Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001598.1 Corchorus capsularis cultivar CVL-1 contig01598, 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: 4306
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36


Found at i:2285 original size:20 final size:21

Alignment explanation


    Indices: 2250--2292  Score: 70
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       2240 ATATTGTTAT

                                  
       2250 TCAATTCATTTTTTTAACTAAA
          1 TCAATTCA-TTTTTTAACTAAA

                                 
       2272 TCAATTCA-TTTTTAACTAAA
          1 TCAATTCATTTTTTAACTAAA

             
       2292 T
          1 T

       2293 TATTGTTGTG


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

Matches are distributed among these distances:
  20   13  0.62
  22    8  0.38

ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49


Consensus pattern (21 bp):   
TCAATTCATTTTTTAACTAAA

Found at i:3248 original size:19 final size:20

Alignment explanation


    Indices: 3213--3258  Score: 67
    Period size: 19  Copynumber: 2.4  Consensus size: 20

       3203 AAAAAAAACG

                                
       3213 GGGCGGGACAAGGCGGGGCA
          1 GGGCGGGACAAGGCGGGGCA

                      *         
       3233 GGGCGGGA-ATGGCGGGGCA
          1 GGGCGGGACAAGGCGGGGCA

            *      
       3252 AGGCGGG
          1 GGGCGGG

       3259 TTTTGCCATC


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  19   16  0.67
  20    8  0.33

ACGTcount: A:0.17, C:0.17, G:0.63, T:0.02


Consensus pattern (20 bp):   
GGGCGGGACAAGGCGGGGCA

Found at i:3465 original size:17 final size:17

Alignment explanation


    Indices: 3443--3475  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       3433 TTGAGAAAAA

                       *     
       3443 AAACTATTAACCTAAAC
          1 AAACTATTAACATAAAC

                            
       3460 AAACTATTAACATAAA
          1 AAACTATTAACATAAA

       3476 ATGTGTCTTG


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

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24


Consensus pattern (17 bp):   
AAACTATTAACATAAAC
Done.