Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012831.1 Corchorus olitorius cultivar O-4 contig12864, 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: 24647
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33


Found at i:2940 original size:14 final size:14

Alignment explanation


    Indices: 2912--2956  Score: 58
    Period size: 15  Copynumber: 3.3  Consensus size: 14

       2902 TAAAAGTCTC

                          
       2912 AAAACC-TTT-TTG
          1 AAAACCTTTTCTTG

                          
       2924 AAAACCTTTTCTTG
          1 AAAACCTTTTCTTG

                  *        
       2938 AAAACAATTTTCTTG
          1 AAAAC-CTTTTCTTG

                
       2953 AAAA
          1 AAAA

       2957 ACATGTTTTG


Statistics
Matches: 29,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  12    6  0.21
  13    3  0.10
  14    8  0.28
  15   12  0.41

ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38


Consensus pattern (14 bp):   
AAAACCTTTTCTTG

Found at i:11673 original size:27 final size:27

Alignment explanation


    Indices: 11643--11716  Score: 103
    Period size: 27  Copynumber: 2.7  Consensus size: 27

      11633 TTGAACTAAA

                                       
      11643 AAATGACCAAAATGCCCCTGAACGTGC
          1 AAATGACCAAAATGCCCCTGAACGTGC

                        *     * * *   *
      11670 AAATGACCAAAACGCCCCAGGATGTGT
          1 AAATGACCAAAATGCCCCTGAACGTGC

                                
      11697 AAATGACCAAAATGCCCCTG
          1 AAATGACCAAAATGCCCCTG

      11717 GGTGCCCCTA


Statistics
Matches: 40,  Mismatches: 7, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  27   40  1.00

ACGTcount: A:0.38, C:0.28, G:0.19, T:0.15


Consensus pattern (27 bp):   
AAATGACCAAAATGCCCCTGAACGTGC

Found at i:16040 original size:19 final size:18

Alignment explanation


    Indices: 16003--16042  Score: 53
    Period size: 19  Copynumber: 2.2  Consensus size: 18

      15993 TTCTTGAAAT

                        *     
      16003 AATTCTTCAATGGTCTTC
          1 AATTCTTCAATGATCTTC

                        *      
      16021 AATTCTTCTAATTATCTTC
          1 AATTCTTC-AATGATCTTC

               
      16040 AAT
          1 AAT

      16043 AAATCTTCAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18    8  0.42
  19   11  0.58

ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47


Consensus pattern (18 bp):   
AATTCTTCAATGATCTTC

Found at i:21307 original size:22 final size:22

Alignment explanation


    Indices: 21282--21326  Score: 72
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      21272 CGGCCTCCAG

                        *     *   
      21282 GGAAGGAGTTCAGCAGAAGATT
          1 GGAAGGAGTTCAACAGAAAATT

                                  
      21304 GGAAGGAGTTCAACAGAAAATT
          1 GGAAGGAGTTCAACAGAAAATT

             
      21326 G
          1 G

      21327 ATGAGGAGAG


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.40, C:0.09, G:0.33, T:0.18


Consensus pattern (22 bp):   
GGAAGGAGTTCAACAGAAAATT
Done.