Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011491.1 Corchorus olitorius cultivar O-4 contig11524, 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: 2989
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29


Found at i:190 original size:17 final size:18

Alignment explanation


    Indices: 164--222  Score: 77
    Period size: 17  Copynumber: 3.4  Consensus size: 18

        154 ATCAAAATCA

                 *            
        164 AACCCAAGCCCGAACCCG
          1 AACCCGAGCCCGAACCCG

                              
        182 -ACCCGAGCCCGAACCCG
          1 AACCCGAGCCCGAACCCG

                 *       *    
        199 AACCCCA-CCCGAGCCCG
          1 AACCCGAGCCCGAACCCG

                   
        216 AACCCGA
          1 AACCCGA

        223 AAATACCCGA


Statistics
Matches: 36,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  17   31  0.86
  18    5  0.14

ACGTcount: A:0.29, C:0.53, G:0.19, T:0.00


Consensus pattern (18 bp):   
AACCCGAGCCCGAACCCG

Found at i:198 original size:23 final size:23

Alignment explanation


    Indices: 172--223  Score: 95
    Period size: 23  Copynumber: 2.3  Consensus size: 23

        162 CAAACCCAAG

                     *             
        172 CCCGAACCCGACCCGAGCCCGAA
          1 CCCGAACCCCACCCGAGCCCGAA

                                   
        195 CCCGAACCCCACCCGAGCCCGAA
          1 CCCGAACCCCACCCGAGCCCGAA

                  
        218 CCCGAA
          1 CCCGAA

        224 AATACCCGAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  23   28  1.00

ACGTcount: A:0.27, C:0.54, G:0.19, T:0.00


Consensus pattern (23 bp):   
CCCGAACCCCACCCGAGCCCGAA

Found at i:233 original size:16 final size:16

Alignment explanation


    Indices: 212--334  Score: 126
    Period size: 16  Copynumber: 7.8  Consensus size: 16

        202 CCCACCCGAG

                            
        212 CCCGAACCCGAAAATA
          1 CCCGAACCCGAAAATA

                        *    
        228 CCCGAACCCG-ACATAA
          1 CCCGAACCCGAAAAT-A

                 *          
        244 CCCGAGCCCGAAAATA
          1 CCCGAACCCGAAAATA

                        **   
        260 CCCGAACCCG-ACTTAA
          1 CCCGAACCCGAAAAT-A

                 *          
        276 CCCGAGCCCGAAAATA
          1 CCCGAACCCGAAAATA

                            
        292 CCCGAACCCGAAAATA
          1 CCCGAACCCGAAAATA

            *     *      *  
        308 TCCGAATCCG-AAGTA
          1 CCCGAACCCGAAAATA

                   *    
        323 CCCGAACACGAA
          1 CCCGAACCCGAA

        335 CCCGCCCAAT


Statistics
Matches: 86,  Mismatches: 16, Indels: 10
        0.77            0.14        0.09

Matches are distributed among these distances:
  15   16  0.19
  16   65  0.76
  17    5  0.06

ACGTcount: A:0.38, C:0.38, G:0.15, T:0.08


Consensus pattern (16 bp):   
CCCGAACCCGAAAATA

Found at i:238 original size:6 final size:6

Alignment explanation


    Indices: 172--223  Score: 63
    Period size: 6  Copynumber: 9.0  Consensus size: 6

        162 CAAACCCAAG

                               *                   *       *       
        172 CCCGAA CCCG-A CCCGAG CCCGAA CCCGAA CCC-CA CCCGAG CCCGAA
          1 CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA

                  
        218 CCCGAA
          1 CCCGAA

        224 AATACCCGAA


Statistics
Matches: 38,  Mismatches: 6, Indels: 4
        0.79            0.12        0.08

Matches are distributed among these distances:
   5    9  0.24
   6   29  0.76

ACGTcount: A:0.27, C:0.54, G:0.19, T:0.00


Consensus pattern (6 bp):   
CCCGAA

Found at i:254 original size:32 final size:32

Alignment explanation


    Indices: 212--302  Score: 164
    Period size: 32  Copynumber: 2.8  Consensus size: 32

        202 CCCACCCGAG

                 *                          
        212 CCCGAACCCGAAAATACCCGAACCCGACATAA
          1 CCCGAGCCCGAAAATACCCGAACCCGACATAA

                                        *   
        244 CCCGAGCCCGAAAATACCCGAACCCGACTTAA
          1 CCCGAGCCCGAAAATACCCGAACCCGACATAA

                                       
        276 CCCGAGCCCGAAAATACCCGAACCCGA
          1 CCCGAGCCCGAAAATACCCGAACCCGA

        303 AAATATCCGA


Statistics
Matches: 57,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  32   57  1.00

ACGTcount: A:0.36, C:0.42, G:0.15, T:0.07


Consensus pattern (32 bp):   
CCCGAGCCCGAAAATACCCGAACCCGACATAA

Done.