Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009286.1 Kokia drynarioides strain JFW-HI SEQ_123992, 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: 10190
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37


Found at i:2322 original size:23 final size:23

Alignment explanation


    Indices: 2303--2363  Score: 104
    Period size: 23  Copynumber: 2.7  Consensus size: 23

       2293 TGATTAAAGG

                                   
       2303 TTAATGTGATTTATGCTTAAATA
          1 TTAATGTGATTTATGCTTAAATA

                          *        
       2326 TTAATGTGATTTATACTTAAATA
          1 TTAATGTGATTTATGCTTAAATA

               *           
       2349 TTATTGTGATTTATG
          1 TTAATGTGATTTATG

       2364 TGTAAATTGG


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  23   35  1.00

ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51


Consensus pattern (23 bp):   
TTAATGTGATTTATGCTTAAATA

Found at i:2369 original size:23 final size:22

Alignment explanation


    Indices: 2303--2370  Score: 91
    Period size: 23  Copynumber: 3.0  Consensus size: 22

       2293 TGATTAAAGG

                                   
       2303 TTAATGTGATTTATGCTTAAATA
          1 TTAATGTGATTTATG-TTAAATA

                           *       
       2326 TTAATGTGATTTATACTTAAATA
          1 TTAATGTGATTTAT-GTTAAATA

               *                  
       2349 TTATTGTGATTTATGTGTAAAT
          1 TTAATGTGATTTATGT-TAAAT

       2371 TGGATACATG


Statistics
Matches: 40,  Mismatches: 3, Indels: 4
        0.85            0.06        0.09

Matches are distributed among these distances:
  22    1  0.03
  23   39  0.98

ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50


Consensus pattern (22 bp):   
TTAATGTGATTTATGTTAAATA

Found at i:5777 original size:23 final size:23

Alignment explanation


    Indices: 5721--5770  Score: 73
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       5711 TCATGCGCTA

                      *            
       5721 TATGCTTAAAGATTAATATAATT
          1 TATGCTTAAATATTAATATAATT

                             * *   
       5744 TATGCTTAAATATTAATGTGATT
          1 TATGCTTAAATATTAATATAATT

                
       5767 TATG
          1 TATG

       5771 TGTAAATGGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  23   24  1.00

ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46


Consensus pattern (23 bp):   
TATGCTTAAATATTAATATAATT

Found at i:8300 original size:21 final size:23

Alignment explanation


    Indices: 8261--8309  Score: 59
    Period size: 22  Copynumber: 2.2  Consensus size: 23

       8251 TATCTAATCT

                                   
       8261 ATTAGAGCAATGTTTAAAT-TTA
          1 ATTAGAGCAATGTTTAAATATTA

            *                       
       8283 TTTAGAG-AA-GTTTAAAATATTA
          1 ATTAGAGCAATGTTT-AAATATTA

                 
       8305 ATTAG
          1 ATTAG

       8310 TAGTTAGAAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  20    4  0.17
  21    6  0.26
  22   13  0.57

ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41


Consensus pattern (23 bp):   
ATTAGAGCAATGTTTAAATATTA

Found at i:9909 original size:34 final size:34

Alignment explanation


    Indices: 9833--9926  Score: 100
    Period size: 34  Copynumber: 2.8  Consensus size: 34

       9823 TATTTATATT

                     *        * *      *      
       9833 GTCAGTTTAACTAACTAGTGTTGGGCAGACATTC
          1 GTCAGTTTATCTAACTAGAGCTGGGCAAACATTC

               *              *                
       9867 GTCGGTTTATCTAACTAGCGCTGGGCACAACA-TC
          1 GTCAGTTTATCTAACTAGAGCTGGGCA-AACATTC

              *        *              
       9901 GTTAGTTTATCCAACTAGAGCTGGGC
          1 GTCAGTTTATCTAACTAGAGCTGGGC

       9927 TCACGATCGA


Statistics
Matches: 50,  Mismatches: 9, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  34   47  0.94
  35    3  0.06

ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30


Consensus pattern (34 bp):   
GTCAGTTTATCTAACTAGAGCTGGGCAAACATTC
Done.