Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016405.1 Corchorus olitorius cultivar O-4 contig16438, 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: 50062
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:818 original size:3 final size:3

Alignment explanation


    Indices: 810--840  Score: 53
    Period size: 3  Copynumber: 10.0  Consensus size: 3

        800 ACTTTATTTC

                                                    
        810 TCT TCT TCT TCT TCT TCT TCT TCTT TCT TCT
          1 TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT

        841 AATTCCAAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   3   24  0.89
   4    3  0.11

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (3 bp):   
TCT

Found at i:35953 original size:67 final size:67

Alignment explanation


    Indices: 35873--36006  Score: 268
    Period size: 67  Copynumber: 2.0  Consensus size: 67

      35863 CACCCAGAAA

                                                                             
      35873 AAAAAATGAGAGAATGGAGTAATAAGAAGAAAAACCCCTGATACGGTATTACCAAAAGAAAGAAC
          1 AAAAAATGAGAGAATGGAGTAATAAGAAGAAAAACCCCTGATACGGTATTACCAAAAGAAAGAAC

              
      35938 CC
         66 CC

                                                                             
      35940 AAAAAATGAGAGAATGGAGTAATAAGAAGAAAAACCCCTGATACGGTATTACCAAAAGAAAGAAC
          1 AAAAAATGAGAGAATGGAGTAATAAGAAGAAAAACCCCTGATACGGTATTACCAAAAGAAAGAAC

              
      36005 CC
         66 CC

      36007 TGATATGGAA


Statistics
Matches: 67,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  67   67  1.00

ACGTcount: A:0.52, C:0.15, G:0.19, T:0.13


Consensus pattern (67 bp):   
AAAAAATGAGAGAATGGAGTAATAAGAAGAAAAACCCCTGATACGGTATTACCAAAAGAAAGAAC
CC

Found at i:45651 original size:36 final size:35

Alignment explanation


    Indices: 45583--45665  Score: 96
    Period size: 34  Copynumber: 2.3  Consensus size: 35

      45573 GTGCTAAAAT

                 *   *             *             
      45583 AACTGCAAATTTATTAATTACTTGCCAAAAAAAAAGA
          1 AACTGTAAAATTATTAATTACTTACC--AAAAAAAGA

                                       *       
      45620 AACTGTAAAATTATT-ATTACTTACCACAAAAAGA
          1 AACTGTAAAATTATTAATTACTTACCAAAAAAAGA

             *          
      45654 AGCTGTAAAATT
          1 AACTGTAAAATT

      45666 GTAACCGGCC


Statistics
Matches: 41,  Mismatches: 5, Indels: 3
        0.84            0.10        0.06

Matches are distributed among these distances:
  34   19  0.46
  36    9  0.22
  37   13  0.32

ACGTcount: A:0.49, C:0.13, G:0.08, T:0.29


Consensus pattern (35 bp):   
AACTGTAAAATTATTAATTACTTACCAAAAAAAGA

Found at i:45898 original size:2 final size:2

Alignment explanation


    Indices: 45891--45926  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      45881 TGCTTAGTGG

                                                                 
      45891 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      45927 TCATGAGCCT


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

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:47828 original size:28 final size:28

Alignment explanation


    Indices: 47768--47828  Score: 65
    Period size: 28  Copynumber: 2.2  Consensus size: 28

      47758 CCTTTTCCTT

                                   *     
      47768 TCTTTGCCTTCAATTTGTTTTCCCTTTTC
          1 TCTTTGCCTT-AATTTGTTTTCCATTTTC

                                          
      47797 -CTTTGCCTT-ATTTGCTTTT-CATTTCTC
          1 TCTTTGCCTTAATTTG-TTTTCCATTT-TC

                 
      47824 TCTTT
          1 TCTTT

      47829 CTTTTTCTTT


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  26    9  0.32
  27    6  0.21
  28   13  0.46

ACGTcount: A:0.07, C:0.26, G:0.07, T:0.61


Consensus pattern (28 bp):   
TCTTTGCCTTAATTTGTTTTCCATTTTC
Done.