Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014354.1 Kokia drynarioides strain JFW-HI SEQ_129391, 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: 16901
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31


Found at i:5827 original size:48 final size:48

Alignment explanation


    Indices: 5766--5887  Score: 199
    Period size: 48  Copynumber: 2.5  Consensus size: 48

       5756 TTAAGTGTTT

                *                                        *  
       5766 TTTTTTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCATCAAGTG
          1 TTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCATCAACTG

                                        *          *  *     
       5814 TTTTGTTTGTTAAATGCATCTTTGTTTAGTAATCTGCATTATTAACTG
          1 TTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCATCAACTG

                                      
       5862 TTTTGTTTGTTAAATGCATCTTTGTT
          1 TTTTGTTTGTTAAATGCATCTTTGTT

       5888 AAATGCCTTG


Statistics
Matches: 69,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  48   69  1.00

ACGTcount: A:0.22, C:0.11, G:0.14, T:0.53


Consensus pattern (48 bp):   
TTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCATCAACTG

Found at i:5900 original size:48 final size:46

Alignment explanation


    Indices: 5766--5902  Score: 152
    Period size: 48  Copynumber: 2.8  Consensus size: 46

       5756 TTAAGTGTTT

                *                                   *     *  
       5766 TTTTTTTTGTTAAATGCATCTTTGTTTAATAATC-TGCATCATCAAGTG
          1 TTTTGTTTGTTAAATGCATCTTTG-TT-A-AATCTTGCATTATCAACTG

                                                       *     
       5814 TTTTGTTTGTTAAATGCATCTTTGTTTAGTAATC-TGCATTATTAACTG
          1 TTTTGTTTGTTAAATGCATCTTTG-TTA--AATCTTGCATTATCAACTG

                                                     
       5862 TTTTGTTTGTTAAATGCATCTTTGTTAAATGCCTTGCATTA
          1 TTTTGTTTGTTAAATGCATCTTTGTTAAAT--CTTGCATTA

       5903 ATGCATCAGT


Statistics
Matches: 81,  Mismatches: 4, Indels: 8
        0.87            0.04        0.09

Matches are distributed among these distances:
  45    3  0.04
  47    5  0.06
  48   73  0.90

ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51


Consensus pattern (46 bp):   
TTTTGTTTGTTAAATGCATCTTTGTTAAATCTTGCATTATCAACTG

Found at i:13814 original size:17 final size:18

Alignment explanation


    Indices: 13772--13806  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      13762 AGTTTGAGAC

                              
      13772 AAATTAATTTCATGTTTG
          1 AAATTAATTTCATGTTTG

                             
      13790 AAATTAATTTCATGTTT
          1 AAATTAATTTCATGTTT

      13807 TAATTAATAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51


Consensus pattern (18 bp):   
AAATTAATTTCATGTTTG

Found at i:13868 original size:32 final size:32

Alignment explanation


    Indices: 13832--13894  Score: 90
    Period size: 32  Copynumber: 2.0  Consensus size: 32

      13822 AGCTGAAATT

                           * *              
      13832 AATTAGCCGATTAATGTGTCTCAGGTACATGC
          1 AATTAGCCGATTAATATATCTCAGGTACATGC

                   *           *           
      13864 AATTAGCTGATTAATATATTTCAGGTACATG
          1 AATTAGCCGATTAATATATCTCAGGTACATG

      13895 TATGGATGGC


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  32   27  1.00

ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35


Consensus pattern (32 bp):   
AATTAGCCGATTAATATATCTCAGGTACATGC

Found at i:15308 original size:48 final size:48

Alignment explanation


    Indices: 15236--15357  Score: 190
    Period size: 48  Copynumber: 2.5  Consensus size: 48

      15226 TTAATGCAAG

                               *           *                
      15236 GCATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAAGAT
          1 GCATTTAACAAACAAAACACTTAATAATGCAAATTACTAAACAAAGAT

                                                *     *     
      15284 GCATTTAACAAACAAAACACTTAATAATGCAAATTATTAAACGAAGAT
          1 GCATTTAACAAACAAAACACTTAATAATGCAAATTACTAAACAAAGAT

                         *            
      15332 GCATTTAACAAAAAAAAACACTTAAT
          1 GCATTTAAC-AAACAAAACACTTAAT

      15358 GAAGCATAAA


Statistics
Matches: 68,  Mismatches: 5, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
  48   53  0.78
  49   15  0.22

ACGTcount: A:0.53, C:0.15, G:0.08, T:0.24


Consensus pattern (48 bp):   
GCATTTAACAAACAAAACACTTAATAATGCAAATTACTAAACAAAGAT

Found at i:16827 original size:60 final size:60

Alignment explanation


    Indices: 16734--16855  Score: 226
    Period size: 60  Copynumber: 2.0  Consensus size: 60

      16724 GGTTCGGGTT

                                   *                                    
      16734 TTAGGTTTAATTTATATTATATATGAGCCCAATATTGTATTATCAGCTCTTATTATTTTA
          1 TTAGGTTTAATTTATATTATATAAGAGCCCAATATTGTATTATCAGCTCTTATTATTTTA

                         *                                              
      16794 TTAGGTTTAATTTTTATTATATAAGAGCCCAATATTGTATTATCAGCTCTTATTATTTTA
          1 TTAGGTTTAATTTATATTATATAAGAGCCCAATATTGTATTATCAGCTCTTATTATTTTA

              
      16854 TT
          1 TT

      16856 GTTATTTTTA


Statistics
Matches: 60,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  60   60  1.00

ACGTcount: A:0.30, C:0.10, G:0.10, T:0.51


Consensus pattern (60 bp):   
TTAGGTTTAATTTATATTATATAAGAGCCCAATATTGTATTATCAGCTCTTATTATTTTA
Done.