Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014083.1 Kokia drynarioides strain JFW-HI SEQ_129114, 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: 5278
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36


Found at i:1093 original size:23 final size:23

Alignment explanation


    Indices: 1062--1124  Score: 81
    Period size: 23  Copynumber: 2.7  Consensus size: 23

       1052 TACATAGCGC

                     *      * *     
       1062 AAATCAGTAGGCACACGAGGTACG
          1 AAAT-AGTAAGCACACAAAGTACG

                                *  
       1086 AAATAGTAAGCACACAAAGTGCG
          1 AAATAGTAAGCACACAAAGTACG

                            
       1109 AAATAGTAAGCACACA
          1 AAATAGTAAGCACACA

       1125 CAGTGCTGAA


Statistics
Matches: 35,  Mismatches: 4, Indels: 1
        0.88            0.10        0.03

Matches are distributed among these distances:
  23   31  0.89
  24    4  0.11

ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13


Consensus pattern (23 bp):   
AAATAGTAAGCACACAAAGTACG

Found at i:1129 original size:23 final size:23

Alignment explanation


    Indices: 1084--1130  Score: 85
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1074 ACACGAGGTA

                                   
       1084 CGAAATAGTAAGCACACAAAGTG
          1 CGAAATAGTAAGCACACAAAGTG

                              *    
       1107 CGAAATAGTAAGCACACACAGTG
          1 CGAAATAGTAAGCACACAAAGTG

             
       1130 C
          1 C

       1131 TGAACAGTAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13


Consensus pattern (23 bp):   
CGAAATAGTAAGCACACAAAGTG

Found at i:1139 original size:23 final size:23

Alignment explanation


    Indices: 1019--1142  Score: 76
    Period size: 23  Copynumber: 5.4  Consensus size: 23

       1009 CGAAGTACTT

                           *       
       1019 AACAGTAAGCACACACAGT--GA
          1 AACAGTAAGCACACAAAGTGCGA

                    *  **   *  *    
       1040 AATCAGTAGGCGTACATAGCGC-A
          1 AA-CAGTAAGCACACAAAGTGCGA

                    *      * *  *   
       1063 AATCAGTAGGCACACGAGGTACGA
          1 AA-CAGTAAGCACACAAAGTGCGA

              *                    
       1087 AATAGTAAGCACACAAAGTGCGA
          1 AACAGTAAGCACACAAAGTGCGA

              *            *        
       1110 AATAGTAAGCACACACAGTGCTG-
          1 AACAGTAAGCACACAAAGTGC-GA

                      
       1133 AACAGTAAGC
          1 AACAGTAAGC

       1143 GCGCTAGCGT


Statistics
Matches: 79,  Mismatches: 19, Indels: 8
        0.75            0.18        0.08

Matches are distributed among these distances:
  21    2  0.03
  22   12  0.15
  23   61  0.77
  24    4  0.05

ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14


Consensus pattern (23 bp):   
AACAGTAAGCACACAAAGTGCGA

Found at i:1243 original size:24 final size:26

Alignment explanation


    Indices: 1205--1252  Score: 66
    Period size: 24  Copynumber: 1.9  Consensus size: 26

       1195 TCTACATGGG

                                       
       1205 CATAATCTCTCATAT-TCATCATTTCT
          1 CATAATCTCTCATATATCA-CATTTCT

                                    
       1231 CATAAT-T-TCATATATCACATTT
          1 CATAATCTCTCATATATCACATTT

       1253 ATATTTCTCT


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24   11  0.52
  25    4  0.19
  26    6  0.29

ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46


Consensus pattern (26 bp):   
CATAATCTCTCATATATCACATTTCT
Done.