Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014022.1 Corchorus olitorius cultivar O-4 contig14055, 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: 7935
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32


Found at i:882 original size:137 final size:138

Alignment explanation


    Indices: 680--939  Score: 373
    Period size: 137  Copynumber: 1.9  Consensus size: 138

        670 ACTTTTATAG

                                                                             
        680 TTTTACACAACTAAAAACGCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTAATTT
          1 TTTTACACAACTAAAAACGCTATTTTTATTTAATT-AA-CTAATATCCTTATAACTATTTAATTT

                          *                  *                 *             
        745 TTACCATTTTACTATTTTAATTAAAAAA-CTTATATATATTAGAAGTTTTTTAAATATACTTTTA
         64 TTACCATTTTACTAATTTAATTAAAAAATCTTAGATATATTAGAA-TTTTTAAAATATACTTTTA

                       
        809 TAGTCTTACAC
        128 TAGTCTTACAC

                  *          **                                 *      *     
        820 TTTTACTCAACTAAAAATTCTATTTTTTATTTAATT-A-TAATATCCTTATACCTATTTTATTTT
          1 TTTTACACAACTAAAAACGCTA-TTTTTATTTAATTAACTAATATCCTTATAACTATTTAATTTT

              **                                                     
        883 TATTATTTTACTAATTTAATTAAAAAATCTTAGATATATTAGAATTTTTAAAATATA
         65 TACCATTTTACTAATTTAATTAAAAAATCTTAGATATATTAGAATTTTTAAAATATA

        940 TTTCTTAAAT


Statistics
Matches: 108,  Mismatches: 10, Indels: 7
        0.86            0.08        0.06

Matches are distributed among these distances:
 137   60  0.56
 138   15  0.14
 139    1  0.01
 140   19  0.18
 141   13  0.12

ACGTcount: A:0.38, C:0.10, G:0.02, T:0.49


Consensus pattern (138 bp):   
TTTTACACAACTAAAAACGCTATTTTTATTTAATTAACTAATATCCTTATAACTATTTAATTTTT
ACCATTTTACTAATTTAATTAAAAAATCTTAGATATATTAGAATTTTTAAAATATACTTTTATAG
TCTTACAC

Found at i:1594 original size:16 final size:17

Alignment explanation


    Indices: 1559--1597  Score: 53
    Period size: 16  Copynumber: 2.4  Consensus size: 17

       1549 GGTTTTGGCA

                        *    
       1559 TCGGGTTCTTGGGTTAT
          1 TCGGGTTCTTGGATTAT

                           * 
       1576 TCGGGTT-TTGGATTTT
          1 TCGGGTTCTTGGATTAT

                  
       1592 TCGGGT
          1 TCGGGT

       1598 CTAGGGTTTG


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  16   13  0.65
  17    7  0.35

ACGTcount: A:0.05, C:0.10, G:0.36, T:0.49


Consensus pattern (17 bp):   
TCGGGTTCTTGGATTAT

Found at i:2103 original size:30 final size:30

Alignment explanation


    Indices: 2067--2128  Score: 106
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       2057 ATATTTATAT

                            *             
       2067 TGACTTTCCTCTTATATCCTCAAATTTTAA
          1 TGACTTTCCTCTTATACCCTCAAATTTTAA

                   *                      
       2097 TGACTTTTCTCTTATACCCTCAAATTTTAA
          1 TGACTTTCCTCTTATACCCTCAAATTTTAA

              
       2127 TG
          1 TG

       2129 GCTTATTAAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   30  1.00

ACGTcount: A:0.26, C:0.23, G:0.05, T:0.47


Consensus pattern (30 bp):   
TGACTTTCCTCTTATACCCTCAAATTTTAA

Found at i:3851 original size:61 final size:61

Alignment explanation


    Indices: 3756--3878  Score: 246
    Period size: 61  Copynumber: 2.0  Consensus size: 61

       3746 TCTTGACATC

                                                                         
       3756 GGGCGCATGGCAAAACTTGTCCTCATCATATTGAAAGACTGGATTCAAATAAAATGCAGCA
          1 GGGCGCATGGCAAAACTTGTCCTCATCATATTGAAAGACTGGATTCAAATAAAATGCAGCA

                                                                         
       3817 GGGCGCATGGCAAAACTTGTCCTCATCATATTGAAAGACTGGATTCAAATAAAATGCAGCA
          1 GGGCGCATGGCAAAACTTGTCCTCATCATATTGAAAGACTGGATTCAAATAAAATGCAGCA

             
       3878 G
          1 G

       3879 CATGTATATT


Statistics
Matches: 62,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  61   62  1.00

ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23


Consensus pattern (61 bp):   
GGGCGCATGGCAAAACTTGTCCTCATCATATTGAAAGACTGGATTCAAATAAAATGCAGCA
Done.