Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010887.1 Corchorus capsularis cultivar CVL-1 contig10908, 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: 21307
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:7349 original size:31 final size:31

Alignment explanation


    Indices: 7311--7373  Score: 126
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       7301 AATGTTACTT

                                           
       7311 GTTTTAAATGAATGTCGTTATACTATTACAA
          1 GTTTTAAATGAATGTCGTTATACTATTACAA

                                           
       7342 GTTTTAAATGAATGTCGTTATACTATTACAA
          1 GTTTTAAATGAATGTCGTTATACTATTACAA

             
       7373 G
          1 G

       7374 CTTAAGGGAT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41


Consensus pattern (31 bp):   
GTTTTAAATGAATGTCGTTATACTATTACAA

Found at i:19397 original size:30 final size:30

Alignment explanation


    Indices: 19326--19387  Score: 106
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      19316 TCGTCATCTG

                     *                    
      19326 CAGAACTTGAATCATCCAAATCATCATCAA
          1 CAGAACTTGCATCATCCAAATCATCATCAA

                             *            
      19356 CAGAACTTGCATCATCCGAATCATCATCAA
          1 CAGAACTTGCATCATCCAAATCATCATCAA

              
      19386 CA
          1 CA

      19388 TATATTGCAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   30  1.00

ACGTcount: A:0.40, C:0.29, G:0.08, T:0.23


Consensus pattern (30 bp):   
CAGAACTTGCATCATCCAAATCATCATCAA

Found at i:21141 original size:32 final size:32

Alignment explanation


    Indices: 21094--21244  Score: 239
    Period size: 32  Copynumber: 4.7  Consensus size: 32

      21084 GATGACCCGT

                     **                *    
      21094 GCCGCCCCAAGAGGGCGGCTTACCATGAGCAG
          1 GCCGCCCCACTAGGGCGGCTTACCATGGGCAG

                                            
      21126 GCCGCCCCACTAGGGCGGCTTACCATGGGCAG
          1 GCCGCCCCACTAGGGCGGCTTACCATGGGCAG

                 *                          
      21158 GCCGCTCCACTAGGGCGGCTTACCATGGGCAG
          1 GCCGCCCCACTAGGGCGGCTTACCATGGGCAG

                 *                            
      21190 GCCGCTCCACTAGGGCGGCTTCACCATTGGGCAG
          1 GCCGCCCCACTAGGGCGGCTT-ACCA-TGGGCAG

                                 
      21224 GCCGCCCCACTAGGGCGGCTT
          1 GCCGCCCCACTAGGGCGGCTT

      21245 CATTATGAAT


Statistics
Matches: 112,  Mismatches: 5, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
  32   81  0.72
  33    4  0.04
  34   27  0.24

ACGTcount: A:0.16, C:0.36, G:0.34, T:0.14


Consensus pattern (32 bp):   
GCCGCCCCACTAGGGCGGCTTACCATGGGCAG

Found at i:21200 original size:64 final size:66

Alignment explanation


    Indices: 21094--21278  Score: 248
    Period size: 64  Copynumber: 2.8  Consensus size: 66

      21084 GATGACCCGT

                     **                                                      
      21094 GCCGCCCCAAGAGGGCGGCTTACCATGAGCAGGCCGCCCCACTAGGGCGGCTT-ACCA-TGGGCA
          1 GCCGCCCCACTAGGGCGGCTTACCATGAGCAGGCCGCCCCACTAGGGCGGCTTCACCATTGGGCA

             
      21157 G
         66 G

                 *                     *         *                           
      21158 GCCGCTCCACTAGGGCGGCTTACCATGGGCAGGCCGCTCCACTAGGGCGGCTTCACCATTGGGCA
          1 GCCGCCCCACTAGGGCGGCTTACCATGAGCAGGCCGCCCCACTAGGGCGGCTTCACCATTGGGCA

             
      21223 G
         66 G

                                   **    **             *    *     
      21224 GCCGCCCCACTAGGGCGGCTTCATTATGAATAGGCCGCCCCACTGGGGCAGCTTC
          1 GCCGCCCCACTAGGGCGGCTT-ACCATGAGCAGGCCGCCCCACTAGGGCGGCTTC

      21279 GTCAGGGCAG


Statistics
Matches: 104,  Mismatches: 14, Indels: 3
        0.86            0.12        0.02

Matches are distributed among these distances:
  64   48  0.46
  65    4  0.04
  66   27  0.26
  67   25  0.24

ACGTcount: A:0.17, C:0.36, G:0.32, T:0.15


Consensus pattern (66 bp):   
GCCGCCCCACTAGGGCGGCTTACCATGAGCAGGCCGCCCCACTAGGGCGGCTTCACCATTGGGCA
G
Done.