Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020451.1 Corchorus olitorius cultivar O-4 contig20484, 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: 6744
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:27 original size:10 final size:9

Alignment explanation


    Indices: 9--35  Score: 54
    Period size: 9  Copynumber: 3.0  Consensus size: 9

          1 TGCCGCGG

                     
          9 TTATTTTTT
          1 TTATTTTTT

                     
         18 TTATTTTTT
          1 TTATTTTTT

                     
         27 TTATTTTTT
          1 TTATTTTTT

         36 AATTATTAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   18  1.00

ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89


Consensus pattern (9 bp):   
TTATTTTTT

Found at i:4592 original size:13 final size:13

Alignment explanation


    Indices: 4574--4603  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       4564 TTTTGGTGTA

                         
       4574 TATATTATTATAT
          1 TATATTATTATAT

                         
       4587 TATATTATTATAT
          1 TATATTATTATAT

                
       4600 TATA
          1 TATA

       4604 ATAGTAAACA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60


Consensus pattern (13 bp):   
TATATTATTATAT

Found at i:4807 original size:18 final size:20

Alignment explanation


    Indices: 4770--4808  Score: 55
    Period size: 19  Copynumber: 2.0  Consensus size: 20

       4760 AACATAACAA

                         *      
       4770 AATTTCTTTTTGAGTATAAT
          1 AATTTCTTTTTGACTATAAT

                                
       4790 AATTT-TTTTTGACT-TAAT
          1 AATTTCTTTTTGACTATAAT

             
       4808 A
          1 A

       4809 CCTTTTTTAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  18    5  0.28
  19    8  0.44
  20    5  0.28

ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56


Consensus pattern (20 bp):   
AATTTCTTTTTGACTATAAT

Found at i:5167 original size:26 final size:26

Alignment explanation


    Indices: 5137--5197  Score: 86
    Period size: 26  Copynumber: 2.3  Consensus size: 26

       5127 GCAAGAGCTT

                                      
       5137 AATTAACTAATCAATAAAATACCTTA
          1 AATTAACTAATCAATAAAATACCTTA

                         * *         *
       5163 AATTAACTAATCATTCAAATACCTTT
          1 AATTAACTAATCAATAAAATACCTTA

            *        
       5189 GATTAACTA
          1 AATTAACTA

       5198 TACGTAAAGT


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  26   31  1.00

ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34


Consensus pattern (26 bp):   
AATTAACTAATCAATAAAATACCTTA
Done.