Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01003134.1 Corchorus olitorius cultivar O-4 contig03139, 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: 1837
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36


Found at i:1488 original size:34 final size:33

Alignment explanation


    Indices: 1450--1560  Score: 118
    Period size: 37  Copynumber: 3.2  Consensus size: 33

       1440 CTTTGAAAAC

                            *                  
       1450 TAAAACTGAAAAC-GACGGGAACTTTCCCTAAATT
          1 TAAAACTGAAAACTGATGGGAACTTTCCC--AATT

                                   *          
       1484 TAAAACT-AAAACCTGATGGGAAATTTCCCAATT
          1 TAAAACTGAAAA-CTGATGGGAACTTTCCCAATT

                                                 
       1517 TAAAAACTTTGAAAACTGAATGGGAACTTTCCCAATT
          1 T-AAAAC--TGAAAACTG-ATGGGAACTTTCCCAATT

                   
       1554 TGAAAAC
          1 T-AAAAC

       1561 CGGTTAAATT


Statistics
Matches: 66,  Mismatches: 4, Indels: 11
        0.81            0.05        0.14

Matches are distributed among these distances:
  33    9  0.14
  34   13  0.20
  35   13  0.20
  36    4  0.06
  37   27  0.41

ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26


Consensus pattern (33 bp):   
TAAAACTGAAAACTGATGGGAACTTTCCCAATT

Found at i:1609 original size:52 final size:53

Alignment explanation


    Indices: 1516--1664  Score: 212
    Period size: 52  Copynumber: 2.8  Consensus size: 53

       1506 ATTTCCCAAT

                 *                                       *   *    
       1516 TTAAAAACTTTGAAAACTGAATGGGAACTTTCCCAATTTGAAAACCG-GTTAAA
          1 TTAAATACTTTGAAAACTG-ATGGGAACTTTCCCAATTTGAAAACAGAGCTAAA

                                             * *                 
       1569 TTAAATACTTTGAAAACTGATGGGAACTTTCCCGACTTGAAAA-AGAGCTAAA
          1 TTAAATACTTTGAAAACTGATGGGAACTTTCCCAATTTGAAAACAGAGCTAAA

              *           *                             
       1621 TTGAATACTTTGAAGACTGATGGGAACTTTCCCAATTTGAAAAC
          1 TTAAATACTTTGAAAACTGATGGGAACTTTCCCAATTTGAAAAC

       1665 TTAAAAACTT


Statistics
Matches: 85,  Mismatches: 9, Indels: 4
        0.87            0.09        0.04

Matches are distributed among these distances:
  51    1  0.01
  52   66  0.78
  53   18  0.21

ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29


Consensus pattern (53 bp):   
TTAAATACTTTGAAAACTGATGGGAACTTTCCCAATTTGAAAACAGAGCTAAA

Found at i:1661 original size:36 final size:36

Alignment explanation


    Indices: 1621--1739  Score: 168
    Period size: 36  Copynumber: 3.3  Consensus size: 36

       1611 AAGAGCTAAA

                 *        *                     
       1621 TTGAATACTTTGAAGACTGATGGGAACTTTCCCAAT
          1 TTGAAAACTTTGAAAACTGATGGGAACTTTCCCAAT

                       *                         
       1657 TTGAAAAC-TTAAAAACTTGATGGGAACTTTCCCAAT
          1 TTGAAAACTTTGAAAAC-TGATGGGAACTTTCCCAAT

                   *                             
       1693 TTGAAAATTTTGAAAACTGGATGGGAACTTTCCCAAT
          1 TTGAAAACTTTGAAAACT-GATGGGAACTTTCCCAAT

                 *    
       1730 TTGAAGACTT
          1 TTGAAAACTT

       1740 AAACCTGATG


Statistics
Matches: 73,  Mismatches: 7, Indels: 5
        0.86            0.08        0.06

Matches are distributed among these distances:
  35    6  0.08
  36   34  0.47
  37   33  0.45

ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33


Consensus pattern (36 bp):   
TTGAAAACTTTGAAAACTGATGGGAACTTTCCCAAT

Found at i:1718 original size:37 final size:35

Alignment explanation


    Indices: 1629--1734  Score: 158
    Period size: 37  Copynumber: 2.9  Consensus size: 35

       1619 AATTGAATAC

                  *                            
       1629 TTTGAAGACTGATGGGAACTTTCCCAATTTGAAAA
          1 TTTGAAAACTGATGGGAACTTTCCCAATTTGAAAA

            *  *                                
       1664 CTTAAAAACTTGATGGGAACTTTCCCAATTTGAAAA
          1 TTTGAAAAC-TGATGGGAACTTTCCCAATTTGAAAA

                                               
       1700 TTTTGAAAACTGGATGGGAACTTTCCCAATTTGAA
          1 -TTTGAAAACT-GATGGGAACTTTCCCAATTTGAA

       1735 GACTTAAACC


Statistics
Matches: 63,  Mismatches: 5, Indels: 4
        0.88            0.07        0.06

Matches are distributed among these distances:
  35    6  0.10
  36   27  0.43
  37   30  0.48

ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32


Consensus pattern (35 bp):   
TTTGAAAACTGATGGGAACTTTCCCAATTTGAAAA
Done.