Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004932.1 Kokia drynarioides strain JFW-HI SEQ_118635, 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: 3208
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:330 original size:21 final size:19

Alignment explanation


    Indices: 314--351  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 19

        304 ATACATGTCT

                                 
        314 TTAAGGTATC-GAAACATAGC
          1 TTAAGGTATCAG-AACAT-GC

                              
        334 TTAAGGTATCAGAACATG
          1 TTAAGGTATCAGAACATG

        352 GGGGTTATGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  19    1  0.06
  20   15  0.88
  21    1  0.06

ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26


Consensus pattern (19 bp):   
TTAAGGTATCAGAACATGC

Found at i:1017 original size:32 final size:29

Alignment explanation


    Indices: 952--1017  Score: 78
    Period size: 32  Copynumber: 2.2  Consensus size: 29

        942 ATAGTTTAAA

                              *      *   
        952 TATCACATGAAACATTTTCAAAGTATAAG
          1 TATCACATGAAACATTTTAAAAGTACAAG

                                           *
        981 TATCACATGAAACATTTTATTAAAAGTACAAT
          1 TATCACATGAAACA--TT-TTAAAAGTACAAG

                 
       1013 TATCA
          1 TATCA

       1018 AATGTGATCT


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  29   14  0.45
  31    2  0.06
  32   15  0.48

ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33


Consensus pattern (29 bp):   
TATCACATGAAACATTTTAAAAGTACAAG

Found at i:1129 original size:162 final size:162

Alignment explanation


    Indices: 859--1186  Score: 602
    Period size: 162  Copynumber: 2.0  Consensus size: 162

        849 CCTAATTCGA

                                          *                                  
        859 GTGATCTGAATCTCTAACCCCTTAGAGTCTGGAGGTAAAGTAAAAGATGTTTTTTTAAAACATTT
          1 GTGATCTGAATCTCTAACCCCTTAGAGTCTAGAGGTAAAGTAAAAGATGTTTTTTTAAAACATTT

                                                                             
        924 TATAAAAACACAAGTACCATAGTTTAAATATCACATGAAACATTTTCAAAGTATAAGTATCACAT
         66 TATAAAAACACAAGTACCATAGTTTAAATATCACATGAAACATTTTCAAAGTATAAGTATCACAT

                                            
        989 GAAACATTTTATTAAAAGTACAATTATCAAAT
        131 GAAACATTTTATTAAAAGTACAATTATCAAAT

                                                                    *        
       1021 GTGATCTGAATCTCTAACCCCTTAGAGTCTAGAGGTAAAGTAAAAGATGTTTTTTTTAAACATTT
          1 GTGATCTGAATCTCTAACCCCTTAGAGTCTAGAGGTAAAGTAAAAGATGTTTTTTTAAAACATTT

                    *                        *  *             *              
       1086 TATAAAAATACAAGTACCATAGTTTAAATATCATATTAAACATTTTCAAATTATAAGTATCACAT
         66 TATAAAAACACAAGTACCATAGTTTAAATATCACATGAAACATTTTCAAAGTATAAGTATCACAT

                                            
       1151 GAAACATTTTATTAAAAGTACAATTATCAAAT
        131 GAAACATTTTATTAAAAGTACAATTATCAAAT

                
       1183 GTGA
          1 GTGA

       1187 CGTTATCCAT


Statistics
Matches: 160,  Mismatches: 6, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 162  160  1.00

ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34


Consensus pattern (162 bp):   
GTGATCTGAATCTCTAACCCCTTAGAGTCTAGAGGTAAAGTAAAAGATGTTTTTTTAAAACATTT
TATAAAAACACAAGTACCATAGTTTAAATATCACATGAAACATTTTCAAAGTATAAGTATCACAT
GAAACATTTTATTAAAAGTACAATTATCAAAT
Done.