Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007194.1 Corchorus capsularis cultivar CVL-1 contig07215, 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: 23709
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:1724 original size:21 final size:22

Alignment explanation


    Indices: 1684--1724  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

       1674 TAACAGCCAT

                      *  *        
       1684 GGCAGAGATATCTGAAGCAGGA
          1 GGCAGAGATAACTAAAGCAGGA

                                
       1706 GGCAGAG-TAACTAAAGCAG
          1 GGCAGAGATAACTAAAGCAG

       1725 AACGCTCTTG


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   10  0.59
  22    7  0.41

ACGTcount: A:0.39, C:0.15, G:0.34, T:0.12


Consensus pattern (22 bp):   
GGCAGAGATAACTAAAGCAGGA

Found at i:2876 original size:18 final size:19

Alignment explanation


    Indices: 2832--2877  Score: 51
    Period size: 18  Copynumber: 2.5  Consensus size: 19

       2822 GGTTGGGTTT

                               
       2832 AGTTAG-TTTTTTAAGTTC
          1 AGTTAGTTTTTTTAAGTTC

             *            *     
       2850 AATTCAGTTTTTTTGAG-TC
          1 AGTT-AGTTTTTTTAAGTTC

                     
       2869 AGTTAGTTT
          1 AGTTAGTTT

       2878 GAATCTGAGT


Statistics
Matches: 23,  Mismatches: 3, Indels: 4
        0.77            0.10        0.13

Matches are distributed among these distances:
  18    8  0.35
  19    7  0.30
  20    8  0.35

ACGTcount: A:0.22, C:0.07, G:0.17, T:0.54


Consensus pattern (19 bp):   
AGTTAGTTTTTTTAAGTTC

Found at i:14997 original size:22 final size:22

Alignment explanation


    Indices: 14967--15019  Score: 65
    Period size: 22  Copynumber: 2.5  Consensus size: 22

      14957 AGGGAAAAAT

                                  
      14967 AAAAATAAAACAAACAA-ACAA
          1 AAAAATAAAACAAACAACACAA

                       *   *       
      14988 AAAAATTAAAAGAAATAACAC-A
          1 AAAAA-TAAAACAAACAACACAA

                      
      15010 AAAAATAAAA
          1 AAAAATAAAA

      15020 GCGAAGATTG


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  21   10  0.36
  22   16  0.57
  23    2  0.07

ACGTcount: A:0.79, C:0.09, G:0.02, T:0.09


Consensus pattern (22 bp):   
AAAAATAAAACAAACAACACAA

Found at i:15020 original size:21 final size:21

Alignment explanation


    Indices: 14967--15020  Score: 65
    Period size: 21  Copynumber: 2.5  Consensus size: 21

      14957 AGGGAAAAAT

                      *          
      14967 AAAAATAAAACAAACAAACAA
          1 AAAAATAAAAGAAACAAACAA

                            *      
      14988 AAAAATTAAAAGAAA-TAACACA
          1 AAAAA-TAAAAGAAACAAACA-A

                       
      15010 AAAAATAAAAG
          1 AAAAATAAAAG

      15021 CGAAGATTGT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  21   15  0.52
  22   14  0.48

ACGTcount: A:0.78, C:0.09, G:0.04, T:0.09


Consensus pattern (21 bp):   
AAAAATAAAAGAAACAAACAA

Found at i:18631 original size:32 final size:32

Alignment explanation


    Indices: 18590--18654  Score: 130
    Period size: 32  Copynumber: 2.0  Consensus size: 32

      18580 TGATGTTGTC

                                            
      18590 TAGGTAATTTCATTGGCATTACTTGAAAACAT
          1 TAGGTAATTTCATTGGCATTACTTGAAAACAT

                                            
      18622 TAGGTAATTTCATTGGCATTACTTGAAAACAT
          1 TAGGTAATTTCATTGGCATTACTTGAAAACAT

             
      18654 T
          1 T

      18655 GCAGCACTTT


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

Matches are distributed among these distances:
  32   33  1.00

ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38


Consensus pattern (32 bp):   
TAGGTAATTTCATTGGCATTACTTGAAAACAT
Done.