Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006391.1 Kokia drynarioides strain JFW-HI SEQ_120968, 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: 1759
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.28


Found at i:852 original size:21 final size:21

Alignment explanation


    Indices: 814--853  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        804 AAAACCCAAT

                        *        
        814 TTTATTTATTTCGTATTTTTA
          1 TTTATTTATTTCATATTTTTA

                                
        835 TTTATTTATTT-ATCATTTT
          1 TTTATTTATTTCAT-ATTTT

        854 ATAAATGTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    1  0.06
  21   16  0.94

ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72


Consensus pattern (21 bp):   
TTTATTTATTTCATATTTTTA

Found at i:1108 original size:16 final size:18

Alignment explanation


    Indices: 1064--1110  Score: 53
    Period size: 19  Copynumber: 2.6  Consensus size: 18

       1054 ATTTGCAAAT

                                
       1064 TAAAATAACCCAATACTACC
          1 TAAAA-AACCCAATAC-ACC

                              
       1084 TAAAAAACCCAATAC-CC
          1 TAAAAAACCCAATACACC

                *      
       1101 -AAACAACCCA
          1 TAAAAAACCCA

       1111 TTTTAATAAC


Statistics
Matches: 26,  Mismatches: 1, Indels: 4
        0.84            0.03        0.13

Matches are distributed among these distances:
  16    9  0.35
  17    2  0.08
  19   10  0.38
  20    5  0.19

ACGTcount: A:0.53, C:0.34, G:0.00, T:0.13


Consensus pattern (18 bp):   
TAAAAAACCCAATACACC

Found at i:1197 original size:50 final size:50

Alignment explanation


    Indices: 1141--1237  Score: 176
    Period size: 50  Copynumber: 1.9  Consensus size: 50

       1131 AACCTAACTA

                                  *                           
       1141 CCAATACCTAAACAAAACCAAATAGCCCAAACTTAAGTCCAACCTTATAT
          1 CCAATACCTAAACAAAACCAAACAGCCCAAACTTAAGTCCAACCTTATAT

                                      *                    
       1191 CCAATACCTAAACAAAACCAAACAGCTCAAACTTAAGTCCAACCTTA
          1 CCAATACCTAAACAAAACCAAACAGCCCAAACTTAAGTCCAACCTTA

       1238 CAAACCCATA


Statistics
Matches: 45,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  50   45  1.00

ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19


Consensus pattern (50 bp):   
CCAATACCTAAACAAAACCAAACAGCCCAAACTTAAGTCCAACCTTATAT
Done.