Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002359.1 Corchorus capsularis cultivar CVL-1 contig02365, 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, 650

Length: 1084
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25


Found at i:159 original size:6 final size:6

Alignment explanation


    Indices: 148--210  Score: 71
    Period size: 6  Copynumber: 11.2  Consensus size: 6

        138 GGAGTCACTA

                                          *      *                 
        148 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT A-GAAT ACTAAT -CTAAT
          1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT

                   *              
        192 ACTAAT TCTAAT ACTAAT A
          1 ACTAAT ACTAAT ACTAAT A

        211 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:165 original size:11 final size:11

Alignment explanation


    Indices: 144--209  Score: 62
    Period size: 11  Copynumber: 5.5  Consensus size: 11

        134 GCCGGGAGTC

                       
        144 ACTAA-CTAAT
          1 ACTAATCTAAT

                       
        154 ACTAATCTAAT
          1 ACTAATCTAAT

                     *      
        165 ACTAATAGAATAGAAT
          1 ACTAAT---CT--AAT

                       
        181 ACTAATCTAAT
          1 ACTAATCTAAT

                        
        192 ACTAATTCTAAT
          1 ACTAA-TCTAAT

                  
        204 ACTAAT
          1 ACTAAT

        210 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:208 original size:39 final size:37

Alignment explanation


    Indices: 144--218  Score: 132
    Period size: 39  Copynumber: 2.0  Consensus size: 37

        134 GCCGGGAGTC

                                                 
        144 ACTAACTAATACTAATCTAATACTAATAGAATAGAAT
          1 ACTAACTAATACTAATCTAATACTAATAGAATAGAAT

                                                  
        181 ACTAATCTAATACTAATTCTAATACTAATAGAATAGAA
          1 ACTAA-CTAATACTAA-TCTAATACTAATAGAATAGAA

        219 AAATAAGAAT


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
Done.