Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001908.1 Kokia drynarioides strain JFW-HI SEQ_113699, 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: 8466
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:213 original size:41 final size:40

Alignment explanation


    Indices: 165--265  Score: 100
    Period size: 38  Copynumber: 2.6  Consensus size: 40

        155 TCGACTTTGA

                                  ** *              
        165 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
          1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG

             *        **                         *   
        205 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
          1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG

             *                     
        243 GCCGATGAGACACTGGGTGTCAC
          1 GTCGATGAGACACTGGGTGTCAC

        266 TTTATTGCTT


Statistics
Matches: 46,  Mismatches: 11, Indels: 7
        0.72            0.17        0.11

Matches are distributed among these distances:
  37   10  0.22
  38   17  0.37
  39    4  0.09
  40    4  0.09
  41   11  0.24

ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30


Consensus pattern (40 bp):   
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG

Found at i:1984 original size:22 final size:22

Alignment explanation


    Indices: 1937--2015  Score: 64
    Period size: 22  Copynumber: 3.8  Consensus size: 22

       1927 AAATTCCAAA

                                   
       1937 TATTGTAAAAAAT-ATAAA-AA-
          1 TATT-TAAAAAATCATAAATAAT

                             *    
       1957 TA--TAAAAAATCATAACTAAT
          1 TATTTAAAAAATCATAAATAAT

                      *            
       1977 TATTTAAAATTAT-ATAAATAAT
          1 TATTTAAAA-AATCATAAATAAT

                 *            
       1999 TATTTGAAAAATC-TAAA
          1 TATTTAAAAAATCATAAA

       2016 AAAAAAATAA


Statistics
Matches: 47,  Mismatches: 5, Indels: 13
        0.72            0.08        0.20

Matches are distributed among these distances:
  17    8  0.17
  18    4  0.09
  19    2  0.04
  20    4  0.09
  21    6  0.13
  22   21  0.45
  23    2  0.04

ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35


Consensus pattern (22 bp):   
TATTTAAAAAATCATAAATAAT

Found at i:2590 original size:19 final size:17

Alignment explanation


    Indices: 2553--2602  Score: 64
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       2543 TTTTAAGGAT

                        *    
       2553 TTTATATTTTTTTATTA
          1 TTTATATTTTTTAATTA

                               
       2570 TTTATATTTTTAATAATTA
          1 TTTATATTTTT--TAATTA

                          
       2589 TTTATAATTTTTTA
          1 TTTAT-ATTTTTTA

       2603 CCATTTTAAT


Statistics
Matches: 29,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  17   11  0.38
  18    2  0.07
  19   10  0.34
  20    6  0.21

ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70


Consensus pattern (17 bp):   
TTTATATTTTTTAATTA
Done.