Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012720.1 Corchorus olitorius cultivar O-4 contig12753, 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: 30178
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28


Found at i:98 original size:53 final size:53

Alignment explanation


    Indices: 18--148  Score: 262
    Period size: 53  Copynumber: 2.5  Consensus size: 53

          8 AGAGAGAGTT

                                                                 
         18 TATTTGCATCATCTTTGAAACAAATGTTTAATTTGTTTAATTTGGAAGTTGTG
          1 TATTTGCATCATCTTTGAAACAAATGTTTAATTTGTTTAATTTGGAAGTTGTG

                                                                 
         71 TATTTGCATCATCTTTGAAACAAATGTTTAATTTGTTTAATTTGGAAGTTGTG
          1 TATTTGCATCATCTTTGAAACAAATGTTTAATTTGTTTAATTTGGAAGTTGTG

                                     
        124 TATTTGCATCATCTTTGAAACAAAT
          1 TATTTGCATCATCTTTGAAACAAAT

        149 TATATAGAGA


Statistics
Matches: 78,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  53   78  1.00

ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46


Consensus pattern (53 bp):   
TATTTGCATCATCTTTGAAACAAATGTTTAATTTGTTTAATTTGGAAGTTGTG

Found at i:852 original size:41 final size:42

Alignment explanation


    Indices: 787--868  Score: 123
    Period size: 43  Copynumber: 2.0  Consensus size: 42

        777 AAGGGGAAAT

                 *                                    
        787 TTTATGTTTTTCGATTGTA-TTTTTTTTTCAAATATATTTAC
          1 TTTATATTTTTCGATTGTACTTTTTTTTTCAAATATATTTAC

                                                      
        828 TTTATATTTTT-GATTGTACCTTTTTTTTTTCAAATATATTT
          1 TTTATATTTTTCGATTGTA-C-TTTTTTTTTCAAATATATTT

        869 CTAAATTATC


Statistics
Matches: 37,  Mismatches: 1, Indels: 4
        0.88            0.02        0.10

Matches are distributed among these distances:
  40    7  0.19
  41   10  0.27
  43   20  0.54

ACGTcount: A:0.22, C:0.07, G:0.06, T:0.65


Consensus pattern (42 bp):   
TTTATATTTTTCGATTGTACTTTTTTTTTCAAATATATTTAC

Found at i:29259 original size:21 final size:20

Alignment explanation


    Indices: 29231--29278  Score: 62
    Period size: 21  Copynumber: 2.4  Consensus size: 20

      29221 ATCATGTAAA

                           *    
      29231 ATGC-AAATGTGAGATAAAT
          1 ATGCAAAATGTGAGACAAAT

                          *      
      29250 ATGCGAAAATGTGATACAAAT
          1 ATGC-AAAATGTGAGACAAAT

                    
      29271 ATGCAAAA
          1 ATGCAAAA

      29279 GAACGCAACA


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  19    4  0.16
  20    4  0.16
  21   17  0.68

ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23


Consensus pattern (20 bp):   
ATGCAAAATGTGAGACAAAT

Found at i:29435 original size:28 final size:28

Alignment explanation


    Indices: 29368--29503  Score: 86
    Period size: 27  Copynumber: 4.9  Consensus size: 28

      29358 ACTTAAGCAA

                    *       * *         
      29368 TGGA-GTAGAAATGACCACAATGCCCCC
          1 TGGATGTAAAAATGACTAAAATGCCCCC

                * * *                   
      29395 T-GAAGCACAAATGACTAAAATGCCCCC
          1 TGGATGTAAAAATGACTAAAATGCCCCC

                                          
      29422 TAGG-TGTAAAAATGACCT-AAATG-CCCC
          1 T-GGATGTAAAAATGA-CTAAAATGCCCCC

                   **            *      
      29449 TGGATGTGCAAATGACTAAAACG-CCCC
          1 TGGATGTAAAAATGACTAAAATGCCCCC

                  * *         *         
      29476 TGGATTTTGAAAATGACCCAAAATGCCC
          1 TGGA-TGTAAAAATGA-CTAAAATGCCC

      29504 ATAGATGACC


Statistics
Matches: 86,  Mismatches: 14, Indels: 15
        0.75            0.12        0.13

Matches are distributed among these distances:
  26    6  0.07
  27   47  0.55
  28   22  0.26
  29    9  0.10
  30    2  0.02

ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19


Consensus pattern (28 bp):   
TGGATGTAAAAATGACTAAAATGCCCCC

Found at i:29872 original size:50 final size:49

Alignment explanation


    Indices: 29783--30178  Score: 621
    Period size: 50  Copynumber: 7.9  Consensus size: 49

      29773 ATCCTCGAAT

                            *             *   *              
      29783 TTGGCTTGTGGAAAAGTCTATGTTGATAATCGACCCGTATGGAAACGAG
          1 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG

               *                         *                    
      29832 CTTTGCTTGTGGAAAAGCCTATGTTGATAGTTGACTCGTATGGAAACGAG
          1 -TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG

                             *                                
      29882 CTTGGCTTGTGGAAAAGTCTATGTTGATAATTGACTCGTATGGAAACGAG
          1 -TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG

                                                              
      29932 CTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG
          1 -TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG

                                                              
      29982 TGTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG
          1 T-TGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG

                    *           *                             
      30032 TTTGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAG
          1 -TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG

                                *                     *       
      30082 TTCGGCTTGTGGAAAAGCCTGTGTTGATAATTGACTCGTATGTAAACGAG
          1 TT-GGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG

                                *                *         
      30132 TTCGGCTTGTGGAAAAGCCTGTGTTGATAATTGACTCATATGGAAAC
          1 TT-GGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAAC


Statistics
Matches: 328,  Mismatches: 15, Indels: 6
        0.94            0.04        0.02

Matches are distributed among these distances:
  49    3  0.01
  50  324  0.99
  51    1  0.00

ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31


Consensus pattern (49 bp):   
TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAG

Done.