Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010531.1 Corchorus capsularis cultivar CVL-1 contig10552, 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: 10908
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33


Found at i:5085 original size:12 final size:12

Alignment explanation


    Indices: 5070--5132  Score: 66
    Period size: 12  Copynumber: 5.7  Consensus size: 12

       5060 ATTATGCATG

                        
       5070 TTTTTATAGCTA
          1 TTTTTATAGCTA

                        
       5082 TTTTTATA--TA
          1 TTTTTATAGCTA

                         
       5092 GTTTTTATAGCTA
          1 -TTTTTATAGCTA

                        
       5105 TTTTTATA--TA
          1 TTTTTATAGCTA

            *           
       5115 CTTTT-T-GCTA
          1 TTTTTATAGCTA

                    
       5125 TTTTTATA
          1 TTTTTATA

       5133 TGTGTTTTTA


Statistics
Matches: 42,  Mismatches: 2, Indels: 14
        0.72            0.03        0.24

Matches are distributed among these distances:
   9    1  0.02
  10   14  0.33
  11    9  0.21
  12   16  0.38
  13    2  0.05

ACGTcount: A:0.24, C:0.06, G:0.06, T:0.63


Consensus pattern (12 bp):   
TTTTTATAGCTA

Found at i:5099 original size:23 final size:23

Alignment explanation


    Indices: 5069--5142  Score: 100
    Period size: 23  Copynumber: 3.3  Consensus size: 23

       5059 AATTATGCAT

                                   
       5069 GTTTTTATAGCTATTTTTATATA
          1 GTTTTTATAGCTATTTTTATATA

                                   
       5092 GTTTTTATAGCTATTTTTATATA
          1 GTTTTTATAGCTATTTTTATATA

             *                     *
       5115 -CTTTT-T-GCTATTTTTATATGT
          1 GTTTTTATAGCTATTTTTATAT-A

                   
       5136 GTTTTTA
          1 GTTTTTA

       5143 CCCTATTTTG


Statistics
Matches: 45,  Mismatches: 3, Indels: 6
        0.83            0.06        0.11

Matches are distributed among these distances:
  20   13  0.29
  21    1  0.02
  22    8  0.18
  23   23  0.51

ACGTcount: A:0.22, C:0.05, G:0.09, T:0.64


Consensus pattern (23 bp):   
GTTTTTATAGCTATTTTTATATA

Found at i:6681 original size:13 final size:13

Alignment explanation


    Indices: 6663--6689  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       6653 ATAATTATTG

                         
       6663 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

                         
       6676 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

             
       6689 T
          1 T

       6690 CTACTTTAGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63


Consensus pattern (13 bp):   
TTTGCTTTATTAA
Done.