Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008513.1 Corchorus capsularis cultivar CVL-1 contig08534, 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: 2127
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33


Found at i:636 original size:33 final size:32

Alignment explanation


    Indices: 539--643  Score: 129
    Period size: 33  Copynumber: 3.2  Consensus size: 32

        529 TTACAAAGAG

                                           * 
        539 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
          1 TGTTTTAG-TGTTGTTTGCGATGATACTAAATC

              *   *            *    *        
        572 TAATTTGAGTGTTGTTTGCAATGACACTAAATC
          1 T-GTTTTAGTGTTGTTTGCGATGATACTAAATC

                              *              
        605 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
          1 TGTTTT-AGTGTTGTTTGCGATGATACTAAATC

                  
        638 TGTTTT
          1 TGTTTT

        644 GGATGCTAAT


Statistics
Matches: 60,  Mismatches: 10, Indels: 4
        0.81            0.14        0.05

Matches are distributed among these distances:
  32    3  0.05
  33   52  0.87
  34    5  0.08

ACGTcount: A:0.25, C:0.10, G:0.20, T:0.46


Consensus pattern (32 bp):   
TGTTTTAGTGTTGTTTGCGATGATACTAAATC

Found at i:742 original size:32 final size:33

Alignment explanation


    Indices: 662--776  Score: 160
    Period size: 33  Copynumber: 3.5  Consensus size: 33

        652 ATTGTTATGA

                                      *    * 
        662 AAATAATTCTGTTTTGGTTGATCATAACATTGC
          1 AAATAATTCTGTTTTGGTTGATCATAGCATTAC

             *              *                
        695 ACATAATTCTGTTTTGATTGATCATAGCATT-C
          1 AAATAATTCTGTTTTGGTTGATCATAGCATTAC

                      *           *         *
        727 AAATAATTCTATTTTGGTTGATTATAGCATTAA
          1 AAATAATTCTGTTTTGGTTGATCATAGCATTAC

                             
        760 AAATAATTCTGTTTTGG
          1 AAATAATTCTGTTTTGG

        777 ATGAAAAGAA


Statistics
Matches: 72,  Mismatches: 9, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  32   28  0.39
  33   44  0.61

ACGTcount: A:0.31, C:0.10, G:0.14, T:0.44


Consensus pattern (33 bp):   
AAATAATTCTGTTTTGGTTGATCATAGCATTAC

Found at i:1191 original size:30 final size:30

Alignment explanation


    Indices: 1155--1213  Score: 93
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       1145 CAAGGGGGAG

                       *                   
       1155 GGAATGATGCGCCCAAGG-CTTATTATGGAA
          1 GGAATGATGC-ACCAAGGACTTATTATGGAA

                                         
       1185 GGAATGATGCACCAAGGACTTATTATGGA
          1 GGAATGATGCACCAAGGACTTATTATGGA

       1214 CTTGAAGACA


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  29    6  0.22
  30   21  0.78

ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24


Consensus pattern (30 bp):   
GGAATGATGCACCAAGGACTTATTATGGAA
Done.