Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007968.1 Corchorus capsularis cultivar CVL-1 contig07989, 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: 22575
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:2010 original size:12 final size:14

Alignment explanation


    Indices: 1982--2010  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

       1972 AACTGATTTA

                          
       1982 TTTACATATTAATT
          1 TTTACATATTAATT

                          
       1996 TTTAC-TATTAATT
          1 TTTACATATTAATT

              
       2009 TT
          1 TT

       2011 CTAATTAACA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   10  0.67
  14    5  0.33

ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62


Consensus pattern (14 bp):   
TTTACATATTAATT

Found at i:5446 original size:12 final size:12

Alignment explanation


    Indices: 5429--5453  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       5419 GAGATACCAA

                        
       5429 GAAGCAAAACTT
          1 GAAGCAAAACTT

                        
       5441 GAAGCAAAACTT
          1 GAAGCAAAACTT

             
       5453 G
          1 G

       5454 TGGAGCTAAC


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

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16


Consensus pattern (12 bp):   
GAAGCAAAACTT

Found at i:14719 original size:3 final size:3

Alignment explanation


    Indices: 14695--14739  Score: 56
    Period size: 3  Copynumber: 15.3  Consensus size: 3

      14685 ACCTTTTTTT

                         *       *            *                          
      14695 TTC TT- TTC TCC TTC TCC TTC TTC TTT TTC TTC TTC TTC TTC TTC T
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T

      14740 CCCCTTAGAC


Statistics
Matches: 35,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
   2    2  0.06
   3   33  0.94

ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTC

Found at i:17415 original size:15 final size:14

Alignment explanation


    Indices: 17370--17414  Score: 53
    Period size: 13  Copynumber: 3.4  Consensus size: 14

      17360 AAAACATATA

                          
      17370 ATATATTT-TAAAT
          1 ATATATTTATAAAT

                           
      17383 ATAT-TTATATAAA-
          1 ATATATT-TATAAAT

                          
      17396 ATATATTTAT-AAT
          1 ATATATTTATAAAT

                  
      17409 ATATAT
          1 ATATAT

      17415 AATATATTTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 8
        0.78            0.00        0.22

Matches are distributed among these distances:
  12    4  0.14
  13   18  0.64
  14    6  0.21

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (14 bp):   
ATATATTTATAAAT

Found at i:17459 original size:46 final size:46

Alignment explanation


    Indices: 17329--17459  Score: 155
    Period size: 46  Copynumber: 2.9  Consensus size: 46

      17319 ATATTTAAAC

                                                          
      17329 TATATTTTAAATTTTATTTA-TT-TATATAATAAAAAC--ATATAA
          1 TATATTTTAAATTTTATTTATTTATATATAATAAAAACATATATAA

                         *         * *     * * *  *        
      17371 TATATTTTAAA-TATATTTATATAAAATATATTTATAATATATATAA
          1 TATATTTTAAATTTTATTTAT-TTATATATAATAAAAACATATATAA

                                                       
      17417 TATATTTTAAATTTTATTTATTTATATATAATAAAAACATATA
          1 TATATTTTAAATTTTATTTATTTATATATAATAAAAACATATA

      17460 CTCCCTCTGT


Statistics
Matches: 69,  Mismatches: 14, Indels: 8
        0.76            0.15        0.09

Matches are distributed among these distances:
  41    7  0.10
  42   11  0.16
  43    1  0.01
  44    9  0.13
  46   33  0.48
  47    8  0.12

ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50


Consensus pattern (46 bp):   
TATATTTTAAATTTTATTTATTTATATATAATAAAAACATATATAA
Done.