Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008864.1 Corchorus capsularis cultivar CVL-1 contig08885, 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: 1859
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:128 original size:16 final size:16

Alignment explanation


    Indices: 107--150  Score: 70
    Period size: 16  Copynumber: 2.8  Consensus size: 16

         97 TGCTTTTTTT

                            
        107 AAAACCCTAGTTTTCA
          1 AAAACCCTAGTTTTCA

             *        *     
        123 AGAACCCTAGATTTCA
          1 AAAACCCTAGTTTTCA

                        
        139 AAAACCCTAGTT
          1 AAAACCCTAGTT

        151 GCCCTCTGTT


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  16   24  1.00

ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27


Consensus pattern (16 bp):   
AAAACCCTAGTTTTCA

Found at i:1316 original size:23 final size:23

Alignment explanation


    Indices: 1286--1330  Score: 90
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1276 CACTCAAAAG

                                   
       1286 GAGACAAGTCCAAGATTAACTCA
          1 GAGACAAGTCCAAGATTAACTCA

                                  
       1309 GAGACAAGTCCAAGATTAACTC
          1 GAGACAAGTCCAAGATTAACTC

       1331 TTAATGAAAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18


Consensus pattern (23 bp):   
GAGACAAGTCCAAGATTAACTCA

Found at i:1820 original size:27 final size:27

Alignment explanation


    Indices: 1763--1838  Score: 89
    Period size: 27  Copynumber: 2.8  Consensus size: 27

       1753 AAGTGAACTT

                          *   *    *   
       1763 AAAATGACCAAAATACCCTTAAATGCA
          1 AAAATGACCAAAATGCCCCTAAACGCA

                                *    **
       1790 AAAATGACCAAAATGCCCCTGAACGTG
          1 AAAATGACCAAAATGCCCCTAAACGCA

                        *         
       1817 AAAATGACCAAATTGCCCCTAA
          1 AAAATGACCAAAATGCCCCTAA

       1839 TAGCTAATTA


Statistics
Matches: 41,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  27   41  1.00

ACGTcount: A:0.46, C:0.25, G:0.12, T:0.17


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCCTAAACGCA
Done.