Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000082.1 Kokia drynarioides strain JFW-HI SEQ_110705, 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: 2061
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43


Found at i:264 original size:17 final size:17

Alignment explanation


    Indices: 244--276  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        234 TTTTTTATTT

                              
        244 TTTA-AAATATTATAAAA
          1 TTTAGAAAT-TTATAAAA

                            
        261 TTTAGAAATTTATAAA
          1 TTTAGAAATTTATAAA

        277 TATATATATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  17   11  0.73
  18    4  0.27

ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42


Consensus pattern (17 bp):   
TTTAGAAATTTATAAAA

Found at i:397 original size:21 final size:21

Alignment explanation


    Indices: 372--411  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        362 TATCCCTTGA

                                  
        372 ATAATTCTT-ATATAATTTTCT
          1 ATAATT-TTGATATAATTTTCT

                     *         
        393 ATAATTTTGTTATAATTTT
          1 ATAATTTTGATATAATTTT

        412 TAAAAATCAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    2  0.12
  21   15  0.88

ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60


Consensus pattern (21 bp):   
ATAATTTTGATATAATTTTCT

Found at i:1271 original size:17 final size:17

Alignment explanation


    Indices: 1246--1280  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       1236 TTTACATATT

                *            
       1246 TTAAGTTACTTACTTGG
          1 TTAAATTACTTACTTGG

                        *    
       1263 TTAAATTACTTAGTTGG
          1 TTAAATTACTTACTTGG

             
       1280 T
          1 T

       1281 CGCCCATATT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49


Consensus pattern (17 bp):   
TTAAATTACTTACTTGG
Done.