Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015063.1 Corchorus olitorius cultivar O-4 contig15096, 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: 35666
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:12265 original size:18 final size:17

Alignment explanation


    Indices: 12242--12289  Score: 53
    Period size: 16  Copynumber: 2.8  Consensus size: 17

      12232 GAAGCTCCCT

                              
      12242 TTTTTTTCTCTCTTTCTC
          1 TTTTTTTCT-TCTTTCTC

                        *    
      12260 TTTTTTT-TTCTCTCTC
          1 TTTTTTTCTTCTTTCTC

               *          
      12276 TTTATTTCTATCTT
          1 TTTTTTTCT-TCTT

      12290 GGGTTTTTTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 4
        0.78            0.09        0.12

Matches are distributed among these distances:
  16   13  0.52
  17    2  0.08
  18   10  0.40

ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73


Consensus pattern (17 bp):   
TTTTTTTCTTCTTTCTC

Found at i:17672 original size:1 final size:1

Alignment explanation


    Indices: 17666--17691  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

      17656 CAATTGCAGG

                                      
      17666 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

      17692 GGCAAATAGA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:23601 original size:16 final size:16

Alignment explanation


    Indices: 23580--23613  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      23570 AAAAACCCAG

                  *      *  
      23580 AAGAAGGTAAAGATCA
          1 AAGAAGCTAAAGAGCA

                            
      23596 AAGAAGCTAAAGAGCA
          1 AAGAAGCTAAAGAGCA

              
      23612 AA
          1 AA

      23614 AAAGTTTCTT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.59, C:0.09, G:0.24, T:0.09


Consensus pattern (16 bp):   
AAGAAGCTAAAGAGCA

Found at i:24872 original size:142 final size:145

Alignment explanation


    Indices: 24598--24884  Score: 501
    Period size: 142  Copynumber: 2.0  Consensus size: 145

      24588 TTAAGTATAG

                                                                         *   
      24598 TCGAATTCAATTTTGTCCATTTATATTTGTTGTTTGTTTTCAAGGAAAATCTGTTTTTGCTTATT
          1 TCGAATTCAATTTTGTCCATTTATATTTGTTGTTTGTTTTCAAGGAAAATCTGTTTTTGCTCATT

                                                      *                 *    
      24663 CTTTCTTCCTTTGGTTTATGCAGGAAGAAGCTATTGCTACACGTTTGTCTTTTGTTTCTTTTCAA
         66 CTTTCTT-CTTTGGTTTATGCAGGAAGAAGCTATTGCTACACATTTGTCTTTTGTTTCTTGTCAA

                            
      24728 TCCAAACATAATAAAA
        130 TCCAAACATAATAAAA

                                                                             
      24744 TCGAATTCAATTTTGTCCATTTATATTTGTTGTTTGTTTTCAAGGAAAATCTGTTTTTGCTCATT
          1 TCGAATTCAATTTTGTCCATTTATATTTGTTGTTTGTTTTCAAGGAAAATCTGTTTTTGCTCATT

                                                                             
      24809 C-TTC-T-TTTGGTTTATGCAGGAAGAAGCTATTGCTACA-ATCTTGTCTTTTGTTTCTTGTCAA
         66 CTTTCTTCTTTGGTTTATGCAGGAAGAAGCTATTGCTACACAT-TTGTCTTTTGTTTCTTGTCAA

                           
      24870 TCCAAACATAATAAA
        130 TCCAAACATAATAAA

      24885 GTGTGCTACT


Statistics
Matches: 137,  Mismatches: 3, Indels: 6
        0.94            0.02        0.04

Matches are distributed among these distances:
 141    1  0.01
 142   67  0.49
 144    1  0.01
 145    3  0.02
 146   65  0.47

ACGTcount: A:0.24, C:0.15, G:0.14, T:0.47


Consensus pattern (145 bp):   
TCGAATTCAATTTTGTCCATTTATATTTGTTGTTTGTTTTCAAGGAAAATCTGTTTTTGCTCATT
CTTTCTTCTTTGGTTTATGCAGGAAGAAGCTATTGCTACACATTTGTCTTTTGTTTCTTGTCAAT
CCAAACATAATAAAA
Done.