Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022979.1 Corchorus olitorius cultivar O-4 contig23012, 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: 12574
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32


Found at i:1995 original size:76 final size:76

Alignment explanation


    Indices: 1902--2052  Score: 205
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       1892 TGATGAGCTA

                        *           *                                        
       1902 TGACACAGCCCATCTGGGTGATCAGGCAAAACACATGGGTCTTCAA-ACAAACCATGTGGGCACC
          1 TGACACAGCCCACCTGGGTGATCAAGCAAAACACATGGGTCTTCAAGAC-AACCATGTGGGCACC

                        
       1966 CAACTGGAGTCG
         65 CAACTGGAGTCG

                  *            *          *         *      *                 
       1978 TGACACTGCCCACCTGGGTTATCAAGCAAACCACATGGGTGTTCAAGGCAACCATGTGGGCACCC
          1 TGACACAGCCCACCTGGGTGATCAAGCAAAACACATGGGTCTTCAAGACAACCATGTGGGCACCC

             **       
       2043 AGGTGGAGTC
         66 AACTGGAGTC

       2053 AGGGTCCTTG


Statistics
Matches: 65,  Mismatches: 9, Indels: 2
        0.86            0.12        0.03

Matches are distributed among these distances:
  76   64  0.98
  77    1  0.02

ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18


Consensus pattern (76 bp):   
TGACACAGCCCACCTGGGTGATCAAGCAAAACACATGGGTCTTCAAGACAACCATGTGGGCACCC
AACTGGAGTCG

Found at i:4545 original size:18 final size:18

Alignment explanation


    Indices: 4522--4558  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       4512 CTCCTCTTGC

                     *        
       4522 ATGAAAACACTTGTTTTT
          1 ATGAAAACAATTGTTTTT

                        *     
       4540 ATGAAAACAATTTTTTTT
          1 ATGAAAACAATTGTTTTT

             
       4558 A
          1 A

       4559 ACTACCCTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46


Consensus pattern (18 bp):   
ATGAAAACAATTGTTTTT

Found at i:8733 original size:26 final size:26

Alignment explanation


    Indices: 8685--8736  Score: 68
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       8675 CGCAAAACAA

                            ***       
       8685 AAATTAAAAACACAATTTTTTTTTTT
          1 AAATTAAAAACACAATGAATTTTTTT

                       *              
       8711 AAATTAAAAACGCAATGAATTTTTTT
          1 AAATTAAAAACACAATGAATTTTTTT

       8737 TTAGGGAAAA


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  26   22  1.00

ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44


Consensus pattern (26 bp):   
AAATTAAAAACACAATGAATTTTTTT

Found at i:9039 original size:16 final size:15

Alignment explanation


    Indices: 8981--9026  Score: 78
    Period size: 15  Copynumber: 3.2  Consensus size: 15

       8971 AAACAGAGGG

                           
       8981 TTAAAAAG--AACAA
          1 TTAAAAAGAAAACAA

                           
       8994 TTAAAAAGAAAACAA
          1 TTAAAAAGAAAACAA

                           
       9009 TTAAAAAGAAAACAA
          1 TTAAAAAGAAAACAA

               
       9024 TTA
          1 TTA

       9027 TACTAGAAAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    8  0.26
  15   23  0.74

ACGTcount: A:0.70, C:0.07, G:0.07, T:0.17


Consensus pattern (15 bp):   
TTAAAAAGAAAACAA

Found at i:10457 original size:11 final size:11

Alignment explanation


    Indices: 10441--10470  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

      10431 AGTCTTCAAG

                     * 
      10441 TCTTCAAATTA
          1 TCTTCAAATAA

                       
      10452 TCTTCAAATAA
          1 TCTTCAAATAA

                    
      10463 TCTTCAAA
          1 TCTTCAAA

      10471 CACGAACTTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40


Consensus pattern (11 bp):   
TCTTCAAATAA
Done.