Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004848.1 Corchorus capsularis cultivar CVL-1 contig04866, 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: 18629
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:9205 original size:6 final size:6

Alignment explanation


    Indices: 9194--9219  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

       9184 CAAAAAATAC

                                          
       9194 TTTGGT TTTGGT TTTGGT TTTGGT TT
          1 TTTGGT TTTGGT TTTGGT TTTGGT TT

       9220 ATATATTTCC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69


Consensus pattern (6 bp):   
TTTGGT

Found at i:10903 original size:21 final size:20

Alignment explanation


    Indices: 10866--10904  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      10856 TTTAGACGCG

                       *        
      10866 ATTAATTAAAAGCATTAAAT
          1 ATTAATTAAAAACATTAAAT

                               
      10886 ATTAATTAAAAACAATTAA
          1 ATTAATTAAAAAC-ATTAA

      10905 GGAAGGGAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20   12  0.71
  21    5  0.29

ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33


Consensus pattern (20 bp):   
ATTAATTAAAAACATTAAAT

Found at i:11037 original size:74 final size:74

Alignment explanation


    Indices: 10911--11067  Score: 224
    Period size: 74  Copynumber: 2.1  Consensus size: 74

      10901 TTAAGGAAGG

                *                *                  * *             *        
      10911 GAAATGTGTAATTACGAAAAATGGTAGAAGGAAAAGGAATGAGGGAAACTCATAGATAGACTTTT
          1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAAAGGAAACTCATAGAGAGACTTTT

                  *  
      10976 TAGTCATCC
         66 TAGTCACCC

                      *   *                                          * *     
      10985 GAAAAGTGTAGTTATGAAAAAGGGTAGAAGGAAAAGGAATAAAGGAAACTCATAGAGGGGCTTTT
          1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAAAGGAAACTCATAGAGAGACTTTT

                     
      11050 TAGTCACCC
         66 TAGTCACCC

                     
      11059 GAAAAGTGT
          1 GAAAAGTGT

      11068 GAAAAAACCA


Statistics
Matches: 73,  Mismatches: 10, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  74   73  1.00

ACGTcount: A:0.42, C:0.09, G:0.27, T:0.22


Consensus pattern (74 bp):   
GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAAAGGAAACTCATAGAGAGACTTTT
TAGTCACCC

Found at i:16099 original size:25 final size:23

Alignment explanation


    Indices: 16053--16099  Score: 58
    Period size: 25  Copynumber: 2.0  Consensus size: 23

      16043 TAGCTAGCTC

                          *  *     
      16053 CTTTATTTTTCTTTTTTTTTAGT
          1 CTTTATTTTTCTTTATTATTAGT

                                    
      16076 CTTTATATTTTCCTTTATTATTAG
          1 CTTTAT-TTTT-CTTTATTATTAG

      16100 GTACAAAGTC


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  23    6  0.30
  24    4  0.20
  25   10  0.50

ACGTcount: A:0.15, C:0.11, G:0.04, T:0.70


Consensus pattern (23 bp):   
CTTTATTTTTCTTTATTATTAGT

Found at i:18599 original size:2 final size:2

Alignment explanation


    Indices: 18592--18629  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      18582 TATTTAAACC

                                                                    
      18592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.