Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014448.1 Kokia drynarioides strain JFW-HI SEQ_129487, 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: 6619
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34


Found at i:2625 original size:10 final size:9

Alignment explanation


    Indices: 2591--2626  Score: 63
    Period size: 9  Copynumber: 3.9  Consensus size: 9

       2581 AAGTTAATTT

                     
       2591 TAAATTTTG
          1 TAAATTTTG

                     
       2600 TAAATTTTG
          1 TAAATTTTG

                     
       2609 TAAATTTTG
          1 TAAATTTTG

                     
       2618 TAAAATTTT
          1 T-AAATTTT

       2627 AAAATTATTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   9   19  0.73
  10    7  0.27

ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56


Consensus pattern (9 bp):   
TAAATTTTG

Found at i:2631 original size:8 final size:9

Alignment explanation


    Indices: 2586--2632  Score: 53
    Period size: 9  Copynumber: 5.4  Consensus size: 9

       2576 CAATTAAGTT

                     
       2586 AATTT-TAA
          1 AATTTGTAA

             *       
       2594 ATTTTGTAA
          1 AATTTGTAA

             *       
       2603 ATTTTGTAA
          1 AATTTGTAA

             *       
       2612 ATTTTGTAA
          1 AATTTGTAA

                     
       2621 AATTT-TAA
          1 AATTTGTAA

                
       2629 AATT
          1 AATT

       2633 ATTTTATTTT


Statistics
Matches: 36,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
   8   11  0.31
   9   25  0.69

ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53


Consensus pattern (9 bp):   
AATTTGTAA

Found at i:2632 original size:18 final size:16

Alignment explanation


    Indices: 2586--2629  Score: 61
    Period size: 18  Copynumber: 2.6  Consensus size: 16

       2576 CAATTAAGTT

                            
       2586 AATTTTAAATTTTGTA
          1 AATTTTAAATTTTGTA

                               
       2602 AATTTTGTAAATTTTGTAA
          1 AA-TTT-TAAATTTTGT-A

                     
       2621 AATTTTAAA
          1 AATTTTAAA

       2630 ATTATTTTAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  16    2  0.08
  17    7  0.28
  18   13  0.52
  19    3  0.12

ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52


Consensus pattern (16 bp):   
AATTTTAAATTTTGTA
Done.