Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014657.1 Kokia drynarioides strain JFW-HI SEQ_129696, 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: 14396
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33


Found at i:3612 original size:20 final size:21

Alignment explanation


    Indices: 3568--3610  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3558 TTCACTTCGT

                  *    *         
       3568 AATTTTTTCTTTTTTAATTCA
          1 AATTTTCTCTTCTTTAATTCA

                            *    
       3589 AATTTTCTCTTCTTTATTTCA
          1 AATTTTCTCTTCTTTAATTCA

             
       3610 A
          1 A

       3611 TTCGAATTTT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63


Consensus pattern (21 bp):   
AATTTTCTCTTCTTTAATTCA

Found at i:4928 original size:51 final size:50

Alignment explanation


    Indices: 4776--4968  Score: 228
    Period size: 50  Copynumber: 3.8  Consensus size: 50

       4766 ACTTATTTTA

                                *   *                      *    
       4776 ATGATGCAAACTTTAACTAATATGGGAGTTACATAATGCATGAT-ATAATTT
          1 ATGATGCAAAC-TTAACTAACATGAGAGTTACATAATGCATG-TCATTATTT

              *     * *                     *                  
       4827 ATTATGCATATTTAACTAACATGTA-AGTTACTTAATGCATGTCATTATTT
          1 ATGATGCAAACTTAACTAACATG-AGAGTTACATAATGCATGTCATTATTT

                                          *         *          
       4877 ATGATGCAAACTTAACTAATCATGAGAGTTTCATAATGCAAGTCATTATTT
          1 ATGATGCAAACTTAACTAA-CATGAGAGTTACATAATGCATGTCATTATTT

               *    *               *                
       4928 ATGGTGCATACTTAACTAACATGAAAGTTACATAATGCATG
          1 ATGATGCAAACTTAACTAACATGAGAGTTACATAATGCATG

       4969 ATTTTATTAA


Statistics
Matches: 120,  Mismatches: 18, Indels: 9
        0.82            0.12        0.06

Matches are distributed among these distances:
  49    1  0.01
  50   68  0.57
  51   51  0.43

ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36


Consensus pattern (50 bp):   
ATGATGCAAACTTAACTAACATGAGAGTTACATAATGCATGTCATTATTT

Found at i:4976 original size:101 final size:101

Alignment explanation


    Indices: 4776--4968  Score: 273
    Period size: 101  Copynumber: 1.9  Consensus size: 101

       4766 ACTTATTTTA

                                    *               *            *       *   
       4776 ATGATGCAAACTTTAACTAATATGGGAGTTACATAATGCATGATATAATTTATTATGCATATTTA
          1 ATGATGCAAACTTTAACTAATATGAGAGTTACATAATGCAAGATATAATTTATGATGCATACTTA

                     *       *                  
       4841 ACTAACATGTAAGTTACTTAATGCATGTCATTATTT
         66 ACTAACATGAAAGTTACATAATGCATGTCATTATTT

                                           *                *       *        
       4877 ATGATGCAAAC-TTAACTAATCATGAGAGTTTCATAATGCAAG-TCATTATTTATGGTGCATACT
          1 ATGATGCAAACTTTAACTAAT-ATGAGAGTTACATAATGCAAGAT-ATAATTTATGATGCATACT

                                         
       4940 TAACTAACATGAAAGTTACATAATGCATG
         64 TAACTAACATGAAAGTTACATAATGCATG

       4969 ATTTTATTAA


Statistics
Matches: 81,  Mismatches: 9, Indels: 4
        0.86            0.10        0.04

Matches are distributed among these distances:
 100   10  0.12
 101   71  0.88

ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36


Consensus pattern (101 bp):   
ATGATGCAAACTTTAACTAATATGAGAGTTACATAATGCAAGATATAATTTATGATGCATACTTA
ACTAACATGAAAGTTACATAATGCATGTCATTATTT

Found at i:10073 original size:34 final size:34

Alignment explanation


    Indices: 10015--10080  Score: 89
    Period size: 34  Copynumber: 1.9  Consensus size: 34

      10005 ATATATATGG

                           *                  
      10015 AAATGCAATGACAATGTAGATGCAGCGACAATAA
          1 AAATGCAATGACAATATAGATGCAGCGACAATAA

                         *            *      
      10049 AAATGCAATGACATTAATAG-TGCAGGGACAAT
          1 AAATGCAATGACAAT-ATAGATGCAGCGACAAT

      10081 TATACTACAG


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  34   25  0.89
  35    3  0.11

ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20


Consensus pattern (34 bp):   
AAATGCAATGACAATATAGATGCAGCGACAATAA
Done.