Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011655.1 Corchorus capsularis cultivar CVL-1 contig11676, 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: 40362
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:8747 original size:110 final size:110

Alignment explanation


    Indices: 8515--8737  Score: 410
    Period size: 110  Copynumber: 2.0  Consensus size: 110

       8505 CCGATCACAA

                    *                                   *                    
       8515 TTTTGGCGCCGTTGCCGGGGAAGGAAGGAAGCAACAAAAGATTGGAGACAAATTACTACATAAGG
          1 TTTTGGCGTCGTTGCCGGGGAAGGAAGGAAGCAACAAAAGATTGAAGACAAATTACTACATAAGG

                                                         
       8580 ATTTCTTACCCTTATCTTTTTCTTTTTCGTTATTTTATTTTTATT
         66 ATTTCTTACCCTTATCTTTTTCTTTTTCGTTATTTTATTTTTATT

                                          *                            *     
       8625 TTTTGGCGTCGTTGCCGGGGAAGGAAGGAATCAACAAAAGATTGAAGACAAATTACTACCTAAGG
          1 TTTTGGCGTCGTTGCCGGGGAAGGAAGGAAGCAACAAAAGATTGAAGACAAATTACTACATAAGG

                                                         
       8690 ATTTCTTACCCTTATCTTTTTCTTTTTCGTTATTTTATTTTTATT
         66 ATTTCTTACCCTTATCTTTTTCTTTTTCGTTATTTTATTTTTATT

               
       8735 TTT
          1 TTT

       8738 ATTTTTCGTT


Statistics
Matches: 109,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 110  109  1.00

ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41


Consensus pattern (110 bp):   
TTTTGGCGTCGTTGCCGGGGAAGGAAGGAAGCAACAAAAGATTGAAGACAAATTACTACATAAGG
ATTTCTTACCCTTATCTTTTTCTTTTTCGTTATTTTATTTTTATT

Found at i:12039 original size:6 final size:6

Alignment explanation


    Indices: 12028--12059  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

      12018 TATATTCTGC

                                                  
      12028 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT

      12060 TCTTTGCTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5    4  0.15
   6   22  0.85

ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:23277 original size:23 final size:21

Alignment explanation


    Indices: 23231--23278  Score: 53
    Period size: 23  Copynumber: 2.2  Consensus size: 21

      23221 TTGAGAAAAA

                               * 
      23231 TAATTACACTTACATGGTTGC
          1 TAATTACACTTACATGGTTAC

                                    
      23252 TAATTACCACTTACCAT-GTCTAC
          1 TAATTA-CACTTA-CATGGT-TAC

                
      23275 TAAT
          1 TAAT

      23279 AACAAATTTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  21    6  0.26
  22    8  0.35
  23    9  0.39

ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38


Consensus pattern (21 bp):   
TAATTACACTTACATGGTTAC

Found at i:39038 original size:10 final size:10

Alignment explanation


    Indices: 39023--39050  Score: 56
    Period size: 10  Copynumber: 2.8  Consensus size: 10

      39013 ATATATAAAA

                      
      39023 TAACTTTCAC
          1 TAACTTTCAC

                      
      39033 TAACTTTCAC
          1 TAACTTTCAC

                    
      39043 TAACTTTC
          1 TAACTTTC

      39051 TTCAAAAAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   18  1.00

ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43


Consensus pattern (10 bp):   
TAACTTTCAC
Done.