Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021571.1 Corchorus olitorius cultivar O-4 contig21604, 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: 3911
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35


Found at i:671 original size:21 final size:21

Alignment explanation


    Indices: 650--691  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        640 GCCCACATGG

                      *     *     
        650 TTGCCTTGAGCACCCATGTGGT
          1 TTGCC-TGAGAACCCAGGTGGT

                                
        672 TTGCCTGAGAACCCAGGTGG
          1 TTGCCTGAGAACCCAGGTGG

        692 GCAGTGTCAC


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  21   13  0.72
  22    5  0.28

ACGTcount: A:0.17, C:0.26, G:0.31, T:0.26


Consensus pattern (21 bp):   
TTGCCTGAGAACCCAGGTGGT

Found at i:754 original size:76 final size:76

Alignment explanation


    Indices: 625--775  Score: 191
    Period size: 76  Copynumber: 2.0  Consensus size: 76

        615 ACAAGGACCC

                                                                           * 
        625 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
        690 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                            **     
        701 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                   *     
        763 GATGGGCTGTGTC
         63 GATGGGCAGTGTC

        776 TTAGCTCATC


Statistics
Matches: 65,  Mismatches: 7, Indels: 6
        0.83            0.09        0.08

Matches are distributed among these distances:
  75    4  0.06
  76   55  0.85
  77    6  0.09

ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:3232 original size:24 final size:24

Alignment explanation


    Indices: 3205--3255  Score: 93
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       3195 TTTAGTTAGT

                                    
       3205 TTTAGGTTTATTTTTCCTACATTA
          1 TTTAGGTTTATTTTTCCTACATTA

                                *   
       3229 TTTAGGTTTATTTTTCCTACGTTA
          1 TTTAGGTTTATTTTTCCTACATTA

               
       3253 TTT
          1 TTT

       3256 TTTATTCTAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.18, C:0.12, G:0.10, T:0.61


Consensus pattern (24 bp):   
TTTAGGTTTATTTTTCCTACATTA
Done.