Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011877.1 Corchorus olitorius cultivar O-4 contig11910, 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: 14705
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30


Found at i:6205 original size:15 final size:16

Alignment explanation


    Indices: 6181--6220  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       6171 AGAGGTTGAA

                 *          
       6181 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
       6196 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                     
       6212 AGAAAACAA
          1 AGAAAACAA

       6221 AACAAACAAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Found at i:8678 original size:13 final size:14

Alignment explanation


    Indices: 8647--8684  Score: 69
    Period size: 14  Copynumber: 2.8  Consensus size: 14

       8637 AGTTAATTCC

                          
       8647 AAAAACAATTTAAG
          1 AAAAACAATTTAAG

                          
       8661 AAAAACAATTTAAG
          1 AAAAACAATTTAAG

                       
       8675 -AAAACAATTT
          1 AAAAACAATTT

       8685 CAAAAAGTAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  13   10  0.42
  14   14  0.58

ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24


Consensus pattern (14 bp):   
AAAAACAATTTAAG

Found at i:11270 original size:22 final size:22

Alignment explanation


    Indices: 11240--11291  Score: 70
    Period size: 22  Copynumber: 2.4  Consensus size: 22

      11230 AATTCTTGCT

                *                  
      11240 TCTTGAAATAATTCTTCAATAA-
          1 TCTTCAAATAA-TCTTCAATAAG

                     *            
      11262 TCTTCAAATTATCTTCAATAAG
          1 TCTTCAAATAATCTTCAATAAG

                    
      11284 TCTTCAAA
          1 TCTTCAAA

      11292 CACGAACTTC


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  21   10  0.37
  22   17  0.63

ACGTcount: A:0.38, C:0.17, G:0.04, T:0.40


Consensus pattern (22 bp):   
TCTTCAAATAATCTTCAATAAG

Found at i:13769 original size:29 final size:29

Alignment explanation


    Indices: 13714--13770  Score: 71
    Period size: 29  Copynumber: 1.9  Consensus size: 29

      13704 CATGGTTTAG

                              *          
      13714 GGTTACTAACCCTTTTATTTTTATTTTGA
          1 GGTTACTAACCCTTTTATCTTTATTTTGA

                                    *    
      13743 GGTTACTAACACTCTTTT-TCTTTTTTTT
          1 GGTTACTAAC-C-CTTTTATCTTTATTTT

      13771 TTCTTTTTTT


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

Matches are distributed among these distances:
  29   10  0.42
  30    9  0.38
  31    5  0.21

ACGTcount: A:0.18, C:0.16, G:0.09, T:0.58


Consensus pattern (29 bp):   
GGTTACTAACCCTTTTATCTTTATTTTGA
Done.