Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008820.1 Kokia drynarioides strain JFW-HI SEQ_123504, 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: 9687
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36


Found at i:1994 original size:23 final size:23

Alignment explanation


    Indices: 1938--1987  Score: 73
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       1928 TCATGCGCTA

                      *            
       1938 TATGCTTAAAGATTAATATAATT
          1 TATGCTTAAATATTAATATAATT

                             * *   
       1961 TATGCTTAAATATTAATGTGATT
          1 TATGCTTAAATATTAATATAATT

                
       1984 TATG
          1 TATG

       1988 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:4517 original size:21 final size:23

Alignment explanation


    Indices: 4478--4526  Score: 59
    Period size: 22  Copynumber: 2.2  Consensus size: 23

       4468 TATCTAATCT

                                   
       4478 ATTAGAGCAATGTTTAAAT-TTA
          1 ATTAGAGCAATGTTTAAATATTA

            *                       
       4500 TTTAGAG-AA-GTTTAAAATATTA
          1 ATTAGAGCAATGTTT-AAATATTA

                 
       4522 ATTAG
          1 ATTAG

       4527 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:6092 original size:34 final size:34

Alignment explanation


    Indices: 6054--6143  Score: 110
    Period size: 34  Copynumber: 2.6  Consensus size: 34

       6044 TATATTGTCA

                 *        *         *          
       6054 GTTTAACTAACTAGTGTTGGGCA-GACATTCGTCG
          1 GTTTATCTAACTAGAGTTGGGCACAACA-TCGTCG

                          * *                 
       6088 GTTTATCTAACTAGCGCTGGGCACAACATCGTCG
          1 GTTTATCTAACTAGAGTTGGGCACAACATCGTCG

                   *              
       6122 GTTTATCCAACTAGAGTTGGGC
          1 GTTTATCTAACTAGAGTTGGGC

       6144 TCACGATCGA


Statistics
Matches: 48,  Mismatches: 7, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  34   45  0.94
  35    3  0.06

ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30


Consensus pattern (34 bp):   
GTTTATCTAACTAGAGTTGGGCACAACATCGTCG
Done.