Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007796.1 Kokia drynarioides strain JFW-HI SEQ_122430, 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: 3677
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36


Found at i:789 original size:31 final size:29

Alignment explanation


    Indices: 754--834  Score: 92
    Period size: 29  Copynumber: 2.8  Consensus size: 29

        744 TTAATAACTC

                          *         *   *  
        754 AGTGACTAAAATGTTACAATATGATAACGTA
          1 AGTGACTAAAATGTAAC-AT-TGAAAACATA

                       *        *        
        785 AGTGACTAAAACGTAACATTTAAAACATA
          1 AGTGACTAAAATGTAACATTGAAAACATA

                                  
        814 AGTGACTAAAATGTAAC-TTGA
          1 AGTGACTAAAATGTAACATTGA

        835 GACAAACAAA


Statistics
Matches: 43,  Mismatches: 7, Indels: 3
        0.81            0.13        0.06

Matches are distributed among these distances:
  28    3  0.07
  29   23  0.53
  30    2  0.05
  31   15  0.35

ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27


Consensus pattern (29 bp):   
AGTGACTAAAATGTAACATTGAAAACATA

Found at i:1165 original size:22 final size:22

Alignment explanation


    Indices: 1137--1187  Score: 66
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       1127 CAATCTTAAA

                      *           
       1137 TAATAAAAATGAATAAAATTTT
          1 TAATAAAAATCAATAAAATTTT

                          ** *    
       1159 TAATAAAAATCAATTTATTTTT
          1 TAATAAAAATCAATAAAATTTT

                   
       1181 TAATAAA
          1 TAATAAA

       1188 GATATATAAA


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   25  1.00

ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41


Consensus pattern (22 bp):   
TAATAAAAATCAATAAAATTTT

Found at i:2359 original size:48 final size:48

Alignment explanation


    Indices: 2306--2403  Score: 187
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       2296 TTTCGTACCC

                           *                                
       2306 GTGAAGATGATTCCATCTAAAGAATAGATATTTTGGAAAATAGTAATA
          1 GTGAAGATGATTCCAACTAAAGAATAGATATTTTGGAAAATAGTAATA

                                                            
       2354 GTGAAGATGATTCCAACTAAAGAATAGATATTTTGGAAAATAGTAATA
          1 GTGAAGATGATTCCAACTAAAGAATAGATATTTTGGAAAATAGTAATA

              
       2402 GT
          1 GT

       2404 ATAGTAGGAC


Statistics
Matches: 49,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  48   49  1.00

ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31


Consensus pattern (48 bp):   
GTGAAGATGATTCCAACTAAAGAATAGATATTTTGGAAAATAGTAATA

Found at i:3462 original size:28 final size:28

Alignment explanation


    Indices: 3425--3490  Score: 89
    Period size: 30  Copynumber: 2.3  Consensus size: 28

       3415 GAGTTTCACG

                               *        
       3425 TGTATAATTGCAC-CAAATTAAAGTTCA
          1 TGTATAATTGCACACAAATCAAAGTTCA

                            *             
       3452 TGTATCAATTGCACATTAAATCAAAGTTCA
          1 TGTAT-AATTGCACA-CAAATCAAAGTTCA

                     
       3482 TGTATAATT
          1 TGTATAATT

       3491 TTGAGATATA


Statistics
Matches: 34,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  27    5  0.15
  28    8  0.24
  29    4  0.12
  30   17  0.50

ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36


Consensus pattern (28 bp):   
TGTATAATTGCACACAAATCAAAGTTCA
Done.