Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012526.1 Corchorus olitorius cultivar O-4 contig12559, 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: 20801
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:10517 original size:29 final size:29

Alignment explanation


    Indices: 10482--10583  Score: 91
    Period size: 29  Copynumber: 3.4  Consensus size: 29

      10472 CCAAAATGTT

                                         
      10482 CAAATAAGGGCCTGATCTTTTAATTTGAC
          1 CAAATAAGGGCCTGATCTTTTAATTTGAC

                    *      *       *  **    
      10511 CAAATAAGAGCCT-AACGTTTGCCAAAGTG-C
          1 CAAATAAGGGCCTGATC-TTT--TAATTTGAC

                         * *              
      10541 TCAAATAAGGGCCCGGTCTTTTAATTTGAC
          1 -CAAATAAGGGCCTGATCTTTTAATTTGAC

                         
      10571 CAAATAAGGGCCT
          1 CAAATAAGGGCCT

      10584 AACGTTTGCC


Statistics
Matches: 54,  Mismatches: 13, Indels: 12
        0.68            0.16        0.15

Matches are distributed among these distances:
  28    2  0.04
  29   31  0.57
  30    2  0.04
  31   18  0.33
  32    1  0.02

ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27


Consensus pattern (29 bp):   
CAAATAAGGGCCTGATCTTTTAATTTGAC

Found at i:10524 original size:60 final size:60

Alignment explanation


    Indices: 10452--10611  Score: 257
    Period size: 60  Copynumber: 2.7  Consensus size: 60

      10442 CTAATTGCTT

                   *           *        *             *                 
      10452 AAATAAGCGCCTAACGTTTTCCAAAATGTTCAAATAAGGGCCTGATCTTTTAATTTGACC
          1 AAATAAGAGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGACC

                                     *                  *               
      10512 AAATAAGAGCCTAACGTTTGCCAAAGTGCTCAAATAAGGGCCCGGTCTTTTAATTTGACC
          1 AAATAAGAGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGACC

                   *                                
      10572 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
          1 AAATAAGAGCCTAACGTTTGCCAAAATGCTCAAATAAGGG

      10612 TCTGGCATCG


Statistics
Matches: 92,  Mismatches: 8, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  60   92  1.00

ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27


Consensus pattern (60 bp):   
AAATAAGAGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGACC

Found at i:10609 original size:31 final size:30

Alignment explanation


    Indices: 10447--10611  Score: 92
    Period size: 31  Copynumber: 5.5  Consensus size: 30

      10437 TAAGGCTAAT

                *       *                  
      10447 TGCTTAAATAAGCGCCTAACGTTTTCCAAAA
          1 TGCTCAAATAAGGGCCTAACG-TTTCCAAAA

              *                *      *  **
      10478 TGTTCAAATAAGGGCCTGATC-TTT-TAATT
          1 TGCTCAAATAAGGGCCT-AACGTTTCCAAAA

                         *                 *
      10507 TGAC-CAAATAAGAGCCTAACGTTTGCCAAAG
          1 TG-CTCAAATAAGGGCCTAACGTTT-CCAAAA

                                      **  **
      10538 TGCTCAAATAAGGGCC---CGGTCTTTTAATT
          1 TGCTCAAATAAGGGCCTAAC-GT-TTCCAAAA

                                            
      10567 TGAC-CAAATAAGGGCCTAACGTTTGCCAAAA
          1 TG-CTCAAATAAGGGCCTAACGTTT-CCAAAA

                          
      10598 TGCTCAAATAAGGG
          1 TGCTCAAATAAGGG

      10612 TCTGGCATCG


Statistics
Matches: 98,  Mismatches: 22, Indels: 28
        0.66            0.15        0.19

Matches are distributed among these distances:
  28    3  0.03
  29   37  0.38
  30   10  0.10
  31   45  0.46
  32    3  0.03

ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28


Consensus pattern (30 bp):   
TGCTCAAATAAGGGCCTAACGTTTCCAAAA

Found at i:10782 original size:29 final size:29

Alignment explanation


    Indices: 10687--10815  Score: 138
    Period size: 29  Copynumber: 4.4  Consensus size: 29

      10677 AAATGTTAGG

                                          
      10687 CCCTTATTTTG-CCAAATTAAAAGATCGGA
          1 CCCTTA-TTTGACCAAATTAAAAGATCGGA

               *       *   *           * *   
      10716 CCCGTATTTGAGC-ATTTCCAATAACGTTAGG-
          1 CCCTTATTTGACCAAATT--AA-AA-GATCGGA

                                         
      10747 CCCTTATTTGACCAAATTAAAAGATCGGA
          1 CCCTTATTTGACCAAATTAAAAGATCGGA

                                      *  
      10776 CCCTTATTTGACCAAATTAAAAGATCAGA
          1 CCCTTATTTGACCAAATTAAAAGATCGGA

                       
      10805 CCCTTATTTGA
          1 CCCTTATTTGA

      10816 GCATTTTGGC


Statistics
Matches: 82,  Mismatches: 11, Indels: 14
        0.77            0.10        0.13

Matches are distributed among these distances:
  28   11  0.13
  29   47  0.57
  30    4  0.05
  31   13  0.16
  32    7  0.09

ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31


Consensus pattern (29 bp):   
CCCTTATTTGACCAAATTAAAAGATCGGA
Done.