Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010455.1 Corchorus capsularis cultivar CVL-1 contig10476, 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: 12831
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37


Found at i:2498 original size:16 final size:16

Alignment explanation


    Indices: 2460--2564  Score: 151
    Period size: 16  Copynumber: 6.6  Consensus size: 16

       2450 GGCAATTGGG

                         *  
       2460 CGGGTTCGGGTA-CTT
          1 CGGGTTCGGGTATTTT

             *              
       2475 CAGGTTCGGGTATTTT
          1 CGGGTTCGGGTATTTT

                            
       2491 CGGGTTCGGGTATTTT
          1 CGGGTTCGGGTATTTT

                             
       2507 CGGGTTCGGG-ATTTTT
          1 CGGGTTCGGGTA-TTTT

                       *    
       2523 CGGGTTCGGGTTTTTT
          1 CGGGTTCGGGTATTTT

                     *      
       2539 CGGGTTCGGATATTTT
          1 CGGGTTCGGGTATTTT

                      
       2555 CGGGTTCGGG
          1 CGGGTTCGGG

       2565 CTCGGGTCGG


Statistics
Matches: 80,  Mismatches: 7, Indels: 5
        0.87            0.08        0.05

Matches are distributed among these distances:
  15   12  0.15
  16   68  0.85

ACGTcount: A:0.07, C:0.14, G:0.38, T:0.41


Consensus pattern (16 bp):   
CGGGTTCGGGTATTTT

Found at i:2562 original size:6 final size:6

Alignment explanation


    Indices: 2553--2590  Score: 60
    Period size: 6  Copynumber: 6.5  Consensus size: 6

       2543 TTCGGATATT

                          *                              
       2553 TTCGGG TTCGGG CTCGGG -TCGGG TTCGGG TTCGGG TTC
          1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTC

       2591 ACTTTCAATA


Statistics
Matches: 30,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
   5    5  0.17
   6   25  0.83

ACGTcount: A:0.00, C:0.21, G:0.47, T:0.32


Consensus pattern (6 bp):   
TTCGGG

Found at i:2576 original size:17 final size:17

Alignment explanation


    Indices: 2554--2588  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       2544 TCGGATATTT

                             
       2554 TCGGGTTCGGGCTCGGG
          1 TCGGGTTCGGGCTCGGG

                       *     
       2571 TCGGGTTCGGGTTCGGG
          1 TCGGGTTCGGGCTCGGG

             
       2588 T
          1 T

       2589 TCACTTTCAA


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

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.00, C:0.20, G:0.51, T:0.29


Consensus pattern (17 bp):   
TCGGGTTCGGGCTCGGG

Found at i:3572 original size:2 final size:2

Alignment explanation


    Indices: 3565--3591  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       3555 TGTTTAATTG

                                                    
       3565 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

       3592 CTTATACTAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:5782 original size:1 final size:1

Alignment explanation


    Indices: 5776--5801  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

       5766 CAAGTTTGGA

                                      
       5776 TTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTT

       5802 GCATATTATA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:10298 original size:14 final size:14

Alignment explanation


    Indices: 10279--10305  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

      10269 CATAATCAGC

                          
      10279 TACTTATGTAGTAG
          1 TACTTATGTAGTAG

                         
      10293 TACTTATGTAGTA
          1 TACTTATGTAGTA

      10306 ACTGATTCCT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44


Consensus pattern (14 bp):   
TACTTATGTAGTAG
Done.