Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009590.1 Corchorus capsularis cultivar CVL-1 contig09611, 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: 20026
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:70 original size:25 final size:24

Alignment explanation


    Indices: 23--70  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

         13 CTCCTCGTTC

                            *       
         23 TTTAAAGTTTTTTTTTCGTTTTTT
          1 TTTAAAGTTTTTTTTTAGTTTTTT

                                    
         47 TTTAAGAGTTTTTTTTTTAGTTTT
          1 TTTAA-AG-TTTTTTTTTAGTTTT

         71 CTTTGTTATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24    5  0.24
  25    2  0.10
  26   14  0.67

ACGTcount: A:0.15, C:0.02, G:0.10, T:0.73


Consensus pattern (24 bp):   
TTTAAAGTTTTTTTTTAGTTTTTT

Found at i:3700 original size:3 final size:3

Alignment explanation


    Indices: 3692--3719  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       3682 TTTTTGAATC

                                                 
       3692 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G

       3720 GGAGAGAGAG


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

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00


Consensus pattern (3 bp):   
GAA

Found at i:8661 original size:1 final size:1

Alignment explanation


    Indices: 8655--8684  Score: 51
    Period size: 1  Copynumber: 30.0  Consensus size: 1

       8645 TGATATATAT

                   *                      
       8655 AAAAAAAGAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       8685 GAATTTGTTG


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   1   27  1.00

ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00


Consensus pattern (1 bp):   
A

Found at i:8769 original size:30 final size:29

Alignment explanation


    Indices: 8713--8769  Score: 69
    Period size: 30  Copynumber: 1.9  Consensus size: 29

       8703 ATTGCAAATA

                   *      *      *       
       8713 TTTTAAGTACATGGTAAAAGTGTAAATCT
          1 TTTTAAGGACATGGCAAAAGTATAAATCT

                                *       
       8742 TTTTAGAGGACATGGCAAAATTATAAAT
          1 TTTTA-AGGACATGGCAAAAGTATAAAT

       8770 TTTCACCTAC


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  29    5  0.22
  30   18  0.78

ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35


Consensus pattern (29 bp):   
TTTTAAGGACATGGCAAAAGTATAAATCT

Found at i:11572 original size:52 final size:51

Alignment explanation


    Indices: 11509--11609  Score: 159
    Period size: 52  Copynumber: 2.0  Consensus size: 51

      11499 GAATTTCTTC

                                                                 
      11509 ATAGCCTTTATCTTTCATATTTTCACAAAAA-AAAAAACAAACAAACAAACAA
          1 ATAGCCTTTATCTTTCATATTTTCACAAAAACAAAAAA-AAA-AAACAAACAA

                *                             *              
      11561 ATAGTCTTTATCTTTCATATTTTCACAAAAACAACAAAAAAAAACAAAC
          1 ATAGCCTTTATCTTTCATATTTTCACAAAAACAAAAAAAAAAAACAAAC

      11610 TTTTATATGA


Statistics
Matches: 46,  Mismatches: 2, Indels: 3
        0.90            0.04        0.06

Matches are distributed among these distances:
  51    8  0.17
  52   33  0.72
  53    5  0.11

ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27


Consensus pattern (51 bp):   
ATAGCCTTTATCTTTCATATTTTCACAAAAACAAAAAAAAAAAACAAACAA

Found at i:19560 original size:16 final size:16

Alignment explanation


    Indices: 19536--19573  Score: 58
    Period size: 16  Copynumber: 2.4  Consensus size: 16

      19526 TTGATTAATT

                     *      
      19536 ATAAAAAAATAATAAA
          1 ATAAAAAAAAAATAAA

                *           
      19552 ATAATAAAAAAATAAA
          1 ATAAAAAAAAAATAAA

                  
      19568 ATAAAA
          1 ATAAAA

      19574 TCAGTGAAAC


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18


Consensus pattern (16 bp):   
ATAAAAAAAAAATAAA
Done.