Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017867.1 Corchorus olitorius cultivar O-4 contig17900, 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: 31757
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:14 original size:2 final size:2

Alignment explanation


    Indices: 8--42  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

          1 ATAGTAC

                                                                
          8 TA TA TA 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 TA TA TA T

         43 TTGGAAAGTC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:3122 original size:13 final size:14

Alignment explanation


    Indices: 3095--3132  Score: 60
    Period size: 13  Copynumber: 2.8  Consensus size: 14

       3085 AAAAGGGCAA

                          
       3095 AAAAAATAAAAAAG
          1 AAAAAATAAAAAAG

                      *   
       3109 AAAAAA-AAAGAAG
          1 AAAAAATAAAAAAG

                       
       3122 AAAAAATAAAA
          1 AAAAAATAAAA

       3133 CATAAGTAGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  13   12  0.57
  14    9  0.43

ACGTcount: A:0.87, C:0.00, G:0.08, T:0.05


Consensus pattern (14 bp):   
AAAAAATAAAAAAG

Found at i:8888 original size:21 final size:20

Alignment explanation


    Indices: 8864--8907  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 20

       8854 AGAACAATTT

                *                
       8864 TTTTCTCTACTTCATAATTCA
          1 TTTTATCTACTTCAT-ATTCA

                  *             
       8885 TTTTATTTACTTCATATTCA
          1 TTTTATCTACTTCATATTCA

               
       8905 TTT
          1 TTT

       8908 AGGTTTGCAG


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  20    8  0.38
  21   13  0.62

ACGTcount: A:0.23, C:0.18, G:0.00, T:0.59


Consensus pattern (20 bp):   
TTTTATCTACTTCATATTCA

Found at i:12149 original size:15 final size:15

Alignment explanation


    Indices: 12126--12157  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      12116 AGAAATGCCA

                           
      12126 AAGACAAAAGAAAAG
          1 AAGACAAAAGAAAAG

                *          
      12141 AAGAGAAAAGAAAAG
          1 AAGACAAAAGAAAAG

              
      12156 AA
          1 AA

      12158 AAAGGAGATG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00


Consensus pattern (15 bp):   
AAGACAAAAGAAAAG

Found at i:26931 original size:7 final size:7

Alignment explanation


    Indices: 26914--26968  Score: 92
    Period size: 7  Copynumber: 7.7  Consensus size: 7

      26904 ACGCATGAAT

                    
      26914 AAAATGAA
          1 AAAATG-A

                   
      26922 AAAATGA
          1 AAAATGA

                   
      26929 AAAATGA
          1 AAAATGA

                   
      26936 AAAATGA
          1 AAAATGA

                   
      26943 AAAATGA
          1 AAAATGA

                   
      26950 AAAATGA
          1 AAAATGA

                *  
      26957 AAAAAGA
          1 AAAATGA

                 
      26964 AAAAT
          1 AAAAT

      26969 ACAGAATGTG


Statistics
Matches: 45,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
   7   39  0.87
   8    6  0.13

ACGTcount: A:0.75, C:0.00, G:0.13, T:0.13


Consensus pattern (7 bp):   
AAAATGA

Done.