Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008991.1 Kokia drynarioides strain JFW-HI SEQ_123689, 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: 24911
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:816 original size:16 final size:17

Alignment explanation


    Indices: 783--816  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        773 ATGTTTTTAT

                             
        783 AATTAAATATTAATAAA
          1 AATTAAATATTAATAAA

                  *          
        800 AATTAATTATT-ATAAA
          1 AATTAAATATTAATAAA

             
        816 A
          1 A

        817 CAAGCTGAGA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    6  0.38
  17   10  0.62

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (17 bp):   
AATTAAATATTAATAAA

Found at i:2041 original size:29 final size:28

Alignment explanation


    Indices: 1991--2049  Score: 64
    Period size: 29  Copynumber: 2.1  Consensus size: 28

       1981 TACGTGATAG

                  *               *      
       1991 ATAATTGTTGCTCTCTACATAATATAAAA
          1 ATAATTATTGCTCTCTACATAAGA-AAAA

                          * **          
       2020 ATAATTATTGCTCTTTGTATAAGAAAAA
          1 ATAATTATTGCTCTCTACATAAGAAAAA

              
       2048 AT
          1 AT

       2050 GAAATAAAAT


Statistics
Matches: 25,  Mismatches: 5, Indels: 1
        0.81            0.16        0.03

Matches are distributed among these distances:
  28    6  0.24
  29   19  0.76

ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39


Consensus pattern (28 bp):   
ATAATTATTGCTCTCTACATAAGAAAAA

Found at i:3026 original size:22 final size:20

Alignment explanation


    Indices: 2996--3047  Score: 56
    Period size: 22  Copynumber: 2.6  Consensus size: 20

       2986 TTTTAAGTTT

                *                 
       2996 ATAAGTATAAAAGCAATATGTC
          1 ATAAATATAAAAGCAAT-TG-C

                                
       3018 ATAAATATAAAA-CAATTGC
          1 ATAAATATAAAAGCAATTGC

                         
       3037 --AAATATAAAAG
          1 ATAAATATAAAAG

       3048 TACATTCAAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 6
        0.80            0.03        0.17

Matches are distributed among these distances:
  17   10  0.36
  19    1  0.04
  20    2  0.07
  21    4  0.14
  22   11  0.39

ACGTcount: A:0.58, C:0.08, G:0.10, T:0.25


Consensus pattern (20 bp):   
ATAAATATAAAAGCAATTGC

Found at i:4462 original size:2 final size:2

Alignment explanation


    Indices: 4455--4484  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       4445 GTTATGAGTA

                                                        
       4455 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

       4485 GTGAAAAGTA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:12221 original size:2 final size:2

Alignment explanation


    Indices: 12214--12238  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      12204 TTGATGCCTT

                                                 
      12214 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

      12239 GTAGATAAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:24612 original size:22 final size:20

Alignment explanation


    Indices: 24573--24612  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      24563 AATTATTTGA

                   *            
      24573 TAAATATTATTTATAAATTT
          1 TAAATATAATTTATAAATTT

                                
      24593 TAAATATAATGTTATGAAAT
          1 TAAATATAAT-TTAT-AAAT

      24613 AAAAAAATTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    9  0.53
  21    4  0.24
  22    4  0.24

ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47


Consensus pattern (20 bp):   
TAAATATAATTTATAAATTT
Done.