Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012357.1 Corchorus capsularis cultivar CVL-1 contig12378, 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: 12028
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29


Found at i:750 original size:3 final size:3

Alignment explanation


    Indices: 734--768  Score: 52
    Period size: 3  Copynumber: 11.7  Consensus size: 3

        724 CAAACAGTCC

                    *   *                                 
        734 CTT CTT TTT TTT CTT CTT CTT CTT CTT CTT CTT CT
          1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT

        769 CCGATAGCCG


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71


Consensus pattern (3 bp):   
CTT

Found at i:1163 original size:20 final size:21

Alignment explanation


    Indices: 1138--1177  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       1128 AAATACTTAC

                                  
       1138 CTCTCTT-TA-AACCAATGAAT
          1 CTCTCTTATATAACC-ATGAAT

                                
       1158 CTCTCTTATATAACCATGAA
          1 CTCTCTTATATAACCATGAA

       1178 ATTTAACAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  20    7  0.39
  21    7  0.39
  22    4  0.22

ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35


Consensus pattern (21 bp):   
CTCTCTTATATAACCATGAAT

Found at i:9442 original size:16 final size:16

Alignment explanation


    Indices: 9417--9447  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       9407 TTACGCTTGA

                            
       9417 GGTTTCAAAAAAAAGG
          1 GGTTTCAAAAAAAAGG

                 *         
       9433 GGTTTTAAAAAAAAG
          1 GGTTTCAAAAAAAAG

       9448 TTTCAAAGAA


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:0.03, G:0.23, T:0.23


Consensus pattern (16 bp):   
GGTTTCAAAAAAAAGG
Done.