Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021335.1 Corchorus olitorius cultivar O-4 contig21368, 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: 14445
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32


Found at i:703 original size:33 final size:32

Alignment explanation


    Indices: 630--759  Score: 154
    Period size: 32  Copynumber: 4.0  Consensus size: 32

        620 AAAAAATGCA

                            *    **   *      
        630 AAATAGTGGCGTTTCTCG-ACAAAAAGGCCACT
          1 AAATAGTGGCGTTT-TTGTACGGAAATGCCACT

                     *         *            
        662 AAATAGTGGTGTTTTTGTAAGGAAATGCCACT
          1 AAATAGTGGCGTTTTTGTACGGAAATGCCACT

                                      *      
        694 AAAATAGTGGCGTTTTTGTACGGAAACGCCACT
          1 -AAATAGTGGCGTTTTTGTACGGAAATGCCACT

                           **               
        727 AAATAGTGGCGTTTTAATACGGAAATGCCACT
          1 AAATAGTGGCGTTTTTGTACGGAAATGCCACT

             
        759 A
          1 A

        760 TTTAGCGGCG


Statistics
Matches: 84,  Mismatches: 12, Indels: 4
        0.84            0.12        0.04

Matches are distributed among these distances:
  31    2  0.02
  32   53  0.63
  33   29  0.35

ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28


Consensus pattern (32 bp):   
AAATAGTGGCGTTTTTGTACGGAAATGCCACT

Found at i:725 original size:65 final size:65

Alignment explanation


    Indices: 629--759  Score: 174
    Period size: 65  Copynumber: 2.0  Consensus size: 65

        619 TAAAAAATGC

                                      *               *     **               
        629 AAAATAGTGGCGTTTCTCGACAAAAAGGCCACTAAATAGTGGTGTTTTTGTAAGGAAATGCCACT
          1 AAAATAGTGGCGTTTCTCGACAAAAACGCCACTAAATAGTGGCGTTTTAATAAGGAAATGCCACT

                             *    **                             *           
        694 AAAATAGTGGCGTTT-TTGTACGGAAACGCCACTAAATAGTGGCGTTTTAATACGGAAATGCCAC
          1 AAAATAGTGGCGTTTCTCG-ACAAAAACGCCACTAAATAGTGGCGTTTTAATAAGGAAATGCCAC

             
        758 T
         65 T

             
        759 A
          1 A

        760 TTTAGCGGCG


Statistics
Matches: 57,  Mismatches: 8, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  64    2  0.04
  65   55  0.96

ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27


Consensus pattern (65 bp):   
AAAATAGTGGCGTTTCTCGACAAAAACGCCACTAAATAGTGGCGTTTTAATAAGGAAATGCCACT

Found at i:8662 original size:50 final size:50

Alignment explanation


    Indices: 8602--8700  Score: 171
    Period size: 50  Copynumber: 2.0  Consensus size: 50

       8592 AAAAAATGGT

                 *                                            
       8602 TTATCGTACATTTTGGCCTTTGAACTCGCACAAAATTATCAAATAAAACC
          1 TTATCATACATTTTGGCCTTTGAACTCGCACAAAATTATCAAATAAAACC

                                    *            *           
       8652 TTATCATACATTTTGGCCTTTGAATTCGCACAAAATTGTCAAATAAAAC
          1 TTATCATACATTTTGGCCTTTGAACTCGCACAAAATTATCAAATAAAAC

       8701 TTCAAACTAC


Statistics
Matches: 46,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  50   46  1.00

ACGTcount: A:0.36, C:0.20, G:0.10, T:0.33


Consensus pattern (50 bp):   
TTATCATACATTTTGGCCTTTGAACTCGCACAAAATTATCAAATAAAACC

Found at i:9595 original size:30 final size:27

Alignment explanation


    Indices: 9538--9592  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       9528 ATAATAGCCC

                                       
       9538 TCATCCTCCTCAACATTAAGAAGATAA
          1 TCATCCTCCTCAACATTAAGAAGATAA

                                       
       9565 TCATCCTCCTCAACATTAAGAAGATAA
          1 TCATCCTCCTCAACATTAAGAAGATAA

             
       9592 T
          1 T

       9593 AATAAATCTC


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.40, C:0.25, G:0.07, T:0.27


Consensus pattern (27 bp):   
TCATCCTCCTCAACATTAAGAAGATAA

Found at i:9788 original size:37 final size:37

Alignment explanation


    Indices: 9738--9808  Score: 142
    Period size: 37  Copynumber: 1.9  Consensus size: 37

       9728 AAACTCTTTG

                                                 
       9738 GTTTGTTGAAGAAAACATCCTGAACTCTTTGCAAAGA
          1 GTTTGTTGAAGAAAACATCCTGAACTCTTTGCAAAGA

                                              
       9775 GTTTGTTGAAGAAAACATCCTGAACTCTTTGCAA
          1 GTTTGTTGAAGAAAACATCCTGAACTCTTTGCAA

       9809 CATAAATAGA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  37   34  1.00

ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Consensus pattern (37 bp):   
GTTTGTTGAAGAAAACATCCTGAACTCTTTGCAAAGA

Found at i:12567 original size:19 final size:19

Alignment explanation


    Indices: 12543--12580  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      12533 TTTCTCCAAG

                               
      12543 AATTGCCTAGTTAGAAAAT
          1 AATTGCCTAGTTAGAAAAT

                               
      12562 AATTGCCTAGTTAGAAAAT
          1 AATTGCCTAGTTAGAAAAT

      12581 CAACAATGAA


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:0.42, C:0.11, G:0.16, T:0.32


Consensus pattern (19 bp):   
AATTGCCTAGTTAGAAAAT
Done.