Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018097.1 Corchorus olitorius cultivar O-4 contig18130, 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: 51733
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:2894 original size:31 final size:31

Alignment explanation


    Indices: 2837--2895  Score: 75
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       2827 TTCGGCTCAT

                           * *             
       2837 CTGGATTCAGGTCATTCGGGTCTCGGGTCTG
          1 CTGGATTCAGGTCATGCAGGTCTCGGGTCTG

                   *                     
       2868 CTGGATTTAGGGTCATGCAGGT-TCGGGT
          1 CTGGATTCA-GGTCATGCAGGTCTCGGGT

       2896 TTTGGCCTCA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  31   14  0.58
  32   10  0.42

ACGTcount: A:0.12, C:0.19, G:0.37, T:0.32


Consensus pattern (31 bp):   
CTGGATTCAGGTCATGCAGGTCTCGGGTCTG

Found at i:6569 original size:25 final size:25

Alignment explanation


    Indices: 6540--6589  Score: 100
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       6530 TGTGCAATTG

                                     
       6540 AAAAATTTAAAGTTCAGATACTGAT
          1 AAAAATTTAAAGTTCAGATACTGAT

                                     
       6565 AAAAATTTAAAGTTCAGATACTGAT
          1 AAAAATTTAAAGTTCAGATACTGAT

       6590 TTGTCCCTTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32


Consensus pattern (25 bp):   
AAAAATTTAAAGTTCAGATACTGAT

Found at i:7647 original size:8 final size:8

Alignment explanation


    Indices: 7634--7665  Score: 64
    Period size: 8  Copynumber: 4.0  Consensus size: 8

       7624 TGTTGTTCAC

                    
       7634 CACCATCA
          1 CACCATCA

                    
       7642 CACCATCA
          1 CACCATCA

                    
       7650 CACCATCA
          1 CACCATCA

                    
       7658 CACCATCA
          1 CACCATCA

       7666 TACAATTCTT


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

Matches are distributed among these distances:
   8   24  1.00

ACGTcount: A:0.38, C:0.50, G:0.00, T:0.12


Consensus pattern (8 bp):   
CACCATCA

Found at i:38508 original size:88 final size:88

Alignment explanation


    Indices: 38356--38612  Score: 435
    Period size: 88  Copynumber: 2.9  Consensus size: 88

      38346 GATTTTGGTT

                         *                                                   
      38356 ATGATTAGGGTTTGACTGTGTCTGGGTATTAATTCATTTATGTTTTTTTGATAACTTCAACTCGA
          1 ATGATTAGGGTTTCACTGTGTCTGGGTATTAATTCATTTATGTTTTTTTGATAACTTCAACTCGA

                                   
      38421 ATGCAAAATTAATTTGTTCGGTG
         66 ATGCAAAATTAATTTGTTCGGTG

              *     *                      *                    *            
      38444 ATTATTAGAGTTTCACTGTGTCTGGGTATTAGTTCATTTATGTTTTTTTGATTACTTCAACTCGA
          1 ATGATTAGGGTTTCACTGTGTCTGGGTATTAATTCATTTATGTTTTTTTGATAACTTCAACTCGA

                            *        
      38509 ATGCAAAATTAATTCAAGTTCGGTG
         66 ATGCAAAATTAATT--TGTTCGGTG

                                                                             
      38534 ATGATTAGGGTTTCACTGTGTCTGGGTATTAATTCATTTATG-TTTTTTGATAACTTCAACTCGA
          1 ATGATTAGGGTTTCACTGTGTCTGGGTATTAATTCATTTATGTTTTTTTGATAACTTCAACTCGA

                           
      38598 ATGCAAAATTAATTT
         66 ATGCAAAATTAATTT

      38613 TAGTTGTTTC


Statistics
Matches: 156,  Mismatches: 11, Indels: 5
        0.91            0.06        0.03

Matches are distributed among these distances:
  88   74  0.47
  89   35  0.22
  90   47  0.30

ACGTcount: A:0.26, C:0.11, G:0.18, T:0.44


Consensus pattern (88 bp):   
ATGATTAGGGTTTCACTGTGTCTGGGTATTAATTCATTTATGTTTTTTTGATAACTTCAACTCGA
ATGCAAAATTAATTTGTTCGGTG

Found at i:42001 original size:37 final size:39

Alignment explanation


    Indices: 41922--42010  Score: 164
    Period size: 37  Copynumber: 2.3  Consensus size: 39

      41912 CCTTCCTAAT

                                                   
      41922 AGGCTCCAAAATAGGTGCCAAAAGAAAGAAAAGAAAAAA
          1 AGGCTCCAAAATAGGTGCCAAAAGAAAGAAAAGAAAAAA

                                                   
      41961 AGGCTCCAAAATAGGTGCCAAAA-AAAG-AAAGAAAAAA
          1 AGGCTCCAAAATAGGTGCCAAAAGAAAGAAAAGAAAAAA

                         
      41998 AGGCTCCAAAATA
          1 AGGCTCCAAAATA

      42011 AAGACTCAAG


Statistics
Matches: 50,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
  37   23  0.46
  38    4  0.08
  39   23  0.46

ACGTcount: A:0.57, C:0.15, G:0.19, T:0.09


Consensus pattern (39 bp):   
AGGCTCCAAAATAGGTGCCAAAAGAAAGAAAAGAAAAAA

Found at i:48239 original size:3 final size:3

Alignment explanation


    Indices: 48224--48258  Score: 52
    Period size: 3  Copynumber: 11.7  Consensus size: 3

      48214 CTAATGCAAA

                      *                           *       
      48224 CTC CTC CTG CTC CTC CTC CTC CTC CTC CTG CTC CT
          1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT

      48259 ATTGAGGATG


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   3   28  1.00

ACGTcount: A:0.00, C:0.60, G:0.06, T:0.34


Consensus pattern (3 bp):   
CTC

Done.