Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011996.1 Kokia drynarioides strain JFW-HI SEQ_126994, 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: 8299
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:5372 original size:14 final size:14

Alignment explanation


    Indices: 5348--5381  Score: 54
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       5338 TGTCAAGCAA

                          
       5348 TCAGA-GTTAAATG
          1 TCAGATGTTAAATG

                          
       5361 TCAGATGTTAAATG
          1 TCAGATGTTAAATG

                    
       5375 TCA-ATGT
          1 TCAGATGT

       5382 ACTGAAAGTA


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  13    9  0.45
  14   11  0.55

ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35


Consensus pattern (14 bp):   
TCAGATGTTAAATG

Found at i:6929 original size:13 final size:13

Alignment explanation


    Indices: 6905--6943  Score: 53
    Period size: 13  Copynumber: 3.0  Consensus size: 13

       6895 AAATATAATT

                          
       6905 TTTTCTTCTTTTTC
          1 TTTTC-TCTTTTTC

                        *
       6919 TTTTCTCTTTTTT
          1 TTTTCTCTTTTTC

                         
       6932 TTTTCT-TTTTTC
          1 TTTTCTCTTTTTC

       6944 AAGTGACTGA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  12    5  0.22
  13   13  0.57
  14    5  0.22

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (13 bp):   
TTTTCTCTTTTTC

Found at i:6942 original size:11 final size:11

Alignment explanation


    Indices: 6903--6942  Score: 53
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       6893 GCAAATATAA

                  *    
       6903 TTTTTTCTTCT
          1 TTTTTTTTTCT

                         
       6914 TTTTCTTTTCTCT
          1 TTTT-TTTT-TCT

                       
       6927 TTTTTTTTTCT
          1 TTTTTTTTTCT

                 
       6938 TTTTT
          1 TTTTT

       6943 CAAGTGACTG


Statistics
Matches: 26,  Mismatches: 1, Indels: 4
        0.84            0.03        0.13

Matches are distributed among these distances:
  11   12  0.46
  12    7  0.27
  13    7  0.27

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (11 bp):   
TTTTTTTTTCT

Found at i:7547 original size:18 final size:18

Alignment explanation


    Indices: 7524--7566  Score: 52
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       7514 TAACAAAAGG

                   *           
       7524 AATGCAGTGACA-AAATAA
          1 AATGCAGGGACAGAAA-AA

                               
       7542 AATGCAGGGACAGTAAAAA
          1 AATGCAGGGACAG-AAAAA

                  
       7561 AATGCA
          1 AATGCA

       7567 TGAAAATATC


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  18   11  0.50
  19    8  0.36
  20    3  0.14

ACGTcount: A:0.53, C:0.12, G:0.21, T:0.14


Consensus pattern (18 bp):   
AATGCAGGGACAGAAAAA
Done.