Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001699.1 Kokia drynarioides strain JFW-HI SEQ_113385, 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: 25637
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:9807 original size:17 final size:18

Alignment explanation


    Indices: 9785--9825  Score: 52
    Period size: 17  Copynumber: 2.4  Consensus size: 18

       9775 TTAGTTTTCA

                               
       9785 TGCATTCTT-ATTGT-GCT
          1 TGCATTCTTAATTGTCG-T

                              
       9802 TGCATT-TTAATTGTCGT
          1 TGCATTCTTAATTGTCGT

                   
       9819 TGCATTC
          1 TGCATTC

       9826 ATTTTAGTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 5
        0.81            0.00        0.19

Matches are distributed among these distances:
  16    2  0.10
  17   18  0.86
  18    1  0.05

ACGTcount: A:0.15, C:0.17, G:0.17, T:0.51


Consensus pattern (18 bp):   
TGCATTCTTAATTGTCGT

Found at i:12785 original size:6 final size:6

Alignment explanation


    Indices: 12774--12818  Score: 56
    Period size: 6  Copynumber: 7.5  Consensus size: 6

      12764 ATTTCTTTTC

                                      * *                        
      12774 TTCTTT TTCTTT TTCTTT TTCTTC CT-TTT TTCATTT TTCTTT TTC
          1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTC-TTT TTCTTT TTC

      12819 AAGTGACTGA


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
   5    3  0.09
   6   24  0.73
   7    6  0.18

ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78


Consensus pattern (6 bp):   
TTCTTT

Found at i:12810 original size:24 final size:21

Alignment explanation


    Indices: 12765--12818  Score: 74
    Period size: 24  Copynumber: 2.5  Consensus size: 21

      12755 TTATCATAAA

                                 
      12765 TTTC-TTTTCTTCTTTTTCTT
          1 TTTCTTTTTCTTCTTTTTCTT

                                    
      12785 TTTCTTTTTCTTCCTTTTTTCATT
          1 TTTCTTTTTCTT-C-TTTTTC-TT

                      
      12809 TTTCTTTTTC
          1 TTTCTTTTTC

      12819 AAGTGACTGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
  20    4  0.13
  21    7  0.23
  22    1  0.03
  23    6  0.20
  24   12  0.40

ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78


Consensus pattern (21 bp):   
TTTCTTTTTCTTCTTTTTCTT

Found at i:13419 original size:19 final size:19

Alignment explanation


    Indices: 13395--13447  Score: 81
    Period size: 19  Copynumber: 2.8  Consensus size: 19

      13385 CTAACATAAC

                               
      13395 AAAAATGCAATGAAAAAAT
          1 AAAAATGCAATGAAAAAAT

                         *   * 
      13414 AAAAATGCAATGACAAAGT
          1 AAAAATGCAATGAAAAAAT

                            
      13433 AAAAATGC-ATGAAAA
          1 AAAAATGCAATGAAAA

      13448 CTATCTACAG


Statistics
Matches: 31,  Mismatches: 3, Indels: 1
        0.89            0.09        0.03

Matches are distributed among these distances:
  18    6  0.19
  19   25  0.81

ACGTcount: A:0.64, C:0.08, G:0.13, T:0.15


Consensus pattern (19 bp):   
AAAAATGCAATGAAAAAAT

Found at i:25417 original size:16 final size:16

Alignment explanation


    Indices: 25396--25437  Score: 59
    Period size: 16  Copynumber: 2.6  Consensus size: 16

      25386 ATGTGTGAAA

                             
      25396 AAACAT-AAATATAAAT
          1 AAACATGAAA-ATAAAT

                            
      25412 AAACATGAAAATAAAT
          1 AAACATGAAAATAAAT

               *      
      25428 AAAGATGAAA
          1 AAACATGAAA

      25438 TAAGCATAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  16   21  0.88
  17    3  0.12

ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19


Consensus pattern (16 bp):   
AAACATGAAAATAAAT
Done.