Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020968.1 Corchorus olitorius cultivar O-4 contig21001, 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: 2873
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.29


Found at i:221 original size:40 final size:40

Alignment explanation


    Indices: 4--218  Score: 297
    Period size: 40  Copynumber: 5.4  Consensus size: 40

          1 GGT

                           *    *                   
          4 AGGTATTGTTTAAATGCCCAGTTTGCCCTTCCCCACCGGA
          1 AGGTATTGTTTAAATACCCAATTTGCCCTTCCCCACCGGA

                         *                          
         44 AGGTATTGTTTAAGTACCCAATTTGCCCTTCCCCACCGGA
          1 AGGTATTGTTTAAATACCCAATTTGCCCTTCCCCACCGGA

                         *                          
         84 AGGTATTGTTTAAGTACCCAATTTGCCCTTCCCCACCGGA
          1 AGGTATTGTTTAAATACCCAATTTGCCCTTCCCCACCGGA

                                                     
        124 AGGTATTGTTTAAATA-CCAATTTTGCCCTTCCCCACCGGA
          1 AGGTATTGTTTAAATACCCAA-TTTGCCCTTCCCCACCGGA

               **    *     *    *  *            *   
        164 AGGCGTTGTCTAAATTCCCAGTTGGCCCTTCCCCACAGGA
          1 AGGTATTGTTTAAATACCCAATTTGCCCTTCCCCACCGGA

                *    *     
        204 AGGTGTTGTCTAAAT
          1 AGGTATTGTTTAAAT

        219 TCCTGGTTTG


Statistics
Matches: 161,  Mismatches: 12, Indels: 4
        0.91            0.07        0.02

Matches are distributed among these distances:
  39    4  0.02
  40  154  0.96
  41    3  0.02

ACGTcount: A:0.22, C:0.28, G:0.19, T:0.30


Consensus pattern (40 bp):   
AGGTATTGTTTAAATACCCAATTTGCCCTTCCCCACCGGA

Found at i:252 original size:40 final size:40

Alignment explanation


    Indices: 4--244  Score: 257
    Period size: 40  Copynumber: 6.0  Consensus size: 40

          1 GGT

                *    *     *                        
          4 AGGTATTGTTTAAATGCCCAGTTTGCCCTTCCCCACCGGA
          1 AGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCCCACCGGA

                *    *   * *    *                   
         44 AGGTATTGTTTAAGTACCCAATTTGCCCTTCCCCACCGGA
          1 AGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCCCACCGGA

                *    *   * *    *                   
         84 AGGTATTGTTTAAGTACCCAATTTGCCCTTCCCCACCGGA
          1 AGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCCCACCGGA

                *    *     *  * *                   
        124 AGGTATTGTTTAAATACCAATTTTGCCCTTCCCCACCGGA
          1 AGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCCCACCGGA

               *                   *            *   
        164 AGGCGTTGTCTAAATTCCCAGTTGGCCCTTCCCCACAGGA
          1 AGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCCCACCGGA

                              **       *    *       
        204 AGGTGTTGTCTAAATTCCTGGTTTGCCTTTCCTCACCGGA
          1 AGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCCCACCGGA

             
        244 A
          1 A

        245 AATGTTGTTC


Statistics
Matches: 180,  Mismatches: 21, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  40  180  1.00

ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31


Consensus pattern (40 bp):   
AGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCCCACCGGA

Found at i:253 original size:120 final size:120

Alignment explanation


    Indices: 7--253  Score: 287
    Period size: 120  Copynumber: 2.1  Consensus size: 120

          1 GGTAGG

                        *  *                        *     *   *         *    
          7 TATTGTTTAAATGCCCAGTTTGCCCTTCCCCACCGGAAGGTATTGTTTAAGTACCCAATTTGCCC
          1 TATTGTTTAAATACCAAGTTTGCCCTTCCCCACCGGAAGGCATTGTCTAAATACCCAATTGGCCC

                    *            *   *                           **
         72 TTCCCCACCGGAAGGTATTGTTTAAGTACCCAATTTGCCCTTCCCCACCGGAAGG
         66 TTCCCCACAGGAAGGTATTGTCTAAATACCCAATTTGCCCTTCCCCACCGGAAAA

                             *                       *          *    *       
        127 TATTGTTTAAATACCAATTTTGCCCTTCCCCACCGGAAGGCGTTGTCTAAATTCCCAGTTGGCCC
          1 TATTGTTTAAATACCAAGTTTGCCCTTCCCCACCGGAAGGCATTGTCTAAATACCCAATTGGCCC

                            *          *  ***      *    *          
        192 TTCCCCACAGGAAGGTGTTGTCTAAATTCCTGGTTTGCCTTTCCTCACCGGAAAA
         66 TTCCCCACAGGAAGGTATTGTCTAAATACCCAATTTGCCCTTCCCCACCGGAAAA

             *     
        247 TGTTGTT
          1 TATTGTT

        254 CCGAGTTTGC


Statistics
Matches: 104,  Mismatches: 23, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
 120  104  1.00

ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32


Consensus pattern (120 bp):   
TATTGTTTAAATACCAAGTTTGCCCTTCCCCACCGGAAGGCATTGTCTAAATACCCAATTGGCCC
TTCCCCACAGGAAGGTATTGTCTAAATACCCAATTTGCCCTTCCCCACCGGAAAA
Done.