Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008514.1 Corchorus capsularis cultivar CVL-1 contig08535, 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: 8251
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32


Found at i:1393 original size:135 final size:136

Alignment explanation


    Indices: 1122--1395  Score: 532
    Period size: 135  Copynumber: 2.0  Consensus size: 136

       1112 ATTCAAGGGA

                  *                                                          
       1122 ATCGATTAAGCAATGGAGACAAGGAAAGGAAGCACACATGAAGAGCAATTGGAGCTTACGCTTTG
          1 ATCGATCAAGCAATGGAGACAAGGAAAGGAAGCACACATGAAGAGCAATTGGAGCTTACGCTTTG

                                                                             
       1187 CAAAAAATAGAGAAGCTTTCTTGAACTCTAATCTCATTTAATTTCCTATGTTTGATTGATAATTG
         66 CAAAAAATAGAGAAGCTTTCTTGAACTCTAATCTCATTTAATTTCCTATGTTTGATTGATAATTG

                  
       1252 ATGCAT
        131 ATGCAT

                                                                             
       1258 ATCGATCAAGCAATGGAGACAAGGAAAGGAAGCACACATGAAGAGCAATTGGAGCTTACGCTTTG
          1 ATCGATCAAGCAATGGAGACAAGGAAAGGAAGCACACATGAAGAGCAATTGGAGCTTACGCTTTG

                                                                             
       1323 C-AAAAATAGAGAAGCTTTCTTGAACTCTAATCTCATTTAATTTCCTATGTTTGATTGATAATTG
         66 CAAAAAATAGAGAAGCTTTCTTGAACTCTAATCTCATTTAATTTCCTATGTTTGATTGATAATTG

                  
       1387 ATGCAT
        131 ATGCAT

               
       1393 ATC
          1 ATC

       1396 AATTAATTTT


Statistics
Matches: 137,  Mismatches: 1, Indels: 1
        0.99            0.01        0.01

Matches are distributed among these distances:
 135   72  0.53
 136   65  0.47

ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29


Consensus pattern (136 bp):   
ATCGATCAAGCAATGGAGACAAGGAAAGGAAGCACACATGAAGAGCAATTGGAGCTTACGCTTTG
CAAAAAATAGAGAAGCTTTCTTGAACTCTAATCTCATTTAATTTCCTATGTTTGATTGATAATTG
ATGCAT

Found at i:5428 original size:111 final size:111

Alignment explanation


    Indices: 5234--5457  Score: 421
    Period size: 111  Copynumber: 2.0  Consensus size: 111

       5224 ATTTTCCAAG

                                                                 *           
       5234 GACAATTTGGATGAAGAATGGAGCCAATATGATCGTGATTGAAGAGCTCGAAGGGTCAATTTTAT
          1 GACAATTTGGATGAAGAATGGAGCCAATATGATCGTGATTGAAGAGCTCGAAGAGTCAATTTTAT

               *                                          
       5299 CATTATAAGATTGATTTTCAAGAGTTTGAAGCAAAGGAGCAAAGTT
         66 CATCATAAGATTGATTTTCAAGAGTTTGAAGCAAAGGAGCAAAGTT

                                                            *                
       5345 GACAATTTGGATGAAGAATGGAGCCAATATGATCGTGATTGAAGAGCTTGAAGAGTCAATTTTAT
          1 GACAATTTGGATGAAGAATGGAGCCAATATGATCGTGATTGAAGAGCTCGAAGAGTCAATTTTAT

                                                          
       5410 CATCATAAGATTGATTTTCAAGAGTTTGAAGCAAAGGAGCAAAGTT
         66 CATCATAAGATTGATTTTCAAGAGTTTGAAGCAAAGGAGCAAAGTT

              
       5456 GA
          1 GA

       5458 ATTTCAAGGC


Statistics
Matches: 110,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 111  110  1.00

ACGTcount: A:0.37, C:0.10, G:0.25, T:0.29


Consensus pattern (111 bp):   
GACAATTTGGATGAAGAATGGAGCCAATATGATCGTGATTGAAGAGCTCGAAGAGTCAATTTTAT
CATCATAAGATTGATTTTCAAGAGTTTGAAGCAAAGGAGCAAAGTT

Found at i:5530 original size:21 final size:21

Alignment explanation


    Indices: 5504--5552  Score: 71
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       5494 GCACTGGAGT

                       * *       
       5504 ACATGGGGCGCGAGGCAAACC
          1 ACATGGGGCGCCAAGCAAACC

                             *   
       5525 ACATGGGGCGCCAAGCATACC
          1 ACATGGGGCGCCAAGCAAACC

                   
       5546 ACATGGG
          1 ACATGGG

       5553 CCCCCAGCGC


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.29, C:0.29, G:0.35, T:0.08


Consensus pattern (21 bp):   
ACATGGGGCGCCAAGCAAACC

Found at i:8209 original size:21 final size:21

Alignment explanation


    Indices: 8180--8233  Score: 90
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       8170 TGACTGGCCA

                *        *       
       8180 CATGGCCGGCCATTACCATCG
          1 CATGCCCGGCCATCACCATCG

                                 
       8201 CATGCCCGGCCATCACCATCG
          1 CATGCCCGGCCATCACCATCG

                        
       8222 CATGCCCGGCCA
          1 CATGCCCGGCCA

       8234 CCTGACCCGT


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  21   31  1.00

ACGTcount: A:0.19, C:0.44, G:0.22, T:0.15


Consensus pattern (21 bp):   
CATGCCCGGCCATCACCATCG
Done.