Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013073.1 Corchorus olitorius cultivar O-4 contig13106, 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: 15318
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:385 original size:21 final size:20

Alignment explanation


    Indices: 361--411  Score: 59
    Period size: 19  Copynumber: 2.5  Consensus size: 20

        351 TCTAATCTGC

                                 
        361 ACAGTAGTTAATCTAATATAT
          1 ACAGT-GTTAATCTAATATAT

                         *  *   
        382 ACAGTG-TAATCTCATTTAT
          1 ACAGTGTTAATCTAATATAT

                       
        401 ACAGTTGTTAA
          1 ACAG-TGTTAA

        412 ACAGTATCAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  19   15  0.58
  20    3  0.12
  21    8  0.31

ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39


Consensus pattern (20 bp):   
ACAGTGTTAATCTAATATAT

Found at i:6237 original size:29 final size:30

Alignment explanation


    Indices: 6204--6276  Score: 85
    Period size: 29  Copynumber: 2.5  Consensus size: 30

       6194 CTTGTAGCTA

                 *     *                  
       6204 TTGGATGTTTTGCCCCCTCAACTTCAA-TT
          1 TTGGACGTTTTACCCCCTCAACTTCAATTT

                  *       **  *           
       6233 TTGGACATTTTACCTTCTGAACTTCAATTT
          1 TTGGACGTTTTACCCCCTCAACTTCAATTT

                          
       6263 TTGGACGTTTTACC
          1 TTGGACGTTTTACC

       6277 TATTCAAGCT


Statistics
Matches: 36,  Mismatches: 7, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  29   21  0.58
  30   15  0.42

ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44


Consensus pattern (30 bp):   
TTGGACGTTTTACCCCCTCAACTTCAATTT

Found at i:7597 original size:20 final size:20

Alignment explanation


    Indices: 7572--7613  Score: 75
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       7562 ACTATAAAAC

                   *            
       7572 ATGTGATTGCATATATTTGT
          1 ATGTGATAGCATATATTTGT

                                
       7592 ATGTGATAGCATATATTTGT
          1 ATGTGATAGCATATATTTGT

              
       7612 AT
          1 AT

       7614 ATTAATTTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.29, C:0.05, G:0.19, T:0.48


Consensus pattern (20 bp):   
ATGTGATAGCATATATTTGT

Found at i:11620 original size:15 final size:16

Alignment explanation


    Indices: 11579--11620  Score: 52
    Period size: 15  Copynumber: 2.8  Consensus size: 16

      11569 ATGAGCAAAA

                            
      11579 AAAAATTCCAAATGAC
          1 AAAAATTCCAAATGAC

                *         * 
      11595 AAAAGTT-CAAAT-CC
          1 AAAAATTCCAAATGAC

                        
      11609 AAAAATTCCAAA
          1 AAAAATTCCAAA

      11621 AAAATCTCCT


Statistics
Matches: 22,  Mismatches: 3, Indels: 3
        0.79            0.11        0.11

Matches are distributed among these distances:
  14    7  0.32
  15    9  0.41
  16    6  0.27

ACGTcount: A:0.57, C:0.19, G:0.05, T:0.19


Consensus pattern (16 bp):   
AAAAATTCCAAATGAC

Found at i:14646 original size:30 final size:29

Alignment explanation


    Indices: 14605--14662  Score: 98
    Period size: 30  Copynumber: 2.0  Consensus size: 29

      14595 CTAATAAATA

                                         
      14605 ATCATAAACCATAATTAAAAGCCATTATG
          1 ATCATAAACCATAATTAAAAGCCATTATG

                                  *      
      14634 ATCATAAAACCATAATTAAAAGTCATTAT
          1 ATCAT-AAACCATAATTAAAAGCCATTAT

      14663 TTCAGCTTAT


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  29    5  0.19
  30   22  0.81

ACGTcount: A:0.50, C:0.16, G:0.05, T:0.29


Consensus pattern (29 bp):   
ATCATAAACCATAATTAAAAGCCATTATG
Done.