Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004884.1 Corchorus capsularis cultivar CVL-1 contig04902, 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: 10426
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35


Found at i:10 original size:2 final size:2

Alignment explanation


    Indices: 4--31  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

          1 TTC

                                                     
          4 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         32 GTATGACACT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:3316 original size:27 final size:28

Alignment explanation


    Indices: 3260--3316  Score: 105
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       3250 TAACTATTCA

                                        
       3260 TTTTGGGACAAATTGGCCCCTCAACTTT
          1 TTTTGGGACAAATTGGCCCCTCAACTTT

                                 *      
       3288 TTTTGGGACAAATTGGCCCCTTAACTTT
          1 TTTTGGGACAAATTGGCCCCTCAACTTT

             
       3316 T
          1 T

       3317 AAAAACGAGA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  28   28  1.00

ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39


Consensus pattern (28 bp):   
TTTTGGGACAAATTGGCCCCTCAACTTT

Found at i:4043 original size:29 final size:30

Alignment explanation


    Indices: 4008--4088  Score: 110
    Period size: 29  Copynumber: 2.7  Consensus size: 30

       3998 TCTCGTTTTT

                                  *       
       4008 AAAAGTTAAGGGGCCAATTTGTTCCAAAA-
          1 AAAAGTTAAGGGGCCAATTTGTCCCAAAAG

                                           
       4037 AAAAGTTAAGGGGCCAATTTGTCCCAAAATG
          1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA-G

            * *           *      
       4068 GATAGTTAAGGGGCTAATTTG
          1 AAAAGTTAAGGGGCCAATTTG

       4089 GGTATTAAGC


Statistics
Matches: 46,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  29   28  0.61
  31   18  0.39

ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26


Consensus pattern (30 bp):   
AAAAGTTAAGGGGCCAATTTGTCCCAAAAG

Found at i:9682 original size:31 final size:31

Alignment explanation


    Indices: 9644--9720  Score: 111
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       9634 TATATTAAAC

                                           
       9644 AAATAAGGATATAATAAAAATATTAAAAGTT
          1 AAATAAGGATATAATAAAAATATTAAAAGTT

                       *    **             
       9675 AAATAAGGATAAAATAGGAATATTAAAAGTT
          1 AAATAAGGATATAATAAAAATATTAAAAGTT

                            
       9706 AAATAA-GAGTATAAT
          1 AAATAAGGA-TATAAT

       9721 GGCAATTCAA


Statistics
Matches: 41,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  30    2  0.05
  31   39  0.95

ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27


Consensus pattern (31 bp):   
AAATAAGGATATAATAAAAATATTAAAAGTT
Done.