Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006513.1 Kokia drynarioides strain JFW-HI SEQ_121097, 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: 2781
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42


Found at i:887 original size:16 final size:17

Alignment explanation


    Indices: 849--888  Score: 55
    Period size: 17  Copynumber: 2.4  Consensus size: 17

        839 ATTTTAGTAA

                             
        849 AATTTTATATTTTCTAT
          1 AATTTTATATTTTCTAT

             *    *          
        866 AGTTTTGTATTTT-TAT
          1 AATTTTATATTTTCTAT

                   
        882 AATTTTA
          1 AATTTTA

        889 GGTTTTTTCT


Statistics
Matches: 19,  Mismatches: 4, Indels: 1
        0.79            0.17        0.04

Matches are distributed among these distances:
  16    8  0.42
  17   11  0.58

ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65


Consensus pattern (17 bp):   
AATTTTATATTTTCTAT

Found at i:1414 original size:8 final size:9

Alignment explanation


    Indices: 1392--1416  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

       1382 TTTATTTAAA

                     
       1392 TAAAAATAT
          1 TAAAAATAT

                     
       1401 TAAAAATAT
          1 TAAAAATAT

                   
       1410 TAAAAAT
          1 TAAAAAT

       1417 CCTTTGTCTG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (9 bp):   
TAAAAATAT

Found at i:2202 original size:18 final size:18

Alignment explanation


    Indices: 2144--2202  Score: 50
    Period size: 18  Copynumber: 3.2  Consensus size: 18

       2134 TTTATTTTTT

                             * 
       2144 TAAAT-TTGTAAAAAATAA
          1 TAAATATTGT-AAAAATTA

                    *          *
       2162 TAAA-ATTATAAGAAATTGT
          1 TAAATATTGTAA-AAATT-A

                              
       2181 TAAATATTGTAAAAATTA
          1 TAAATATTGTAAAAATTA

                
       2199 TAAA
          1 TAAA

       2203 AAAGCCAAAA


Statistics
Matches: 32,  Mismatches: 5, Indels: 8
        0.71            0.11        0.18

Matches are distributed among these distances:
  17    2  0.06
  18   15  0.47
  19    9  0.28
  20    6  0.19

ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36


Consensus pattern (18 bp):   
TAAATATTGTAAAAATTA
Done.