Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000116.1 Kokia drynarioides strain JFW-HI SEQ_110755, 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, 747

Length: 1245
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39


Found at i:39 original size:18 final size:18

Alignment explanation


    Indices: 5--71  Score: 91
    Period size: 18  Copynumber: 3.8  Consensus size: 18

          1 ATTC

                              
          5 AAAATAAATTT-AAATTT
          1 AAAATAAATTTAAAATTT

                              
         22 AAAATAAATTTAAAATTT
          1 AAAATAAATTTAAAATTT

            *   *        **   
         40 TAAACAAATTTAATTTTT
          1 AAAATAAATTTAAAATTT

                          
         58 AAAATAAATTTAAA
          1 AAAATAAATTTAAA

         72 GGGAGTTTGG


Statistics
Matches: 42,  Mismatches: 7, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  17   11  0.26
  18   31  0.74

ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40


Consensus pattern (18 bp):   
AAAATAAATTTAAAATTT

Found at i:162 original size:23 final size:23

Alignment explanation


    Indices: 109--167  Score: 81
    Period size: 20  Copynumber: 2.7  Consensus size: 23

         99 GCTTCAACAA

                                *  
        109 TATTAATTA-TTAATATAAATAT
          1 TATTAATTACTTAATATAAAGAT

                                   
        131 TATT-A--ACTTAATATAAAGAT
          1 TATTAATTACTTAATATAAAGAT

                             
        151 TATTAATTACTTAATAT
          1 TATTAATTACTTAATAT

        168 TAATAACAAA


Statistics
Matches: 32,  Mismatches: 1, Indels: 7
        0.80            0.03        0.17

Matches are distributed among these distances:
  19    1  0.03
  20   16  0.50
  21    2  0.06
  22    4  0.12
  23    9  0.28

ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47


Consensus pattern (23 bp):   
TATTAATTACTTAATATAAAGAT

Found at i:604 original size:21 final size:21

Alignment explanation


    Indices: 580--628  Score: 89
    Period size: 21  Copynumber: 2.3  Consensus size: 21

        570 AATTGCCTTT

                                 
        580 TTCTTCACGCACGCCCTTCCC
          1 TTCTTCACGCACGCCCTTCCC

                               * 
        601 TTCTTCACGCACGCCCTTCTC
          1 TTCTTCACGCACGCCCTTCCC

                   
        622 TTCTTCA
          1 TTCTTCA

        629 GTCTTATCTT


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.10, C:0.47, G:0.08, T:0.35


Consensus pattern (21 bp):   
TTCTTCACGCACGCCCTTCCC

Found at i:816 original size:18 final size:17

Alignment explanation


    Indices: 774--817  Score: 52
    Period size: 18  Copynumber: 2.5  Consensus size: 17

        764 TGTAATCCTT

                           **
        774 TTTATTGTTTAATTTTG
          1 TTTATTGTTTAATTTAA

                               
        791 TTTAATTGTTTAATTTCAA
          1 TTT-ATTGTTTAATTT-AA

                    
        810 TTTATTGT
          1 TTTATTGT

        818 AATCCTTCGT


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  17    3  0.13
  18   17  0.74
  19    3  0.13

ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66


Consensus pattern (17 bp):   
TTTATTGTTTAATTTAA
Done.