Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014467.1 Kokia drynarioides strain JFW-HI SEQ_129506, 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: 8130
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36


Found at i:6290 original size:30 final size:29

Alignment explanation


    Indices: 6253--6462  Score: 171
    Period size: 30  Copynumber: 7.1  Consensus size: 29

       6243 GTTTATTACT

                               *         
       6253 CCCTAAACTTTTCAAAAATCACATTTTAA
          1 CCCTAAACTTTTCAAAAATTACATTTTAA

                                  ** *  *  
       6282 CCCTTAAAC-TTTCTAAAAATTTGAATTCAA
          1 CCC-TAAACTTTTC-AAAAATTACATTTTAA

                   *                      
       6312 CCCTAAAATTTTCCAAAAATTACATTTTAA
          1 CCCTAAACTTTT-CAAAAATTACATTTTAA

                                    *      *
       6342 CCCCTAAAC-TTTCAAAAAATTTAGA-TTTAG
          1 -CCCTAAACTTTTC-AAAAA-TTACATTTTAA

               *       *                 
       6372 CCCCAAACTTTCCAAAAATTACATTTTAA
          1 CCCTAAACTTTTCAAAAATTACATTTTAA

                              *             
       6401 CCCTTAAAC-TTTCTAAAGATCT-CATTTTAA
          1 CCC-TAAACTTTTC-AAAAAT-TACATTTTAA

                        *         *       
       6431 CCCTAAA-TTTTTATAAAATTATATTTTAA
          1 CCCTAAACTTTTCA-AAAATTACATTTTAA

               
       6460 CCC
          1 CCC

       6463 CAAATTCTTG


Statistics
Matches: 143,  Mismatches: 23, Indels: 30
        0.73            0.12        0.15

Matches are distributed among these distances:
  28    6  0.04
  29   55  0.38
  30   69  0.48
  31   13  0.09

ACGTcount: A:0.40, C:0.22, G:0.02, T:0.37


Consensus pattern (29 bp):   
CCCTAAACTTTTCAAAAATTACATTTTAA

Found at i:6393 original size:59 final size:60

Alignment explanation


    Indices: 6253--6413  Score: 220
    Period size: 60  Copynumber: 2.7  Consensus size: 60

       6243 GTTTATTACT

                        *       *                      *                
       6253 CCCT-AAACTTTTCAAAAATCACATTTTAACCCTTAAACTTTCTAAAAATTTGAATTCAA
          1 CCCTAAAACTTTCCAAAAATTACATTTTAACCCTTAAACTTTCAAAAAATTTGAATTCAA

                    *                        *                        * *
       6312 CCCTAAAATTTTCCAAAAATTACATTTTAACCCCTAAACTTTCAAAAAATTT-AGATTTAG
          1 CCCTAAAACTTTCCAAAAATTACATTTTAACCCTTAAACTTTCAAAAAATTTGA-ATTCAA

                *                                      
       6372 CCC-CAAACTTTCCAAAAATTACATTTTAACCCTTAAACTTTC
          1 CCCTAAAACTTTCCAAAAATTACATTTTAACCCTTAAACTTTC

       6414 TAAAGATCTC


Statistics
Matches: 90,  Mismatches: 10, Indels: 4
        0.87            0.10        0.04

Matches are distributed among these distances:
  59   41  0.46
  60   49  0.54

ACGTcount: A:0.40, C:0.24, G:0.02, T:0.35


Consensus pattern (60 bp):   
CCCTAAAACTTTCCAAAAATTACATTTTAACCCTTAAACTTTCAAAAAATTTGAATTCAA

Found at i:6449 original size:59 final size:58

Alignment explanation


    Indices: 6253--6462  Score: 242
    Period size: 59  Copynumber: 3.6  Consensus size: 58

       6243 GTTTATTACT

                               *                               *    *  
       6253 CCCTAAACTTTTCAAAAATCACATTTTAACCCTTAAACTTTCTAAAAATTTGAATTCAA
          1 CCCTAAACTTTTCAAAAATTACATTTTAACCCTTAAACTTTCTAAAAA-TTCAATTTAA

                   *                         *         *       *       *
       6312 CCCTAAAATTTTCCAAAAATTACATTTTAACCCCTAAACTTTCAAAAAATTTAGATTTAG
          1 CCCTAAACTTTT-CAAAAATTACATTTTAACCCTTAAACTTTCTAAAAATTCA-ATTTAA

               *       *                                  *      *     
       6372 CCCCAAACTTTCCAAAAATTACATTTTAACCCTTAAACTTTCTAAAGATCTCATTTTAA
          1 CCCTAAACTTTTCAAAAATTACATTTTAACCCTTAAACTTTCTAAAAAT-TCAATTTAA

                        *         *          
       6431 CCCTAAA-TTTTTATAAAATTATATTTTAACCC
          1 CCCTAAACTTTTCA-AAAATTACATTTTAACCC

       6463 CAAATTCTTG


Statistics
Matches: 127,  Mismatches: 20, Indels: 8
        0.82            0.13        0.05

Matches are distributed among these distances:
  58    4  0.03
  59   75  0.59
  60   48  0.38

ACGTcount: A:0.40, C:0.22, G:0.02, T:0.37


Consensus pattern (58 bp):   
CCCTAAACTTTTCAAAAATTACATTTTAACCCTTAAACTTTCTAAAAATTCAATTTAA
Done.