Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011970.1 Corchorus capsularis cultivar CVL-1 contig11991, 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: 27827
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:481 original size:30 final size:30

Alignment explanation


    Indices: 414--485  Score: 83
    Period size: 29  Copynumber: 2.4  Consensus size: 30

        404 ACACCGAACC

                                    ****  
        414 GTCAAATAAGCCCCTGAACTATTATTTCAA
          1 GTCAAATAAGCCCCTGAACTATTAAAAAAA

             *                  *         
        444 -CCAAATAAGCCCCTGAACTCTTAAAAAAA
          1 GTCAAATAAGCCCCTGAACTATTAAAAAAA

                         
        473 GTCAAATAAGCCC
          1 GTCAAATAAGCCC

        486 TGTTGCCAAG


Statistics
Matches: 34,  Mismatches: 7, Indels: 2
        0.79            0.16        0.05

Matches are distributed among these distances:
  29   23  0.68
  30   11  0.32

ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22


Consensus pattern (30 bp):   
GTCAAATAAGCCCCTGAACTATTAAAAAAA

Found at i:9760 original size:5 final size:5

Alignment explanation


    Indices: 9750--9774  Score: 50
    Period size: 5  Copynumber: 5.0  Consensus size: 5

       9740 ACGTGTGCTC

                                         
       9750 TCTCA TCTCA TCTCA TCTCA TCTCA
          1 TCTCA TCTCA TCTCA TCTCA TCTCA

       9775 GTATTTTGCT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   20  1.00

ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40


Consensus pattern (5 bp):   
TCTCA

Found at i:14077 original size:7 final size:7

Alignment explanation


    Indices: 14065--14095  Score: 62
    Period size: 7  Copynumber: 4.4  Consensus size: 7

      14055 AAGTAAAGTA

                   
      14065 ATACTCC
          1 ATACTCC

                   
      14072 ATACTCC
          1 ATACTCC

                   
      14079 ATACTCC
          1 ATACTCC

                   
      14086 ATACTCC
          1 ATACTCC

               
      14093 ATA
          1 ATA

      14096 GAGTTGGGAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   24  1.00

ACGTcount: A:0.32, C:0.39, G:0.00, T:0.29


Consensus pattern (7 bp):   
ATACTCC

Found at i:15016 original size:6 final size:6

Alignment explanation


    Indices: 15005--15032  Score: 56
    Period size: 6  Copynumber: 4.7  Consensus size: 6

      14995 AATATCTATC

                                            
      15005 CATTTT CATTTT CATTTT CATTTT CATT
          1 CATTTT CATTTT CATTTT CATTTT CATT

      15033 GATGATTGAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64


Consensus pattern (6 bp):   
CATTTT

Found at i:19737 original size:2 final size:2

Alignment explanation


    Indices: 19730--19754  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      19720 TTGAAACATG

                                                 
      19730 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

      19755 GGTGTATGGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.