Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012536.1 Corchorus capsularis cultivar CVL-1 contig12557, 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: 34638
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:6869 original size:10 final size:10

Alignment explanation


    Indices: 6854--6886  Score: 57
    Period size: 10  Copynumber: 3.3  Consensus size: 10

       6844 AAAACCAACA

                      
       6854 TTTCTCTCTC
          1 TTTCTCTCTC

                     *
       6864 TTTCTCTCTT
          1 TTTCTCTCTC

                      
       6874 TTTCTCTCTC
          1 TTTCTCTCTC

               
       6884 TTT
          1 TTT

       6887 GAAAAGAAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  10   21  1.00

ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67


Consensus pattern (10 bp):   
TTTCTCTCTC

Found at i:21133 original size:82 final size:82

Alignment explanation


    Indices: 20996--21160  Score: 303
    Period size: 82  Copynumber: 2.0  Consensus size: 82

      20986 GATCCGCATC

                                                     *                       
      20996 GCGCACCTGGTTATGGTGGGTGAGTCTCCGAACAGGGGCAGTTGCGTACGCAAGGTCTCGAACCC
          1 GCGCACCTGGTTATGGTGGGTGAGTCTCCGAACAGGGGCAGCTGCGTACGCAAGGTCTCGAACCC

                    *        
      21061 GAGACCTGTTTAAGCTG
         66 GAGACCTGCTTAAGCTG

                  *                                                          
      21078 GCGCACTTGGTTATGGTGGGTGAGTCTCCGAACAGGGGCAGCTGCGTACGCAAGGTCTCGAACCC
          1 GCGCACCTGGTTATGGTGGGTGAGTCTCCGAACAGGGGCAGCTGCGTACGCAAGGTCTCGAACCC

                             
      21143 GAGACCTGCTTAAGCTG
         66 GAGACCTGCTTAAGCTG

             
      21160 G
          1 G

      21161 AACAGGCCGC


Statistics
Matches: 80,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  82   80  1.00

ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21


Consensus pattern (82 bp):   
GCGCACCTGGTTATGGTGGGTGAGTCTCCGAACAGGGGCAGCTGCGTACGCAAGGTCTCGAACCC
GAGACCTGCTTAAGCTG

Found at i:32529 original size:54 final size:56

Alignment explanation


    Indices: 32436--32546  Score: 165
    Period size: 54  Copynumber: 2.0  Consensus size: 56

      32426 ATTCTGGCAG

                                                                     
      32436 TTCCCTTGCTGCCTCTTGCTGGCGACCAGGATCAGCTGCTGCTTGTTGATAATGATC
          1 TTCCCTTGCTGCCTCTTGC-GGCGACCAGGATCAGCTGCTGCTTGTTGATAATGATC

                                                     *        *      
      32493 TTCCCTTGCTGCCTCTT-C-GCGACCAGGATC-GCCTGCTGGTTGTTGATGATGATC
          1 TTCCCTTGCTGCCTCTTGCGGCGACCAGGATCAG-CTGCTGCTTGTTGATAATGATC

      32547 CAAGTTATCA


Statistics
Matches: 51,  Mismatches: 2, Indels: 5
        0.88            0.03        0.09

Matches are distributed among these distances:
  53    1  0.02
  54   32  0.63
  56    1  0.02
  57   17  0.33

ACGTcount: A:0.13, C:0.29, G:0.25, T:0.33


Consensus pattern (56 bp):   
TTCCCTTGCTGCCTCTTGCGGCGACCAGGATCAGCTGCTGCTTGTTGATAATGATC

Found at i:33879 original size:2 final size:2

Alignment explanation


    Indices: 33872--33909  Score: 69
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      33862 AAAATTATCT

                                                                      
      33872 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      33910 GATTTCTTTA


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   34  0.97

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:33897 original size:17 final size:17

Alignment explanation


    Indices: 33875--33908  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      33865 ATTATCTTAT

                             
      33875 ATATATATATATATATA
          1 ATATATATATATATATA

                             
      33892 ATATATATATATATATA
          1 ATATATATATATATATA

      33909 TGATTTCTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (17 bp):   
ATATATATATATATATA
Done.