Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001155.1 Kokia drynarioides strain JFW-HI SEQ_112467, 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: 3472
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33


Found at i:452 original size:19 final size:19

Alignment explanation


    Indices: 391--454  Score: 64
    Period size: 20  Copynumber: 3.4  Consensus size: 19

        381 TTATAATTAA

                               
        391 ATTTAAA-TAAAAATA-TT
          1 ATTTAAATTAAAAATATTT

                                 
        408 A-TT-AATATATAAAATATTT
          1 ATTTAAAT-TA-AAAATATTT

              *                 
        427 GAATTAAATTAAAAATATTT
          1 -ATTTAAATTAAAAATATTT

                    
        447 ATTTAAAT
          1 ATTTAAAT

        455 CCTATTTAAT


Statistics
Matches: 39,  Mismatches: 1, Indels: 12
        0.75            0.02        0.23

Matches are distributed among these distances:
  15    2  0.05
  16    2  0.05
  17    3  0.08
  18    6  0.15
  19    9  0.23
  20   10  0.26
  21    4  0.10
  22    3  0.08

ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44


Consensus pattern (19 bp):   
ATTTAAATTAAAAATATTT

Found at i:2294 original size:17 final size:16

Alignment explanation


    Indices: 2253--2333  Score: 54
    Period size: 17  Copynumber: 4.9  Consensus size: 16

       2243 CTGGGCCCAA

                *    *   *  
       2253 TAAACTTAATTTTTTT
          1 TAAATTTAAATTTATT

                *    *      
       2269 TAAAATTAAGTTTATT
          1 TAAATTTAAATTTATT

                           *  
       2285 CTAAATTTAAATTTGGTT
          1 -TAAATTTAAATTT-ATT

            *        * *    
       2303 GAAATTTAAGTATATT
          1 TAAATTTAAATTTATT

                           
       2319 ATAAATTTAAATTTA
          1 -TAAATTTAAATTTA

       2334 AAATTTATTT


Statistics
Matches: 49,  Mismatches: 13, Indels: 5
        0.73            0.19        0.07

Matches are distributed among these distances:
  16   15  0.31
  17   32  0.65
  18    2  0.04

ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51


Consensus pattern (16 bp):   
TAAATTTAAATTTATT

Found at i:3102 original size:3 final size:3

Alignment explanation


    Indices: 3089--3143  Score: 58
    Period size: 3  Copynumber: 18.0  Consensus size: 3

       3079 CTGATAGCAT

                 *                                             **        
       3089 TAA TGA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA CTGC T-A TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA TAA

                       
       3135 TAA TAA TAA
          1 TAA TAA TAA

       3144 CAAATAAAAA


Statistics
Matches: 44,  Mismatches: 5, Indels: 6
        0.80            0.09        0.11

Matches are distributed among these distances:
   2    1  0.02
   3   39  0.89
   4    4  0.09

ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33


Consensus pattern (3 bp):   
TAA
Done.