Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014498.1 Corchorus capsularis cultivar CVL-1 contig14519, 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: 13819
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33


Found at i:40 original size:2 final size:2

Alignment explanation


    Indices: 33--62  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

         23 TAAATGAATG

                                                        
         33 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         63 TTACCTTGGT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:2702 original size:13 final size:13

Alignment explanation


    Indices: 2684--2709  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       2674 TATATATAAT

                         
       2684 CTATAATCTATAC
          1 CTATAATCTATAC

                         
       2697 CTATAATCTATAC
          1 CTATAATCTATAC

       2710 TAATTATAAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38


Consensus pattern (13 bp):   
CTATAATCTATAC

Found at i:8561 original size:18 final size:19

Alignment explanation


    Indices: 8540--8589  Score: 50
    Period size: 18  Copynumber: 2.7  Consensus size: 19

       8530 ACTCAGACTC

                        *      
       8540 AAAACTAACTGACTTAAAA
          1 AAAACTAACTGAATTAAAA

                             *  
       8559 AAAACTGAACT-AATT-CAA
          1 AAAACT-AACTGAATTAAAA

                  *      
       8577 AAAACTGACTGAA
          1 AAAACTAACTGAA

       8590 CCCAACATAT


Statistics
Matches: 26,  Mismatches: 3, Indels: 5
        0.76            0.09        0.15

Matches are distributed among these distances:
  17    3  0.12
  18   10  0.38
  19    9  0.35
  20    4  0.15

ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20


Consensus pattern (19 bp):   
AAAACTAACTGAATTAAAA

Found at i:9503 original size:7 final size:7

Alignment explanation


    Indices: 9491--9517  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

       9481 TGTAGTCTAA

                   
       9491 TCACAAC
          1 TCACAAC

                   
       9498 TCACAAC
          1 TCACAAC

                   
       9505 TCACAAC
          1 TCACAAC

                  
       9512 TCACAA
          1 TCACAA

       9518 TAATGAAACA


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

Matches are distributed among these distances:
   7   20  1.00

ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15


Consensus pattern (7 bp):   
TCACAAC

Done.