Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002033.1 Corchorus capsularis cultivar CVL-1 contig02037, 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, 690

Length: 1150
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:397 original size:6 final size:6

Alignment explanation


    Indices: 386--448  Score: 71
    Period size: 6  Copynumber: 11.2  Consensus size: 6

        376 GGGATCACTA

                                          *      *                 
        386 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT A-GAAT ACTAAT -CTAAT
          1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT

                   *              
        430 ACTAAT TCTAAT ACTAAT A
          1 ACTAAT ACTAAT ACTAAT A

        449 GAATAGAAAA


Statistics
Matches: 50,  Mismatches: 4, Indels: 6
        0.83            0.07        0.10

Matches are distributed among these distances:
   5   19  0.38
   6   31  0.62

ACGTcount: A:0.49, C:0.14, G:0.03, T:0.33


Consensus pattern (6 bp):   
ACTAAT

Found at i:403 original size:11 final size:11

Alignment explanation


    Indices: 382--447  Score: 62
    Period size: 11  Copynumber: 5.5  Consensus size: 11

        372 AGCCGGGATC

                       
        382 ACTAA-CTAAT
          1 ACTAATCTAAT

                       
        392 ACTAATCTAAT
          1 ACTAATCTAAT

                     *      
        403 ACTAATAGAATAGAAT
          1 ACTAAT---CT--AAT

                       
        419 ACTAATCTAAT
          1 ACTAATCTAAT

                        
        430 ACTAATTCTAAT
          1 ACTAA-TCTAAT

                  
        442 ACTAAT
          1 ACTAAT

        448 AGAATAGAAA


Statistics
Matches: 47,  Mismatches: 2, Indels: 13
        0.76            0.03        0.21

Matches are distributed among these distances:
  10    5  0.11
  11   20  0.43
  12   11  0.23
  13    1  0.02
  14    1  0.02
  16    9  0.19

ACGTcount: A:0.48, C:0.15, G:0.03, T:0.33


Consensus pattern (11 bp):   
ACTAATCTAAT

Found at i:446 original size:39 final size:37

Alignment explanation


    Indices: 382--456  Score: 132
    Period size: 39  Copynumber: 2.0  Consensus size: 37

        372 AGCCGGGATC

                                                 
        382 ACTAACTAATACTAATCTAATACTAATAGAATAGAAT
          1 ACTAACTAATACTAATCTAATACTAATAGAATAGAAT

                                                  
        419 ACTAATCTAATACTAATTCTAATACTAATAGAATAGAA
          1 ACTAA-CTAATACTAA-TCTAATACTAATAGAATAGAA

        457 AAAATGAATA


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  37    5  0.14
  38   10  0.28
  39   21  0.58

ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31


Consensus pattern (37 bp):   
ACTAACTAATACTAATCTAATACTAATAGAATAGAAT

Found at i:983 original size:13 final size:13

Alignment explanation


    Indices: 967--993  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

        957 GAAGGGAATA

                         
        967 AAATAAAAAAAAG
          1 AAATAAAAAAAAG

                         
        980 AAATAAAAAAAAG
          1 AAATAAAAAAAAG

             
        993 A
          1 A

        994 GGGGAAAAAA


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:0.85, C:0.00, G:0.07, T:0.07


Consensus pattern (13 bp):   
AAATAAAAAAAAG
Done.