Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017700.1 Corchorus olitorius cultivar O-4 contig17733, 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: 12945
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31


Found at i:3627 original size:21 final size:21

Alignment explanation


    Indices: 3601--3692  Score: 125
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       3591 AGGGATCGAG

                          *       
       3601 CTGGGCGCTGA-GCCTTGTCGC
          1 CTGGGCGCTGAGGCATT-TCGC

                          *       
       3622 CTGGGCGCTGA-GCCTTGTCGC
          1 CTGGGCGCTGAGGCATT-TCGC

                                *
       3643 CTGGGCGCTGAGGCATTTCGT
          1 CTGGGCGCTGAGGCATTTCGC

                                 
       3664 CTGGGCGCTGAGGCATTTCGC
          1 CTGGGCGCTGAGGCATTTCGC

                    
       3685 CTGGGCGC
          1 CTGGGCGC

       3693 CCAGCGGCAG


Statistics
Matches: 67,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  21   63  0.94
  22    4  0.06

ACGTcount: A:0.07, C:0.30, G:0.39, T:0.24


Consensus pattern (21 bp):   
CTGGGCGCTGAGGCATTTCGC

Found at i:11927 original size:109 final size:109

Alignment explanation


    Indices: 11736--11953  Score: 386
    Period size: 109  Copynumber: 2.0  Consensus size: 109

      11726 TAGTCATTTT

                                                                             
      11736 GGTGCTTGTATTTTTCTTTAAACCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
          1 GGTGCTTGTATTTTTCTTTAAACCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT

                                                        
      11801 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
         66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA

                                  *                                          
      11845 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCA-TGTTGTATTGTTTGGTAT-TAGTGC
          1 GGTGCTTGTATTTTTCTTTAAACCCAATAGTTCATTGCACT-TTGTATTGTTTGGTATGT-GTGC

                                       *                  
      11908 TTATTTAATAGGTTCAATTGAATAAACCACACAATTAATAATAATA
         64 TTATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA

      11954 TATAACAAGT


Statistics
Matches: 105,  Mismatches: 2, Indels: 4
        0.95            0.02        0.04

Matches are distributed among these distances:
 108    2  0.02
 109  103  0.98

ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43


Consensus pattern (109 bp):   
GGTGCTTGTATTTTTCTTTAAACCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA

Found at i:12079 original size:21 final size:22

Alignment explanation


    Indices: 12055--12096  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 22

      12045 TTCAAAAATT

                                  
      12055 TGTAATTTTATTAGT-ATTTTG
          1 TGTAATTTTATTAGTAATTTTG

                        *        
      12076 TGTAATTTTATTTGTAATTTT
          1 TGTAATTTTATTAGTAATTTT

      12097 ATAGATATTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21   14  0.74
  22    5  0.26

ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64


Consensus pattern (22 bp):   
TGTAATTTTATTAGTAATTTTG

Found at i:12093 original size:12 final size:12

Alignment explanation


    Indices: 12052--12098  Score: 55
    Period size: 12  Copynumber: 4.2  Consensus size: 12

      12042 CGTTTCAAAA

                        
      12052 ATTTGTAATTTT
          1 ATTTGTAATTTT

               *        
      12064 ATTAGT-A-TTT
          1 ATTTGTAATTTT

              *         
      12074 -TGTGTAATTTT
          1 ATTTGTAATTTT

                        
      12085 ATTTGTAATTTT
          1 ATTTGTAATTTT

              
      12097 AT
          1 AT

      12099 AGATATTTCT


Statistics
Matches: 28,  Mismatches: 4, Indels: 6
        0.74            0.11        0.16

Matches are distributed among these distances:
   9    3  0.11
  10    4  0.14
  11    4  0.14
  12   17  0.61

ACGTcount: A:0.26, C:0.00, G:0.11, T:0.64


Consensus pattern (12 bp):   
ATTTGTAATTTT
Done.