Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009350.1 Kokia drynarioides strain JFW-HI SEQ_124057, 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: 12130
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:5652 original size:15 final size:15

Alignment explanation


    Indices: 5632--5670  Score: 51
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       5622 TTAACTCGAA

                         * 
       5632 CAATTTCACTCGATT
          1 CAATTTCACTCGACT

                  *        
       5647 CAATTTGACTCGACT
          1 CAATTTCACTCGACT

                     
       5662 CAAATTTCA
          1 C-AATTTCA

       5671 TTTCACTCGA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  15   14  0.70
  16    6  0.30

ACGTcount: A:0.31, C:0.26, G:0.08, T:0.36


Consensus pattern (15 bp):   
CAATTTCACTCGACT

Found at i:11425 original size:15 final size:16

Alignment explanation


    Indices: 11400--11461  Score: 60
    Period size: 15  Copynumber: 4.1  Consensus size: 16

      11390 TCATTAAATT

                            
      11400 TCATATTATATTTTAA
          1 TCATATTATATTTTAA

                            
      11416 TCAT-TTATA-TTTAA
          1 TCATATTATATTTTAA

             *      *       
      11430 -AATATTACATTTTAA
          1 TCATATTATATTTTAA

                *            
      11445 TCA-CTTATATTATTAA
          1 TCATATTATATT-TTAA

             
      11461 T
          1 T

      11462 TTATTACGAA


Statistics
Matches: 37,  Mismatches: 5, Indels: 8
        0.74            0.10        0.16

Matches are distributed among these distances:
  13    2  0.05
  14    9  0.24
  15   16  0.43
  16   10  0.27

ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53


Consensus pattern (16 bp):   
TCATATTATATTTTAA

Found at i:11696 original size:69 final size:69

Alignment explanation


    Indices: 11585--11725  Score: 264
    Period size: 69  Copynumber: 2.0  Consensus size: 69

      11575 TTTTTAAACC

                                                                             
      11585 CTAAATCATCCTTTACATTAGTTACAGAGAAATTGCCTAGAAACCTCTGTTTACTTTCCTTGCAA
          1 CTAAATCATCCTTTACATTAGTTACAGAGAAATTGCCTAGAAACCTCTGTTTACTTTCCTTGCAA

                
      11650 TTAT
         66 TTAT

                   *      *                                                  
      11654 CTAAATCGTCCTTTGCATTAGTTACAGAGAAATTGCCTAGAAACCTCTGTTTACTTTCCTTGCAA
          1 CTAAATCATCCTTTACATTAGTTACAGAGAAATTGCCTAGAAACCTCTGTTTACTTTCCTTGCAA

                
      11719 TTAT
         66 TTAT

               
      11723 CTA
          1 CTA

      11726 TTCTTCTCAT


Statistics
Matches: 70,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  69   70  1.00

ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38


Consensus pattern (69 bp):   
CTAAATCATCCTTTACATTAGTTACAGAGAAATTGCCTAGAAACCTCTGTTTACTTTCCTTGCAA
TTAT
Done.