Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003489.1 Kokia drynarioides strain JFW-HI SEQ_116308, 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: 5351
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31


Found at i:1148 original size:18 final size:17

Alignment explanation


    Indices: 1125--1175  Score: 54
    Period size: 18  Copynumber: 3.1  Consensus size: 17

       1115 AGTTTTTTTC

                              
       1125 TTTCTATTATATTAGTAT
          1 TTTCTATTATATT-GTAT

                    *        
       1143 TTTCTATTCTA-T-T-T
          1 TTTCTATTATATTGTAT

                              
       1157 TTTCTATTATATTCGTAT
          1 TTTCTATTATATT-GTAT

             
       1175 T
          1 T

       1176 AGATTAGTAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 8
        0.73            0.05        0.22

Matches are distributed among these distances:
  14   11  0.41
  15    2  0.07
  17    2  0.07
  18   12  0.44

ACGTcount: A:0.22, C:0.10, G:0.04, T:0.65


Consensus pattern (17 bp):   
TTTCTATTATATTGTAT

Found at i:1188 original size:27 final size:27

Alignment explanation


    Indices: 1158--1213  Score: 94
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       1148 ATTCTATTTT

                        *              
       1158 TTCTATTATATTCGTATTAGATTAGTA
          1 TTCTATTATATTAGTATTAGATTAGTA

                   *                   
       1185 TTCTATTCTATTAGTATTAGATTAGTA
          1 TTCTATTATATTAGTATTAGATTAGTA

              
       1212 TT
          1 TT

       1214 AGTTAGTGAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  27   27  1.00

ACGTcount: A:0.29, C:0.07, G:0.11, T:0.54


Consensus pattern (27 bp):   
TTCTATTATATTAGTATTAGATTAGTA

Found at i:4866 original size:14 final size:16

Alignment explanation


    Indices: 4843--4880  Score: 53
    Period size: 14  Copynumber: 2.5  Consensus size: 16

       4833 TGGAAGATGG

                            
       4843 ATAAAAAAAA-AGAA-
          1 ATAAAAAAAATAGAAT

                 *          
       4857 ATAAATAAAATAGAAT
          1 ATAAAAAAAATAGAAT

                    
       4873 ATAAAAAA
          1 ATAAAAAA

       4881 GATAAAGATA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  14    9  0.45
  15    4  0.20
  16    7  0.35

ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16


Consensus pattern (16 bp):   
ATAAAAAAAATAGAAT
Done.