Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015704.1 Corchorus capsularis cultivar CVL-1 contig15725, 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: 24613
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31


Found at i:4754 original size:22 final size:22

Alignment explanation


    Indices: 4706--4788  Score: 76
    Period size: 22  Copynumber: 3.8  Consensus size: 22

       4696 CATTATGTGG

                        *    * * *
       4706 CCGAATCTCACGACCACTATGG
          1 CCGAATCTCACGGCCACCAAGA

            *         *     *    *
       4728 TCGAATCTCATGGCCAGCAAGG
          1 CCGAATCTCACGGCCACCAAGA

                       *       *  
       4750 CCGAATCTCACAGCCACCATGA
          1 CCGAATCTCACGGCCACCAAGA

                             
       4772 CCGAATCTCACGGCCAC
          1 CCGAATCTCACGGCCAC

       4789 GTTTTTCTCA


Statistics
Matches: 48,  Mismatches: 13, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  22   48  1.00

ACGTcount: A:0.28, C:0.37, G:0.19, T:0.16


Consensus pattern (22 bp):   
CCGAATCTCACGGCCACCAAGA

Found at i:4754 original size:44 final size:44

Alignment explanation


    Indices: 4704--4787  Score: 116
    Period size: 44  Copynumber: 1.9  Consensus size: 44

       4694 TCCATTATGT

                                *   **         *         
       4704 GGCCGAATCTCAC-GACCACTATGGTCGAATCTCATGGCCAGCAA
          1 GGCCGAATCTCACAG-CCACCATGACCGAATCTCACGGCCAGCAA

                                                    
       4748 GGCCGAATCTCACAGCCACCATGACCGAATCTCACGGCCA
          1 GGCCGAATCTCACAGCCACCATGACCGAATCTCACGGCCA

       4788 CGTTTTTCTC


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  44   34  0.97
  45    1  0.03

ACGTcount: A:0.27, C:0.36, G:0.21, T:0.15


Consensus pattern (44 bp):   
GGCCGAATCTCACAGCCACCATGACCGAATCTCACGGCCAGCAA

Found at i:5174 original size:78 final size:78

Alignment explanation


    Indices: 5054--5204  Score: 275
    Period size: 78  Copynumber: 1.9  Consensus size: 78

       5044 ATAATTAAAA

                                *                              *             
       5054 AGGAATGGAAAAAGGGGAAATTATCCCCAAGTGTAATGAAGAATTAAAATTGCCCCCAAGATGTA
          1 AGGAATGGAAAAAGGGGAAACTATCCCCAAGTGTAATGAAGAATTAAAATTACCCCCAAGATGTA

                         
       5119 ATCAACTATAATT
         66 ATCAACTATAATT

                    *                                                        
       5132 AGGAATGGGAAAAGGGGAAACTATCCCCAAGTGTAATGAAGAATTAAAATTACCCCCAAGATGTA
          1 AGGAATGGAAAAAGGGGAAACTATCCCCAAGTGTAATGAAGAATTAAAATTACCCCCAAGATGTA

                    
       5197 ATCAACTA
         66 ATCAACTA

       5205 AACTAATGTC


Statistics
Matches: 70,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  78   70  1.00

ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21


Consensus pattern (78 bp):   
AGGAATGGAAAAAGGGGAAACTATCCCCAAGTGTAATGAAGAATTAAAATTACCCCCAAGATGTA
ATCAACTATAATT

Found at i:7779 original size:2 final size:2

Alignment explanation


    Indices: 7772--7827  Score: 71
    Period size: 2  Copynumber: 28.5  Consensus size: 2

       7762 AATAGATGGT

                                                          *             * 
       7772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TA TA -A TA CA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                                   
       7812 TA TA TA TA CTA TA TA T
          1 TA TA TA TA -TA TA TA T

       7828 TATTTTTAAC


Statistics
Matches: 48,  Mismatches: 3, Indels: 6
        0.84            0.05        0.11

Matches are distributed among these distances:
   1    2  0.04
   2   44  0.92
   3    2  0.04

ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:8725 original size:21 final size:21

Alignment explanation


    Indices: 8687--8726  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       8677 ATAACTTCAC

                       * *       
       8687 AATATATATTATACTATATAA
          1 AATATATATTAAAATATATAA

                   *           
       8708 AATATATTTTAAAATATAT
          1 AATATATATTAAAATATAT

       8727 GGCTAGAAAA


Statistics
Matches: 16,  Mismatches: 3, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   16  1.00

ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45


Consensus pattern (21 bp):   
AATATATATTAAAATATATAA
Done.