Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015797.1 Corchorus capsularis cultivar CVL-1 contig15818, 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: 9906
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28


Found at i:1978 original size:15 final size:16

Alignment explanation


    Indices: 1946--1979  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       1936 AAGAAGAATT

                 *          
       1946 TAAAATTAAATCTAAC
          1 TAAAAGTAAATCTAAC

                            
       1962 TAAAAGTAAAT-TAAC
          1 TAAAAGTAAATCTAAC

               
       1977 TAA
          1 TAA

       1980 GAGAGCAATC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29


Consensus pattern (16 bp):   
TAAAAGTAAATCTAAC

Found at i:3497 original size:20 final size:21

Alignment explanation


    Indices: 3459--3497  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 21

       3449 TAGAAAATAA

                          *      
       3459 GGTAAAAATGCATATAAAAGT
          1 GGTAAAAATGCATAGAAAAGT

                      *        
       3480 GGTAAAAA-GTATAGAAAA
          1 GGTAAAAATGCATAGAAAA

       3498 ATAGCCATAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    8  0.50
  21    8  0.50

ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21


Consensus pattern (21 bp):   
GGTAAAAATGCATAGAAAAGT

Found at i:8164 original size:21 final size:21

Alignment explanation


    Indices: 8136--8189  Score: 56
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       8126 ACTAGCGCTG

                                 
       8136 GGCG-CCCATGTGGTAAGCCT
          1 GGCGCCCCATGTGGTAAGCCT

                     **    **    
       8156 GGCGCCCCACCTGGTTTGCCT
          1 GGCGCCCCATGTGGTAAGCCT

            *            
       8177 CGCGCCCCATGTG
          1 GGCGCCCCATGTG

       8190 CTCCAGTGCT


Statistics
Matches: 26,  Mismatches: 7, Indels: 1
        0.76            0.21        0.03

Matches are distributed among these distances:
  20    4  0.15
  21   22  0.85

ACGTcount: A:0.09, C:0.39, G:0.31, T:0.20


Consensus pattern (21 bp):   
GGCGCCCCATGTGGTAAGCCT

Found at i:9144 original size:13 final size:13

Alignment explanation


    Indices: 9126--9160  Score: 61
    Period size: 13  Copynumber: 2.7  Consensus size: 13

       9116 GATCTAAATC

                   *     
       9126 TAAAGCAGATTAA
          1 TAAAGCAAATTAA

                         
       9139 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                     
       9152 TAAAGCAAA
          1 TAAAGCAAA

       9161 CAATAATTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   21  1.00

ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20


Consensus pattern (13 bp):   
TAAAGCAAATTAA
Done.