Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007811.1 Kokia drynarioides strain JFW-HI SEQ_122447, 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: 5815
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:2534 original size:21 final size:21

Alignment explanation


    Indices: 2508--2549  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2498 TAAAATCACA

                                  
       2508 TTTAATGCAACCA-TCGAAACT
          1 TTTAATGCAACCACT-GAAACT

                                 
       2529 TTTAATGCAACCACTGAAACT
          1 TTTAATGCAACCACTGAAACT

       2550 CTCCCGTCAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  21   19  0.95
  22    1  0.05

ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29


Consensus pattern (21 bp):   
TTTAATGCAACCACTGAAACT

Found at i:3105 original size:63 final size:62

Alignment explanation


    Indices: 3038--3223  Score: 184
    Period size: 63  Copynumber: 2.9  Consensus size: 62

       3028 AACATTTATA

                            *    *                                      *  
       3038 AAAATTTAATTTAATAATTATCTTAATAATATTTTATTAATTTAATATTAAAGTAATTATCTT
          1 AAAATTTAATTTAATATTTATTTTAATAATATTTTATTAATTTAATATTAAAGT-ATTATATT

                  *        *                                          *      
       3101 AAAATTAAATTTAATGTTTATTTTGTAAATAAATATTTTATTAATTTAA-A-T-AAGTTTTAATA
          1 AAAATTTAATTTAATATTTA-TTT-T-AAT-AATATTTTATTAATTTAATATTAAAGTATT-ATA

              
       3163 TT
         61 TT

                      *                        *                         
       3165 -AAATTTAATCTAATATTTATATTTACA-AATATTATATTAATTTAATATTAAAGTGATTA
          1 AAAATTTAATTTAATATTTAT-TTTA-ATAATATTTTATTAATTTAATATTAAAGT-ATTA

       3224 AGTTTACTCA


Statistics
Matches: 101,  Mismatches: 11, Indels: 22
        0.75            0.08        0.16

Matches are distributed among these distances:
  60   17  0.17
  61    2  0.02
  62    4  0.04
  63   42  0.42
  64   12  0.12
  65    2  0.02
  66    4  0.04
  67   18  0.18

ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50


Consensus pattern (62 bp):   
AAAATTTAATTTAATATTTATTTTAATAATATTTTATTAATTTAATATTAAAGTATTATATT

Found at i:3186 original size:23 final size:21

Alignment explanation


    Indices: 3126--3187  Score: 56
    Period size: 23  Copynumber: 2.8  Consensus size: 21

       3116 GTTTATTTTG

                                  
       3126 TAAATAAATATTT-TATTAATT
          1 TAAAT-AATATTTATATTAATT

                                    
       3147 TAAATAAGT-TTTAATATTAAATT
          1 TAAATAA-TATTT-ATATT-AATT

                *             
       3170 TAATCTAATATTTATATT
          1 TAA-ATAATATTTATATT

       3188 TACAAATATT


Statistics
Matches: 34,  Mismatches: 1, Indels: 10
        0.76            0.02        0.22

Matches are distributed among these distances:
  20    5  0.15
  21    6  0.18
  22    4  0.12
  23   13  0.38
  24    6  0.18

ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52


Consensus pattern (21 bp):   
TAAATAATATTTATATTAATT
Done.