Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008914.1 Corchorus capsularis cultivar CVL-1 contig08935, 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: 28626
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:9770 original size:14 final size:15

Alignment explanation


    Indices: 9751--9779  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

       9741 CTGATTAGGG

                           
       9751 GGTGGTTGA-TTGGA
          1 GGTGGTTGAGTTGGA

                           
       9765 GGTGGTTGAGTTGGA
          1 GGTGGTTGAGTTGGA

       9780 ACGGCAGCAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    9  0.64
  15    5  0.36

ACGTcount: A:0.14, C:0.00, G:0.52, T:0.34


Consensus pattern (15 bp):   
GGTGGTTGAGTTGGA

Found at i:12209 original size:14 final size:15

Alignment explanation


    Indices: 12182--12221  Score: 55
    Period size: 14  Copynumber: 2.7  Consensus size: 15

      12172 CAGACCTAAC

                *          
      12182 AAAACAAAAGAAAAA
          1 AAAAGAAAAGAAAAA

                           
      12197 AAAAGAAAA-AAAAA
          1 AAAAGAAAAGAAAAA

            *          
      12211 GAAAGAAAAGA
          1 AAAAGAAAAGA

      12222 CATCCACTCC


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  14   13  0.59
  15    9  0.41

ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00


Consensus pattern (15 bp):   
AAAAGAAAAGAAAAA

Found at i:12221 original size:9 final size:10

Alignment explanation


    Indices: 12182--12219  Score: 58
    Period size: 10  Copynumber: 3.7  Consensus size: 10

      12172 CAGACCTAAC

                *     
      12182 AAAACAAAAG
          1 AAAAAAAAAG

                      
      12192 AAAAAAAAAG
          1 AAAAAAAAAG

                      
      12202 AAAAAAAAAG
          1 AAAAAAAAAG

                    
      12212 AAAGAAAA
          1 AAA-AAAA

      12220 GACATCCACT


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  10   22  0.85
  11    4  0.15

ACGTcount: A:0.87, C:0.03, G:0.11, T:0.00


Consensus pattern (10 bp):   
AAAAAAAAAG
Done.