Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012829.1 Corchorus capsularis cultivar CVL-1 contig12850, 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: 16539
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:2818 original size:19 final size:19

Alignment explanation


    Indices: 2794--2849  Score: 63
    Period size: 19  Copynumber: 3.3  Consensus size: 19

       2784 GTGTGTGTGA

                               
       2794 TTGTTTGGTTTGGTAGATG
          1 TTGTTTGGTTTGGTAGATG

                               
       2813 TTGTTT-G-TT-GT-G--G
          1 TTGTTTGGTTTGGTAGATG

                               
       2826 -TGTTTGGTTTGGTAGATG
          1 TTGTTTGGTTTGGTAGATG

                  
       2844 TTGTTT
          1 TTGTTT

       2850 TCTGCGGTGT


Statistics
Matches: 30,  Mismatches: 0, Indels: 14
        0.68            0.00        0.32

Matches are distributed among these distances:
  12    5  0.17
  13    2  0.07
  14    2  0.07
  15    3  0.10
  16    3  0.10
  17    2  0.07
  18    2  0.07
  19   11  0.37

ACGTcount: A:0.07, C:0.00, G:0.36, T:0.57


Consensus pattern (19 bp):   
TTGTTTGGTTTGGTAGATG

Found at i:2833 original size:31 final size:31

Alignment explanation


    Indices: 2795--2875  Score: 137
    Period size: 31  Copynumber: 2.6  Consensus size: 31

       2785 TGTGTGTGAT

                                         *  
       2795 TGTTTGGTTTGGTAGATGTTGTTTGT-TGTGG
          1 TGTTTGGTTTGGTAGATGTTGTTT-TCTGCGG

                                           
       2826 TGTTTGGTTTGGTAGATGTTGTTTTCTGCGG
          1 TGTTTGGTTTGGTAGATGTTGTTTTCTGCGG

                               
       2857 TGTTTGGTTTGGTAGATGT
          1 TGTTTGGTTTGGTAGATGT

       2876 GATGATTAGT


Statistics
Matches: 48,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  30    1  0.02
  31   47  0.98

ACGTcount: A:0.07, C:0.02, G:0.37, T:0.53


Consensus pattern (31 bp):   
TGTTTGGTTTGGTAGATGTTGTTTTCTGCGG

Found at i:2926 original size:25 final size:25

Alignment explanation


    Indices: 2892--2939  Score: 69
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       2882 TAGTTTGTTT

                *         *  *       
       2892 GAGATCGAGCGAGAGTGCTCAAATA
          1 GAGACCGAGCGAGAATGATCAAATA

                                   
       2917 GAGACCGAGCGAGAATGATCAAA
          1 GAGACCGAGCGAGAATGATCAAA

       2940 GATTGGTTGG


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  25   20  1.00

ACGTcount: A:0.40, C:0.17, G:0.31, T:0.12


Consensus pattern (25 bp):   
GAGACCGAGCGAGAATGATCAAATA

Found at i:10479 original size:59 final size:60

Alignment explanation


    Indices: 10412--10534  Score: 239
    Period size: 59  Copynumber: 2.1  Consensus size: 60

      10402 GAGATTAAAT

                                                                        
      10412 TTAGGTAGACTAAGGAGCTCAATCAATTAATAATGAGAGTTGGATAATTTTTT-TGCTTA
          1 TTAGGTAGACTAAGGAGCTCAATCAATTAATAATGAGAGTTGGATAATTTTTTCTGCTTA

                                                                        
      10471 TTAGGTAGACTAAGGAGCTCAATCAATTAATAATGAGAGTTGGATAATTTTTTCTGCTTA
          1 TTAGGTAGACTAAGGAGCTCAATCAATTAATAATGAGAGTTGGATAATTTTTTCTGCTTA

                
      10531 TTAG
          1 TTAG

      10535 CCTTTTTTGC


Statistics
Matches: 63,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  59   53  0.84
  60   10  0.16

ACGTcount: A:0.33, C:0.09, G:0.20, T:0.37


Consensus pattern (60 bp):   
TTAGGTAGACTAAGGAGCTCAATCAATTAATAATGAGAGTTGGATAATTTTTTCTGCTTA

Found at i:11837 original size:45 final size:45

Alignment explanation


    Indices: 11786--11872  Score: 147
    Period size: 45  Copynumber: 1.9  Consensus size: 45

      11776 AATAGAGTAG

                                                         
      11786 TGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGGA
          1 TGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGGA

                                    *  *         *    
      11831 TGGAATTACTAAAAGATCCCTACCTCGGATTAATGATGAGCT
          1 TGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCT

      11873 ATAGAAGTAA


Statistics
Matches: 39,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  45   39  1.00

ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26


Consensus pattern (45 bp):   
TGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGGA

Found at i:12772 original size:2 final size:2

Alignment explanation


    Indices: 12765--12793  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      12755 AGTAGATTTA

                                                       
      12765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      12794 AAGTATAAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.