Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015862.1 Corchorus olitorius cultivar O-4 contig15895, 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: 9289
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32


Found at i:2855 original size:21 final size:21

Alignment explanation


    Indices: 2829--2878  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       2819 GGAATGGCGA

                        **       
       2829 TGGCACGGGCATGGCCGGTGG
          1 TGGCACGGGCATAACCGGTGG

                      *          
       2850 TGGCACGGGCTTAACCGGTGG
          1 TGGCACGGGCATAACCGGTGG

             *      
       2871 TAGCACGG
          1 TGGCACGG

       2879 TGAATGGGCG


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.14, C:0.24, G:0.46, T:0.16


Consensus pattern (21 bp):   
TGGCACGGGCATAACCGGTGG

Found at i:5834 original size:27 final size:27

Alignment explanation


    Indices: 5804--5879  Score: 116
    Period size: 28  Copynumber: 2.8  Consensus size: 27

       5794 ACGCAGAAAT

                          *            
       5804 TTTTTTTTTTTAAAGACGCAAAAACCC
          1 TTTTTTTTTTTAAAAACGCAAAAACCC

                                      * 
       5831 TTTTTTTTTTTATAAAACGCAAAAACTC
          1 TTTTTTTTTTTA-AAAACGCAAAAACCC

                      *          
       5859 TTTTTTTTTTCAAAAACGCAA
          1 TTTTTTTTTTTAAAAACGCAA

       5880 CAACAAAAAA


Statistics
Matches: 45,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
  27   21  0.47
  28   24  0.53

ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45


Consensus pattern (27 bp):   
TTTTTTTTTTTAAAAACGCAAAAACCC

Found at i:5917 original size:22 final size:21

Alignment explanation


    Indices: 5870--5917  Score: 53
    Period size: 22  Copynumber: 2.2  Consensus size: 21

       5860 TTTTTTTTTC

                      *           
       5870 AAAAACGCAACAACAAAAAATT
          1 AAAAACGCAAAAACAAAAAA-T

                                   
       5892 AAAAACGCAAAAAATCAAAAAA-
          1 AAAAACGC-AAAAA-CAAAAAAT

                
       5914 AAAA
          1 AAAA

       5918 TTAATTTTTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  22   12  0.52
  23    4  0.17
  24    7  0.30

ACGTcount: A:0.75, C:0.15, G:0.04, T:0.06


Consensus pattern (21 bp):   
AAAAACGCAAAAACAAAAAAT

Found at i:6339 original size:16 final size:15

Alignment explanation


    Indices: 6301--6342  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       6291 ACAGAGGTTG

                           
       6301 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
       6316 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       6331 ACTAGAAAACAA
          1 AC-AGAAAACAA

       6343 AGCAGAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:9189 original size:57 final size:57

Alignment explanation


    Indices: 9073--9189  Score: 166
    Period size: 57  Copynumber: 2.0  Consensus size: 57

       9063 TATCAATTTC

                    *                       *                         
       9073 CTTTCACATAATAAATGTTATGATAATAAATCCTATCCCCTATCTCTACTTAATTATT
          1 CTTTCACACAATAAATGTTA-GATAATAAATCATATCCCCTATCTCTACTTAATTATT

                                        *                              
       9131 CTTTCACACAATAAATGTTA-A-AATAATTCATATCCCCCCTATCTCTACTTAATTATT
          1 CTTTCACACAATAAATGTTAGATAATAAATCATAT--CCCCTATCTCTACTTAATTATT

              
       9188 CT
          1 CT

       9190 ACAAAATAAA


Statistics
Matches: 54,  Mismatches: 3, Indels: 5
        0.87            0.05        0.08

Matches are distributed among these distances:
  55   10  0.19
  56    1  0.02
  57   24  0.44
  58   19  0.35

ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40


Consensus pattern (57 bp):   
CTTTCACACAATAAATGTTAGATAATAAATCATATCCCCTATCTCTACTTAATTATT
Done.