Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019540.1 Corchorus olitorius cultivar O-4 contig19573, 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: 15852
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32


Found at i:2937 original size:19 final size:19

Alignment explanation


    Indices: 2913--2955  Score: 86
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       2903 CCAATGAAAG

                               
       2913 GATATATAATAGAGCAACA
          1 GATATATAATAGAGCAACA

                               
       2932 GATATATAATAGAGCAACA
          1 GATATATAATAGAGCAACA

                 
       2951 GATAT
          1 GATAT

       2956 TCGCCAGAGG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   24  1.00

ACGTcount: A:0.51, C:0.09, G:0.16, T:0.23


Consensus pattern (19 bp):   
GATATATAATAGAGCAACA

Found at i:7961 original size:18 final size:18

Alignment explanation


    Indices: 7938--7972  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       7928 AGTTAATGTC

                              
       7938 GATGGGGATTCAAAAACT
          1 GATGGGGATTCAAAAACT

                             
       7956 GATGGGGATTCAAAAAC
          1 GATGGGGATTCAAAAAC

       7973 ATACAAGGTG


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

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.40, C:0.11, G:0.29, T:0.20


Consensus pattern (18 bp):   
GATGGGGATTCAAAAACT

Found at i:8774 original size:23 final size:23

Alignment explanation


    Indices: 8740--8784  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       8730 ATCTTCTAAT

                   *     *         
       8740 CAATCTATGGTATGTTAATCATC
          1 CAATCTACGGTATATTAATCATC

                                  
       8763 CAATCTACGGTATATTAATCAT
          1 CAATCTACGGTATATTAATCAT

       8785 TCATTCATAC


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38


Consensus pattern (23 bp):   
CAATCTACGGTATATTAATCATC

Found at i:10939 original size:2 final size:2

Alignment explanation


    Indices: 10932--10972  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      10922 TTTCTTAATC

                                                                         
      10932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      10973 AGAGAATTCA


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:13450 original size:28 final size:27

Alignment explanation


    Indices: 13408--13468  Score: 70
    Period size: 28  Copynumber: 2.2  Consensus size: 27

      13398 ACCAATTCTA

                     **            *     
      13408 GGGTAAAATGGTAATTTCT-TCATTATAG
          1 GGGTAAAATCATAATTT-TATCAATA-AG

                                       
      13436 GGGTAAAATCATAATTTTATCAATAAG
          1 GGGTAAAATCATAATTTTATCAATAAG

                  
      13463 GGGTAA
          1 GGGTAA

      13469 TATAGTAAAT


Statistics
Matches: 29,  Mismatches: 3, Indels: 3
        0.83            0.09        0.09

Matches are distributed among these distances:
  27    9  0.31
  28   20  0.69

ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34


Consensus pattern (27 bp):   
GGGTAAAATCATAATTTTATCAATAAG
Done.