Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014393.1 Corchorus capsularis cultivar CVL-1 contig14414, 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: 31350
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31


Found at i:7287 original size:37 final size:37

Alignment explanation


    Indices: 7234--7324  Score: 130
    Period size: 37  Copynumber: 2.5  Consensus size: 37

       7224 GATACTACCA

                       *        *                 
       7234 CACATACCAAACACCACCTTGGATTTAAGA-AGATTAC
          1 CACATACCAAATACCACCTTAGATTTAAGACA-ATTAC

                                                 
       7271 CACATACCAAATACCACCTTAGATTTAAGACAATTAC
          1 CACATACCAAATACCACCTTAGATTTAAGACAATTAC

                 *      *    
       7308 CACATTCCAAATGCCAC
          1 CACATACCAAATACCAC

       7325 TCGAAGGAAA


Statistics
Matches: 49,  Mismatches: 4, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  37   48  0.98
  38    1  0.02

ACGTcount: A:0.41, C:0.30, G:0.08, T:0.22


Consensus pattern (37 bp):   
CACATACCAAATACCACCTTAGATTTAAGACAATTAC

Found at i:13804 original size:31 final size:30

Alignment explanation


    Indices: 13751--13850  Score: 110
    Period size: 31  Copynumber: 3.3  Consensus size: 30

      13741 TTTTGTGCAC

                          *  *       *    
      13751 GTGGCATGCACGTGCCATTTTTTGAAACAT
          1 GTGGCATGCACGTGTCACTTTTTGATACAT

                                     *    *
      13781 GTGGCATGCCACGTGTCACTTTTTGGTACAC
          1 GTGGCATG-CACGTGTCACTTTTTGATACAT

               * *     *                   
      13812 GTGACGTGACATGTGTCACTTTTTGATACAT
          1 GTGGCATG-CACGTGTCACTTTTTGATACAT

                    
      13843 GTGGCATG
          1 GTGGCATG

      13851 ACTTTTTGGT


Statistics
Matches: 56,  Mismatches: 13, Indels: 1
        0.80            0.19        0.01

Matches are distributed among these distances:
  30    8  0.14
  31   48  0.86

ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34


Consensus pattern (30 bp):   
GTGGCATGCACGTGTCACTTTTTGATACAT

Found at i:13856 original size:53 final size:53

Alignment explanation


    Indices: 13798--13900  Score: 143
    Period size: 53  Copynumber: 1.9  Consensus size: 53

      13788 GCCACGTGTC

                                     **                 *        
      13798 ACTTTTTGGTACACGTGACGTGACATGTGTCACTTTTTGATACATGTGGCATG
          1 ACTTTTTGGTACACGTGACGTGACACATGTCACTTTTTGATACACGTGGCATG

                         *   *    *                *          
      13851 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
          1 ACTTTTTGGTACACGTGACGTGACACATGTCACTTTTTGATACACGTGGC

      13901 GTGCCACGTC


Statistics
Matches: 43,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  53   43  1.00

ACGTcount: A:0.18, C:0.19, G:0.25, T:0.37


Consensus pattern (53 bp):   
ACTTTTTGGTACACGTGACGTGACACATGTCACTTTTTGATACACGTGGCATG

Found at i:31303 original size:2 final size:2

Alignment explanation


    Indices: 31296--31350  Score: 110
    Period size: 2  Copynumber: 27.5  Consensus size: 2

      31286 CAAGAAAGGG

                                                                          
      31296 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

                               
      31338 GA GA GA GA GA GA G
          1 GA GA GA GA GA GA G


Statistics
Matches: 53,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   53  1.00

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


Consensus pattern (2 bp):   
GA

Done.