Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021489.1 Corchorus olitorius cultivar O-4 contig21522, 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: 11104
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:2007 original size:21 final size:21

Alignment explanation


    Indices: 1982--2023  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1972 GCAATACTGA

                   *             
       1982 ACTAATCTTTAATACATAGAC
          1 ACTAATCCTTAATACATAGAC

                                 
       2003 ACTAATCCTTAATACATAGAC
          1 ACTAATCCTTAATACATAGAC

       2024 CCCAAAATTG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31


Consensus pattern (21 bp):   
ACTAATCCTTAATACATAGAC

Found at i:5622 original size:31 final size:31

Alignment explanation


    Indices: 5587--5648  Score: 88
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       5577 ATTTTACCCT

                                           
       5587 TTAAACTTTCAAAATTTTATCATTTCGCCCC
          1 TTAAACTTTCAAAATTTTATCATTTCGCCCC

                 *   *        *      *     
       5618 TTAAATTTTTAAAATTTTGTCATTTTGCCCC
          1 TTAAACTTTCAAAATTTTATCATTTCGCCCC

       5649 ATGCTCTATC


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47


Consensus pattern (31 bp):   
TTAAACTTTCAAAATTTTATCATTTCGCCCC

Found at i:6916 original size:2 final size:2

Alignment explanation


    Indices: 6909--6950  Score: 52
    Period size: 2  Copynumber: 21.5  Consensus size: 2

       6899 TAGCTTTGTT

                                        *                                  
       6909 TA TA TA TA TA T- TA T- TGA AA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA

             
       6950 T
          1 T

       6951 TTGTGATTAA


Statistics
Matches: 35,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
   1    2  0.06
   2   33  0.94

ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:8303 original size:33 final size:34

Alignment explanation


    Indices: 8255--8323  Score: 104
    Period size: 37  Copynumber: 2.0  Consensus size: 34

       8245 CATCGACGGT

                                              
       8255 TGTTGTCAG-AAAAAAAGACTTGTCTATTTCTAA
          1 TGTTGTCAGAAAAAAAAGACTTGTCTATTTCTAA

                                                
       8288 TGTTGTCAAAGAAAAAAAAAGACTTGTCTATTTCTA
          1 TGTTGTC--AG-AAAAAAAAGACTTGTCTATTTCTA

       8324 CAGAACAGTA


Statistics
Matches: 32,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
  33    7  0.22
  35    2  0.06
  37   23  0.72

ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35


Consensus pattern (34 bp):   
TGTTGTCAGAAAAAAAAGACTTGTCTATTTCTAA

Found at i:8422 original size:31 final size:31

Alignment explanation


    Indices: 8370--8474  Score: 101
    Period size: 31  Copynumber: 3.5  Consensus size: 31

       8360 ATTAAGGCTG

                  *        * *           * 
       8370 AAATCTTAAAT-AGGTCCCCGAACTTTGTCA
          1 AAATCTCAAATAAGGGCTCCGAACTTTGTGA

                                            
       8400 TAAATCTCAAATAAGGG-TCCGAACTTTG-GA
          1 -AAATCTCAAATAAGGGCTCCGAACTTTGTGA

               **                     *     
       8430 AAAGGTCAAATAAGGGCTCC-AACTTCGTGAA
          1 AAATCTCAAATAAGGGCTCCGAACTTTGTG-A

                          
       8461 AAATCTCAAATAAG
          1 AAATCTCAAATAAG

       8475 TCCATACACT


Statistics
Matches: 61,  Mismatches: 9, Indels: 8
        0.78            0.12        0.10

Matches are distributed among these distances:
  29   20  0.33
  30    5  0.08
  31   33  0.54
  32    3  0.05

ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25


Consensus pattern (31 bp):   
AAATCTCAAATAAGGGCTCCGAACTTTGTGA

Found at i:8593 original size:21 final size:22

Alignment explanation


    Indices: 8560--8606  Score: 60
    Period size: 21  Copynumber: 2.2  Consensus size: 22

       8550 TTCCATTTTA

                    *    *        
       8560 TTTATTTCTTTTTCATTTAATT
          1 TTTATTTCCTTTTAATTTAATT

                               *  
       8582 TTTA-TTCCTTTTAATTTATTT
          1 TTTATTTCCTTTTAATTTAATT

                
       8603 TTTA
          1 TTTA

       8607 CCGTTTAAAA


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  21   18  0.82
  22    4  0.18

ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72


Consensus pattern (22 bp):   
TTTATTTCCTTTTAATTTAATT
Done.