Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010512.1 Corchorus capsularis cultivar CVL-1 contig10533, 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: 22240
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32


Found at i:1596 original size:14 final size:14

Alignment explanation


    Indices: 1555--1597  Score: 50
    Period size: 14  Copynumber: 3.0  Consensus size: 14

       1545 GGAATAAAAG

                          
       1555 TTTGGTAGACAATT
          1 TTTGGTAGACAATT

                ** *       
       1569 TTGTTTTGGACAATT
          1 TT-TGGTAGACAATT

                          
       1584 TTTGGTAGACAATT
          1 TTTGGTAGACAATT

       1598 AAACATAGTA


Statistics
Matches: 22,  Mismatches: 6, Indels: 2
        0.73            0.20        0.07

Matches are distributed among these distances:
  14   11  0.50
  15   11  0.50

ACGTcount: A:0.26, C:0.07, G:0.21, T:0.47


Consensus pattern (14 bp):   
TTTGGTAGACAATT

Found at i:1992 original size:24 final size:24

Alignment explanation


    Indices: 1960--2007  Score: 87
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       1950 CCAAATTTAC

                              *     
       1960 CCTCATGTCCAAAATTGACTTAAT
          1 CCTCATGTCCAAAATTGAATTAAT

                                    
       1984 CCTCATGTCCAAAATTGAATTAAT
          1 CCTCATGTCCAAAATTGAATTAAT

       2008 TGTTAGAATT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.35, C:0.23, G:0.08, T:0.33


Consensus pattern (24 bp):   
CCTCATGTCCAAAATTGAATTAAT

Found at i:7932 original size:3 final size:3

Alignment explanation


    Indices: 7926--7969  Score: 54
    Period size: 3  Copynumber: 14.7  Consensus size: 3

       7916 TGTTGTATTC

                                *                    *                 
       7926 TAT TAT TAT TA- TAT AAT TAT TAT TAT TAT AAAT TAT TAT TAT TA
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TA

       7970 AGCTCGCATT


Statistics
Matches: 35,  Mismatches: 4, Indels: 4
        0.81            0.09        0.09

Matches are distributed among these distances:
   2    2  0.06
   3   31  0.89
   4    2  0.06

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (3 bp):   
TAT

Found at i:10230 original size:16 final size:16

Alignment explanation


    Indices: 10205--10235  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      10195 AAGAAAAAAA

                            
      10205 AGAGAGAAAGAGAGTG
          1 AGAGAGAAAGAGAGTG

                 *         
      10221 AGAGATAAAGAGAGT
          1 AGAGAGAAAGAGAGT

      10236 TGCTGCTGCT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.52, C:0.00, G:0.39, T:0.10


Consensus pattern (16 bp):   
AGAGAGAAAGAGAGTG

Found at i:18136 original size:11 final size:11

Alignment explanation


    Indices: 18120--18154  Score: 61
    Period size: 11  Copynumber: 3.2  Consensus size: 11

      18110 TTTTTCTGTT

                       
      18120 TTTTGTTTTTG
          1 TTTTGTTTTTG

                     * 
      18131 TTTTGTTTTCG
          1 TTTTGTTTTTG

                       
      18142 TTTTGTTTTTG
          1 TTTTGTTTTTG

              
      18153 TT
          1 TT

      18155 GTGCTGTCAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  11   22  1.00

ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80


Consensus pattern (11 bp):   
TTTTGTTTTTG

Found at i:21838 original size:49 final size:49

Alignment explanation


    Indices: 21766--21863  Score: 151
    Period size: 49  Copynumber: 2.0  Consensus size: 49

      21756 AAAAAATTCA

                       *     *          *           *        
      21766 AATCAAATCAATTTCTTGATAAGAGGAAGAAGTAATTAATTCCAATTGT
          1 AATCAAATCAAGTTCTTAATAAGAGGAAAAAGTAATTAATACCAATTGT

                                                       *     
      21815 AATCAAATCAAGTTCTTAATAAGAGGAAAAAGTAATTAATACCTATTGT
          1 AATCAAATCAAGTTCTTAATAAGAGGAAAAAGTAATTAATACCAATTGT

      21864 TTTAAATTCA


Statistics
Matches: 44,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  49   44  1.00

ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32


Consensus pattern (49 bp):   
AATCAAATCAAGTTCTTAATAAGAGGAAAAAGTAATTAATACCAATTGT
Done.