Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013906.1 Kokia drynarioides strain JFW-HI SEQ_128935, 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: 1861
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.31


Found at i:351 original size:15 final size:15

Alignment explanation


    Indices: 331--373  Score: 72
    Period size: 15  Copynumber: 3.0  Consensus size: 15

        321 AACATATATT

                           
        331 CAATAAAATGCAAAG
          1 CAATAAAATGCAAAG

                           
        346 CAATAAAATGCAAA-
          1 CAATAAAATGCAAAG

                           
        360 -AATAAAATGCAAAG
          1 CAATAAAATGCAAAG

        374 GATCACAAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  13   13  0.48
  15   14  0.52

ACGTcount: A:0.63, C:0.12, G:0.12, T:0.14


Consensus pattern (15 bp):   
CAATAAAATGCAAAG

Found at i:1292 original size:45 final size:46

Alignment explanation


    Indices: 1232--1353  Score: 151
    Period size: 45  Copynumber: 2.7  Consensus size: 46

       1222 AGTGCTGGGG

                            *                       *      
       1232 AAACAGTAAGCACACACAGTGC-AATCCAGTAGGCACACACAGTGC-
          1 AAACAGTAAGCACACAAAGTGCAAAT-CAGTAGGCACACAAAGTGCA

              *     *       *  *                          
       1277 AATCAGTAGGCACACATAGCGCAAATCAGTAGGCACACAAAGTGCA
          1 AAACAGTAAGCACACAAAGTGCAAATCAGTAGGCACACAAAGTGCA

                                            
       1323 AAACAGTAAGCACACAAAGTGCGAAA-CAGTA
          1 AAACAGTAAGCACACAAAGTGC-AAATCAGTA

       1354 AGAGCGCTAG


Statistics
Matches: 65,  Mismatches: 9, Indels: 5
        0.82            0.11        0.06

Matches are distributed among these distances:
  45   36  0.55
  46   26  0.40
  47    3  0.05

ACGTcount: A:0.43, C:0.25, G:0.20, T:0.11


Consensus pattern (46 bp):   
AAACAGTAAGCACACAAAGTGCAAATCAGTAGGCACACAAAGTGCA

Found at i:1354 original size:23 final size:22

Alignment explanation


    Indices: 1232--1355  Score: 131
    Period size: 23  Copynumber: 5.5  Consensus size: 22

       1222 AGTGCTGGGG

                            *     
       1232 AAACAGTAAGCACACACAGTGC
          1 AAACAGTAAGCACACAAAGTGC

               *     *       *     
       1254 AATCCAGTAGGCACACACAGTGC
          1 AA-ACAGTAAGCACACAAAGTGC

              *     *       *  *  
       1277 AATCAGTAGGCACACATAGCGC
          1 AAACAGTAAGCACACAAAGTGC

                     *             
       1299 AAATCAGTAGGCACACAAAGTGC
          1 AAA-CAGTAAGCACACAAAGTGC

                                   
       1322 AAAACAGTAAGCACACAAAGTGC
          1 -AAACAGTAAGCACACAAAGTGC

                       
       1345 GAAACAGTAAG
          1 -AAACAGTAAG

       1356 AGCGCTAGCG


Statistics
Matches: 89,  Mismatches: 10, Indels: 5
        0.86            0.10        0.05

Matches are distributed among these distances:
  22   21  0.24
  23   65  0.73
  24    3  0.03

ACGTcount: A:0.44, C:0.24, G:0.21, T:0.11


Consensus pattern (22 bp):   
AAACAGTAAGCACACAAAGTGC
Done.