Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006757.1 Corchorus capsularis cultivar CVL-1 contig06778, 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: 12234
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Found at i:5606 original size:32 final size:32

Alignment explanation


    Indices: 5560--5625  Score: 96
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       5550 TTGAGTCAGG

                *               *           
       5560 TCGGGTTAAATTTGGATCAGGTTGAATCGGGT
          1 TCGGATTAAATTTGGATCAGATTGAATCGGGT

                           *         *      
       5592 TCGGATTAAATTTGGGTCAGATTGATTCGGGT
          1 TCGGATTAAATTTGGATCAGATTGAATCGGGT

              
       5624 TC
          1 TC

       5626 AGATCCATTT


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

Matches are distributed among these distances:
  32   30  1.00

ACGTcount: A:0.21, C:0.11, G:0.32, T:0.36


Consensus pattern (32 bp):   
TCGGATTAAATTTGGATCAGATTGAATCGGGT

Found at i:5638 original size:32 final size:32

Alignment explanation


    Indices: 5567--5642  Score: 89
    Period size: 32  Copynumber: 2.4  Consensus size: 32

       5557 AGGTCGGGTT

                    *    *             *   *
       5567 AAATTTGGATCAGGTTGAATCGGGTTCGGATT
          1 AAATTTGGGTCAGATTGAATCGGGTTCAGATC

                              *             
       5599 AAATTTGGGTCAGATTGATTCGGGTTCAGATC
          1 AAATTTGGGTCAGATTGAATCGGGTTCAGATC

            * *         
       5631 CATTTTGGGTCA
          1 AAATTTGGGTCA

       5643 TGTTAATTCA


Statistics
Matches: 37,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  32   37  1.00

ACGTcount: A:0.24, C:0.12, G:0.29, T:0.36


Consensus pattern (32 bp):   
AAATTTGGGTCAGATTGAATCGGGTTCAGATC

Found at i:7044 original size:11 final size:11

Alignment explanation


    Indices: 6989--7046  Score: 59
    Period size: 11  Copynumber: 5.5  Consensus size: 11

       6979 TCGTTTGGCA

                        
       6989 TTGTTTTCG-TT
          1 TTGTTTT-GTTT

              *        
       7000 TTCTTTT-TTT
          1 TTGTTTTGTTT

                       
       7010 TT-TTTTGTTT
          1 TTGTTTTGTTT

                  **   
       7020 TTGTTTCATTT
          1 TTGTTTTGTTT

                       
       7031 TTGTTTTGTTT
          1 TTGTTTTGTTT

                 
       7042 TTGTT
          1 TTGTT

       7047 ATGCTGTCTA


Statistics
Matches: 39,  Mismatches: 5, Indels: 6
        0.78            0.10        0.12

Matches are distributed among these distances:
   9    4  0.10
  10    9  0.23
  11   26  0.67

ACGTcount: A:0.02, C:0.05, G:0.12, T:0.81


Consensus pattern (11 bp):   
TTGTTTTGTTT

Found at i:10705 original size:16 final size:16

Alignment explanation


    Indices: 10684--10718  Score: 61
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      10674 ACAATTCAGA

                         *  
      10684 AAGCAGAAAAGCTTTG
          1 AAGCAGAAAAGCTCTG

                            
      10700 AAGCAGAAAAGCTCTG
          1 AAGCAGAAAAGCTCTG

               
      10716 AAG
          1 AAG

      10719 TATTTCAGAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.46, C:0.14, G:0.26, T:0.14


Consensus pattern (16 bp):   
AAGCAGAAAAGCTCTG
Done.