Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006121.1 Corchorus capsularis cultivar CVL-1 contig06139, 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: 29510
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:786 original size:18 final size:18

Alignment explanation


    Indices: 748--803  Score: 51
    Period size: 18  Copynumber: 2.9  Consensus size: 18

        738 CTCACCAAAT

                                
        748 TTTTTTTGAAAAAAATTATA
          1 TTTTTTT-AAAAAAA-TATA

                    *          
        768 TATTTTTTTAAAAAA-ATA
          1 T-TTTTTTAAAAAAATATA

                  *           
        786 TTTTTTAATAAAAAATAT
          1 TTTTTTTA-AAAAAATAT

        804 GACGTGGCAT


Statistics
Matches: 30,  Mismatches: 3, Indels: 7
        0.75            0.08        0.17

Matches are distributed among these distances:
  17    5  0.17
  18   10  0.33
  19    2  0.07
  20    7  0.23
  21    6  0.20

ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50


Consensus pattern (18 bp):   
TTTTTTTAAAAAAATATA

Found at i:798 original size:17 final size:16

Alignment explanation


    Indices: 767--803  Score: 56
    Period size: 16  Copynumber: 2.2  Consensus size: 16

        757 AAAAAATTAT

                     *      
        767 ATATTTTTTTAAAAAA
          1 ATATTTTTTAAAAAAA

                             
        783 ATATTTTTTAATAAAAA
          1 ATATTTTTTAA-AAAAA

                
        800 ATAT
          1 ATAT

        804 GACGTGGCAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  16   10  0.53
  17    9  0.47

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (16 bp):   
ATATTTTTTAAAAAAA

Found at i:29293 original size:21 final size:22

Alignment explanation


    Indices: 29267--29309  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

      29257 TTTACGTGAA

                                  
      29267 TTACTAAATACCGCCC-CCTTT
          1 TTACTAAATACCGCCCTCCTTT

                  **              
      29288 TTACTAGGTACCGCCCTCCTTT
          1 TTACTAAATACCGCCCTCCTTT

      29310 GGACAATTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   14  0.74
  22    5  0.26

ACGTcount: A:0.19, C:0.37, G:0.09, T:0.35


Consensus pattern (22 bp):   
TTACTAAATACCGCCCTCCTTT
Done.