Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023933.1 Corchorus olitorius cultivar O-4 contig23966, 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: 10853
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:5698 original size:74 final size:74

Alignment explanation


    Indices: 5607--5755  Score: 246
    Period size: 74  Copynumber: 2.0  Consensus size: 74

       5597 GTAAATAATG

                                                                       *     
       5607 TTAGGTGTGTTTCGCGTAGAATGACCTATGAAATTAGATAAAATTTAGGCCTGATTTGATATTGT
          1 TTAGGTGTGTTTCGCGTAGAATGACCTATGAAATTAGATAAAATTTAGGCCTGATTTGACATTGT

                     
       5672 GTTTGAAGA
         66 GTTTGAAGA

                                            *                  *         *   
       5681 TTAGGTGTG-TTCGGCGTAGAATGACCTATGAGATTAGATAAAATTTAGGCTTGATTTGACGTTG
          1 TTAGGTGTGTTTC-GCGTAGAATGACCTATGAAATTAGATAAAATTTAGGCCTGATTTGACATTG

                      
       5745 TGTTTGAAGA
         65 TGTTTGAAGA

             
       5755 T
          1 T

       5756 AAAAATACTG


Statistics
Matches: 70,  Mismatches: 4, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  73    3  0.04
  74   67  0.96

ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38


Consensus pattern (74 bp):   
TTAGGTGTGTTTCGCGTAGAATGACCTATGAAATTAGATAAAATTTAGGCCTGATTTGACATTGT
GTTTGAAGA

Found at i:8456 original size:7 final size:7

Alignment explanation


    Indices: 8444--8504  Score: 50
    Period size: 8  Copynumber: 8.0  Consensus size: 7

       8434 AGTTAGGGCA

                   
       8444 TTTTTTG
          1 TTTTTTG

                   
       8451 TTTTTTG
          1 TTTTTTG

                  **
       8458 TTTTGTCC
          1 TTTT-TTG

                   *
       8466 TTTTTATT
          1 TTTTT-TG

                    
       8474 TTTGTTTG
          1 TTT-TTTG

                    
       8482 TATTTTTG
          1 T-TTTTTG

                    
       8490 ATTTTTTG
          1 -TTTTTTG

                   
       8498 TTTTTTG
          1 TTTTTTG

       8505 GGTTGTGCTT


Statistics
Matches: 44,  Mismatches: 5, Indels: 10
        0.75            0.08        0.17

Matches are distributed among these distances:
   7   19  0.43
   8   20  0.45
   9    5  0.11

ACGTcount: A:0.05, C:0.03, G:0.13, T:0.79


Consensus pattern (7 bp):   
TTTTTTG

Found at i:8475 original size:20 final size:21

Alignment explanation


    Indices: 8445--8501  Score: 68
    Period size: 20  Copynumber: 2.9  Consensus size: 21

       8435 GTTAGGGCAT

                                 *
       8445 TTTTTG-TTTTTTGTTTTGTCC
          1 TTTTTGATTTTTTGTTTTGT-A

                                 
       8466 TTTTT-A-TTTTTG-TTTGTA
          1 TTTTTGATTTTTTGTTTTGTA

                              
       8484 TTTTTGATTTTTTGTTTT
          1 TTTTTGATTTTTTGTTTT

       8502 TTGGGTTGTG


Statistics
Matches: 31,  Mismatches: 1, Indels: 8
        0.77            0.03        0.20

Matches are distributed among these distances:
  18    5  0.16
  19    6  0.19
  20   12  0.39
  21    8  0.26

ACGTcount: A:0.05, C:0.04, G:0.12, T:0.79


Consensus pattern (21 bp):   
TTTTTGATTTTTTGTTTTGTA

Done.