Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004157.1 Corchorus capsularis cultivar CVL-1 contig04165, 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: 7828
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36


Found at i:2091 original size:28 final size:28

Alignment explanation


    Indices: 2011--2092  Score: 87
    Period size: 28  Copynumber: 2.9  Consensus size: 28

       2001 ATTTCATTAG

                                      *  
       2011 CTAAATAGGTATTATTATAGTTTTGTTAT
          1 CTAAATAGGTATTATTATAG-TTTGTCAT

            * *          *                
       2040 TTGAATAGGTTACATATTAT--TTTGTCAT
          1 CTAAATAGG-TA-TTATTATAGTTTGTCAT

                                     
       2068 CTAAATAGGTATTATTATAGTTTGT
          1 CTAAATAGGTATTATTATAGTTTGT

       2093 ACATGGACAG


Statistics
Matches: 42,  Mismatches: 7, Indels: 9
        0.72            0.12        0.16

Matches are distributed among these distances:
  26    6  0.14
  27    2  0.05
  28   19  0.45
  29    7  0.17
  30    2  0.05
  31    6  0.14

ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50


Consensus pattern (28 bp):   
CTAAATAGGTATTATTATAGTTTGTCAT

Found at i:6810 original size:235 final size:235

Alignment explanation


    Indices: 6399--6856  Score: 756
    Period size: 235  Copynumber: 1.9  Consensus size: 235

       6389 TGTGTAATAT

                           *                            *             *      
       6399 ATATACTAAATATTATTTGAAAGACCCAAGGAATTTACCAAAGGTCCCTTTTGAGAATTGATGAG
          1 ATATACTAAATATTACTTGAAAGACCCAAGGAATTTACCAAAGGCCCCTTTTGAGAATCGATGAG

               **         *                                                  
       6464 GAGGTTCTATTTGACCTCTTTTTGTCCTTTTCCGTCTTTTTTCACTTGTCAAATTACTAAGAAAA
         66 GAGCCTCTATTTGAACTCTTTTTGTCCTTTTCCGTCTTTTTTCACTTGTCAAATTACTAAGAAAA

            *                 *           *      *                           
       6529 TCCTAGGTTAGTTTCTAGTCAATTCTTGCTGTTGAACTCTTTTTTGTAATTATCATTTCCTTTCA
        131 CCCTAGGTTAGTTTCTAGCCAATTCTTGCTCTTGAACCCTTTTTTGTAATTATCATTTCCTTTCA

                                                    
       6594 CATAAATTCAATGTTATAACATAAATGTTATATATATTAA
        196 CATAAATTCAATGTTATAACATAAATGTTATATATATTAA

                                    * * *                          *         
       6634 ATATACTAAATATTACTTGAAAGATCTAGGGAATTTACCAAAGGCCCCTTTTGAGGATCGATGAG
          1 ATATACTAAATATTACTTGAAAGACCCAAGGAATTTACCAAAGGCCCCTTTTGAGAATCGATGAG

                                            *                               *
       6699 GAGCCTCTATTTGAACTCTTTTTGTCCTTTTCTGTCTTTTTTCACTTG-CTAAATTACTAAGAAG
         66 GAGCCTCTATTTGAACTCTTTTTGTCCTTTTCCGTCTTTTTTCACTTGTC-AAATTACTAAGAAA

                                                                             
       6763 ACCCTAGGTTAGTTTCTAGCCAATTCTTGCTCTTGAACCCTTTTTTGTAATTATCATTTCCTTTC
        130 ACCCTAGGTTAGTTTCTAGCCAATTCTTGCTCTTGAACCCTTTTTTGTAATTATCATTTCCTTTC

                                         
       6828 ACATAAATTCAATGTTATAACATAAATGT
        195 ACATAAATTCAATGTTATAACATAAATGT

       6857 CATAATAAAT


Statistics
Matches: 206,  Mismatches: 16, Indels: 2
        0.92            0.07        0.01

Matches are distributed among these distances:
 234    1  0.00
 235  205  1.00

ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41


Consensus pattern (235 bp):   
ATATACTAAATATTACTTGAAAGACCCAAGGAATTTACCAAAGGCCCCTTTTGAGAATCGATGAG
GAGCCTCTATTTGAACTCTTTTTGTCCTTTTCCGTCTTTTTTCACTTGTCAAATTACTAAGAAAA
CCCTAGGTTAGTTTCTAGCCAATTCTTGCTCTTGAACCCTTTTTTGTAATTATCATTTCCTTTCA
CATAAATTCAATGTTATAACATAAATGTTATATATATTAA

Found at i:7591 original size:9 final size:9

Alignment explanation


    Indices: 7564--7606  Score: 61
    Period size: 9  Copynumber: 4.9  Consensus size: 9

       7554 TTGATTCTCT

                    *
       7564 AAAACAAAG
          1 AAAACAAAA

            *        
       7573 TAAA-AAAA
          1 AAAACAAAA

                     
       7581 AAAACAAAA
          1 AAAACAAAA

                     
       7590 AAAACAAAA
          1 AAAACAAAA

                    
       7599 AAAACAAA
          1 AAAACAAA

       7607 GTTTTAAACA


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
   8    6  0.20
   9   24  0.80

ACGTcount: A:0.86, C:0.09, G:0.02, T:0.02


Consensus pattern (9 bp):   
AAAACAAAA
Done.