Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023557.1 Corchorus olitorius cultivar O-4 contig23590, 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: 17572
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:68 original size:2 final size:2

Alignment explanation


    Indices: 61--95  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

         51 ATACTATTAG

                                                                
         61 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         96 TTTAATAATG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:2723 original size:40 final size:40

Alignment explanation


    Indices: 2678--2761  Score: 123
    Period size: 40  Copynumber: 2.1  Consensus size: 40

       2668 CATAGATCAC

                   *        **      *               
       2678 ACAATAATATTTTAACTGACACTTGAACAACTTCAATCGG
          1 ACAATAACATTTTAACCAACACTTAAACAACTTCAATCGG

                                *                   
       2718 ACAATAACATTTTAACCAACGCTTAAACAACTTCAATCGG
          1 ACAATAACATTTTAACCAACACTTAAACAACTTCAATCGG

                
       2758 ACAA
          1 ACAA

       2762 GTGGACTGAA


Statistics
Matches: 39,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  40   39  1.00

ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26


Consensus pattern (40 bp):   
ACAATAACATTTTAACCAACACTTAAACAACTTCAATCGG

Found at i:3837 original size:307 final size:306

Alignment explanation


    Indices: 3260--3873  Score: 1061
    Period size: 307  Copynumber: 2.0  Consensus size: 306

       3250 AGTCCTTCAT

                                                         *                   
       3260 TGAAGTTGTAGATTATGGAATTACATCTTAATAGACACTTGAATCGCCTTGATTGGACAAATAGA
          1 TGAAGTTGTAGATTATGGAATTACATCTTAATAGACACTTGAATCACCTTGATTGGACAAATAGA

                      *                           *                          
       3325 AAAAAATACCGAAATAAAAGCCAACGCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATA
         66 AAAAAATACCAAAATAAAAGCCAACGCGTTAAATCGTCAAACCCATAATTGTAAAGGATTAAATA

                                                        *                    
       3390 ACATAAAACATAAAACTATGAGGATTATTAAATAAATAATCCGGCAAAAAATATTAGTTTATGGA
        131 ACATAAAACATAAAACTATGAGGATTATTAAATAAATAATCCGGAAAAAAATATTAGTTTATGGA

                              *                                 *            
       3455 GAATGAGACCCACAAATAGTAATTTTTTCACAAAGTTCCAAAACGCCCTCGGCCATCAAACCAAA
        196 GAATGAGACCCACAAATAATAATTTTTTCACAAAGTTCCAAAACGCCCTCGGACATCAAACCAAA

                                 *     *      *            
       3520 TAACAAAAAACCGAGCATGAAGGTACTGAAATACCCCTCACCATTTG
        261 TAACAAAAAACCGAGCATGAAAGTACTAAAATA-ACCTCACCATTTG

                                                                             
       3567 TGAAGTTGTAGATTATGGAATTACATCTTAATAGACACTTGAATCACCTTGATTGGACAAATAGA
          1 TGAAGTTGTAGATTATGGAATTACATCTTAATAGACACTTGAATCACCTTGATTGGACAAATAGA

                                    *                              *         
       3632 AAAAAATACCAAAATAAAAGCCAATGCGTTAAATCGTCAAACCCATAATTGTAAATGATTAAATA
         66 AAAAAATACCAAAATAAAAGCCAACGCGTTAAATCGTCAAACCCATAATTGTAAAGGATTAAATA

            *                                                                
       3697 GCATAAAACATAAAACTATGAGGATTATTAAATAAATAATCCGGTAAAAAAATATTAGTTTATGG
        131 ACATAAAACATAAAACTATGAGGATTATTAAATAAATAATCCGG-AAAAAAATATTAGTTTATGG

                       *                                                     
       3762 AGAATGAGACCTACAAATAATAA-TTTTTCACAAAGTTCCAAAACGCCCTC-GACATCAAACCAA
        195 AGAATGAGACCCACAAATAATAATTTTTTCACAAAGTTCCAAAACGCCCTCGGACATCAAACCAA

                                *                           
       3825 ATAACGAAAAAACCGAGCATTAAAGTACTAAAATAACCTCACCATTTG
        260 ATAAC-AAAAAACCGAGCATGAAAGTACTAAAATAACCTCACCATTTG

             
       3873 T
          1 T

       3874 TCTTCGGTGA


Statistics
Matches: 291,  Mismatches: 14, Indels: 5
        0.94            0.05        0.02

Matches are distributed among these distances:
 306   30  0.10
 307  221  0.76
 308   40  0.14

ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25


Consensus pattern (306 bp):   
TGAAGTTGTAGATTATGGAATTACATCTTAATAGACACTTGAATCACCTTGATTGGACAAATAGA
AAAAAATACCAAAATAAAAGCCAACGCGTTAAATCGTCAAACCCATAATTGTAAAGGATTAAATA
ACATAAAACATAAAACTATGAGGATTATTAAATAAATAATCCGGAAAAAAATATTAGTTTATGGA
GAATGAGACCCACAAATAATAATTTTTTCACAAAGTTCCAAAACGCCCTCGGACATCAAACCAAA
TAACAAAAAACCGAGCATGAAAGTACTAAAATAACCTCACCATTTG

Found at i:3950 original size:13 final size:13

Alignment explanation


    Indices: 3932--3958  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       3922 CTTTCCAACT

                         
       3932 TTAATATATTGTA
          1 TTAATATATTGTA

                         
       3945 TTAATATATTGTA
          1 TTAATATATTGTA

             
       3958 T
          1 T

       3959 AGATGTATAG


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:0.37, C:0.00, G:0.07, T:0.56


Consensus pattern (13 bp):   
TTAATATATTGTA

Found at i:9504 original size:3 final size:3

Alignment explanation


    Indices: 9498--9527  Score: 51
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       9488 CCCCTTTTTT

                                            *      
       9498 TTC TTC TTC TTC TTC TTC TTC TTC ATC TTC
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC

       9528 CGGTTGCCGG


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63


Consensus pattern (3 bp):   
TTC

Done.