Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022602.1 Corchorus olitorius cultivar O-4 contig22635, 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: 29443
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:1453 original size:27 final size:29

Alignment explanation


    Indices: 1392--1460  Score: 106
    Period size: 29  Copynumber: 2.4  Consensus size: 29

       1382 TTAATTCAGT

                                         
       1392 ACCACTATATATAGTATTTTTTTTGCCAA
          1 ACCACTATATATAGTATTTTTTTTGCCAA

                    *                 *  
       1421 ACCACTATTTATAGTA-TTTTTTTGCTAA
          1 ACCACTATATATAGTATTTTTTTTGCCAA

                         
       1449 A-CACTATATATA
          1 ACCACTATATATA

       1461 AGTACTTAAT


Statistics
Matches: 37,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  27   10  0.27
  28   12  0.32
  29   15  0.41

ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45


Consensus pattern (29 bp):   
ACCACTATATATAGTATTTTTTTTGCCAA

Found at i:4971 original size:2 final size:2

Alignment explanation


    Indices: 4954--4990  Score: 58
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       4944 GCTAAAAAGT

                           *                                        
       4954 TA TA -A TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       4991 AACAAAAACA


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.97

ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46


Consensus pattern (2 bp):   
TA

Found at i:15781 original size:23 final size:23

Alignment explanation


    Indices: 15750--15815  Score: 64
    Period size: 23  Copynumber: 2.9  Consensus size: 23

      15740 AGCAATTTAT

                *               *  
      15750 TATACATGCCTAAATATGAACAA
          1 TATATATGCCTAAATATGAAAAA

                          *          
      15773 TATATATG-CTGGATATAT-AAAAA
          1 TATATATGCCT--AAATATGAAAAA

               *                
      15796 TATCTATGCCTAAATATGAA
          1 TATATATGCCTAAATATGAA

      15816 GGGAGAAAAT


Statistics
Matches: 34,  Mismatches: 5, Indels: 8
        0.72            0.11        0.17

Matches are distributed among these distances:
  22    7  0.21
  23   20  0.59
  24    7  0.21

ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32


Consensus pattern (23 bp):   
TATATATGCCTAAATATGAAAAA

Found at i:18537 original size:18 final size:18

Alignment explanation


    Indices: 18516--18561  Score: 58
    Period size: 18  Copynumber: 2.6  Consensus size: 18

      18506 AATGGTAACG

                               
      18516 GAAATGGCAATGGC-ATCA
          1 GAAATGGCAATGGCAAT-A

                *            *
      18534 GAAACGGCAATGGCAATG
          1 GAAATGGCAATGGCAATA

                      
      18552 GAAATGGCAA
          1 GAAATGGCAA

      18562 GCCGTGGTAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  18   22  0.92
  19    2  0.08

ACGTcount: A:0.41, C:0.15, G:0.30, T:0.13


Consensus pattern (18 bp):   
GAAATGGCAATGGCAATA

Found at i:27903 original size:32 final size:34

Alignment explanation


    Indices: 27838--27905  Score: 88
    Period size: 32  Copynumber: 2.1  Consensus size: 34

      27828 GTCCAACCCA

                                      *       
      27838 ACTTGTCTGCCTATTAATTGTCTGCTTCAATCTG
          1 ACTTGTCTGCCTATTAATTGTCTGCTCCAATCTG

                                    *          
      27872 ACTTGTTCTG-CT-TTAATTG-CTTCTCCAATCTG
          1 ACTTG-TCTGCCTATTAATTGTCTGCTCCAATCTG

              
      27904 AC
          1 AC

      27906 CTCTCAGAAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  32   13  0.42
  33    7  0.23
  34    7  0.23
  35    4  0.13

ACGTcount: A:0.18, C:0.25, G:0.13, T:0.44


Consensus pattern (34 bp):   
ACTTGTCTGCCTATTAATTGTCTGCTCCAATCTG
Done.