Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022509.1 Corchorus olitorius cultivar O-4 contig22542, 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: 18148
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:152 original size:23 final size:23

Alignment explanation


    Indices: 105--152  Score: 60
    Period size: 23  Copynumber: 2.1  Consensus size: 23

         95 TGTTAAACGC

                      *         *  
        105 GGAGCAATTTTGGAACGGTAGTT
          1 GGAGCAATTTGGGAACGGTAATT

                         *  *      
        128 GGAGCAATTTGGGTACTGTAATT
          1 GGAGCAATTTGGGAACGGTAATT

              
        151 GG
          1 GG

        153 TGGGTATGCC


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.25, C:0.08, G:0.35, T:0.31


Consensus pattern (23 bp):   
GGAGCAATTTGGGAACGGTAATT

Found at i:17476 original size:71 final size:72

Alignment explanation


    Indices: 17355--17530  Score: 246
    Period size: 71  Copynumber: 2.4  Consensus size: 72

      17345 ATCGTACTAT

                    *                          *       * *                   
      17355 AAAGGAGCAAAAGGTACAATCAATAAAGCAGGATATAGAAATTTCTAATTTTCCCATC-ACTACA
          1 AAAGGAGCCAAAGGTACAATCAATAAAGCAGGATAAAGAAATTCCCAATTTTCCCATCGACTACA

                 * 
      17419 AATCTGC
         66 AATCTAC

             *                  *                 *             *            
      17426 AGAGGAGCCAAAGGTACAATGAATAAAGCAGGATAAAGGAATTCCCAATTTTTCCATCGTACTAC
          1 AAAGGAGCCAAAGGTACAATCAATAAAGCAGGATAAAGAAATTCCCAATTTTCCCATCG-ACTAC

              *     
      17491 AATTCTAC
         65 AAATCTAC

                                            
      17499 AAAGGAGCCAAAGGTACAATCAATAAAGCAGG
          1 AAAGGAGCCAAAGGTACAATCAATAAAGCAGG

      17531 TGCAGAGTAA


Statistics
Matches: 91,  Mismatches: 12, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  71   50  0.55
  73   41  0.45

ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21


Consensus pattern (72 bp):   
AAAGGAGCCAAAGGTACAATCAATAAAGCAGGATAAAGAAATTCCCAATTTTCCCATCGACTACA
AATCTAC

Found at i:18106 original size:7 final size:7

Alignment explanation


    Indices: 18090--18120  Score: 55
    Period size: 7  Copynumber: 4.6  Consensus size: 7

      18080 TCTCTGATGC

                   
      18090 AAAA-AA
          1 AAAAGAA

                   
      18096 AAAAGAA
          1 AAAAGAA

                   
      18103 AAAAGAA
          1 AAAAGAA

                   
      18110 AAAAGAA
          1 AAAAGAA

                
      18117 AAAA
          1 AAAA

      18121 ACAATAAGAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6    4  0.17
   7   20  0.83

ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00


Consensus pattern (7 bp):   
AAAAGAA

Done.