Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001069.1 Corchorus capsularis cultivar CVL-1 contig01069, 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: 14057
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:1844 original size:1 final size:1

Alignment explanation


    Indices: 1840--1871  Score: 55
    Period size: 1  Copynumber: 32.0  Consensus size: 1

       1830 TGTCATGCAG

                                     *      
       1840 AAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       1872 GAGAAAATTG


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   1   29  1.00

ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00


Consensus pattern (1 bp):   
A

Found at i:1872 original size:7 final size:7

Alignment explanation


    Indices: 1838--1878  Score: 50
    Period size: 7  Copynumber: 6.0  Consensus size: 7

       1828 TTTGTCATGC

                   
       1838 AGAAAAA
          1 AGAAAAA

                   
       1845 A-AAAAA
          1 AGAAAAA

                   
       1851 A-AAAAA
          1 AGAAAAA

             *     
       1857 AAAAAAA
          1 AGAAAAA

                   
       1864 AGAAAAA
          1 AGAAAAA

                    
       1871 AGAGAAAA
          1 AGA-AAAA

       1879 TTGGAGACAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 3
        0.89            0.03        0.09

Matches are distributed among these distances:
   6   12  0.39
   7   15  0.48
   8    4  0.13

ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00


Consensus pattern (7 bp):   
AGAAAAA

Found at i:1876 original size:9 final size:9

Alignment explanation


    Indices: 1838--1878  Score: 57
    Period size: 9  Copynumber: 4.7  Consensus size: 9

       1828 TTTGTCATGC

                     
       1838 AGAAAAAAA
          1 AGAAAAAAA

                     
       1847 A-AAAAAAA
          1 AGAAAAAAA

             *       
       1855 AAAAAAAAA
          1 AGAAAAAAA

                    *
       1864 AGAAAAAAG
          1 AGAAAAAAA

                  
       1873 AGAAAA
          1 AGAAAA

       1879 TTGGAGACAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   8    8  0.28
   9   21  0.72

ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00


Consensus pattern (9 bp):   
AGAAAAAAA

Found at i:4820 original size:93 final size:93

Alignment explanation


    Indices: 4661--4841  Score: 245
    Period size: 93  Copynumber: 1.9  Consensus size: 93

       4651 AACCTTCAAT

                                                            *     *          
       4661 TTTCTTAATATTTTCTATGTAATTTTACATGGTGCCCACCCTTAAATGGTCATAGATGCCCACCC
          1 TTTCTTAATATTTTCTATGTAATTTTACATGGTGCCCACCCTTAAATGATCATAAATGCCCACCC

                                        
       4726 TCAATTAATTAACTCGTCAAAATGCCCA
         66 TCAATTAATTAACTCGTCAAAATGCCCA

                          *                   **        **     *      **     
       4754 TTTCTTAATATTTTGTATGTAATTTTACATGGTGTTCACCCTTATTTGATCCTAAATGTTCACCC
          1 TTTCTTAATATTTTCTATGTAATTTTACATGGTGCCCACCCTTAAATGATCATAAATGCCCACCC

                  *     * *        
       4819 TCAATTGATTAATTTGTCAAAAT
         66 TCAATTAATTAACTCGTCAAAAT

       4842 ATCTTTGAAT


Statistics
Matches: 75,  Mismatches: 13, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  93   75  1.00

ACGTcount: A:0.28, C:0.20, G:0.10, T:0.41


Consensus pattern (93 bp):   
TTTCTTAATATTTTCTATGTAATTTTACATGGTGCCCACCCTTAAATGATCATAAATGCCCACCC
TCAATTAATTAACTCGTCAAAATGCCCA

Found at i:5980 original size:59 final size:59

Alignment explanation


    Indices: 5888--6015  Score: 231
    Period size: 59  Copynumber: 2.2  Consensus size: 59

       5878 TTCTCTCATT

                                        *                        *     
       5888 CTTCATATTTTCTTCTTCTCCATATTCTGTTGTCTCTCTATTCTCTTGTCTTTTACATA
          1 CTTCATATTTTCTTCTTCTCCATATTCTATTGTCTCTCTATTCTCTTGTCTTTAACATA

                                                                       
       5947 CTTCATATTTTCTTCTTCTCCATATTCTATTGTCTCTCTATTCTCTTGTCTTTAACATA
          1 CTTCATATTTTCTTCTTCTCCATATTCTATTGTCTCTCTATTCTCTTGTCTTTAACATA

                       
       6006 CTTCA-ATTTT
          1 CTTCATATTTT

       6016 ACTCCATTGT


Statistics
Matches: 67,  Mismatches: 2, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  58    5  0.07
  59   62  0.93

ACGTcount: A:0.16, C:0.25, G:0.04, T:0.55


Consensus pattern (59 bp):   
CTTCATATTTTCTTCTTCTCCATATTCTATTGTCTCTCTATTCTCTTGTCTTTAACATA
Done.