Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003610.1 Corchorus capsularis cultivar CVL-1 contig03618, 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: 9040
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Found at i:494 original size:68 final size:68

Alignment explanation


    Indices: 409--540  Score: 237
    Period size: 68  Copynumber: 1.9  Consensus size: 68

        399 ATTTTTATCA

                                    **                                       
        409 AAAAGATTAATGAAGGAGGAAATTGTGGATCTAACATATTGTAATTAGAATGTAATTAATCAATC
          1 AAAAGATTAATGAAGGAGGAAATTACGGATCTAACATATTGTAATTAGAATGTAATTAATCAATC

               
        474 AAT
         66 AAT

                       *                                                    
        477 AAAAGATTAATTAAGGAGGAAATTACGGATCTAACATATTGTAATTAGAATGTAATTAATCAAT
          1 AAAAGATTAATGAAGGAGGAAATTACGGATCTAACATATTGTAATTAGAATGTAATTAATCAAT

        541 TAATTAGATA


Statistics
Matches: 61,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  68   61  1.00

ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31


Consensus pattern (68 bp):   
AAAAGATTAATGAAGGAGGAAATTACGGATCTAACATATTGTAATTAGAATGTAATTAATCAATC
AAT

Found at i:4003 original size:75 final size:75

Alignment explanation


    Indices: 3919--4091  Score: 188
    Period size: 75  Copynumber: 2.3  Consensus size: 75

       3909 GATGCTCAAA

                *                                                      *     
       3919 ATTTAAATTCGAATCAGAAACCTAATAAAGTGAATCAGCTTCAAGATGTTG-CAAATCATCATCA
          1 ATTTGAATTCGAATCAGAAACCTAATAAAGTGAATCAGCTTCAAGATGTTGCCAAA-CACCATCA

                   *   
       3983 GAAAACTTAGT
         65 GAAAACTCAGT

                      *  *          *  * *        *         *     *          
       3994 ATTTGAATTCAAAACAGGAAA-CTGATCAGGTGAATCATCTTCAAGATTTTGCCTAACACCATCA
          1 ATTTGAATTCGAATCA-GAAACCTAATAAAGTGAATCAGCTTCAAGATGTTGCCAAACACCATCA

                     * 
       4058 GAAAACTCATT
         65 GAAAACTCAGT

                          *  *     
       4069 ATTTGAATTCGAATTAGCAACCT
          1 ATTTGAATTCGAATCAGAAACCT

       4092 GAGAAGAGTT


Statistics
Matches: 79,  Mismatches: 16, Indels: 6
        0.78            0.16        0.06

Matches are distributed among these distances:
  74    3  0.04
  75   69  0.87
  76    7  0.09

ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29


Consensus pattern (75 bp):   
ATTTGAATTCGAATCAGAAACCTAATAAAGTGAATCAGCTTCAAGATGTTGCCAAACACCATCAG
AAAACTCAGT

Found at i:8938 original size:2 final size:2

Alignment explanation


    Indices: 8931--8970  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       8921 GTTGCTTTTG

                                                                       
       8931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       8971 GATAGTAACA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.