Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013925.1 Corchorus capsularis cultivar CVL-1 contig13946, 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: 8643
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32


Found at i:7091 original size:41 final size:41

Alignment explanation


    Indices: 7046--7186  Score: 133
    Period size: 41  Copynumber: 3.4  Consensus size: 41

       7036 CTTGTGTTAC

                                                      
       7046 ATGTGCTT-AGGGAATTTGATATAGATGCCTCTATGTTATAA
          1 ATGTGCTTGA-GGAATTTGATATAGATGCCTCTATGTTATAA

                         *      * *  *        *        
       7087 ATGTGCTTGAGGACTTTAGAGAGAGTTGCC-CTTTTGTTATAA
          1 ATGTGCTTGAGGAATTT-GATATAGATGCCTC-TATGTTATAA

            *    *   *   *         *   *    *        
       7129 TTGTGTTTGGGGACTTTGATATAAATGTCTCTGTGTTATAA
          1 ATGTGCTTGAGGAATTTGATATAGATGCCTCTATGTTATAA

                             
       7170 ATGTGCTTGAGGAATTT
          1 ATGTGCTTGAGGAATTT

       7187 TGAAGAGAAT


Statistics
Matches: 78,  Mismatches: 18, Indels: 8
        0.75            0.17        0.08

Matches are distributed among these distances:
  41   44  0.56
  42   34  0.44

ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41


Consensus pattern (41 bp):   
ATGTGCTTGAGGAATTTGATATAGATGCCTCTATGTTATAA

Found at i:7940 original size:12 final size:13

Alignment explanation


    Indices: 7925--7958  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

       7915 AATCTAAATC

                   *     
       7925 TAAAGCAGATT-A
          1 TAAAGCAAATTAA

                         
       7937 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                     
       7950 TAAAGCAAA
          1 TAAAGCAAA

       7959 CAATAATTAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12   10  0.50
  13   10  0.50

ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21


Consensus pattern (13 bp):   
TAAAGCAAATTAA

Done.