Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006967.1 Corchorus capsularis cultivar CVL-1 contig06988, 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: 16226
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:3326 original size:30 final size:30

Alignment explanation


    Indices: 3285--3347  Score: 83
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       3275 TCTTCAAGGG

                *       *                  
       3285 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
          1 GGAGAGAATGATACG-CCAAGGACTTATCAT

                                       *  
       3315 GGAGAGAATGATACGCCAAGGACTTATTAT
          1 GGAGAGAATGATACGCCAAGGACTTATCAT

               
       3345 GGA
          1 GGA

       3348 CTTGAAGACA


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  29    6  0.21
  30   23  0.79

ACGTcount: A:0.32, C:0.16, G:0.32, T:0.21


Consensus pattern (30 bp):   
GGAGAGAATGATACGCCAAGGACTTATCAT

Found at i:13264 original size:20 final size:21

Alignment explanation


    Indices: 13239--13286  Score: 62
    Period size: 20  Copynumber: 2.3  Consensus size: 21

      13229 TAAACAGATT

                     *        *  
      13239 AATTAAAAAGAAAGC-AATTA
          1 AATTAAAAACAAAGCAAAGTA

                        *        
      13259 AATTAAAAACAAGGCAAAGTA
          1 AATTAAAAACAAAGCAAAGTA

                   
      13280 AATTAAA
          1 AATTAAA

      13287 TCTAAATCTA


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  20   13  0.54
  21   11  0.46

ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19


Consensus pattern (21 bp):   
AATTAAAAACAAAGCAAAGTA

Found at i:14852 original size:242 final size:244

Alignment explanation


    Indices: 14425--14912  Score: 890
    Period size: 242  Copynumber: 2.0  Consensus size: 244

      14415 GTCAAACAAG

                                                                             
      14425 GTGATACAAATCTAGTTGTATTAGATTCAAATCCACCCTTTGAATATCCACCAAAGTCGACTTGA
          1 GTGATACAAATCTAGTTGTATTAGATTCAAATCCACCCTTTGAATATCCACCAAAGTCGACTTGA

                                                                             
      14490 ACTTCTTCAACTCCTAGACTTGTATGTCGATGACCTTCACAAAGCTATCCCTCCTCTTTCGTCGG
         66 ACTTCTTCAACTCCTAGACTTGTATGTCGATGACCTTCACAAAGCTATCCCTCCTCTTTCGTCGG

                                *                                            
      14555 ACTTAAGCACTCAATTAGACTTGCAATTGAATTCTCAAGATCACAAGATTCACAAACAACTAAGT
        131 ACTTAAGCACTCAATTAGACCTGCAATTGAATTCTCAAGATCACAAGATTCACAAACAACTAAGT

                                                    *        
      14620 TATCTCAACCTAATTGCTTGCTAGGACTCTACAAGATGAAGAACCCTAA
        196 TATCTCAACCTAATTGCTTGCTAGGACTCTACAAGATGAACAACCCTAA

                   *                                                         
      14669 GTGATACGAATCTAGTTGTATTAGATTCAAAT-C-CCCTTTGAATATCCACCAAAGTCGACTTGA
          1 GTGATACAAATCTAGTTGTATTAGATTCAAATCCACCCTTTGAATATCCACCAAAGTCGACTTGA

                                                                 *           
      14732 ACTTCTTCAACTCCTAGACTTGTATGTCGATGACCTTCACAAAGCTATCCCTCTTCTTTCGTCGG
         66 ACTTCTTCAACTCCTAGACTTGTATGTCGATGACCTTCACAAAGCTATCCCTCCTCTTTCGTCGG

            *      *                                                         
      14797 CCTTAAGTACTCAATTAGACCTGCAATTGAATTCTCAAGATCACAAGATTCACAAACAACTAAGT
        131 ACTTAAGCACTCAATTAGACCTGCAATTGAATTCTCAAGATCACAAGATTCACAAACAACTAAGT

                                               *      *      
      14862 TATCTCAACCTAATTGCTTGCTAGGACTCTACAAGGTGAACAGCCCTAA
        196 TATCTCAACCTAATTGCTTGCTAGGACTCTACAAGATGAACAACCCTAA

              
      14911 GT
          1 GT

      14913 TTGCTCAAAC


Statistics
Matches: 236,  Mismatches: 8, Indels: 2
        0.96            0.03        0.01

Matches are distributed among these distances:
 242  204  0.86
 243    1  0.00
 244   31  0.13

ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30


Consensus pattern (244 bp):   
GTGATACAAATCTAGTTGTATTAGATTCAAATCCACCCTTTGAATATCCACCAAAGTCGACTTGA
ACTTCTTCAACTCCTAGACTTGTATGTCGATGACCTTCACAAAGCTATCCCTCCTCTTTCGTCGG
ACTTAAGCACTCAATTAGACCTGCAATTGAATTCTCAAGATCACAAGATTCACAAACAACTAAGT
TATCTCAACCTAATTGCTTGCTAGGACTCTACAAGATGAACAACCCTAA
Done.