Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016225.1 Corchorus capsularis cultivar CVL-1 contig16246, 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: 17717
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31


Found at i:5225 original size:144 final size:144

Alignment explanation


    Indices: 4965--5253  Score: 535
    Period size: 144  Copynumber: 2.0  Consensus size: 144

       4955 GATTTGTTCC

                  *                                                          
       4965 AAGCGATTTTTTCAAGTGTGCCTAGGGTTTGTGGTATTTGTTCTCAAGGACATTATACTGATAAG
          1 AAGCGAATTTTTCAAGTGTGCCTAGGGTTTGTGGTATTTGTTCTCAAGGACATTATACTGATAAG

                                                                             
       5030 TGCCCTACTTTGGAAGAAAACAAGCAAGGAGTCAATGTTGTGGGAATACAAGGAGCTTATCAAAG
         66 TGCCCTACTTTGGAAGAAAACAAGCAAGGAGTCAATGTTGTGGGAATACAAGGAGCTTATCAAAG

                          
       5095 GAAGCGTGAACCTT
        131 GAAGCGTGAACCTT

                                            *                        *       
       5109 AAGCGAATTTTTCAAGTGTGCCTAGGGTTTGTTGTATTTGTTCTCAAGGACATTATAGTGATAAG
          1 AAGCGAATTTTTCAAGTGTGCCTAGGGTTTGTGGTATTTGTTCTCAAGGACATTATACTGATAAG

                                                                             
       5174 TGCCCTACTTTGGAA-AACAACAAGCAAGGAGTCAATGTTGTGGGAATACAAGGAGCTTATCAAA
         66 TGCCCTACTTTGGAAGAA-AACAAGCAAGGAGTCAATGTTGTGGGAATACAAGGAGCTTATCAAA

                           
       5238 GGAAGCGTGAACCTT
        130 GGAAGCGTGAACCTT

             
       5253 A
          1 A

       5254 TTGGAGACCT


Statistics
Matches: 141,  Mismatches: 3, Indels: 2
        0.97            0.02        0.01

Matches are distributed among these distances:
 143    2  0.01
 144  139  0.99

ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29


Consensus pattern (144 bp):   
AAGCGAATTTTTCAAGTGTGCCTAGGGTTTGTGGTATTTGTTCTCAAGGACATTATACTGATAAG
TGCCCTACTTTGGAAGAAAACAAGCAAGGAGTCAATGTTGTGGGAATACAAGGAGCTTATCAAAG
GAAGCGTGAACCTT

Found at i:7381 original size:42 final size:42

Alignment explanation


    Indices: 7322--7418  Score: 185
    Period size: 42  Copynumber: 2.3  Consensus size: 42

       7312 CACCTGCCCG

                                                      
       7322 GCCATGCCCGGCCTTGTCCGCTCCTTCCACGCATCATACCGT
          1 GCCATGCCCGGCCTTGTCCGCTCCTTCCACGCATCATACCGT

                                                   *  
       7364 GCCATGCCCGGCCTTGTCCGCTCCTTCCACGCATCATACTGT
          1 GCCATGCCCGGCCTTGTCCGCTCCTTCCACGCATCATACCGT

                         
       7406 GCCATGCCCGGCC
          1 GCCATGCCCGGCC

       7419 ATGCGAGCTT


Statistics
Matches: 54,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   54  1.00

ACGTcount: A:0.11, C:0.45, G:0.21, T:0.23


Consensus pattern (42 bp):   
GCCATGCCCGGCCTTGTCCGCTCCTTCCACGCATCATACCGT
Done.