Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001039.1 Corchorus capsularis cultivar CVL-1 contig01039, 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: 16924
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34


Found at i:14 original size:2 final size:2

Alignment explanation


    Indices: 8--49  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

          1 CTAGTGG

                                                                          
          8 TA TA 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 TA TA

         50 CATAAATTTA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:14644 original size:42 final size:42

Alignment explanation


    Indices: 14585--14675  Score: 155
    Period size: 42  Copynumber: 2.1  Consensus size: 42

      14575 AACAGCCTAG

                                      *               
      14585 TTCTTCACAAGTTGTTGGCGACATGACACTGAGACCATGCAA
          1 TTCTTCACAAGTTGTTGGCGACATGAAACTGAGACCATGCAA

                                  *                   
      14627 TTCTTCACAAGTTGTTGGCGACGTGAAACTGAGACCATGCAA
          1 TTCTTCACAAGTTGTTGGCGACATGAAACTGAGACCATGCAA

                   
      14669 TATCTTC
          1 T-TCTTC

      14676 CTTTTGAATC


Statistics
Matches: 46,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  42   41  0.89
  43    5  0.11

ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29


Consensus pattern (42 bp):   
TTCTTCACAAGTTGTTGGCGACATGAAACTGAGACCATGCAA

Found at i:16698 original size:2 final size:2

Alignment explanation


    Indices: 16686--16742  Score: 51
    Period size: 2  Copynumber: 25.0  Consensus size: 2

      16676 ATTCATTCTC

                                                                            
      16686 TA TA TA CTA TA TA CTA TA TA TA TA TA TA TA TA CTA TA CTA TA CTA
          1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA -TA TA -TA

                            
      16731 TA CTA TA CTA TA
          1 TA -TA TA -TA TA

      16743 CTATTGTCTT


Statistics
Matches: 48,  Mismatches: 0, Indels: 14
        0.77            0.00        0.23

Matches are distributed among these distances:
   2   34  0.71
   3   14  0.29

ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44


Consensus pattern (2 bp):   
TA

Found at i:16703 original size:5 final size:5

Alignment explanation


    Indices: 16688--16746  Score: 74
    Period size: 5  Copynumber: 12.6  Consensus size: 5

      16678 TCATTCTCTA

                                                                        
      16688 TATAC TATA- TACTA- TATA- TATA- TATA- TATAC TATAC TATAC TATAC
          1 TATAC TATAC TA-TAC TATAC TATAC TATAC TATAC TATAC TATAC TATAC

                           
      16734 TATAC TATAC TAT
          1 TATAC TATAC TAT

      16747 TGTCTTTCCT


Statistics
Matches: 52,  Mismatches: 0, Indels: 4
        0.93            0.00        0.07

Matches are distributed among these distances:
   4   16  0.31
   5   36  0.69

ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44


Consensus pattern (5 bp):   
TATAC

Done.