGTCAACGGTCAAC

             *    *      
       2490 AATCAATGGTCAA
          1 AGTCAACGGTCAA

       2503 TGGATCATGT


Statistics
Matches: 33,  Mismatches: 6, Indels: 4
        0.77            0.14        0.09

Matches are distributed among these distances:
  13    1  0.03
  14   31  0.94
  15    1  0.03

ACGTcount: A:0.36, C:0.24, G:0.18, T:0.20


Consensus pattern (14 bp):   
AGTCAACGGTCAAC

Found at i:3787 original size:33 final size:33

Alignment explanation


    Indices: 3750--3818  Score: 120
    Period size: 33  Copynumber: 2.1  Consensus size: 33

       3740 ACGGAGTAAG

                                           * 
       3750 AATAGGATCGTAGGGCTAGAGGATGAGGATGTT
          1 AATAGGATCGTAGGGCTAGAGGATGAGGATGGT

                       *                     
       3783 AATAGGATCGTGGGGCTAGAGGATGAGGATGGT
          1 AATAGGATCGTAGGGCTAGAGGATGAGGATGGT

               
       3816 AAT
          1 AAT

       3819 GTTGGAAAAT


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.30, C:0.06, G:0.41, T:0.23


Consensus pattern (33 bp):   
AATAGGATCGTAGGGCTAGAGGATGAGGATGGT

Found at i:4273 original size:23 final size:23

Alignment explanation


    Indices: 4238--4291  Score: 92
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       4228 ACCAATTATT

                                   
       4238 ATTAT-TTTGTAACTCTCCTACC
          1 ATTATGTTTGTAACTCTCCTACC

                                   
       4260 ATTATGTTTGTAACTCTCCTACC
          1 ATTATGTTTGTAACTCTCCTACC

              *      
       4283 ATAATGTTT
          1 ATTATGTTT

       4292 TGATTTAAAT


Statistics
Matches: 30,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  22    5  0.17
  23   25  0.83

ACGTcount: A:0.24, C:0.22, G:0.07, T:0.46


Consensus pattern (23 bp):   
ATTATGTTTGTAACTCTCCTACC

Found at i:7797 original size:23 final size:23

Alignment explanation


    Indices: 7767--7811  Score: 81
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       7757 GTATCTGTCA

                     *             
       7767 TTATGTTTGTAACTCTCTTGCCT
          1 TTATGTTTGCAACTCTCTTGCCT

                                  
       7790 TTATGTTTGCAACTCTCTTGCC
          1 TTATGTTTGCAACTCTCTTGCC

       7812 ATAATATTTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.13, C:0.24, G:0.13, T:0.49


Consensus pattern (23 bp):   
TTATGTTTGCAACTCTCTTGCCT

Found at i:10497 original size:21 final size:20

Alignment explanation


    Indices: 10431--10500  Score: 70
    Period size: 21  Copynumber: 3.4  Consensus size: 20

      10421 CAGTAACAAA

                                 
      10431 CTTCTACTGATACTTGTAATG
          1 CTTCTACTGATACTTGT-ATG

            *              *     *
      10452 GTTCTACTGATACAAGTGTA-C
          1 CTTCTACTGATAC--TTGTATG

                                 
      10473 CTTCTACTGATACTTGATATG
          1 CTTCTACTGATACTTG-TATG

                   
      10494 CTTCTAC
          1 CTTCTAC

      10501 AAATACTATA


Statistics
Matches: 39,  Mismatches: 6, Indels: 8
        0.74            0.11        0.15

Matches are distributed among these distances:
  19    2  0.05
  20    2  0.05
  21   31  0.79
  22    1  0.03
  23    3  0.08

ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40


Consensus pattern (20 bp):   
CTTCTACTGATACTTGTATG
Done.