Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021759.1 Corchorus olitorius cultivar O-4 contig21792, 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: 22485
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34


Found at i:135 original size:29 final size:30

Alignment explanation


    Indices: 63--137  Score: 98
    Period size: 31  Copynumber: 2.5  Consensus size: 30

         53 TAGACAAAAT

                        *                  
         63 ACAAAAAAGTCCTTTATGTTTTTCATTTGGG
          1 ACAAAAAAGTCCCTTATGTTTTT-ATTTGGG

                    *                     
         94 ACAAAAAAATCCCTTATGTTTTT-TTTGGG
          1 ACAAAAAAGTCCCTTATGTTTTTATTTGGG

                 **        
        123 ACAAATTAGTCCCTT
          1 ACAAAAAAGTCCCTT

        138 GCTGAGATGG


Statistics
Matches: 39,  Mismatches: 5, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  29   18  0.46
  31   21  0.54

ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40


Consensus pattern (30 bp):   
ACAAAAAAGTCCCTTATGTTTTTATTTGGG

Found at i:296 original size:29 final size:30

Alignment explanation


    Indices: 254--327  Score: 87
    Period size: 29  Copynumber: 2.5  Consensus size: 30

        244 CTCATTTTTG

                *                *  *     
        254 AAACGTAAGGGATTAATTTGTGCCGAAA-A
          1 AAACATAAGGGATTAATTTGTCCCAAAACA

                     *     *               
        283 AAACATAAGAGATTATTTTGTCCCAAAAGCA
          1 AAACATAAGGGATTAATTTGTCCCAAAA-CA

                          
        314 AAACATAAGGGATT
          1 AAACATAAGGGATT

        328 TTTTTGGCTA


Statistics
Matches: 37,  Mismatches: 6, Indels: 2
        0.82            0.13        0.04

Matches are distributed among these distances:
  29   23  0.62
  31   14  0.38

ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24


Consensus pattern (30 bp):   
AAACATAAGGGATTAATTTGTCCCAAAACA

Found at i:20731 original size:22 final size:23

Alignment explanation


    Indices: 20693--20735  Score: 70
    Period size: 22  Copynumber: 1.9  Consensus size: 23

      20683 AATCCTAATC

                                   
      20693 CTGGTACGAATAGTAAAACCTTT
          1 CTGGTACGAATAGTAAAACCTTT

                  *              
      20716 CTGGTAGGAA-AGTAAAACCT
          1 CTGGTACGAATAGTAAAACCT

      20736 ACTCCTTCTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  22   10  0.53
  23    9  0.47

ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26


Consensus pattern (23 bp):   
CTGGTACGAATAGTAAAACCTTT
Done.