Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013764.1 Corchorus olitorius cultivar O-4 contig13797, 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: 1717
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34


Found at i:814 original size:21 final size:21

Alignment explanation


    Indices: 790--856  Score: 57
    Period size: 21  Copynumber: 3.2  Consensus size: 21

        780 AATTCTCTGT

                                 
        790 AAATTAAGAAATACTCAACTC
          1 AAATTAAGAAATACTCAACTC

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

                                 
        832 AAATTAAGAAATACTCAACTC
          1 AAATTAAGAAATACTCAACTC

                
        853 AAAT
          1 AAAT

        857 CCTAATCCTT


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:836 original size:42 final size:42

Alignment explanation


    Indices: 777--857  Score: 153
    Period size: 42  Copynumber: 1.9  Consensus size: 42

        767 GCTAAGTCTT

                                                      
        777 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
          1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA

                     *                             
        819 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
          1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC

        858 CTAATCCTTA


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:995 original size:56 final size:56

Alignment explanation


    Indices: 923--1091  Score: 329
    Period size: 56  Copynumber: 3.0  Consensus size: 56

        913 TTTATTTTGT

                                                                    
        923 AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA

                                        *                           
        979 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA

                                                                    
       1035 AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA

             
       1091 A
          1 A

       1092 AGGAAACGAA


Statistics
Matches: 111,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  56  111  1.00

ACGTcount: A:0.40, C:0.02, G:0.24, T:0.35


Consensus pattern (56 bp):   
AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA

Found at i:1287 original size:7 final size:7

Alignment explanation


    Indices: 1275--1303  Score: 51
    Period size: 7  Copynumber: 4.3  Consensus size: 7

       1265 AAATAATATG

                   
       1275 TAGTATA
          1 TAGTATA

                   
       1282 TAGTATA
          1 TAGTATA

                   
       1289 TAGTATA
          1 TAGTATA

                   
       1296 TA-TATA
          1 TAGTATA

              
       1302 TA
          1 TA

       1304 TTATCATAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6    6  0.27
   7   16  0.73

ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45


Consensus pattern (7 bp):   
TAGTATA

Found at i:1294 original size:14 final size:13

Alignment explanation


    Indices: 1270--1303  Score: 50
    Period size: 14  Copynumber: 2.5  Consensus size: 13

       1260 GTTTCAAATA

                *        
       1270 ATATGTAGTATAT
          1 ATATATAGTATAT

                          
       1283 AGTATATAGTATAT
          1 A-TATATAGTATAT

                   
       1297 ATATATA
          1 ATATATA

       1304 TTATCATAAA


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

Matches are distributed among these distances:
  13    7  0.37
  14   12  0.63

ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44


Consensus pattern (13 bp):   
ATATATAGTATAT
Done.