Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007862.1 Corchorus capsularis cultivar CVL-1 contig07883, 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: 4068
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33


Found at i:2683 original size:6 final size:6

Alignment explanation


    Indices: 2658--2706  Score: 53
    Period size: 6  Copynumber: 7.5  Consensus size: 6

       2648 TTTATCCTCT

                        *                                           
       2658 TTTTCA TTTTCC TTCATTCA TTTTCA TTTTCA TTTTTTCA TTTTCA TTT
          1 TTTTCA TTTTCA TT--TTCA TTTTCA TTTTCA --TTTTCA TTTTCA TTT

       2707 ATATGGAAAT


Statistics
Matches: 37,  Mismatches: 2, Indels: 8
        0.79            0.04        0.17

Matches are distributed among these distances:
   6   26  0.70
   8   11  0.30

ACGTcount: A:0.14, C:0.18, G:0.00, T:0.67


Consensus pattern (6 bp):   
TTTTCA

Found at i:2683 original size:20 final size:20

Alignment explanation


    Indices: 2658--2706  Score: 71
    Period size: 20  Copynumber: 2.5  Consensus size: 20

       2648 TTTATCCTCT

                       *        
       2658 TTTTCATTTTCCTTCATTCA
          1 TTTTCATTTTCATTCATTCA

                          **    
       2678 TTTTCATTTTCATTTTTTCA
          1 TTTTCATTTTCATTCATTCA

                     
       2698 TTTTCATTT
          1 TTTTCATTT

       2707 ATATGGAAAT


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   26  1.00

ACGTcount: A:0.14, C:0.18, G:0.00, T:0.67


Consensus pattern (20 bp):   
TTTTCATTTTCATTCATTCA

Found at i:2695 original size:14 final size:14

Alignment explanation


    Indices: 2678--2706  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       2668 CCTTCATTCA

                          
       2678 TTTTCATTTTCATT
          1 TTTTCATTTTCATT

                          
       2692 TTTTCATTTTCATT
          1 TTTTCATTTTCATT

             
       2706 T
          1 T

       2707 ATATGGAAAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72


Consensus pattern (14 bp):   
TTTTCATTTTCATT

Found at i:2932 original size:69 final size:70

Alignment explanation


    Indices: 2783--3030  Score: 399
    Period size: 70  Copynumber: 3.5  Consensus size: 70

       2773 GTCTTGGAAG

                     *                               *      *                
       2783 ACTGACTTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATTCTTGGATGGAACCAAG
          1 ACTGAC-TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCGCTGAATACTTGGATGGAACCAAG

                  
       2848 GCTTGA
         65 GCTTGA

                                                         * *               * 
       2854 ACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCGCTG-CTGCTTGGATGGAACCAAAG
          1 ACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCGCTGAATACTTGGATGGAACCAAGG

                 
       2918 CTTGA
         66 CTTGA

                                                                             
       2923 ACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCGCTGAATACTTGGATGGAACCAAGG
          1 ACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCGCTGAATACTTGGATGGAACCAAGG

                 
       2988 CTTGA
         66 CTTGA

               *                     *   *        
       2993 ACTTACTCGTATGGAAACGAGTTTGACTTATGGAAAAG
          1 ACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG

       3031 TCGAAGCATT


Statistics
Matches: 165,  Mismatches: 11, Indels: 3
        0.92            0.06        0.02

Matches are distributed among these distances:
  69   66  0.40
  70   93  0.56
  71    6  0.04

ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26


Consensus pattern (70 bp):   
ACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCGCTGAATACTTGGATGGAACCAAGG
CTTGA

Found at i:3598 original size:50 final size:50

Alignment explanation


    Indices: 3493--3591  Score: 146
    Period size: 50  Copynumber: 2.0  Consensus size: 50

       3483 AAAATGCCCT

                               *                              
       3493 TTGAAAAGCAAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATC
          1 TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAATGCAATCTTATC

                   * *              *                         
       3543 TTGAAAATCGAATTTTGATATTGGTCAT-ACAAATGGAATGCAATCTTAT
          1 TTGAAAAGCAAATTTTGATATTGGAC-TCACAAATGGAATGCAATCTTAT

       3592 TGTGAAACTT


Statistics
Matches: 44,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  50   43  0.98
  51    1  0.02

ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34


Consensus pattern (50 bp):   
TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAATGCAATCTTATC
Done.