Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023027.1 Corchorus olitorius cultivar O-4 contig23060, 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: 21021
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:9534 original size:7 final size:7

Alignment explanation


    Indices: 9519--9552  Score: 59
    Period size: 7  Copynumber: 4.9  Consensus size: 7

       9509 TATTTTTTGT

                *  
       9519 TGTTCAA
          1 TGTTGAA

                   
       9526 TGTTGAA
          1 TGTTGAA

                   
       9533 TGTTGAA
          1 TGTTGAA

                   
       9540 TGTTGAA
          1 TGTTGAA

                  
       9547 TGTTGA
          1 TGTTGA

       9553 TACACTTGCA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   7   26  1.00

ACGTcount: A:0.26, C:0.03, G:0.26, T:0.44


Consensus pattern (7 bp):   
TGTTGAA

Found at i:10737 original size:2 final size:2

Alignment explanation


    Indices: 10730--10758  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      10720 TTAATCTCAT

                                                       
      10730 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      10759 TACTAAGTGC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:19572 original size:23 final size:23

Alignment explanation


    Indices: 19546--19618  Score: 76
    Period size: 23  Copynumber: 3.1  Consensus size: 23

      19536 ATCAGCCCTA

                                   
      19546 TTTTTTACTTTTCATCACCCTTG
          1 TTTTTTACTTTTCATCACCCTTG

                         * *    *     
      19569 -TTTTTACAAGTTGTGATCAACCTTG
          1 TTTTTTAC---TTTTCATCACCCTTG

             *                     
      19594 TCTTTTACTTTTCATCACCCTTG
          1 TTTTTTACTTTTCATCACCCTTG

              
      19617 TT
          1 TT

      19619 GTTACAAGGT


Statistics
Matches: 38,  Mismatches: 8, Indels: 8
        0.70            0.15        0.15

Matches are distributed among these distances:
  22    7  0.18
  23   13  0.34
  25   12  0.32
  26    6  0.16

ACGTcount: A:0.16, C:0.23, G:0.08, T:0.52


Consensus pattern (23 bp):   
TTTTTTACTTTTCATCACCCTTG
Done.