Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013924.1 Corchorus capsularis cultivar CVL-1 contig13945, 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: 19732
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:2654 original size:2 final size:2

Alignment explanation


    Indices: 2647--2675  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       2637 AATTTAGAAG

                                                       
       2647 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2676 TGCGTTGGAG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:5865 original size:34 final size:33

Alignment explanation


    Indices: 5827--5907  Score: 101
    Period size: 33  Copynumber: 2.4  Consensus size: 33

       5817 AAACACCGGA

                                  * *       *  
       5827 ATATAGGGGCGTTTG-CGACAAGGGAAACGCCGCT
          1 ATATAGGGGCGTTTGTC--CAACGCAAACGCCACT

                                 *           
       5861 ATATAGGGGCGTTTGTCCAACTCAAACGCCACT
          1 ATATAGGGGCGTTTGTCCAACGCAAACGCCACT

                          
       5894 ATATAGGGGCGTTT
          1 ATATAGGGGCGTTT

       5908 TTTATTGGAA


Statistics
Matches: 42,  Mismatches: 4, Indels: 3
        0.86            0.08        0.06

Matches are distributed among these distances:
  33   26  0.62
  34   15  0.36
  35    1  0.02

ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23


Consensus pattern (33 bp):   
ATATAGGGGCGTTTGTCCAACGCAAACGCCACT

Found at i:8598 original size:39 final size:39

Alignment explanation


    Indices: 8555--8633  Score: 149
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       8545 GTCTTCTATC

                              *                    
       8555 GATTGGGAGCAAAAGAAATTAGGGATTTTTTATGGTTTT
          1 GATTGGGAGCAAAAGAAACTAGGGATTTTTTATGGTTTT

                                                   
       8594 GATTGGGAGCAAAAGAAACTAGGGATTTTTTATGGTTTT
          1 GATTGGGAGCAAAAGAAACTAGGGATTTTTTATGGTTTT

             
       8633 G
          1 G

       8634 TTGTTGGGGG


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  39   39  1.00

ACGTcount: A:0.30, C:0.04, G:0.29, T:0.37


Consensus pattern (39 bp):   
GATTGGGAGCAAAAGAAACTAGGGATTTTTTATGGTTTT

Found at i:18804 original size:75 final size:75

Alignment explanation


    Indices: 18646--18809  Score: 170
    Period size: 75  Copynumber: 2.2  Consensus size: 75

      18636 CGGGTTGCTA

                                         **  *                          * *  
      18646 ATTCGAATTCAAATAATGAATTTCCTGATGGTGTTAGGCAAAATCTTAAAGATGATTCACCTGAT
          1 ATTCGAATTCAAATAATGAATTTCCTGATAATGATAGGCAAAATCTTAAAGATGATTCACATCAT

                      
      18711 CAGATTCCTG
         66 CAGATTCCTG

            *  *           *        *            *    *     *   *            
      18721 TTTTGAATTCAAATAGT-AAGTTTTCTGATAATGATATGCAACATCTTGAAGCTGATTCACATCA
          1 ATTCGAATTCAAATAATGAA-TTTCCTGATAATGATAGGCAAAATCTTAAAGATGATTCACATCA

                    *   
      18785 TCATG-TTTCTG
         65 TCA-GATTCCTG

                          
      18796 ATTCGAATTCAAAT
          1 ATTCGAATTCAAAT

      18810 TTTGAGCATC


Statistics
Matches: 71,  Mismatches: 16, Indels: 4
        0.78            0.18        0.04

Matches are distributed among these distances:
  74    2  0.03
  75   68  0.96
  76    1  0.01

ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37


Consensus pattern (75 bp):   
ATTCGAATTCAAATAATGAATTTCCTGATAATGATAGGCAAAATCTTAAAGATGATTCACATCAT
CAGATTCCTG
Done.