Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023066.1 Corchorus olitorius cultivar O-4 contig23099, 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: 17889
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--38  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

                                                                    
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         39 ACACCAAGAT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:224 original size:24 final size:26

Alignment explanation


    Indices: 197--245  Score: 66
    Period size: 26  Copynumber: 1.9  Consensus size: 26

        187 TCCTCCATGT

                 *                    
        197 GAGTTTTAG-ATGCTAATT-TAAATG
          1 GAGTTCTAGAATGCTAATTCTAAATG

                                     
        221 GAGTTCTAGATATGCTAATTCTAAA
          1 GAGTTCTAGA-ATGCTAATTCTAAA

        246 AACTAAAAGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  24    8  0.38
  26    9  0.43
  27    4  0.19

ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39


Consensus pattern (26 bp):   
GAGTTCTAGAATGCTAATTCTAAATG

Found at i:8826 original size:49 final size:49

Alignment explanation


    Indices: 8754--8903  Score: 264
    Period size: 49  Copynumber: 3.1  Consensus size: 49

       8744 TAGCTTAATG

                                            *                
       8754 TGGTCTTTGGCAATAGAATGTGATATATAGTGATATTCTTACATCTATA
          1 TGGTCTTTGGCAATAGAATGTGATATATAGTGGTATTCTTACATCTATA

                                                        *    
       8803 TGGTCTTTGGCAATAGAATGTGATATATAGTGGTATTCTTACATTTATA
          1 TGGTCTTTGGCAATAGAATGTGATATATAGTGGTATTCTTACATCTATA

                         *                       *           
       8852 TGGTCTTTGGCAAAAGAATGTGATATATAGTGGTATTTTTACATCTATA
          1 TGGTCTTTGGCAATAGAATGTGATATATAGTGGTATTCTTACATCTATA

               
       8901 TGG
          1 TGG

       8904 GATATTATTA


Statistics
Matches: 96,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  49   96  1.00

ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41


Consensus pattern (49 bp):   
TGGTCTTTGGCAATAGAATGTGATATATAGTGGTATTCTTACATCTATA

Found at i:16462 original size:4 final size:4

Alignment explanation


    Indices: 16453--16629  Score: 345
    Period size: 4  Copynumber: 44.2  Consensus size: 4

      16443 ATTCAACATG

                                                            *          
      16453 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTG TGTA TGTA
          1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA

                                                                       
      16501 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
          1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA

                                                                       
      16549 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
          1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA

                                                     
      16597 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
          1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T

      16630 ATGACATGTA


Statistics
Matches: 171,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
   4  171  1.00

ACGTcount: A:0.24, C:0.00, G:0.25, T:0.50


Consensus pattern (4 bp):   
TGTA

Done.