Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015216.1 Corchorus olitorius cultivar O-4 contig15249, 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: 29096
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:13326 original size:37 final size:37

Alignment explanation


    Indices: 13282--13352  Score: 124
    Period size: 37  Copynumber: 1.9  Consensus size: 37

      13272 CTTGATCAAC

                        *  *                     
      13282 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
          1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA

                                              
      13319 ATACATGTCTTTCCAAATAGACATAACTTTATGA
          1 ATACATGTCTTTCCAAATAGACATAACTTTATGA

      13353 ATAATTATGT


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  37   32  1.00

ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38


Consensus pattern (37 bp):   
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA

Found at i:15125 original size:26 final size:25

Alignment explanation


    Indices: 15087--15138  Score: 59
    Period size: 26  Copynumber: 2.0  Consensus size: 25

      15077 TTTCTTACAA

                                      
      15087 AAATAATAGAAATAAACATTAGATAT
          1 AAATAATAGAAATAAAC-TTAGATAT

                *   *    *      *    
      15113 AAATCATATAAATGAACTTATATAT
          1 AAATAATAGAAATAAACTTAGATAT

             
      15138 A
          1 A

      15139 TCTCATTGAC


Statistics
Matches: 22,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  25    8  0.36
  26   14  0.64

ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31


Consensus pattern (25 bp):   
AAATAATAGAAATAAACTTAGATAT

Found at i:15813 original size:37 final size:37

Alignment explanation


    Indices: 15769--15839  Score: 124
    Period size: 37  Copynumber: 1.9  Consensus size: 37

      15759 CTTGATCAAC

                        *  *                     
      15769 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
          1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA

                                              
      15806 ATACATGTCTTTCCAAATAGACATAACTTTATGA
          1 ATACATGTCTTTCCAAATAGACATAACTTTATGA

      15840 ATAATTATGT


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  37   32  1.00

ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38


Consensus pattern (37 bp):   
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA

Found at i:18722 original size:67 final size:65

Alignment explanation


    Indices: 18638--18880  Score: 251
    Period size: 65  Copynumber: 3.7  Consensus size: 65

      18628 ATGATGAAAC

                                              *                              
      18638 TGACCCTTTC-ACCGAAAGGGTATTTTTGGAAATCAAAATACTAAACTTGAATGCAAAAAGAC-A
          1 TGACCC-TTCGACCGAAAGGGTA-TTTTGGAAATAAAAATACTAAACTTGAATGC-AAAAGACGA

               
      18701 AGA
         63 AGA

                     *                      * *         *    *    *          
      18704 TTGACCCTTTGACCGAAAGGGTATTTTTGGAATTGAAAATACTACACTTAAATGTAAAAGACGGA
          1 -TGACCCTTCGACCGAAAGGGTA-TTTTGGAAATAAAAATACTAAACTTGAATGCAAAAGAC-GA

               
      18769 A-A
         63 AGA

                              *                   * *          *          *  
      18771 TGACCCTTCGACCGAAAGTGTATTTTGGAAA-AAAGAAAATTAAACTTGAAGGCAAAAGACGGAG
          1 TGACCCTTCGACCGAAAGGGTATTTTGGAAATAAA-AATACTAAACTTGAATGCAAAAGACGAAG

             
      18835 A
         65 A

                        *                   *            
      18836 TGACCCTTCGACTGAAAGGGTATTTTGGAAAAAAGAAAATACTAA
          1 TGACCCTTCGACCGAAAGGGTATTTTGG-AAATA-AAAATACTAA

      18881 TGACCTTTGG


Statistics
Matches: 147,  Mismatches: 21, Indels: 16
        0.80            0.11        0.09

Matches are distributed among these distances:
  64    4  0.03
  65   54  0.37
  66   32  0.22
  67   53  0.36
  68    4  0.03

ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24


Consensus pattern (65 bp):   
TGACCCTTCGACCGAAAGGGTATTTTGGAAATAAAAATACTAAACTTGAATGCAAAAGACGAAGA

Found at i:26120 original size:22 final size:21

Alignment explanation


    Indices: 26080--26120  Score: 64
    Period size: 22  Copynumber: 1.9  Consensus size: 21

      26070 TTGTTTGATG

                          *      
      26080 CAATTTGGCCCCTGCTTTATT
          1 CAATTTGGCCCCTGATTTATT

                                
      26101 CAATTTGGCCCCCTGATTTA
          1 CAATTTGG-CCCCTGATTTA

      26121 GAATATTTAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21    8  0.44
  22   10  0.56

ACGTcount: A:0.17, C:0.29, G:0.15, T:0.39


Consensus pattern (21 bp):   
CAATTTGGCCCCTGATTTATT
Done.