Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024249.1 Corchorus olitorius cultivar O-4 contig24282, 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: 5638
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32


Found at i:1878 original size:43 final size:43

Alignment explanation


    Indices: 1817--1898  Score: 164
    Period size: 43  Copynumber: 1.9  Consensus size: 43

       1807 CAAACTTAAA

                                                       
       1817 CCTTAGCAAAGTGGTAAGCAAGGGTCGAATCCCACGAGGCTAC
          1 CCTTAGCAAAGTGGTAAGCAAGGGTCGAATCCCACGAGGCTAC

                                                   
       1860 CCTTAGCAAAGTGGTAAGCAAGGGTCGAATCCCACGAGG
          1 CCTTAGCAAAGTGGTAAGCAAGGGTCGAATCCCACGAGG

       1899 AGGTAGCTAT


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  43   39  1.00

ACGTcount: A:0.30, C:0.24, G:0.29, T:0.16


Consensus pattern (43 bp):   
CCTTAGCAAAGTGGTAAGCAAGGGTCGAATCCCACGAGGCTAC

Found at i:1978 original size:141 final size:141

Alignment explanation


    Indices: 1724--1996  Score: 546
    Period size: 141  Copynumber: 1.9  Consensus size: 141

       1714 TAGATGCTTT

                                                                             
       1724 GCAAAGTGGTAAGCAAGGGTCGAATCCCACGAGGAGGTAGCTATCCTTTTACACAAGAAAATCAC
          1 GCAAAGTGGTAAGCAAGGGTCGAATCCCACGAGGAGGTAGCTATCCTTTTACACAAGAAAATCAC

                                                                             
       1789 CACGCTTATTTATCTTCACAAACTTAAACCTTAGCAAAGTGGTAAGCAAGGGTCGAATCCCACGA
         66 CACGCTTATTTATCTTCACAAACTTAAACCTTAGCAAAGTGGTAAGCAAGGGTCGAATCCCACGA

                       
       1854 GGCTACCCTTA
        131 GGCTACCCTTA

                                                                             
       1865 GCAAAGTGGTAAGCAAGGGTCGAATCCCACGAGGAGGTAGCTATCCTTTTACACAAGAAAATCAC
          1 GCAAAGTGGTAAGCAAGGGTCGAATCCCACGAGGAGGTAGCTATCCTTTTACACAAGAAAATCAC

                                                                             
       1930 CACGCTTATTTATCTTCACAAACTTAAACCTTAGCAAAGTGGTAAGCAAGGGTCGAATCCCACGA
         66 CACGCTTATTTATCTTCACAAACTTAAACCTTAGCAAAGTGGTAAGCAAGGGTCGAATCCCACGA

              
       1995 GG
        131 GG

       1997 AGGTAGCTAT


Statistics
Matches: 132,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 141  132  1.00

ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22


Consensus pattern (141 bp):   
GCAAAGTGGTAAGCAAGGGTCGAATCCCACGAGGAGGTAGCTATCCTTTTACACAAGAAAATCAC
CACGCTTATTTATCTTCACAAACTTAAACCTTAGCAAAGTGGTAAGCAAGGGTCGAATCCCACGA
GGCTACCCTTA

Found at i:3402 original size:29 final size:30

Alignment explanation


    Indices: 3327--3434  Score: 137
    Period size: 31  Copynumber: 3.6  Consensus size: 30

       3317 GACGGCTAAA

                                      *    
       3327 TGCTCAATTTGGTCCTAAACCTTTGAGCGAG
          1 TGCTCAATTTGGTCCTAAACCTTTGAACG-G

            *                             
       3358 CGCTCAATTTGGTCCTAAACCTTTGAAC-G
          1 TGCTCAATTTGGTCCTAAACCTTTGAACGG

                      **       *          
       3387 TGCTCAATTTCATCCTAAATCTTTGAACGG
          1 TGCTCAATTTGGTCCTAAACCTTTGAACGG

                       *      
       3417 TCGCTCAATTTAGTCCTA
          1 T-GCTCAATTTGGTCCTA

       3435 TTTCTGACGG


Statistics
Matches: 67,  Mismatches: 8, Indels: 4
        0.85            0.10        0.05

Matches are distributed among these distances:
  29   25  0.37
  30    2  0.03
  31   40  0.60

ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34


Consensus pattern (30 bp):   
TGCTCAATTTGGTCCTAAACCTTTGAACGG

Found at i:3566 original size:42 final size:43

Alignment explanation


    Indices: 3507--3594  Score: 169
    Period size: 42  Copynumber: 2.1  Consensus size: 43

       3497 GCTCAATAAA

                                                       
       3507 ATAGCCACGTGGCTATTTCTAAAGT-AAAAAAAAGCCACATGG
          1 ATAGCCACGTGGCTATTTCTAAAGTAAAAAAAAAGCCACATGG

                                                       
       3549 ATAGCCACGTGGCTATTTCTAAAGTAAAAAAAAAGCCACATGG
          1 ATAGCCACGTGGCTATTTCTAAAGTAAAAAAAAAGCCACATGG

               
       3592 ATA
          1 ATA

       3595 ATGATAAATC


Statistics
Matches: 45,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  42   25  0.56
  43   20  0.44

ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22


Consensus pattern (43 bp):   
ATAGCCACGTGGCTATTTCTAAAGTAAAAAAAAAGCCACATGG

Done.