Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015361.1 Corchorus capsularis cultivar CVL-1 contig15382, 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: 11986
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:980 original size:142 final size:142

Alignment explanation


    Indices: 724--1009  Score: 572
    Period size: 142  Copynumber: 2.0  Consensus size: 142

        714 TATGCCTTAT

                                                                             
        724 ATTTGGTATATTTGTGTTTATAGGTATTAAAGTGAAGAAAAGTGCAAAATCACCATTTTTGTACC
          1 ATTTGGTATATTTGTGTTTATAGGTATTAAAGTGAAGAAAAGTGCAAAATCACCATTTTTGTACC

                                                                             
        789 TTTTTGGAGCCTTTTTGGATGATTATTTATACAAATATTTTCCAAGGGCATTTTGGATGAAGAAT
         66 TTTTTGGAGCCTTTTTGGATGATTATTTATACAAATATTTTCCAAGGGCATTTTGGATGAAGAAT

                        
        854 GGAGGCAACATG
        131 GGAGGCAACATG

                                                                             
        866 ATTTGGTATATTTGTGTTTATAGGTATTAAAGTGAAGAAAAGTGCAAAATCACCATTTTTGTACC
          1 ATTTGGTATATTTGTGTTTATAGGTATTAAAGTGAAGAAAAGTGCAAAATCACCATTTTTGTACC

                                                                             
        931 TTTTTGGAGCCTTTTTGGATGATTATTTATACAAATATTTTCCAAGGGCATTTTGGATGAAGAAT
         66 TTTTTGGAGCCTTTTTGGATGATTATTTATACAAATATTTTCCAAGGGCATTTTGGATGAAGAAT

                        
        996 GGAGGCAACATG
        131 GGAGGCAACATG

              
       1008 AT
          1 AT

       1010 CGTGATTGAA


Statistics
Matches: 144,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 142  144  1.00

ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38


Consensus pattern (142 bp):   
ATTTGGTATATTTGTGTTTATAGGTATTAAAGTGAAGAAAAGTGCAAAATCACCATTTTTGTACC
TTTTTGGAGCCTTTTTGGATGATTATTTATACAAATATTTTCCAAGGGCATTTTGGATGAAGAAT
GGAGGCAACATG

Found at i:4619 original size:23 final size:23

Alignment explanation


    Indices: 4573--4624  Score: 59
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       4563 TTAACTAATT

                               *   
       4573 AAGAAAACTAAAGCAAATTGTAA
          1 AAGAAAACTAAAGCAAATTATAA

             *    *     *   *      
       4596 AGGAAACCTAAATCAATTTATAA
          1 AAGAAAACTAAAGCAAATTATAA

                  
       4619 AAGAAA
          1 AAGAAA

       4625 TCAAAGTATC


Statistics
Matches: 23,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.60, C:0.10, G:0.12, T:0.19


Consensus pattern (23 bp):   
AAGAAAACTAAAGCAAATTATAA

Found at i:7793 original size:14 final size:14

Alignment explanation


    Indices: 7774--7800  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       7764 AAGATAAGGC

                          
       7774 TATGTGTTCAAAAG
          1 TATGTGTTCAAAAG

                         
       7788 TATGTGTTCAAAA
          1 TATGTGTTCAAAA

       7801 TACAAGACTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37


Consensus pattern (14 bp):   
TATGTGTTCAAAAG
Done.