Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008167.1 Kokia drynarioides strain JFW-HI SEQ_122826, 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: 6012
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29


Found at i:1571 original size:15 final size:13

Alignment explanation


    Indices: 1547--1585  Score: 51
    Period size: 16  Copynumber: 2.8  Consensus size: 13

       1537 TGCATATGCA

                         
       1547 TACATGCATTCAT
          1 TACATGCATTCAT

                            
       1560 TAGCATTGCATTTCAT
          1 TA-CA-TGCA-TTCAT

                      
       1576 TACATGCATT
          1 TACATGCATT

       1586 AAATTTCATA


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

Matches are distributed among these distances:
  13    4  0.17
  14    6  0.26
  15    6  0.26
  16    7  0.30

ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41


Consensus pattern (13 bp):   
TACATGCATTCAT

Found at i:1621 original size:20 final size:20

Alignment explanation


    Indices: 1596--1638  Score: 54
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       1586 AAATTTCATA

                                  
       1596 AAAT-AATAATAATA-AATAAT
          1 AAATAAATAA-AATATAA-AAT

                                
       1616 AAATAAATAAAATATAAAAT
          1 AAATAAATAAAATATAAAAT

               
       1636 AAA
          1 AAA

       1639 AATCCTCACA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  20   14  0.67
  21    7  0.33

ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26


Consensus pattern (20 bp):   
AAATAAATAAAATATAAAAT

Found at i:1833 original size:60 final size:60

Alignment explanation


    Indices: 1765--1886  Score: 190
    Period size: 60  Copynumber: 2.0  Consensus size: 60

       1755 TATATTCAAA

                                             **              *          
       1765 GAAAGGAATGGAGAGGGTAACCTATCAAGAATTTGTCCCTACACCCTCGGAAGTGTTTAG
          1 GAAAGGAATGGAGAGGGTAACCTATCAAGAATTCATCCCTACACCCTCGAAAGTGTTTAG

                                 *               *      *               
       1825 GAAAGGAATGGAGAGGGTAACTTATCAAGAATTCATCTCTACACTCTCGAAAGTGTTTAG
          1 GAAAGGAATGGAGAGGGTAACCTATCAAGAATTCATCCCTACACCCTCGAAAGTGTTTAG

              
       1885 GA
          1 GA

       1887 CAACTAGACT


Statistics
Matches: 56,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  60   56  1.00

ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25


Consensus pattern (60 bp):   
GAAAGGAATGGAGAGGGTAACCTATCAAGAATTCATCCCTACACCCTCGAAAGTGTTTAG

Found at i:5919 original size:54 final size:54

Alignment explanation


    Indices: 5857--6011  Score: 168
    Period size: 54  Copynumber: 3.0  Consensus size: 54

       5847 GACCTCCAAT

                                                      * *          
       5857 CTTTTACCCCTAATCCAGAGGGGCAAATTAAAG-CAACCATCTAGTCTTTTACCC
          1 CTTTTACCCCTAATCCAGAGGGGCAAATTAAAGTC-ACCATCCAATCTTTTACCC

                     *               *                            
       5911 CTTTTACCCTTAATCCAGAGGGGCAGATTAAAGTCACCATCCAA-----T----
          1 CTTTTACCCCTAATCCAGAGGGGCAAATTAAAGTCACCATCCAATCTTTTACCC

                          **      *                               
       5956 CTTTTACCCCTAATTTAGAGGGACAAATTAAAGTCACCATCCAATCTTTTACCC
          1 CTTTTACCCCTAATCCAGAGGGGCAAATTAAAGTCACCATCCAATCTTTTACCC

              
       6010 CT
          1 CT

       6012 A


Statistics
Matches: 82,  Mismatches: 9, Indels: 20
        0.74            0.08        0.18

Matches are distributed among these distances:
  45   39  0.48
  49    1  0.01
  50    1  0.01
  54   40  0.49
  55    1  0.01

ACGTcount: A:0.30, C:0.28, G:0.12, T:0.29


Consensus pattern (54 bp):   
CTTTTACCCCTAATCCAGAGGGGCAAATTAAAGTCACCATCCAATCTTTTACCC

Found at i:5976 original size:45 final size:45

Alignment explanation


    Indices: 5911--6012  Score: 159
    Period size: 45  Copynumber: 2.3  Consensus size: 45

       5901 TCTTTTACCC

                     *            *  *                   
       5911 CTTTTACCCTTAATCCAGAGGGGCAGATTAAAGTCACCATCCAAT
          1 CTTTTACCCCTAATCCAGAGGGACAAATTAAAGTCACCATCCAAT

                          **                             
       5956 CTTTTACCCCTAATTTAGAGGGACAAATTAAAGTCACCATCCAAT
          1 CTTTTACCCCTAATCCAGAGGGACAAATTAAAGTCACCATCCAAT

                        
       6001 CTTTTACCCCTA
          1 CTTTTACCCCTA


Statistics
Matches: 52,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  45   52  1.00

ACGTcount: A:0.31, C:0.27, G:0.12, T:0.29


Consensus pattern (45 bp):   
CTTTTACCCCTAATCCAGAGGGACAAATTAAAGTCACCATCCAAT
Done.