Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001172.1 Corchorus olitorius cultivar O-4 contig01172, 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: 2071
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30


Found at i:670 original size:21 final size:21

Alignment explanation


    Indices: 637--677  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        627 ATATATATAA

                           *     
        637 ATATATATAATTAAATATATT
          1 ATATATATAATTAAAAATATT

                                 
        658 ATATGATAT-ATTAAAAATAT
          1 ATAT-ATATAATTAAAAATAT

        678 GTGTCGGTCG


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21   14  0.78
  22    4  0.22

ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44


Consensus pattern (21 bp):   
ATATATATAATTAAAAATATT

Found at i:1887 original size:32 final size:32

Alignment explanation


    Indices: 1851--1921  Score: 124
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       1841 TTTCCCTAAA

                                            
       1851 TTGAAAATTTTGAAAAACTTGAATTGAATACT
          1 TTGAAAATTTTGAAAAACTTGAATTGAATACT

                          **                
       1883 TTGAAAATTTTGAATGACTTGAATTGAATACT
          1 TTGAAAATTTTGAAAAACTTGAATTGAATACT

                   
       1915 TTGAAAA
          1 TTGAAAA

       1922 ACTTGAATTG


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  32   37  1.00

ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38


Consensus pattern (32 bp):   
TTGAAAATTTTGAAAAACTTGAATTGAATACT

Found at i:1909 original size:23 final size:23

Alignment explanation


    Indices: 1883--1949  Score: 64
    Period size: 23  Copynumber: 3.0  Consensus size: 23

       1873 ATTGAATACT

                   *      **       
       1883 TTGAAAATTTTGAATGACTTGAA
          1 TTGAAAACTTTGAAAAACTTGAA

                 *                 
       1906 TTGAATACTTTGAAAAACTTGAA
          1 TTGAAAACTTTGAAAAACTTGAA

                ***               
       1929 TTGATTGCTTTG-AAAACTTGA
          1 TTGAAAACTTTGAAAAACTTGA

       1950 TGGGATCTTT


Statistics
Matches: 38,  Mismatches: 6, Indels: 1
        0.84            0.13        0.02

Matches are distributed among these distances:
  22    9  0.24
  23   29  0.76

ACGTcount: A:0.37, C:0.07, G:0.16, T:0.39


Consensus pattern (23 bp):   
TTGAAAACTTTGAAAAACTTGAA

Found at i:1928 original size:32 final size:32

Alignment explanation


    Indices: 1867--1929  Score: 108
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       1857 ATTTTGAAAA

                                   **       
       1867 ACTTGAATTGAATACTTTGAAAATTTTGAATG
          1 ACTTGAATTGAATACTTTGAAAAACTTGAATG

                                           
       1899 ACTTGAATTGAATACTTTGAAAAACTTGAAT
          1 ACTTGAATTGAATACTTTGAAAAACTTGAAT

       1930 TGATTGCTTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  32   29  1.00

ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38


Consensus pattern (32 bp):   
ACTTGAATTGAATACTTTGAAAAACTTGAATG

Found at i:2023 original size:37 final size:37

Alignment explanation


    Indices: 1939--2047  Score: 139
    Period size: 37  Copynumber: 2.9  Consensus size: 37

       1929 TTGATTGCTT

                            *                     *
       1939 TGAAAACTTGATGGGATCTTTCCCTAA-ATTGAAAACTT
          1 TGAAAACTTGATGGGAACTTTCCC-AATA-TGAAAACTA

             *         *                         
       1977 TAAAAACTTGACGGGAACTTTCCCAATATGAAAACTA
          1 TGAAAACTTGATGGGAACTTTCCCAATATGAAAACTA

                *                      *      
       2014 TGAAGACTTGATGGGAACTTTCCCAATTTGAAAA
          1 TGAAAACTTGATGGGAACTTTCCCAATATGAAAA

       2048 ACTAAATTGA


Statistics
Matches: 62,  Mismatches: 8, Indels: 3
        0.85            0.11        0.04

Matches are distributed among these distances:
  37   40  0.65
  38   22  0.35

ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29


Consensus pattern (37 bp):   
TGAAAACTTGATGGGAACTTTCCCAATATGAAAACTA
Done.