Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014284.1 Corchorus capsularis cultivar CVL-1 contig14305, 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: 14680
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--59  Score: 118
    Period size: 2  Copynumber: 29.5  Consensus size: 2

                                                                          
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                     
         43 TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC T

         60 TTAAATTTTA


Statistics
Matches: 57,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   57  1.00

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


Consensus pattern (2 bp):   
TC

Found at i:4589 original size:1 final size:1

Alignment explanation


    Indices: 4583--4629  Score: 94
    Period size: 1  Copynumber: 47.0  Consensus size: 1

       4573 TTGATTAAAG

                                                           
       4583 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       4630 GACTTCTGTT


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   46  1.00

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


Consensus pattern (1 bp):   
T

Found at i:13838 original size:41 final size:40

Alignment explanation


    Indices: 13778--13856  Score: 113
    Period size: 41  Copynumber: 1.9  Consensus size: 40

      13768 ATTTATAACT

                      *                             
      13778 AGGGGCTAAATCTGAATTTAATTTCTTACCTTAATTATCA
          1 AGGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATCA

                           *         *  *          
      13818 AGGGGCCTAAACCTGGATTTAATTTGTTTCCTTAATTAT
          1 AGGGG-CTAAACCTGAATTTAATTTCTTACCTTAATTAT

      13857 TTGGAGGGAC


Statistics
Matches: 34,  Mismatches: 4, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  40    5  0.15
  41   29  0.85

ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41


Consensus pattern (40 bp):   
AGGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATCA

Found at i:14203 original size:2 final size:2

Alignment explanation


    Indices: 14196--14223  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      14186 AATGGGTAGA

                                                     
      14196 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

      14224 TACAAACATA


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

Done.