Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004711.1 Corchorus capsularis cultivar CVL-1 contig04727, 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, 610

Length: 1017
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.25


Found at i:127 original size:6 final size:6

Alignment explanation


    Indices: 116--178  Score: 71
    Period size: 6  Copynumber: 11.2  Consensus size: 6

        106 GGGATCACTA

                                          *      *                 
        116 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT A-GAAT ACTAAT -CTAAT
          1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT

                   *              
        160 ACTAAT TCTAAT ACTAAT A
          1 ACTAAT ACTAAT ACTAAT A

        179 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:133 original size:11 final size:11

Alignment explanation


    Indices: 112--177  Score: 62
    Period size: 11  Copynumber: 5.5  Consensus size: 11

        102 AGCCGGGATC

                       
        112 ACTAA-CTAAT
          1 ACTAATCTAAT

                       
        122 ACTAATCTAAT
          1 ACTAATCTAAT

                     *      
        133 ACTAATAGAATAGAAT
          1 ACTAAT---CT--AAT

                       
        149 ACTAATCTAAT
          1 ACTAATCTAAT

                        
        160 ACTAATTCTAAT
          1 ACTAA-TCTAAT

                  
        172 ACTAAT
          1 ACTAAT

        178 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:176 original size:39 final size:37

Alignment explanation


    Indices: 112--186  Score: 132
    Period size: 39  Copynumber: 2.0  Consensus size: 37

        102 AGCCGGGATC

                                                 
        112 ACTAACTAATACTAATCTAATACTAATAGAATAGAAT
          1 ACTAACTAATACTAATCTAATACTAATAGAATAGAAT

                                                  
        149 ACTAATCTAATACTAATTCTAATACTAATAGAATAGAA
          1 ACTAA-CTAATACTAA-TCTAATACTAATAGAATAGAA

        187 AAAATAGAAT


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:194 original size:14 final size:14

Alignment explanation


    Indices: 175--202  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

        165 TTCTAATACT

                          
        175 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

                          
        189 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

        203 TACTAATAGA


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

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14


Consensus pattern (14 bp):   
AATAGAATAGAAAA

Found at i:212 original size:18 final size:18

Alignment explanation


    Indices: 169--219  Score: 74
    Period size: 18  Copynumber: 3.1  Consensus size: 18

        159 TACTAATTCT

                              
        169 AATACTAATAGAATAG-A
          1 AATACTAATAGAATAGAA

                              
        186 AA-A--AATAGAATAGAA
          1 AATACTAATAGAATAGAA

                              
        201 AATACTAATAGAATAGAA
          1 AATACTAATAGAATAGAA

             
        219 A
          1 A

        220 GAAAAGAACT


Statistics
Matches: 30,  Mismatches: 0, Indels: 7
        0.81            0.00        0.19

Matches are distributed among these distances:
  14   10  0.33
  15    3  0.10
  16    2  0.07
  17    2  0.07
  18   13  0.43

ACGTcount: A:0.65, C:0.04, G:0.12, T:0.20


Consensus pattern (18 bp):   
AATACTAATAGAATAGAA
Done.