Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014859.1 Corchorus capsularis cultivar CVL-1 contig14880, 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: 16101
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37


Found at i:543 original size:17 final size:17

Alignment explanation


    Indices: 521--554  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

        511 GATCTATTAG

                             
        521 TTTACACAATTAGATTT
          1 TTTACACAATTAGATTT

                   **        
        538 TTTACACTGTTAGATTT
          1 TTTACACAATTAGATTT

        555 CAAGATATTA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50


Consensus pattern (17 bp):   
TTTACACAATTAGATTT

Found at i:3656 original size:31 final size:31

Alignment explanation


    Indices: 3618--3695  Score: 156
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       3608 CATTAACTAC

                                           
       3618 CAGAAGATTGGGTTTACTAGCATATTATTAG
          1 CAGAAGATTGGGTTTACTAGCATATTATTAG

                                           
       3649 CAGAAGATTGGGTTTACTAGCATATTATTAG
          1 CAGAAGATTGGGTTTACTAGCATATTATTAG

                            
       3680 CAGAAGATTGGGTTTA
          1 CAGAAGATTGGGTTTA

       3696 TCAAAGCTGG


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   47  1.00

ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35


Consensus pattern (31 bp):   
CAGAAGATTGGGTTTACTAGCATATTATTAG

Found at i:6635 original size:1 final size:1

Alignment explanation


    Indices: 6631--6665  Score: 61
    Period size: 1  Copynumber: 35.0  Consensus size: 1

       6621 TCTTTTTTTT

                 *                             
       6631 GGGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
          1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

       6666 TGTTAGATCA


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

Matches are distributed among these distances:
   1   32  1.00

ACGTcount: A:0.00, C:0.03, G:0.97, T:0.00


Consensus pattern (1 bp):   
G

Found at i:15683 original size:13 final size:13

Alignment explanation


    Indices: 15667--15691  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      15657 TTGGATTTCC

                         
      15667 AAATAATATTTAT
          1 AAATAATATTTAT

                        
      15680 AAATAATATTTA
          1 AAATAATATTTA

      15692 GAACATTGAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (13 bp):   
AAATAATATTTAT
Done.