Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023840.1 Corchorus olitorius cultivar O-4 contig23873, 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: 14203
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:4876 original size:39 final size:40

Alignment explanation


    Indices: 4820--4900  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       4810 TTTAATTCCT

                                                    
       4820 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

                     *          *                   
       4860 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

              
       4899 AT
          1 AT

       4901 TCTTAGGTAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:5252 original size:204 final size:206

Alignment explanation


    Indices: 5010--5425  Score: 748
    Period size: 208  Copynumber: 2.0  Consensus size: 206

       5000 TTCCTTAATA

                                                                             
       5010 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
          1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA

                                                               *             
       5075 ATTTAATAAATCAACCACTAATGTTCAACTA-ATTTTTTTTGGTATAG-TTCTATA-TATATAAT
         66 ATTTAATAAATCAACCACTAATGTTCAACTACATTTTTTTTGGTATAGTTTATATATTATATAAT

             *                                                               
       5137 AGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC
        131 AATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC

                       
       5202 ATTCACCATTG
        196 ATTCACCATTG

                      *                                                      
       5213 ATAAATAAATTGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
          1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT

                                   *         *                               
       5278 AATTTAATAAATCAACCACTAATTTTCAACTACTTTTTTTTTGGTATAGTTTTATATATTATATA
         65 AATTTAATAAATCAACCACTAATGTTCAACTACATTTTTTTTGGTATAG-TTTATATATTATATA

                                                                             
       5343 ATAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATA
        129 ATAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATA

                         
       5408 ACATTCACCATTG
        194 ACATTCACCATTG

                 
       5421 ATAAA
          1 ATAAA

       5426 GTTATTAAGC


Statistics
Matches: 203,  Mismatches: 5, Indels: 5
        0.95            0.02        0.02

Matches are distributed among these distances:
 203   15  0.07
 204   79  0.39
 205   15  0.07
 207    6  0.03
 208   88  0.43

ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45


Consensus pattern (206 bp):   
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTACATTTTTTTTGGTATAGTTTATATATTATATAAT
AATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC
ATTCACCATTG

Found at i:5986 original size:35 final size:36

Alignment explanation


    Indices: 5940--6008  Score: 113
    Period size: 35  Copynumber: 1.9  Consensus size: 36

       5930 GAGATTTTGG

                         *      *               
       5940 AGAAATATGATAATCAAAATTACAAAA-ATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAGATGTAATA

                                              
       5975 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAGATGTAA

       6009 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  35   25  0.81
  36    6  0.19

ACGTcount: A:0.59, C:0.09, G:0.10, T:0.22


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAGATGTAATA

Found at i:11220 original size:5 final size:5

Alignment explanation


    Indices: 11210--11238  Score: 58
    Period size: 5  Copynumber: 5.8  Consensus size: 5

      11200 CCTTCTGTGT

                                              
      11210 CAGAA CAGAA CAGAA CAGAA CAGAA CAGA
          1 CAGAA CAGAA CAGAA CAGAA CAGAA CAGA

      11239 GAGTTGAAAA


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

Matches are distributed among these distances:
   5   24  1.00

ACGTcount: A:0.59, C:0.21, G:0.21, T:0.00


Consensus pattern (5 bp):   
CAGAA

Found at i:13533 original size:12 final size:13

Alignment explanation


    Indices: 13516--13544  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

      13506 ATTAGCTTTT

                         
      13516 AAAA-TTAAAAAA
          1 AAAATTTAAAAAA

                         
      13528 AAAATTTAAAAAA
          1 AAAATTTAAAAAA

                
      13541 AAAA
          1 AAAA

      13545 GAAGAAAAGC


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12    4  0.25
  13   12  0.75

ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17


Consensus pattern (13 bp):   
AAAATTTAAAAAA
Done.