Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007498.1 Kokia drynarioides strain JFW-HI SEQ_122122, 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: 25652
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--41  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

                                                                         
          1 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T

         42 GATTGTGAAT


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:1973 original size:29 final size:29

Alignment explanation


    Indices: 1941--1996  Score: 76
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       1931 TCATTTTTGG

                                         
       1941 TCACCCAATTATAAAAAGTTACAAAATAA
          1 TCACCCAATTATAAAAAGTTACAAAATAA

                **      **             
       1970 TCACTTAATTATTCAAAGTTACAAAAT
          1 TCACCCAATTATAAAAAGTTACAAAAT

       1997 TAATGGTGAT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  29   23  1.00

ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30


Consensus pattern (29 bp):   
TCACCCAATTATAAAAAGTTACAAAATAA

Found at i:2138 original size:59 final size:59

Alignment explanation


    Indices: 2027--2142  Score: 175
    Period size: 59  Copynumber: 2.0  Consensus size: 59

       2017 ATAAGAATGA

                      *                                                
       2027 AATTGAGTGATCATTTTGTAACTTTTTATAGTTAGATGACCATAAAAGAAATTTACTTT
          1 AATTGAGTGACCATTTTGTAACTTTTTATAGTTAGATGACCATAAAAGAAATTTACTTT

                                                                        
       2086 AATTGAGTGACCATTTTGTAACTTTTTCATAGTT-GATTGACCA-ATAAA-AAATTTACT
          1 AATTGAGTGACCATTTTGTAACTTTTT-ATAGTTAGA-TGACCATA-AAAGAAATTTACT

       2143 AATAATTGGA


Statistics
Matches: 53,  Mismatches: 1, Indels: 6
        0.88            0.02        0.10

Matches are distributed among these distances:
  59   38  0.72
  60   15  0.28

ACGTcount: A:0.35, C:0.10, G:0.13, T:0.41


Consensus pattern (59 bp):   
AATTGAGTGACCATTTTGTAACTTTTTATAGTTAGATGACCATAAAAGAAATTTACTTT

Found at i:14573 original size:19 final size:17

Alignment explanation


    Indices: 14549--14608  Score: 59
    Period size: 17  Copynumber: 3.4  Consensus size: 17

      14539 TATTTTTAAA

                               
      14549 ATTTAAAAATTCAAAAAAT
          1 ATTTAAAAATT--AAAAAT

                  *          
      14568 ATTTAATAATTAAAAAT
          1 ATTTAAAAATTAAAAAT

             *                
      14585 AATT-AAAATTATAAAAT
          1 ATTTAAAAATTA-AAAAT

              *    
      14602 ATATAAA
          1 ATTTAAA

      14609 TTTTAATATA


Statistics
Matches: 34,  Mismatches: 5, Indels: 5
        0.77            0.11        0.11

Matches are distributed among these distances:
  16    6  0.18
  17   16  0.47
  18    2  0.06
  19   10  0.29

ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35


Consensus pattern (17 bp):   
ATTTAAAAATTAAAAAT

Found at i:14619 original size:16 final size:16

Alignment explanation


    Indices: 14590--14632  Score: 50
    Period size: 16  Copynumber: 2.7  Consensus size: 16

      14580 AAAATAATTA

                 *          
      14590 AAATTATAAAATATAT
          1 AAATTTTAAAATATAT

                     *    * 
      14606 AAATTTTAATATATTT
          1 AAATTTTAAAATATAT

              *        
      14622 AATTTTTAAAA
          1 AAATTTTAAAA

      14633 AATTATTTAA


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  16   22  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (16 bp):   
AAATTTTAAAATATAT
Done.