Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016002.1 Corchorus olitorius cultivar O-4 contig16035, 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: 17047
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:1585 original size:23 final size:23

Alignment explanation


    Indices: 1555--1598  Score: 70
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       1545 TTATTACCTC

                                   
       1555 TTTTGATTTTCTGATTTTTCTCT
          1 TTTTGATTTTCTGATTTTTCTCT

                        **       
       1578 TTTTGATTTTCTTCTTTTTCT
          1 TTTTGATTTTCTGATTTTTCT

       1599 ATCTCTAGAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  23   19  1.00

ACGTcount: A:0.07, C:0.14, G:0.07, T:0.73


Consensus pattern (23 bp):   
TTTTGATTTTCTGATTTTTCTCT

Found at i:4476 original size:20 final size:20

Alignment explanation


    Indices: 4451--4496  Score: 92
    Period size: 20  Copynumber: 2.3  Consensus size: 20

       4441 GATTGAAAGC

                                
       4451 TGAATGCCTTATGTCCTGAA
          1 TGAATGCCTTATGTCCTGAA

                                
       4471 TGAATGCCTTATGTCCTGAA
          1 TGAATGCCTTATGTCCTGAA

                  
       4491 TGAATG
          1 TGAATG

       4497 GTAAAGCTGC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   26  1.00

ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35


Consensus pattern (20 bp):   
TGAATGCCTTATGTCCTGAA

Found at i:5409 original size:26 final size:26

Alignment explanation


    Indices: 5295--5417  Score: 120
    Period size: 28  Copynumber: 4.5  Consensus size: 26

       5285 TTGAAGTGAC

                       *        *       
       5295 CCAAAATGCCCTTGGATGTGCAAAATGA
          1 CCAAAATGCCCCTGG-TGT-AAAAATGA

                      *     **          
       5323 CCAAAATGCCTCTGGACATACAAAATGA
          1 CCAAAATGCCCCTGG-TGTA-AAAATGA

                       * *             
       5351 CCAAAATGCCCTTAGTGTAAAAACTGA
          1 CCAAAATGCCCCTGGTGTAAAAA-TGA

                   *                  
       5378 CCAAAATACCCCTGGTGTAAAAATGA
          1 CCAAAATGCCCCTGGTGTAAAAATGA

             *            
       5404 CAAAAATGCCCCTG
          1 CCAAAATGCCCCTG

       5418 AGCTGACCCT


Statistics
Matches: 78,  Mismatches: 15, Indels: 6
        0.79            0.15        0.06

Matches are distributed among these distances:
  26   19  0.24
  27   25  0.32
  28   34  0.44

ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20


Consensus pattern (26 bp):   
CCAAAATGCCCCTGGTGTAAAAATGA

Found at i:8056 original size:21 final size:21

Alignment explanation


    Indices: 8032--8086  Score: 74
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       8022 CATCCATTCA

                           **    
       8032 CCGTGCCACCACCGGTTAAGC
          1 CCGTGCCACCACCGGCCAAGC

                              *  
       8053 CCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGCCAAGC

                    *    
       8074 CCGTGCCATCACC
          1 CCGTGCCACCACC

       8087 ATTCCAAGCC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCCAAGC
Done.