Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017630.1 Corchorus olitorius cultivar O-4 contig17663, 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: 33478
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33


Found at i:4660 original size:108 final size:109

Alignment explanation


    Indices: 4526--4743  Score: 370
    Period size: 108  Copynumber: 2.0  Consensus size: 109

       4516 ATTAATCAAA

                                 *                                           
       4526 ATTTAATGTGATTATCAAAAAGTTGAAAAAAAAATTAAAAGATC-AATTTTTTTATGAAAT-AAA
          1 ATTTAATGTGATTATCAAAAAATTG-AAAAAAAATTAAAAGATCGAATTTTTTTATGAAATGAAA

                              *                           
       4589 GGATGTTTTC-TTTTTTGTTGAATAATAAAAGATGTTTTCGATCTT
         65 -GATGTTTTCTTTTTTTGGTGAATAATAAAAGATGTTTTCGATCTT

                                                         *                   
       4634 ATTTAATGTGATTATCAAAAAATTGAAAAAAAATTAAAAGATCGATTTTTTTTATGAAATGAAAG
          1 ATTTAATGTGATTATCAAAAAATTGAAAAAAAATTAAAAGATCGAATTTTTTTATGAAATGAAAG

                                                        
       4699 ATGTTTTCTTTTTTTGGTGAATAATAAAAGATGTTTTCGATCTT
         66 ATGTTTTCTTTTTTTGGTGAATAATAAAAGATGTTTTCGATCTT

             
       4743 A
          1 A

       4744 CATATCAAAT


Statistics
Matches: 104,  Mismatches: 3, Indels: 5
        0.93            0.03        0.04

Matches are distributed among these distances:
 107   18  0.17
 108   48  0.46
 109   38  0.37

ACGTcount: A:0.40, C:0.05, G:0.13, T:0.42


Consensus pattern (109 bp):   
ATTTAATGTGATTATCAAAAAATTGAAAAAAAATTAAAAGATCGAATTTTTTTATGAAATGAAAG
ATGTTTTCTTTTTTTGGTGAATAATAAAAGATGTTTTCGATCTT

Found at i:11006 original size:40 final size:40

Alignment explanation


    Indices: 10914--11006  Score: 100
    Period size: 40  Copynumber: 2.3  Consensus size: 40

      10904 TGCTCGGTTA

                        *                   *       
      10914 AGTCCCTGATTTTAGATTTTATCTTCTGATTTGTGCAATG
          1 AGTCCCTGATTTAAGATTTTATCTTCTGATTTATGCAATG

              *                       * *              
      10954 AGGCCCTAGATTTAAGATTTTA-CTTGTTATTTATGCAATTTG
          1 AGTCCCT-GATTTAAGATTTTATCTTCTGATTTATGCAA--TG

                        
      10996 A-TCCCTGATTT
          1 AGTCCCTGATTT

      11007 TAGAAATTGT


Statistics
Matches: 44,  Mismatches: 6, Indels: 6
        0.79            0.11        0.11

Matches are distributed among these distances:
  40   24  0.55
  41   17  0.39
  42    3  0.07

ACGTcount: A:0.23, C:0.15, G:0.16, T:0.46


Consensus pattern (40 bp):   
AGTCCCTGATTTAAGATTTTATCTTCTGATTTATGCAATG

Found at i:21131 original size:107 final size:107

Alignment explanation


    Indices: 20940--21154  Score: 403
    Period size: 107  Copynumber: 2.0  Consensus size: 107

      20930 CAATATGAGA

                *                                 *                   *      
      20940 TATGTGAACCTTGTTTATTGGGTAAGATGACCAAAGCTTCTTTCACCAAACAAAGTGAGAGAGCC
          1 TATGGGAACCTTGTTTATTGGGTAAGATGACCAAAGCTCCTTTCACCAAACAAAGTGAAAGAGCC

                                                      
      21005 AGTGATTTATTGGGCCTCATACATACTGATGTTTGTGGACCT
         66 AGTGATTTATTGGGCCTCATACATACTGATGTTTGTGGACCT

                                                                             
      21047 TATGGGAACCTTGTTTATTGGGTAAGATGACCAAAGCTCCTTTCACCAAACAAAGTGAAAGAGCC
          1 TATGGGAACCTTGTTTATTGGGTAAGATGACCAAAGCTCCTTTCACCAAACAAAGTGAAAGAGCC

                                                      
      21112 AGTGATTTATTGGGCCTCATACATACTGATGTTTGTGGACCT
         66 AGTGATTTATTGGGCCTCATACATACTGATGTTTGTGGACCT

             
      21154 T
          1 T

      21155 TAAAACAAAC


Statistics
Matches: 105,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 107  105  1.00

ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31


Consensus pattern (107 bp):   
TATGGGAACCTTGTTTATTGGGTAAGATGACCAAAGCTCCTTTCACCAAACAAAGTGAAAGAGCC
AGTGATTTATTGGGCCTCATACATACTGATGTTTGTGGACCT

Found at i:32613 original size:41 final size:37

Alignment explanation


    Indices: 32516--32623  Score: 207
    Period size: 37  Copynumber: 2.9  Consensus size: 37

      32506 TGAAATAATC

                      *                          
      32516 AAGTTTTACGCTAAGTTAATTAATTTGTTTGTTTAGA
          1 AAGTTTTACGGTAAGTTAATTAATTTGTTTGTTTAGA

                                                 
      32553 AAGTTTTACGGTAAGTTAATTAATTTGTTTGTTTAGA
          1 AAGTTTTACGGTAAGTTAATTAATTTGTTTGTTTAGA

                                              
      32590 AAGTTTTACGGTAAGTTAATTAATTTGTTTGTTT
          1 AAGTTTTACGGTAAGTTAATTAATTTGTTTGTTT

      32624 TTCCCTCAAA


Statistics
Matches: 70,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  37   70  1.00

ACGTcount: A:0.29, C:0.04, G:0.18, T:0.50


Consensus pattern (37 bp):   
AAGTTTTACGGTAAGTTAATTAATTTGTTTGTTTAGA
Done.