Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015820.1 Corchorus capsularis cultivar CVL-1 contig15841, 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: 11127
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31


Found at i:747 original size:15 final size:15

Alignment explanation


    Indices: 723--771  Score: 64
    Period size: 15  Copynumber: 3.3  Consensus size: 15

        713 GGAGAAAAGG

                 *         
        723 GGATCCCTTATCAAT
          1 GGATCTCTTATCAAT

                         * 
        738 GGATCTCTTAT-ACT
          1 GGATCTCTTATCAAT

                            
        752 GGAATCTCTTATCAAT
          1 GG-ATCTCTTATCAAT

                
        768 GGAT
          1 GGAT

        772 AAAGGAGAAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  14    4  0.14
  15   21  0.72
  16    4  0.14

ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37


Consensus pattern (15 bp):   
GGATCTCTTATCAAT

Found at i:2696 original size:68 final size:68

Alignment explanation


    Indices: 2587--2722  Score: 254
    Period size: 68  Copynumber: 2.0  Consensus size: 68

       2577 AAAACACCCT

                                                                 *   *       
       2587 TCATACGACAAGCATTATACTCTACTCAGGTGCGATAGCCAGAAGAAATACCCTGCATGGAGGAA
          1 TCATACGACAAGCATTATACTCTACTCAGGTGCGATAGCCAGAAGAAATACCCCGCAGGGAGGAA

               
       2652 GGC
         66 GGC

                                                                             
       2655 TCATACGACAAGCATTATACTCTACTCAGGTGCGATAGCCAGAAGAAATACCCCGCAGGGAGGAA
          1 TCATACGACAAGCATTATACTCTACTCAGGTGCGATAGCCAGAAGAAATACCCCGCAGGGAGGAA

               
       2720 GGC
         66 GGC

       2723 GTCTGTTTTG


Statistics
Matches: 66,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  68   66  1.00

ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18


Consensus pattern (68 bp):   
TCATACGACAAGCATTATACTCTACTCAGGTGCGATAGCCAGAAGAAATACCCCGCAGGGAGGAA
GGC

Found at i:8469 original size:21 final size:21

Alignment explanation


    Indices: 8442--8488  Score: 85
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       8432 CTTCATGATA

                                 
       8442 ACTTTGCAGACCATTATTTTT
          1 ACTTTGCAGACCATTATTTTT

            *                    
       8463 TCTTTGCAGACCATTATTTTT
          1 ACTTTGCAGACCATTATTTTT

                 
       8484 ACTTT
          1 ACTTT

       8489 TTTTTTTTGA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.21, C:0.19, G:0.09, T:0.51


Consensus pattern (21 bp):   
ACTTTGCAGACCATTATTTTT
Done.