Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002418.1 Kokia drynarioides strain JFW-HI SEQ_114516, 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: 5354
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35


Found at i:1766 original size:20 final size:20

Alignment explanation


    Indices: 1742--1801  Score: 72
    Period size: 19  Copynumber: 3.0  Consensus size: 20

       1732 AAAAATACAA

                                  
       1742 AAAAAATTCAAAAATACTTT-T
          1 AAAAAATTC-AAAATA-TTTAT

                                
       1763 AAAAAATTCAAAATATTTAT
          1 AAAAAATTCAAAATATTTAT

                     *          
       1783 -AAAAATTCCAAA-ATTTAT
          1 AAAAAATTCAAAATATTTAT

             
       1801 A
          1 A

       1802 TTTTTTTAAA


Statistics
Matches: 36,  Mismatches: 1, Indels: 6
        0.84            0.02        0.14

Matches are distributed among these distances:
  18    6  0.17
  19   14  0.39
  20    7  0.19
  21    9  0.25

ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33


Consensus pattern (20 bp):   
AAAAAATTCAAAATATTTAT

Found at i:1766 original size:21 final size:18

Alignment explanation


    Indices: 1742--1796  Score: 65
    Period size: 20  Copynumber: 2.8  Consensus size: 18

       1732 AAAAATACAA

                                 
       1742 AAAAAATTCAAAAATACTTTT
          1 AAAAAATTC-AAAATA--TTT

                              
       1763 AAAAAATTCAAAATATTT
          1 AAAAAATTCAAAATATTT

                            
       1781 ATAAAAATTCCAAAAT
          1 A-AAAAATT-CAAAAT

       1797 TTATATTTTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 5
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    4  0.12
  19    7  0.22
  20   12  0.38
  21    9  0.28

ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31


Consensus pattern (18 bp):   
AAAAAATTCAAAATATTT

Found at i:2758 original size:27 final size:26

Alignment explanation


    Indices: 2715--2804  Score: 78
    Period size: 27  Copynumber: 3.4  Consensus size: 26

       2705 TTTTTAAAGT

                                  *     
       2715 TTAAAGATTT-TAT-TTTTATTTTTATA
          1 TTAAA-ATTTATATATTTTATTATTA-A

                                    *  
       2741 TTAAAATTTATATATTTTATTAATAAA
          1 TTAAAATTTATATATTTTATT-ATTAA

               *      *                 
       2768 TT-TAATTTAAATATTTTTATTAATTAA
          1 TTAAAATTTATATA-TTTTATT-ATTAA

                      
       2795 TTAAAATTTA
          1 TTAAAATTTA

       2805 AGTTGAGCTG


Statistics
Matches: 53,  Mismatches: 6, Indels: 8
        0.79            0.09        0.12

Matches are distributed among these distances:
  25    4  0.08
  26   17  0.32
  27   24  0.45
  28    8  0.15

ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58


Consensus pattern (26 bp):   
TTAAAATTTATATATTTTATTATTAA

Found at i:2781 original size:26 final size:28

Alignment explanation


    Indices: 2725--2805  Score: 94
    Period size: 27  Copynumber: 3.0  Consensus size: 28

       2715 TTAAAGATTT

                      **  *           * 
       2725 TATTTTTATTTTTATATTAAAATTTATA
          1 TATTTTTATTAATAAATTAAAATTTAAA

                               *        
       2753 TA-TTTTATTAATAAATT-TAATTTAAA
          1 TATTTTTATTAATAAATTAAAATTTAAA

                         *             
       2779 TATTTTTATTAATTAATTAAAATTTAA
          1 TATTTTTATTAATAAATTAAAATTTAA

       2806 GTTGAGCTGA


Statistics
Matches: 44,  Mismatches: 7, Indels: 4
        0.80            0.13        0.07

Matches are distributed among these distances:
  26    9  0.20
  27   26  0.59
  28    9  0.20

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (28 bp):   
TATTTTTATTAATAAATTAAAATTTAAA

Found at i:3562 original size:13 final size:13

Alignment explanation


    Indices: 3544--3568  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       3534 TTCAAGTATT

                         
       3544 TTTTTAATTAATG
          1 TTTTTAATTAATG

                        
       3557 TTTTTAATTAAT
          1 TTTTTAATTAAT

       3569 AAATATATTA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64


Consensus pattern (13 bp):   
TTTTTAATTAATG
Done.