Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002479.1 Corchorus capsularis cultivar CVL-1 contig02485, 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, 600

Length: 1000
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35

Warning! 3 characters in sequence are not A, C, G, or T


Found at i:173 original size:17 final size:17

Alignment explanation


    Indices: 151--185  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        141 TTTGTTTTGT

                              
        151 AGTCT-ATCTAAAAGAAA
          1 AGTCTAATCTAAAA-AAA

                             
        168 AGTCTAATCTAAAAAAA
          1 AGTCTAATCTAAAAAAA

             
        185 A
          1 A

        186 AATAGGAGAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    9  0.53
  18    8  0.47

ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23


Consensus pattern (17 bp):   
AGTCTAATCTAAAAAAA

Found at i:186 original size:18 final size:17

Alignment explanation


    Indices: 151--186  Score: 54
    Period size: 18  Copynumber: 2.1  Consensus size: 17

        141 TTTGTTTTGT

                         *   
        151 AGTCTATCTAAAAGAAA
          1 AGTCTATCTAAAAAAAA

                              
        168 AGTCTAATCTAAAAAAAA
          1 AGTCT-ATCTAAAAAAAA

             
        186 A
          1 A

        187 ATAGGAGATC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    5  0.29
  18   12  0.71

ACGTcount: A:0.58, C:0.11, G:0.08, T:0.22


Consensus pattern (17 bp):   
AGTCTATCTAAAAAAAA

Found at i:799 original size:13 final size:13

Alignment explanation


    Indices: 781--818  Score: 53
    Period size: 12  Copynumber: 3.1  Consensus size: 13

        771 GCTGACAAAT

                         
        781 TACAATTATACAA
          1 TACAATTATACAA

                        *
        794 TACAATTATA-AG
          1 TACAATTATACAA

                         
        806 TACAATT-TACAA
          1 TACAATTATACAA

             
        818 T
          1 T

        819 TTATACCAAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  11    2  0.09
  12   10  0.45
  13   10  0.45

ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34


Consensus pattern (13 bp):   
TACAATTATACAA

Found at i:897 original size:15 final size:15

Alignment explanation


    Indices: 877--914  Score: 58
    Period size: 15  Copynumber: 2.5  Consensus size: 15

        867 TTTTTANCTA

                   *       
        877 TTATTTATATATTAT
          1 TTATTTAGATATTAT

                    *      
        892 TTATTTAGGTATTAT
          1 TTATTTAGATATTAT

                    
        907 TTATTTAG
          1 TTATTTAG

        915 TAAAAATTTN


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   21  1.00

ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63


Consensus pattern (15 bp):   
TTATTTAGATATTAT
Done.