Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013084.1 Kokia drynarioides strain JFW-HI SEQ_128102, 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: 5121
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25


Found at i:3257 original size:19 final size:19

Alignment explanation


    Indices: 3233--3270  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       3223 TATCGAGGTT

                               
       3233 GAAATACCTTCCCTCCGAG
          1 GAAATACCTTCCCTCCGAG

                               
       3252 GAAATACCTTCCCTCCGAG
          1 GAAATACCTTCCCTCCGAG

       3271 TCTTAATCGA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.26, C:0.37, G:0.16, T:0.21


Consensus pattern (19 bp):   
GAAATACCTTCCCTCCGAG

Found at i:4680 original size:67 final size:67

Alignment explanation


    Indices: 4569--4728  Score: 293
    Period size: 67  Copynumber: 2.4  Consensus size: 67

       4559 ATAAAATGGT

                                                   *            *            
       4569 TAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCGATGTGATGAAGTCTTCGAAT
          1 TAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGAGCTCGATGTGATCAAGTCTTCGAAT

              
       4634 CC
         66 CC

                                                                             
       4636 TAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGAGCTCGATGTGATCAAGTCTTCGAAT
          1 TAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGAGCTCGATGTGATCAAGTCTTCGAAT

              
       4701 CC
         66 CC

            *                         
       4703 CAGCTTCCTGATGAGATACAGAGAAG
          1 TAGCTTCCTGATGAGATACAGAGAAG

       4729 CGGATTGAAA


Statistics
Matches: 90,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  67   90  1.00

ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24


Consensus pattern (67 bp):   
TAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGAGCTCGATGTGATCAAGTCTTCGAAT
CC

Found at i:5068 original size:206 final size:201

Alignment explanation


    Indices: 4706--5099  Score: 585
    Period size: 206  Copynumber: 1.9  Consensus size: 201

       4696 CGAATCCCAG

                                     *                                       
       4706 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTAAGGCGATCATCTTCCTGATGAGATAC
          1 CTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGTAAGGCGATCATCTTCCTGATGAGATAC

                     *  *   *  *                                             
       4771 AAAGAAGAATACCAACTCAGGACTCGATGAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGAT
         66 AAAGAAGAAAACAAACCCACGACTCGATGAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGAT

             *         *                                      *              
       4836 ATTGAGAAGCAGGTCAAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAA
        131 ACTGAGAAGCAAGTCAAAGCAATAAAATGGTTAGCTTCCTGATGAGATACCGAGAAGTGAACCAA

                  
       4901 ATTCAT
        196 ATTCAT

                                                  * *   *                    
       4907 CTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATAC
          1 CTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGTAAGGCGATCATCTTCCTGATGAGATAC

                   *                           *                             
       4972 TGAGAAGTAGACCAAATCAAACCCACG-CTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGA
         66 --A-AAGAAGA--AAA-CAAACCCACGACTCGATGAGAGCAAATCTTCGAACCCCAGCTTCCTGA

                                      *                                      
       5036 TGAGATACTGAGAAGCAAGTCGAAA-TAATAAAATGGTTAGCTTCCTGATGAGATACCGAGAAGT
        125 TGAGATACTGAGAAGCAAGTC-AAAGCAATAAAATGGTTAGCTTCCTGATGAGATACCGAGAAGT

       5100 ATACCAACTC


Statistics
Matches: 172,  Mismatches: 14, Indels: 9
        0.88            0.07        0.05

Matches are distributed among these distances:
 201   61  0.35
 203    1  0.01
 204    6  0.03
 206   94  0.55
 207   10  0.06

ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22


Consensus pattern (201 bp):   
CTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGTAAGGCGATCATCTTCCTGATGAGATAC
AAAGAAGAAAACAAACCCACGACTCGATGAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGAT
ACTGAGAAGCAAGTCAAAGCAATAAAATGGTTAGCTTCCTGATGAGATACCGAGAAGTGAACCAA
ATTCAT
Done.