Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014218.1 Corchorus capsularis cultivar CVL-1 contig14239, 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: 7203
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33


Found at i:3738 original size:60 final size:60

Alignment explanation


    Indices: 3580--3740  Score: 214
    Period size: 60  Copynumber: 2.7  Consensus size: 60

       3570 GCTAATTGTT

                    *   *        *                *    *       *      * 
       3580 CAAATAAGAGCCCAACGTTTGACAAAATGCTCAAATAAAGGCCTGATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC

            *                     * *                                   
       3640 GAAATAAGGGCCTAACGTTTGCTAGAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC
          1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC

                      *                  *           
       3700 CAAATAAGGGTCTAACGTTTGCCAAAATGTTCAAATAAGGG
          1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG

       3741 TCTGCTTCAT


Statistics
Matches: 86,  Mismatches: 15, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  60   86  1.00

ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26


Consensus pattern (60 bp):   
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC

Found at i:3812 original size:18 final size:18

Alignment explanation


    Indices: 3789--3824  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       3779 ATTTGAGCAT

                     *        
       3789 TTTCGATAATGTTAGGCC
          1 TTTCGATAACGTTAGGCC

                              
       3807 TTTCGATAACGTTAGGCC
          1 TTTCGATAACGTTAGGCC

       3825 ATTATTTGGC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36


Consensus pattern (18 bp):   
TTTCGATAACGTTAGGCC

Found at i:3858 original size:29 final size:29

Alignment explanation


    Indices: 3821--3890  Score: 113
    Period size: 29  Copynumber: 2.4  Consensus size: 29

       3811 GATAACGTTA

                                         
       3821 GGCCATTATTTGGCCAAATTAAATGATCG
          1 GGCCATTATTTGGCCAAATTAAATGATCG

                *                *       
       3850 GGCCCTTATTTGGCCAAATTAGATGATCG
          1 GGCCATTATTTGGCCAAATTAAATGATCG

                *       
       3879 GGCCTTTATTTG
          1 GGCCATTATTTG

       3891 AGCATTTTCG


Statistics
Matches: 38,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   38  1.00

ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34


Consensus pattern (29 bp):   
GGCCATTATTTGGCCAAATTAAATGATCG

Found at i:4377 original size:4 final size:4

Alignment explanation


    Indices: 4368--4401  Score: 54
    Period size: 4  Copynumber: 9.0  Consensus size: 4

       4358 AAAGAAGAAC

                                                        
       4368 AAGA AAGA AAGA AAGA AAGA AAGA AA-A AA-A AAGA
          1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA

       4402 TGAGCATAGC


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   3    6  0.21
   4   23  0.79

ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00


Consensus pattern (4 bp):   
AAGA

Done.