Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024291.1 Corchorus olitorius cultivar O-4 contig24324, 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: 9609
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31


Found at i:5417 original size:69 final size:68

Alignment explanation


    Indices: 5306--5444  Score: 208
    Period size: 69  Copynumber: 2.0  Consensus size: 68

       5296 ATCTAAAGTT

                     *              *                               *        
       5306 TTCTGTCCTGAGCATTGTGCTTACTTACTATTACATTATTGCAGCATATT-TATTAGATTTTATT
          1 TTCTGTCCTAAGCATTGTGCTTACCTACTATTACATTATTGCAGCATATTGT-TTACA-TTTATT

                 
       5370 TGAAA
         64 TGAAA

                  *                    *                                     
       5375 TTCTGTTCTAAGCATTGTGCTTACCTATTATTACATTATTGCAGCATATTGTTTACATTTATTTG
          1 TTCTGTCCTAAGCATTGTGCTTACCTACTATTACATTATTGCAGCATATTGTTTACATTTATTTG

               
       5440 AAA
         66 AAA

              
       5443 TT
          1 TT

       5445 TACTATATAC


Statistics
Matches: 64,  Mismatches: 5, Indels: 3
        0.89            0.07        0.04

Matches are distributed among these distances:
  68   13  0.20
  69   50  0.78
  70    1  0.02

ACGTcount: A:0.26, C:0.14, G:0.12, T:0.47


Consensus pattern (68 bp):   
TTCTGTCCTAAGCATTGTGCTTACCTACTATTACATTATTGCAGCATATTGTTTACATTTATTTG
AAA

Found at i:5721 original size:12 final size:12

Alignment explanation


    Indices: 5703--5737  Score: 52
    Period size: 12  Copynumber: 2.9  Consensus size: 12

       5693 GCATTGACTG

                   *    
       5703 AAATTCTTCCTC
          1 AAATTCTCCCTC

            *           
       5715 GAATTCTCCCTC
          1 AAATTCTCCCTC

                       
       5727 AAATTCTCCCT
          1 AAATTCTCCCT

       5738 GGTATGTTGA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.23, C:0.37, G:0.03, T:0.37


Consensus pattern (12 bp):   
AAATTCTCCCTC

Found at i:6644 original size:150 final size:150

Alignment explanation


    Indices: 6368--6656  Score: 542
    Period size: 150  Copynumber: 1.9  Consensus size: 150

       6358 CTAACCCATT

                                                           *                 
       6368 TGCGATGGACAATAGTTTGAATTCATAACAACTACGACGAATATTAATGCACTTGCGACGGACTA
          1 TGCGATGGACAATAGTTTGAATTCATAACAACTACGACGAATATTAACGCACTTGCGACGGACTA

                                                    *  *                     
       6433 ACACTAATCAACGACGGATAAATACAAACATTTCTAACAATTGTGACGTACAAATTCCAGTTCTG
         66 ACACTAATCAACGACGGATAAATACAAACATTTCTAACAACTGCGACGTACAAATTCCAGTTCTG

                                
       6498 CGACAGACATCTCGAACAAC
        131 CGACAGACATCTCGAACAAC

                                                                             
       6518 TGCGATGGACAATAGTTTGAATTCATAACAACTACGACGAATATTAACGCACTTGCGACGGACTA
          1 TGCGATGGACAATAGTTTGAATTCATAACAACTACGACGAATATTAACGCACTTGCGACGGACTA

                                                                    *        
       6583 ACACTAATCAACGACGGATAAATACAAACATTTCTAACAACTGCGACGTACAAATTGCAGTTCTG
         66 ACACTAATCAACGACGGATAAATACAAACATTTCTAACAACTGCGACGTACAAATTCCAGTTCTG

                     
       6648 CGACAGACA
        131 CGACAGACA

       6657 GCGACAGACA


Statistics
Matches: 135,  Mismatches: 4, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 150  135  1.00

ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23


Consensus pattern (150 bp):   
TGCGATGGACAATAGTTTGAATTCATAACAACTACGACGAATATTAACGCACTTGCGACGGACTA
ACACTAATCAACGACGGATAAATACAAACATTTCTAACAACTGCGACGTACAAATTCCAGTTCTG
CGACAGACATCTCGAACAAC

Found at i:9183 original size:19 final size:20

Alignment explanation


    Indices: 9147--9187  Score: 59
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       9137 ACCCAAAATT

                                
       9147 AAAAAGAAATATATAAAAGA
          1 AAAAAGAAATATATAAAAGA

                                 
       9167 AAAAAGAGAATA-A-AAAAGA
          1 AAAAAGA-AATATATAAAAGA

              
       9186 AA
          1 AA

       9188 GGGGAGAGAC


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  19    8  0.40
  20    8  0.40
  21    4  0.20

ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10


Consensus pattern (20 bp):   
AAAAAGAAATATATAAAAGA
Done.