Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000912.1 Corchorus capsularis cultivar CVL-1 contig00912, 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: 11768
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1661 original size:10 final size:9

Alignment explanation


    Indices: 1642--1679  Score: 53
    Period size: 9  Copynumber: 4.4  Consensus size: 9

       1632 AGTTAATGCC

                     
       1642 AAAAA-AAA
          1 AAAAAGAAA

                *    
       1650 AAAAGGAAA
          1 AAAAAGAAA

                     
       1659 AAAAAGAAA
          1 AAAAAGAAA

                     
       1668 AAAAA-AAA
          1 AAAAAGAAA

                
       1676 AAAA
          1 AAAA

       1680 CCCTTTCACC


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
   8   11  0.41
   9   16  0.59

ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00


Consensus pattern (9 bp):   
AAAAAGAAA

Found at i:2937 original size:20 final size:21

Alignment explanation


    Indices: 2898--2939  Score: 59
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       2888 TTATAAAGAA

                         *       
       2898 AACTCACAATTCCGTGAGAGT
          1 AACTCACAATTCCATGAGAGT

                       *         
       2919 AACTCAC-ATTTCATGAGAGT
          1 AACTCACAATTCCATGAGAGT

             
       2939 A
          1 A

       2940 GAACCTAAGA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  20   12  0.63
  21    7  0.37

ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26


Consensus pattern (21 bp):   
AACTCACAATTCCATGAGAGT

Found at i:9280 original size:32 final size:33

Alignment explanation


    Indices: 9237--9344  Score: 161
    Period size: 30  Copynumber: 3.4  Consensus size: 33

       9227 CGAAACGCAC

                  *          *               
       9237 TTGTTACGTGTTTTATTCGATCACTT-CCTTAG
          1 TTGTTATGTGTTTTATTTGATCACTTCCCTTAG

                                 *           
       9269 TTGTTATGTGTTTTATTTGATAACTTCCCTTAG
          1 TTGTTATGTGTTTTATTTGATCACTTCCCTTAG

                                             
       9302 TTGTTA--TG-TTTATTTGATCACTTCCCTTAG
          1 TTGTTATGTGTTTTATTTGATCACTTCCCTTAG

                         
       9332 TTGTTATGTGTTT
          1 TTGTTATGTGTTT

       9345 GACATGATGA


Statistics
Matches: 68,  Mismatches: 4, Indels: 7
        0.86            0.05        0.09

Matches are distributed among these distances:
  30   27  0.40
  31    2  0.03
  32   25  0.37
  33   14  0.21

ACGTcount: A:0.16, C:0.14, G:0.16, T:0.55


Consensus pattern (33 bp):   
TTGTTATGTGTTTTATTTGATCACTTCCCTTAG

Done.