Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020239.1 Corchorus olitorius cultivar O-4 contig20272, 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: 27870
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33


Found at i:30 original size:21 final size:22

Alignment explanation


    Indices: 4--53  Score: 59
    Period size: 21  Copynumber: 2.3  Consensus size: 22

          1 TTT

                    *              
          4 TTTTTAGCGTTTT-TTTTAA-TC
          1 TTTTTAG-ATTTTCTTTTAATTC

                                   
         25 TTTTTAGATTTTCTTTTAATTTC
          1 TTTTTAGATTTTCTTTTAA-TTC

                  
         48 TTTTTA
          1 TTTTTA

         54 TCTTTTAATA


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  20    4  0.16
  21   13  0.52
  23    8  0.32

ACGTcount: A:0.16, C:0.08, G:0.06, T:0.70


Consensus pattern (22 bp):   
TTTTTAGATTTTCTTTTAATTC

Found at i:582 original size:13 final size:13

Alignment explanation


    Indices: 566--591  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

        556 CATGTATGTA

                         
        566 TAATATTCTCTTT
          1 TAATATTCTCTTT

                         
        579 TAATATTCTCTTT
          1 TAATATTCTCTTT

        592 AAAATACCAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62


Consensus pattern (13 bp):   
TAATATTCTCTTT

Found at i:6808 original size:4 final size:4

Alignment explanation


    Indices: 6763--6801  Score: 78
    Period size: 4  Copynumber: 9.8  Consensus size: 4

       6753 AAAAAAAAAA

                                                            
       6763 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
          1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA

       6802 AAGAAAGTTA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   35  1.00

ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00


Consensus pattern (4 bp):   
AAAG

Found at i:11903 original size:13 final size:13

Alignment explanation


    Indices: 11885--11911  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

      11875 CTTTAACTTT

                         
      11885 CCTTTTTTAGAAG
          1 CCTTTTTTAGAAG

                         
      11898 CCTTTTTTAGAAG
          1 CCTTTTTTAGAAG

             
      11911 C
          1 C

      11912 AAACGTAGTC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44


Consensus pattern (13 bp):   
CCTTTTTTAGAAG

Found at i:16327 original size:65 final size:65

Alignment explanation


    Indices: 16250--16382  Score: 257
    Period size: 65  Copynumber: 2.0  Consensus size: 65

      16240 CTTTCTCTCC

                                                                             
      16250 AAAAATCCCAACCATATCTCTGCAATTTCATCATCATCAAACAAACCCAGATTATTGTTACAAAG
          1 AAAAATCCCAACCATATCTCTGCAATTTCATCATCATCAAACAAACCCAGATTATTGTTACAAAG

                         *                                                   
      16315 AAAAATCCCAACCCTATCTCTGCAATTTCATCATCATCAAACAAACCCAGATTATTGTTACAAAG
          1 AAAAATCCCAACCATATCTCTGCAATTTCATCATCATCAAACAAACCCAGATTATTGTTACAAAG

               
      16380 AAA
          1 AAA

      16383 GCCCATATTC


Statistics
Matches: 67,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  65   67  1.00

ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26


Consensus pattern (65 bp):   
AAAAATCCCAACCATATCTCTGCAATTTCATCATCATCAAACAAACCCAGATTATTGTTACAAAG

Found at i:23881 original size:89 final size:88

Alignment explanation


    Indices: 23664--23926  Score: 422
    Period size: 89  Copynumber: 2.9  Consensus size: 88

      23654 GATTTTGGTT

                         *                                                   
      23664 ATGATTAGGGTTTAACTGTGTCTGGGTATTAGTTCATTTATTATGTTTTTTGATAACTTCAACTC
          1 ATGATTAGGGTTTCACTGTGTCTGGGTATTAGTTCA--T-TTATGTTTTTTGATAACTTCAACTC

                                      
      23729 GAATGCAAAATTAATTT-GTTCGGTG
         63 GAATGCAAAATTAATTTAGTTCGGTG

              *                                                            * 
      23754 ATTATTAGGGTTTCACTGTGTCTGGGTATTAGTTCATTTATGTTTTTTGATAACTTCAACTCGTA
          1 ATGATTAGGGTTTCACTGTGTCTGGGTATTAGTTCATTTATGTTTTTTGATAACTTCAACTCGAA

                                    
      23819 TGCAAAATTAATTTAAGTTCGGTG
         66 TGCAAAATTAATTT-AGTTCGGTG

                                              *                              
      23843 ATGATTAGGGTTTCACTGTGTCTGGGTATTCA-TACATTTATGTTTTTTGATAACTTCAACTCGA
          1 ATGATTAGGGTTTCACTGTGTCTGGGTATT-AGTTCATTTATGTTTTTTGATAACTTCAACTCGA

                                
      23907 ATGCAAAATTAATTTTAGTT
         65 ATGCAAAATTAA-TTTAGTT

      23927 GTTTCTTTCT


Statistics
Matches: 163,  Mismatches: 6, Indels: 9
        0.92            0.03        0.05

Matches are distributed among these distances:
  87   41  0.25
  88    1  0.01
  89   83  0.51
  90   38  0.23

ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44


Consensus pattern (88 bp):   
ATGATTAGGGTTTCACTGTGTCTGGGTATTAGTTCATTTATGTTTTTTGATAACTTCAACTCGAA
TGCAAAATTAATTTAGTTCGGTG
Done.