Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022304.1 Corchorus olitorius cultivar O-4 contig22337, 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: 15628
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35


Found at i:414 original size:30 final size:30

Alignment explanation


    Indices: 380--458  Score: 76
    Period size: 30  Copynumber: 2.6  Consensus size: 30

        370 TTGAAAAGTT

                                           
        380 TGGTAAGGTTGTGAAAGTTGA-GAAAAAGAA
          1 TGGTAAGGTTGTGAAAGTTGAGGAAAAAG-A

                                       * *  
        410 TGGT-AGGTTTGTGAGAA-TTGAGGAAGATGA
          1 TGGTAAGG-TTGTGA-AAGTTGAGGAAAAAGA

                                
        440 TGGTAAGGTT-TGGAAAGTT
          1 TGGTAAGGTTGT-GAAAGTT

        459 TGAAAAGAAA


Statistics
Matches: 41,  Mismatches: 2, Indels: 12
        0.75            0.04        0.22

Matches are distributed among these distances:
  29    6  0.15
  30   25  0.61
  31   10  0.24

ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29


Consensus pattern (30 bp):   
TGGTAAGGTTGTGAAAGTTGAGGAAAAAGA

Found at i:1787 original size:19 final size:18

Alignment explanation


    Indices: 1758--1793  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1748 ATCTAACTTA

                              
       1758 TTTTTATTTTTATTTTAG
          1 TTTTTATTTTTATTTTAG

                        *     
       1776 TTTTTATGTTTTCTTTTA
          1 TTTTTAT-TTTTATTTTA

       1794 ATTTAATTCT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.14, C:0.03, G:0.06, T:0.78


Consensus pattern (18 bp):   
TTTTTATTTTTATTTTAG

Found at i:2104 original size:26 final size:26

Alignment explanation


    Indices: 2061--2115  Score: 67
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       2051 GAAAAAAAAA

                              *       
       2061 TTGCATTTTTGCATTTTTGTTTATGT
          1 TTGCATTTTTGCATTTTTCTTTATGT

                       *           *   
       2087 TTGCATATTTTTCA-TTTTCTTTTTGT
          1 TTGCAT-TTTTGCATTTTTCTTTATGT

               
       2113 TTG
          1 TTG

       2116 TATAAATTGC


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  26   19  0.76
  27    6  0.24

ACGTcount: A:0.11, C:0.09, G:0.13, T:0.67


Consensus pattern (26 bp):   
TTGCATTTTTGCATTTTTCTTTATGT

Found at i:4972 original size:23 final size:23

Alignment explanation


    Indices: 4918--4972  Score: 67
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       4908 ACACTTAAAT

                                   
       4918 TTCTATTTTTAATTTGTTCTATC
          1 TTCTATTTTTAATTTGTTCTATC

              *        *            
       4941 TTTTATTTTTATTTTGTT-TAATC
          1 TTCTATTTTTAATTTGTTCT-ATC

                *    
       4964 TTCTCTTTT
          1 TTCTATTTT

       4973 CTTTGATTTC


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  22    1  0.04
  23   26  0.96

ACGTcount: A:0.15, C:0.11, G:0.04, T:0.71


Consensus pattern (23 bp):   
TTCTATTTTTAATTTGTTCTATC

Found at i:10147 original size:8 final size:8

Alignment explanation


    Indices: 10134--10159  Score: 52
    Period size: 8  Copynumber: 3.2  Consensus size: 8

      10124 TTATTTTTCA

                    
      10134 TATCTTAC
          1 TATCTTAC

                    
      10142 TATCTTAC
          1 TATCTTAC

                    
      10150 TATCTTAC
          1 TATCTTAC

              
      10158 TA
          1 TA

      10160 CTATATAAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   18  1.00

ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50


Consensus pattern (8 bp):   
TATCTTAC
Done.