Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015363.1 Kokia drynarioides strain JFW-HI SEQ_130410, 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: 8396
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.34

Warning! 52 characters in sequence are not A, C, G, or T


Found at i:4437 original size:29 final size:30

Alignment explanation


    Indices: 4403--4465  Score: 85
    Period size: 29  Copynumber: 2.1  Consensus size: 30

       4393 GATTTATATA

                     *                     
       4403 ATTTTCGTATTTAATTT-TTTCTTTAG-ATT
          1 ATTTTCGTAATTAATTTATTT-TTTAGAATT

                                    *     
       4432 ATTTTCGTAATTAATTTATTTTTTTGAATT
          1 ATTTTCGTAATTAATTTATTTTTTAGAATT

                
       4462 ATTT
          1 ATTT

       4466 AAAAAACTCA


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  29   20  0.67
  30   10  0.33

ACGTcount: A:0.24, C:0.05, G:0.06, T:0.65


Consensus pattern (30 bp):   
ATTTTCGTAATTAATTTATTTTTTAGAATT

Found at i:5728 original size:150 final size:150

Alignment explanation


    Indices: 5457--5745  Score: 551
    Period size: 150  Copynumber: 1.9  Consensus size: 150

       5447 AAAAAAAAAA

                                                                  *          
       5457 AAATTGGCATTGGTGGTTGTTTTTAAATTGAATTTTAAAATCTAGGTAGTTAGCGTTAACGTCTC
          1 AAATTGGCATTGGTGGTTGTTTTTAAATTGAATTTTAAAATCTAGGTAGTTAGCATTAACGTCTC

                                                               *             
       5522 CTATATTTAATATATTTAAGGGTACCATATATAGATGCAAATGTGGATTGGTTGGGTTGAATCTG
         66 CTATATTTAATATATTTAAGGGTACCATATATAGATGCAAATGTGGATTGGGTGGGTTGAATCTG

                                
       5587 ATCTAACCATATATAGATGC
        131 ATCTAACCATATATAGATGC

                                                     *                       
       5607 AAATTGGCATTGGTGGTTGTTTTTAAATTGAATTTTAAAATTTAGGTAGTTAGCATTAACGTCTC
          1 AAATTGGCATTGGTGGTTGTTTTTAAATTGAATTTTAAAATCTAGGTAGTTAGCATTAACGTCTC

                                                                             
       5672 CTATATTTAATATATTTAAGGGTACCATATATAGATGCAAATGTGGATTGGGTGGGTTGAATCTG
         66 CTATATTTAATATATTTAAGGGTACCATATATAGATGCAAATGTGGATTGGGTGGGTTGAATCTG

                     
       5737 ATCTAACCA
        131 ATCTAACCA

       5746 AGGGTGGAGT


Statistics
Matches: 136,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 150  136  1.00

ACGTcount: A:0.31, C:0.10, G:0.21, T:0.39


Consensus pattern (150 bp):   
AAATTGGCATTGGTGGTTGTTTTTAAATTGAATTTTAAAATCTAGGTAGTTAGCATTAACGTCTC
CTATATTTAATATATTTAAGGGTACCATATATAGATGCAAATGTGGATTGGGTGGGTTGAATCTG
ATCTAACCATATATAGATGC

Found at i:6769 original size:14 final size:14

Alignment explanation


    Indices: 6750--6799  Score: 57
    Period size: 14  Copynumber: 3.4  Consensus size: 14

       6740 AAATATTCAA

                          
       6750 ATAATAACAACAAT
          1 ATAATAACAACAAT

                            
       6764 ATAATAACAAAACAAT
          1 ATAATAAC--AACAAT

                           
       6780 AATAA-AACAACAAT
          1 -ATAATAACAACAAT

             *    
       6794 AAAATA
          1 ATAATA

       6800 GTAGTTCTTT


Statistics
Matches: 31,  Mismatches: 1, Indels: 8
        0.77            0.03        0.20

Matches are distributed among these distances:
  13    3  0.10
  14   15  0.48
  16    9  0.29
  17    4  0.13

ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18


Consensus pattern (14 bp):   
ATAATAACAACAAT
Done.