Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000423.1 Corchorus capsularis cultivar CVL-1 contig00423, 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: 3976
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31


Found at i:625 original size:16 final size:16

Alignment explanation


    Indices: 603--644  Score: 59
    Period size: 15  Copynumber: 2.7  Consensus size: 16

        593 AATAAGTACT

                           *
        603 ATAACCCGAAATCGAT
          1 ATAACCCGAAATCGAG

            *               
        619 TTAACCCG-AATCGAG
          1 ATAACCCGAAATCGAG

                       
        634 ATAACCCGAAA
          1 ATAACCCGAAA

        645 CCGACAAAAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17


Consensus pattern (16 bp):   
ATAACCCGAAATCGAG

Found at i:3902 original size:31 final size:31

Alignment explanation


    Indices: 3865--3975  Score: 154
    Period size: 31  Copynumber: 3.6  Consensus size: 31

       3855 GCACATATAA

                                           
       3865 CAAAAGGTGACACGTGACACGCCACGTGTAC
          1 CAAAAGGTGACACGTGACACGCCACGTGTAC

                          *      *   *      
       3896 CAAAAGGTGACACATTG-CACACCATGTGTAC
          1 CAAAAGGTGACAC-GTGACACGCCACGTGTAC

                            *          *   
       3927 CAAAAGGTGACACGTGGCACGCCACGTATAC
          1 CAAAAGGTGACACGTGACACGCCACGTGTAC

                               
       3958 CAAAA-GTGACACGTGACA
          1 CAAAAGGTGACACGTGACA

       3976 T


Statistics
Matches: 70,  Mismatches: 8, Indels: 5
        0.84            0.10        0.06

Matches are distributed among these distances:
  30   14  0.20
  31   54  0.77
  32    2  0.03

ACGTcount: A:0.35, C:0.27, G:0.23, T:0.14


Consensus pattern (31 bp):   
CAAAAGGTGACACGTGACACGCCACGTGTAC

Found at i:3969 original size:30 final size:31

Alignment explanation


    Indices: 3841--3972  Score: 149
    Period size: 31  Copynumber: 4.2  Consensus size: 31

       3831 GACAAAAATA

                              *    *         
       3841 ACACGTGGGCACACGCACATATAACAAAAGGTG
          1 ACACGT-GGCACAC-CACGTATACCAAAAGGTG

                   *   *      *            
       3874 ACACGTGACACGCCACGTGTACCAAAAGGTG
          1 ACACGTGGCACACCACGTATACCAAAAGGTG

                * *        *  *            
       3905 ACACATTGCACACCATGTGTACCAAAAGGTG
          1 ACACGTGGCACACCACGTATACCAAAAGGTG

                       *                   
       3936 ACACGTGGCACGCCACGTATACCAAAA-GTG
          1 ACACGTGGCACACCACGTATACCAAAAGGTG

                   
       3966 ACACGTG
          1 ACACGTG

       3973 ACAT


Statistics
Matches: 84,  Mismatches: 15, Indels: 3
        0.82            0.15        0.03

Matches are distributed among these distances:
  30   10  0.12
  31   63  0.75
  32    5  0.06
  33    6  0.07

ACGTcount: A:0.35, C:0.27, G:0.23, T:0.14


Consensus pattern (31 bp):   
ACACGTGGCACACCACGTATACCAAAAGGTG
Done.