Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008721.1 Corchorus capsularis cultivar CVL-1 contig08742, 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: 18076
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:45 original size:30 final size:30

Alignment explanation


    Indices: 1--127  Score: 200
    Period size: 30  Copynumber: 4.2  Consensus size: 30

                                           
          1 GTCATGATTTTTGCAATTGACACCAGAAGTT
          1 GTCATGA-TTTTGCAATTGACACCAGAAGTT

                                          
         32 GTCATGATTTTGCAATTGACACCAGAAGTT
          1 GTCATGATTTTGCAATTGACACCAGAAGTT

                                  **    * 
         62 GTCATGATTTTGCAATTGACACTTGAAGAT
          1 GTCATGATTTTGCAATTGACACCAGAAGTT

                        *                  
         92 GTCATGATTTATTCAATTGACACCAGAAGTT
          1 GTCATGATTT-TGCAATTGACACCAGAAGTT

                 
        123 GTCAT
          1 GTCAT

        128 ATACACCATG


Statistics
Matches: 88,  Mismatches: 7, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  30   60  0.68
  31   28  0.32

ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35


Consensus pattern (30 bp):   
GTCATGATTTTGCAATTGACACCAGAAGTT

Found at i:113 original size:61 final size:61

Alignment explanation


    Indices: 1--127  Score: 202
    Period size: 61  Copynumber: 2.1  Consensus size: 61

                                         *                               
          1 GTCATGATTTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTT
          1 GTCATGATTTTTGCAATTGACACCAGAAGATGTCATGATTTTGCAATTGACACCAGAAGTT

                                   **                  *                  
         62 GTCATGA-TTTTGCAATTGACACTTGAAGATGTCATGATTTATTCAATTGACACCAGAAGTT
          1 GTCATGATTTTTGCAATTGACACCAGAAGATGTCATGATTT-TGCAATTGACACCAGAAGTT

                 
        123 GTCAT
          1 GTCAT

        128 ATACACCATG


Statistics
Matches: 61,  Mismatches: 4, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  60   30  0.49
  61   31  0.51

ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35


Consensus pattern (61 bp):   
GTCATGATTTTTGCAATTGACACCAGAAGATGTCATGATTTTGCAATTGACACCAGAAGTT

Found at i:389 original size:118 final size:118

Alignment explanation


    Indices: 181--418  Score: 413
    Period size: 118  Copynumber: 2.0  Consensus size: 118

        171 ATAACTAATT

                                             *                               
        181 CCCATTTGACACTAGAAGTTATCATTGTGCTTTGATTACATGACTAGACAAATTCTGTCTAAGGA
          1 CCCATTTGACACTAGAAGTTATCATTGTGCTTTAATTACATGACTAGACAAATTCTGTCTAAGGA

                        *                                *       
        246 GTTGGATTTTAAGTGAGACCGTTTGTGACTCCTCCATCTTTCCTGGGAATTTA
         66 GTTGGATTTTAACTGAGACCGTTTGTGACTCCTCCATCTTTCCTGAGAATTTA

                                *                     *    *                 
        299 CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
          1 CCCATTTGACACTAGAAGTTATCATTGTGCTTTAATTACATGACTAGACAAATTCTGTCTAAGGA

                              *                                  
        364 GTTGGATTTTAACTGAGATCGTTTGTGACTCCTCCATCTTTCCTGAGAATTTA
         66 GTTGGATTTTAACTGAGACCGTTTGTGACTCCTCCATCTTTCCTGAGAATTTA

              
        417 CC
          1 CC

        419 TGGTGTAATT


Statistics
Matches: 113,  Mismatches: 7, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 118  113  1.00

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


Consensus pattern (118 bp):   
CCCATTTGACACTAGAAGTTATCATTGTGCTTTAATTACATGACTAGACAAATTCTGTCTAAGGA
GTTGGATTTTAACTGAGACCGTTTGTGACTCCTCCATCTTTCCTGAGAATTTA

Found at i:18012 original size:2 final size:2

Alignment explanation


    Indices: 18005--18037  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      17995 ATATTTAATT

                                                             
      18005 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      18038 GAGAGGGCGG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.