Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004550.1 Corchorus capsularis cultivar CVL-1 contig04561, 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, 636

Length: 1061
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34


Found at i:79 original size:18 final size:18

Alignment explanation


    Indices: 56--117  Score: 70
    Period size: 22  Copynumber: 3.2  Consensus size: 18

         46 AAATTTTTTA

                              
         56 AAAATAAAATTTATATAT
          1 AAAATAAAATTTATATAT

                               
         74 AAAATAAAATTTTATATAT
          1 AAAATAAAA-TTTATATAT

                  *               
         93 ATATAAAAATATATTTATATAT
          1 A-A-AATAA-A-ATTTATATAT

               
        115 AAA
          1 AAA

        118 CGAAAAGAGG


Statistics
Matches: 38,  Mismatches: 1, Indels: 8
        0.81            0.02        0.17

Matches are distributed among these distances:
  18    9  0.24
  19   10  0.26
  20    2  0.05
  21    5  0.13
  22   11  0.29
  23    1  0.03

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (18 bp):   
AAAATAAAATTTATATAT

Found at i:91 original size:17 final size:17

Alignment explanation


    Indices: 46--91  Score: 67
    Period size: 18  Copynumber: 2.7  Consensus size: 17

         36 AATTTTTTAT

                   *         
         46 AAATTTTTTA-AAAATA
          1 AAATTTTATATAAAATA

                              
         62 AAATTTATATATAAAATA
          1 AAATTT-TATATAAAATA

                        
         80 AAATTTTATATA
          1 AAATTTTATATA

         92 TATATAAAAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  16    6  0.22
  17    9  0.33
  18   12  0.44

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (17 bp):   
AAATTTTATATAAAATA

Found at i:108 original size:23 final size:22

Alignment explanation


    Indices: 67--115  Score: 64
    Period size: 23  Copynumber: 2.2  Consensus size: 22

         57 AAATAAAATT

                                   
         67 TATATATAAAATAAAATTTTATA
          1 TATATATAAAATAAAA-TTTATA

                           *       
         90 TATATATAAAA-ATATATTTATA
          1 TATATATAAAATA-AAATTTATA

                
        112 TATA
          1 TATA

        116 AACGAAAAGA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  22   11  0.46
  23   13  0.54

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (22 bp):   
TATATATAAAATAAAATTTATA

Found at i:829 original size:14 final size:14

Alignment explanation


    Indices: 812--842  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

        802 GATGGATATA

                          
        812 TATCGTATAATTCT
          1 TATCGTATAATTCT

                          
        826 TATCGTATAATTCT
          1 TATCGTATAATTCT

               
        840 TAT
          1 TAT

        843 ATATTGTACA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52


Consensus pattern (14 bp):   
TATCGTATAATTCT
Done.