Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005071.1 Kokia drynarioides strain JFW-HI SEQ_118874, 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: 12620
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:574 original size:22 final size:22

Alignment explanation


    Indices: 549--590  Score: 68
    Period size: 22  Copynumber: 1.9  Consensus size: 22

        539 CAATAGTCGG

                                   
        549 TCAACGATC-AGTCAACGGTTGA
          1 TCAACGATCGA-TCAACGGTTGA

                                
        571 TCAACGATCGATCAACGGTT
          1 TCAACGATCGATCAACGGTT

        591 TGACTTGGTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  22   18  0.95
  23    1  0.05

ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24


Consensus pattern (22 bp):   
TCAACGATCGATCAACGGTTGA

Found at i:648 original size:15 final size:16

Alignment explanation


    Indices: 612--648  Score: 58
    Period size: 16  Copynumber: 2.4  Consensus size: 16

        602 AGGTTTGGAC

                      *     
        612 TTGGGTCAAATGGTTA
          1 TTGGGTCAAAAGGTTA

                            
        628 TTGGGTCAAAAGGTT-
          1 TTGGGTCAAAAGGTTA

                  
        643 TTGGGT
          1 TTGGGT

        649 TATTAGGTCT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  15    6  0.30
  16   14  0.70

ACGTcount: A:0.22, C:0.05, G:0.35, T:0.38


Consensus pattern (16 bp):   
TTGGGTCAAAAGGTTA

Found at i:1515 original size:18 final size:17

Alignment explanation


    Indices: 1498--1555  Score: 66
    Period size: 18  Copynumber: 3.4  Consensus size: 17

       1488 CTGGAGTGGT

                             *
       1498 GAGCTCACATAAATTGGT
          1 GAGCTCACATAAA-TGGC

            *                
       1516 AAGCTCAC--AAATGGC
          1 GAGCTCACATAAATGGC

                              
       1531 GAGCTCACATAAAGTGGC
          1 GAGCTCACATAAA-TGGC

                   
       1549 GAGCTCA
          1 GAGCTCA

       1556 TTAACTTTTA


Statistics
Matches: 34,  Mismatches: 3, Indels: 6
        0.79            0.07        0.14

Matches are distributed among these distances:
  15   10  0.29
  16    3  0.09
  17    3  0.09
  18   18  0.53

ACGTcount: A:0.34, C:0.22, G:0.24, T:0.19


Consensus pattern (17 bp):   
GAGCTCACATAAATGGC

Found at i:6050 original size:18 final size:18

Alignment explanation


    Indices: 6027--6061  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       6017 TCATCCGGAG

                   *          
       6027 TGGTGAGGTCACATAAAT
          1 TGGTGAGCTCACATAAAT

                             
       6045 TGGTGAGCTCACATAAA
          1 TGGTGAGCTCACATAAA

       6062 GTGACGAGCT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26


Consensus pattern (18 bp):   
TGGTGAGCTCACATAAAT

Found at i:6070 original size:18 final size:18

Alignment explanation


    Indices: 6035--6073  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       6025 AGTGGTGAGG

                     *  **    
       6035 TCACATAAATTGGTGAGC
          1 TCACATAAAGTGACGAGC

                              
       6053 TCACATAAAGTGACGAGC
          1 TCACATAAAGTGACGAGC

               
       6071 TCA
          1 TCA

       6074 TTAACTTTAG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23


Consensus pattern (18 bp):   
TCACATAAAGTGACGAGC
Done.