Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005872.1 Corchorus capsularis cultivar CVL-1 contig05890, 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: 7010
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32


Found at i:1114 original size:6 final size:6

Alignment explanation


    Indices: 1103--1132  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       1093 ATTAATTTGC

                                              
       1103 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA

       1133 ATTGCTTTGC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50


Consensus pattern (6 bp):   
TTTAGA

Found at i:3610 original size:39 final size:43

Alignment explanation


    Indices: 3501--3615  Score: 148
    Period size: 45  Copynumber: 2.7  Consensus size: 43

       3491 ACATTTTCAA

                                                     *   
       3501 TTTAAGTAATTCCAAAAGAAGATTTTGGGAAAACAAAGAGTTTCT
          1 TTTAAGTAATTCCAAAAGAAGATTTT-GGAAAAC-AAGAGTGTCT

               *              *                        
       3546 TTTGAGTAATTCCAAAAGGAGATTTTGGAAAAC-A-AGTGT-T
          1 TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACAAGAGTGTCT

                     *                     
       3586 TTTAAG-AAATCCAAAAGAAGATTTTGGAAA
          1 TTTAAGTAATTCCAAAAGAAGATTTTGGAAA

       3616 TTAATAAAAT


Statistics
Matches: 64,  Mismatches: 6, Indels: 6
        0.84            0.08        0.08

Matches are distributed among these distances:
  39   22  0.34
  40    6  0.09
  41    4  0.06
  42    1  0.02
  44    7  0.11
  45   24  0.38

ACGTcount: A:0.43, C:0.08, G:0.19, T:0.30


Consensus pattern (43 bp):   
TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACAAGAGTGTCT

Found at i:4533 original size:13 final size:13

Alignment explanation


    Indices: 4515--4539  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       4505 TTAAGGTGAT

                         
       4515 CTTAAGTGTTTTC
          1 CTTAAGTGTTTTC

                        
       4528 CTTAAGTGTTTT
          1 CTTAAGTGTTTT

       4540 GTCTTTGGTA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.16, C:0.12, G:0.16, T:0.56


Consensus pattern (13 bp):   
CTTAAGTGTTTTC
Done.