Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016611.1 Corchorus olitorius cultivar O-4 contig16644, 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: 9368
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:1839 original size:21 final size:21

Alignment explanation


    Indices: 1815--1881  Score: 57
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       1805 AATTCTCTGT

                                 
       1815 AAATTAAGAAATACTCAACTC
          1 AAATTAAGAAATACTCAACTC

                *         *   **  *
       1836 AAATCATAGAAA-ATTC-TTTGT
          1 AAATTA-AGAAATACTCAACT-C

                                 
       1857 AAATTAAGAAATACTCAACTC
          1 AAATTAAGAAATACTCAACTC

                
       1878 AAAT
          1 AAAT

       1882 CTCAAATCCT


Statistics
Matches: 32,  Mismatches: 10, Indels: 8
        0.64            0.20        0.16

Matches are distributed among these distances:
  20    6  0.19
  21   20  0.62
  22    6  0.19

ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28


Consensus pattern (21 bp):   
AAATTAAGAAATACTCAACTC

Found at i:1861 original size:42 final size:42

Alignment explanation


    Indices: 1802--1882  Score: 153
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       1792 GCTAAGTCTT

                                                      
       1802 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
          1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA

                     *                             
       1844 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
          1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC

       1883 TCAAATCCTG


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  42   38  1.00

ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30


Consensus pattern (42 bp):   
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA

Found at i:2026 original size:56 final size:56

Alignment explanation


    Indices: 1954--2061  Score: 189
    Period size: 56  Copynumber: 1.9  Consensus size: 56

       1944 TTTATTTTGT

                                        *            *              
       1954 AGAATAATTAAATAGAGATAGGGGGATATGATTTATTATAATATTTATTGTGCAAA
          1 AGAATAATTAAATAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGCAAA

                       *                                        
       2010 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTG
          1 AGAATAATTAAATAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTG

       2062 TGAAAGGAAA


Statistics
Matches: 49,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  56   49  1.00

ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35


Consensus pattern (56 bp):   
AGAATAATTAAATAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGCAAA

Found at i:2255 original size:2 final size:2

Alignment explanation


    Indices: 2248--2281  Score: 59
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       2238 TTTCAAAATA

                                                              
       2248 AT AT AT AT AT AGT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A

       2282 GCAATGAAGC


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   29  0.94
   3    2  0.06

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:6157 original size:2 final size:2

Alignment explanation


    Indices: 6150--6219  Score: 95
    Period size: 2  Copynumber: 35.0  Consensus size: 2

       6140 CATGAAATAG

                                       *      *                          *
       6150 AT AT AT AT AT AT AT AT AT GT AT AC AT AT AT AT AT AT AT AT AC
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

             *     *                                 
       6192 AC AT AC 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

       6220 GTTAGAAAAT


Statistics
Matches: 60,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   60  1.00

ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44


Consensus pattern (2 bp):   
AT

Done.