Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020325.1 Corchorus olitorius cultivar O-4 contig20358, 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: 19585
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:3071 original size:13 final size:13

Alignment explanation


    Indices: 3053--3077  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       3043 TCCATATTAA

                         
       3053 TTTATTTTTTATT
          1 TTTATTTTTTATT

                        
       3066 TTTATTTTTTAT
          1 TTTATTTTTTAT

       3078 AAGTACCTAC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84


Consensus pattern (13 bp):   
TTTATTTTTTATT

Found at i:5340 original size:13 final size:13

Alignment explanation


    Indices: 5322--5354  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       5312 AATAATATTT

                         
       5322 AACTATTTGAAGG
          1 AACTATTTGAAGG

                         
       5335 AACTATTTGAAGG
          1 AACTATTTGAAGG

              *    
       5348 AAATATT
          1 AACTATT

       5355 ACAAGAGTAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33


Consensus pattern (13 bp):   
AACTATTTGAAGG

Found at i:5679 original size:35 final size:35

Alignment explanation


    Indices: 5607--5682  Score: 98
    Period size: 35  Copynumber: 2.2  Consensus size: 35

       5597 AACATGTCCC

                     *                     *   
       5607 TGTTGGCCATTATTAACTAAGCTTTCCATGATACT
          1 TGTTGGCCACTATTAACTAAGCTTTCCATGACACT

                    *     *               * *  
       5642 TGTTGGCCCCTATTGACTAAGCTTTCCATGGCGCT
          1 TGTTGGCCACTATTAACTAAGCTTTCCATGACACT

                  
       5677 TGTTGG
          1 TGTTGG

       5683 GAGAACTCAA


Statistics
Matches: 35,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  35   35  1.00

ACGTcount: A:0.18, C:0.22, G:0.21, T:0.38


Consensus pattern (35 bp):   
TGTTGGCCACTATTAACTAAGCTTTCCATGACACT

Found at i:9800 original size:3 final size:3

Alignment explanation


    Indices: 9792--9817  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       9782 CTTTTAAGAA

                                              
       9792 ATT ATT ATT ATT ATT ATT ATT ATT AT
          1 ATT ATT ATT ATT ATT ATT ATT ATT AT

       9818 ATCTATATAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
ATT

Found at i:11180 original size:6 final size:6

Alignment explanation


    Indices: 11169--11215  Score: 85
    Period size: 6  Copynumber: 7.7  Consensus size: 6

      11159 AATAAACTCC

                                                                  
      11169 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCTT TTTTCT TTTTCT TTTT
          1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT TTTT

      11216 ACCTAGATAA


Statistics
Matches: 40,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   6   34  0.85
   7    6  0.15

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (6 bp):   
TTTTCT

Found at i:17886 original size:21 final size:22

Alignment explanation


    Indices: 17862--17902  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

      17852 GTTTATAATA

                *                 
      17862 TTCTTGGGTCA-TCGGGTTATC
          1 TTCTCGGGTCATTCGGGTTATC

                     *          
      17883 TTCTCGGGTTATTCGGGTTA
          1 TTCTCGGGTCATTCGGGTTA

      17903 CGAGTTTGTC


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    9  0.53
  22    8  0.47

ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44


Consensus pattern (22 bp):   
TTCTCGGGTCATTCGGGTTATC
Done.