Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013357.1 Corchorus capsularis cultivar CVL-1 contig13378, 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: 49994
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:6132 original size:3 final size:3

Alignment explanation


    Indices: 6124--6155  Score: 57
    Period size: 3  Copynumber: 11.0  Consensus size: 3

       6114 GTAATATTAC

                                                       
       6124 AAG AAG AAG AAG AAG AAG AAG AAG AAG -AG AAG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG

       6156 GCTGGCTAGT


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2    2  0.07
   3   26  0.93

ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:7722 original size:21 final size:23

Alignment explanation


    Indices: 7680--7722  Score: 54
    Period size: 21  Copynumber: 2.0  Consensus size: 23

       7670 ACTTACTATA

                            **     
       7680 ATAATTATTATTAAAACTAAAAT
          1 ATAATTATTATTAAAAAGAAAAT

                                  
       7703 ATAATT-TT-TTAAAAAGAAAA
          1 ATAATTATTATTAAAAAGAAAA

       7723 CCCAGAGCTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  21   10  0.56
  22    2  0.11
  23    6  0.33

ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37


Consensus pattern (23 bp):   
ATAATTATTATTAAAAAGAAAAT

Found at i:18837 original size:3 final size:3

Alignment explanation


    Indices: 18826--18856  Score: 53
    Period size: 3  Copynumber: 10.3  Consensus size: 3

      18816 CAAGGAGGAT

                 *                                   
      18826 ATC AGC ATC ATC ATC ATC ATC ATC ATC ATC A
          1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A

      18857 GAATGGGTAT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.35, C:0.32, G:0.03, T:0.29


Consensus pattern (3 bp):   
ATC

Found at i:29435 original size:7 final size:7

Alignment explanation


    Indices: 29423--29449  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

      29413 GAGATACGCT

                   
      29423 AAAGGGA
          1 AAAGGGA

                   
      29430 AAAGGGA
          1 AAAGGGA

                   
      29437 AAAGGGA
          1 AAAGGGA

                  
      29444 AAAGGG
          1 AAAGGG

      29450 GCTTCCACAA


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:0.56, C:0.00, G:0.44, T:0.00


Consensus pattern (7 bp):   
AAAGGGA

Done.