Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012574.1 Corchorus capsularis cultivar CVL-1 contig12595, 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: 28578
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33


Found at i:16756 original size:25 final size:27

Alignment explanation


    Indices: 16722--16789  Score: 90
    Period size: 25  Copynumber: 2.6  Consensus size: 27

      16712 CTTTTCCTTC

                                        
      16722 AAAAAAATGTTTGAGCT-T-CCCTAA-A
          1 AAAAAAATGTTTGAGCTCTGCCC-AATA

                                *      
      16747 AAAAAAATGTTTGAGCTCTGGCCAATA
          1 AAAAAAATGTTTGAGCTCTGCCCAATA

                             
      16774 AAAAAAA-GTTTGAGCT
          1 AAAAAAATGTTTGAGCT

      16790 AACCCACAAC


Statistics
Matches: 39,  Mismatches: 1, Indels: 5
        0.87            0.02        0.11

Matches are distributed among these distances:
  25   17  0.44
  26   12  0.31
  27   10  0.26

ACGTcount: A:0.44, C:0.13, G:0.16, T:0.26


Consensus pattern (27 bp):   
AAAAAAATGTTTGAGCTCTGCCCAATA

Found at i:24844 original size:77 final size:77

Alignment explanation


    Indices: 24717--24862  Score: 258
    Period size: 77  Copynumber: 1.9  Consensus size: 77

      24707 GATCAAAAAA

                            *                                                
      24717 GGGTTGCTAAATAACGTCCCATAATTGCTATTCACCGCCTCATTTTTTACCCTTTCGCCCTTTAG
          1 GGGTTGCTAAATAACGCCCCATAATTGCTATTCACCGCCTCATTTTTTACCCTTTCGCCCTTTAG

                        
      24782 TCCAGAAATAGG
         66 TCCAGAAATAGG

                         *                                                   
      24794 GGGTTGCTAAATACCGCCCCATAATTGCTATTCACCGCC-CAATTTTTTACCCTTTCGCCCTTTA
          1 GGGTTGCTAAATAACGCCCCATAATTGCTATTCACCGCCTC-ATTTTTTACCCTTTCGCCCTTTA

                 
      24858 GTCCA
         65 GTCCA

      24863 TTTTCAAACT


Statistics
Matches: 66,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  76    1  0.02
  77   65  0.98

ACGTcount: A:0.22, C:0.30, G:0.14, T:0.34


Consensus pattern (77 bp):   
GGGTTGCTAAATAACGCCCCATAATTGCTATTCACCGCCTCATTTTTTACCCTTTCGCCCTTTAG
TCCAGAAATAGG

Found at i:28226 original size:12 final size:12

Alignment explanation


    Indices: 28209--28233  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      28199 GGCAGACACG

                        
      28209 TGCAAATGTATT
          1 TGCAAATGTATT

                        
      28221 TGCAAATGTATT
          1 TGCAAATGTATT

             
      28233 T
          1 T

      28234 CAGTAGTATT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44


Consensus pattern (12 bp):   
TGCAAATGTATT

Found at i:28464 original size:8 final size:8

Alignment explanation


    Indices: 28451--28510  Score: 120
    Period size: 8  Copynumber: 7.5  Consensus size: 8

      28441 TAACCAAAAA

                    
      28451 CCGGGGTC
          1 CCGGGGTC

                    
      28459 CCGGGGTC
          1 CCGGGGTC

                    
      28467 CCGGGGTC
          1 CCGGGGTC

                    
      28475 CCGGGGTC
          1 CCGGGGTC

                    
      28483 CCGGGGTC
          1 CCGGGGTC

                    
      28491 CCGGGGTC
          1 CCGGGGTC

                    
      28499 CCGGGGTC
          1 CCGGGGTC

                
      28507 CCGG
          1 CCGG

      28511 TTGGGGGTCA


Statistics
Matches: 52,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   52  1.00

ACGTcount: A:0.00, C:0.38, G:0.50, T:0.12


Consensus pattern (8 bp):   
CCGGGGTC

Found at i:28549 original size:23 final size:23

Alignment explanation


    Indices: 28505--28554  Score: 64
    Period size: 23  Copynumber: 2.2  Consensus size: 23

      28495 GGTCCCGGGG

                                  *
      28505 TCCCGGTTGGGGGTCAACTGGGC
          1 TCCCGGTTGGGGGTCAACTGGGA

                    *     *  *     
      28528 TCCCGGTTTGGGGTGAAGTGGGA
          1 TCCCGGTTGGGGGTCAACTGGGA

                
      28551 TCCC
          1 TCCC

      28555 ACTTCGACCC


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.10, C:0.24, G:0.42, T:0.24


Consensus pattern (23 bp):   
TCCCGGTTGGGGGTCAACTGGGA
Done.