Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008766.1 Corchorus olitorius cultivar O-4 contig08793, 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, 605

Length: 1009
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:558 original size:21 final size:20

Alignment explanation


    Indices: 523--606  Score: 65
    Period size: 19  Copynumber: 4.3  Consensus size: 20

        513 CCGTTTAGTA

                                
        523 ATATT-TATAAT-TAAATAT
          1 ATATTATATAATATAAATAT

                                 
        541 ATATTATATATATATAAA-AT
          1 ATATTATATA-ATATAAATAT

                   *              
        561 AATATTAGAT-ATATATAAT-T
          1 -ATATTATATAATATA-AATAT

             *                  
        581 ACA-TATATAATA-AAATAT
          1 ATATTATATAATATAAATAT

                    
        599 ATAATTAT
          1 AT-ATTAT

        607 TAAACGGTTT


Statistics
Matches: 52,  Mismatches: 4, Indels: 18
        0.70            0.05        0.24

Matches are distributed among these distances:
  17    3  0.06
  18   12  0.23
  19   15  0.29
  20   10  0.19
  21   12  0.23

ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44


Consensus pattern (20 bp):   
ATATTATATAATATAAATAT

Found at i:588 original size:12 final size:12

Alignment explanation


    Indices: 528--605  Score: 74
    Period size: 12  Copynumber: 6.7  Consensus size: 12

        518 TAGTAATATT

                        
        528 TATAATTAAATA
          1 TATAATTAAATA

                    *   
        540 TAT-ATTATATA
          1 TATAATTAAATA

                  *     
        551 TAT-ATAAAATA
          1 TATAATTAAATA

                          
        562 -AT-ATTAGATATA
          1 TATAATTA-A-ATA

                    *   
        574 TATAATTACATA
          1 TATAATTAAATA

                  *     
        586 TATAATAAAATA
          1 TATAATTAAATA

                    
        598 TATAATTA
          1 TATAATTA

        606 TTAAACGGTT


Statistics
Matches: 54,  Mismatches: 8, Indels: 8
        0.77            0.11        0.11

Matches are distributed among these distances:
  10    5  0.09
  11   17  0.31
  12   26  0.48
  13    2  0.04
  14    4  0.07

ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42


Consensus pattern (12 bp):   
TATAATTAAATA
Done.