Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024089.1 Corchorus olitorius cultivar O-4 contig24122, 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: 26330
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34


Found at i:7645 original size:19 final size:19

Alignment explanation


    Indices: 7623--7661  Score: 62
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       7613 GTTACTTTCC

                                
       7623 TGTAGTTTTGTTTT-GTTTT
          1 TGTA-TTTTGTTTTCGTTTT

                               
       7642 TGTATTTTGTTTTCGTTTT
          1 TGTATTTTGTTTTCGTTTT

             
       7661 T
          1 T

       7662 TTGTTTTTGT


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

Matches are distributed among these distances:
  18    9  0.47
  19   10  0.53

ACGTcount: A:0.05, C:0.03, G:0.18, T:0.74


Consensus pattern (19 bp):   
TGTATTTTGTTTTCGTTTT

Found at i:7651 original size:13 final size:13

Alignment explanation


    Indices: 7633--7676  Score: 52
    Period size: 13  Copynumber: 3.3  Consensus size: 13

       7623 TGTAGTTTTG

                         
       7633 TTTTGTTTTTGTA
          1 TTTTGTTTTTGTA

                     *   *
       7646 TTTTGTTTTCGTTT
          1 TTTTGTTTTTG-TA

                        *
       7660 TTTTGTTTTTGTG
          1 TTTTGTTTTTGTA

                
       7673 TTTT
          1 TTTT

       7677 TCTTAACTTT


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

Matches are distributed among these distances:
  13   15  0.58
  14   11  0.42

ACGTcount: A:0.02, C:0.02, G:0.16, T:0.80


Consensus pattern (13 bp):   
TTTTGTTTTTGTA

Found at i:7676 original size:14 final size:13

Alignment explanation


    Indices: 7633--7677  Score: 54
    Period size: 14  Copynumber: 3.3  Consensus size: 13

       7623 TGTAGTTTTG

                        *
       7633 TTTTGTTTTTGTA
          1 TTTTGTTTTTGTT

                     *    
       7646 TTTTGTTTTCGTTT
          1 TTTTGTTTTTG-TT

                          
       7660 TTTTGTTTTTGTGT
          1 TTTTGTTTTTGT-T

                
       7674 TTTT
          1 TTTT

       7678 CTTAACTTTG


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  13   11  0.41
  14   16  0.59

ACGTcount: A:0.02, C:0.02, G:0.16, T:0.80


Consensus pattern (13 bp):   
TTTTGTTTTTGTT

Found at i:21956 original size:15 final size:16

Alignment explanation


    Indices: 21936--21968  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

      21926 TATCAAGTTT

                       *    
      21936 AACCTTAA-TTTTAAG
          1 AACCTTAAGTTGTAAG

                            
      21951 AACCTTAAGTTGTAAG
          1 AACCTTAAGTTGTAAG

              
      21967 AA
          1 AA

      21969 GTTAAATTTA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15    8  0.50
  16    8  0.50

ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33


Consensus pattern (16 bp):   
AACCTTAAGTTGTAAG

Found at i:24971 original size:16 final size:16

Alignment explanation


    Indices: 24947--24983  Score: 56
    Period size: 16  Copynumber: 2.3  Consensus size: 16

      24937 CGGCTGCCTT

                *           
      24947 TTACGATTTTGCCAAA
          1 TTACAATTTTGCCAAA

                       *    
      24963 TTACAATTTTGGCAAA
          1 TTACAATTTTGCCAAA

                 
      24979 TTACA
          1 TTACA

      24984 TAAACCTAAT


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

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38


Consensus pattern (16 bp):   
TTACAATTTTGCCAAA
Done.