Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007228.1 Kokia drynarioides strain JFW-HI SEQ_121843, 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: 5273
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35


Found at i:2234 original size:44 final size:44

Alignment explanation


    Indices: 2171--2260  Score: 180
    Period size: 44  Copynumber: 2.0  Consensus size: 44

       2161 TCTATTTGTC

                                                        
       2171 ATTATCAATTTGTCACCAAGTTATTTTCCTCGAGAAATTATGTA
          1 ATTATCAATTTGTCACCAAGTTATTTTCCTCGAGAAATTATGTA

                                                        
       2215 ATTATCAATTTGTCACCAAGTTATTTTCCTCGAGAAATTATGTA
          1 ATTATCAATTTGTCACCAAGTTATTTTCCTCGAGAAATTATGTA

              
       2259 AT
          1 AT

       2261 AGTGTCAATA


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  44   46  1.00

ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41


Consensus pattern (44 bp):   
ATTATCAATTTGTCACCAAGTTATTTTCCTCGAGAAATTATGTA

Found at i:2432 original size:41 final size:40

Alignment explanation


    Indices: 2387--2463  Score: 109
    Period size: 40  Copynumber: 1.9  Consensus size: 40

       2377 AAAATTTTAA

                     *    *   *                      
       2387 AAATAAAAATAATATTCAGTTTTCTCTTTAAAGAAAATTAT
          1 AAAT-AAAAGAATACTCAATTTTCTCTTTAAAGAAAATTAT

                   *                            
       2428 AAATAAAGGAATACTCAATTTTCTCTTTAAAGAAAA
          1 AAATAAAAGAATACTCAATTTTCTCTTTAAAGAAAA

       2464 ACACAAATAA


Statistics
Matches: 32,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  40   28  0.88
  41    4  0.12

ACGTcount: A:0.49, C:0.09, G:0.06, T:0.35


Consensus pattern (40 bp):   
AAATAAAAGAATACTCAATTTTCTCTTTAAAGAAAATTAT

Found at i:2472 original size:40 final size:40

Alignment explanation


    Indices: 2397--2474  Score: 111
    Period size: 40  Copynumber: 1.9  Consensus size: 40

       2387 AAATAAAAAT

                *   *                  ** *         
       2397 AATATTCAGTTTTCTCTTTAAAGAAAATTATAAATAAAGG
          1 AATACTCAATTTTCTCTTTAAAGAAAAACACAAATAAAGG

                                                  
       2437 AATACTCAATTTTCTCTTTAAAGAAAAACACAAATAAA
          1 AATACTCAATTTTCTCTTTAAAGAAAAACACAAATAAA

       2475 AACTTTGATC


Statistics
Matches: 33,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  40   33  1.00

ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33


Consensus pattern (40 bp):   
AATACTCAATTTTCTCTTTAAAGAAAAACACAAATAAAGG

Found at i:4007 original size:16 final size:15

Alignment explanation


    Indices: 3982--4015  Score: 50
    Period size: 16  Copynumber: 2.2  Consensus size: 15

       3972 TAAAAAAAAG

                 *          
       3982 AATTACAATTTATGTA
          1 AATTAAAATTTAT-TA

                           
       3998 AATTAAAATTTATTA
          1 AATTAAAATTTATTA

               
       4013 AAT
          1 AAT

       4016 ATCAAAGAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    5  0.29
  16   12  0.71

ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44


Consensus pattern (15 bp):   
AATTAAAATTTATTA
Done.