Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009073.1 Kokia drynarioides strain JFW-HI SEQ_123773, 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: 11979
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:422 original size:23 final size:23

Alignment explanation


    Indices: 347--422  Score: 68
    Period size: 23  Copynumber: 3.2  Consensus size: 23

        337 AGGATAGTGG

                                   
        347 TGAAAAGGGTTATGAAATTCACT
          1 TGAAAAGGGTTATGAAATTCACT

                    *             *     
        370 TG-AAA-GATTATTTGGGACAACTC-CT
          1 TGAAAAGGGTTA--T--GA-AATTCACT

                                   
        395 TGAAAAGGGTTATGAAATTCACT
          1 TGAAAAGGGTTATGAAATTCACT

                 
        418 TGAAA
          1 TGAAA

        423 TTCATTATGT


Statistics
Matches: 41,  Mismatches: 4, Indels: 16
        0.67            0.07        0.26

Matches are distributed among these distances:
  21    4  0.10
  22    7  0.17
  23   12  0.29
  25    7  0.17
  26    7  0.17
  27    4  0.10

ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30


Consensus pattern (23 bp):   
TGAAAAGGGTTATGAAATTCACT

Found at i:4376 original size:32 final size:33

Alignment explanation


    Indices: 4340--4403  Score: 103
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       4330 TGTAGTTATA

                                *            
       4340 TTTAATGAATGTA-TTAGAGTAGATGTATCTAC
          1 TTTAATGAATGTATTTAGAGAAGATGTATCTAC

                  *                         
       4372 TTTAATTAATGTATTTAGAGAAGATGTATCTA
          1 TTTAATGAATGTATTTAGAGAAGATGTATCTA

       4404 GTAGTCATGC


Statistics
Matches: 29,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  32   12  0.41
  33   17  0.59

ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42


Consensus pattern (33 bp):   
TTTAATGAATGTATTTAGAGAAGATGTATCTAC

Found at i:7169 original size:30 final size:31

Alignment explanation


    Indices: 7111--7184  Score: 77
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       7101 TAGATTCGTC

                                *   *      
       7111 TATATTG-TTT-TTTTAATTCTTTTAAA-TT
          1 TATATTGTTTTATTTTAATTATTTAAAATTT

                                            
       7139 TATATTGTTTTATTTTAA-TATTTAATAATTT
          1 TATATTGTTTTATTTTAATTATTTAA-AATTT

                            
       7170 TATCATT-TTTTATTT
          1 TAT-ATTGTTTTATTT

       7185 GTTGAAATTT


Statistics
Matches: 39,  Mismatches: 2, Indels: 7
        0.81            0.04        0.15

Matches are distributed among these distances:
  28    7  0.18
  29    8  0.21
  30    8  0.21
  31   13  0.33
  32    3  0.08

ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68


Consensus pattern (31 bp):   
TATATTGTTTTATTTTAATTATTTAAAATTT

Found at i:9486 original size:29 final size:29

Alignment explanation


    Indices: 9427--9485  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       9417 TTTGGTTTAA

                             *           
       9427 TGTGCAATTGTATAAATGAATTTTAATTT
          1 TGTGCAATTGTATAAATAAATTTTAATTT

                     *    *          *    
       9456 TGTGCAATTTTATACATCAAATTTTGATTT
          1 TGTGCAATTGTATAAAT-AAATTTTAATTT

       9486 GATCTAACTC


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  29   15  0.60
  30   10  0.40

ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49


Consensus pattern (29 bp):   
TGTGCAATTGTATAAATAAATTTTAATTT

Found at i:10273 original size:15 final size:14

Alignment explanation


    Indices: 10253--10296  Score: 56
    Period size: 14  Copynumber: 3.1  Consensus size: 14

      10243 CCTGGCCACC

                           
      10253 AATATTAATTTCTTT
          1 AATATTAATTT-TTT

                          
      10268 AATATT-ATTTTTT
          1 AATATTAATTTTTT

                           
      10281 -ATATATAATTTTTT
          1 AATAT-TAATTTTTT

              
      10295 AA
          1 AA

      10297 AAAATATATA


Statistics
Matches: 26,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  12    4  0.15
  13    4  0.15
  14   11  0.42
  15    7  0.27

ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61


Consensus pattern (14 bp):   
AATATTAATTTTTT

Done.