Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006844.1 Corchorus olitorius cultivar O-4 contig06869, 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, 763

Length: 1273
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34


Found at i:71 original size:3 final size:3

Alignment explanation


    Indices: 65--97  Score: 50
    Period size: 3  Copynumber: 11.0  Consensus size: 3

         55 TTAGGAGGAA

                                                        
         65 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT

         98 TTTGGAATAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   2    2  0.07
   3   23  0.82
   4    3  0.11

ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30


Consensus pattern (3 bp):   
AAT

Found at i:817 original size:29 final size:29

Alignment explanation


    Indices: 783--903  Score: 179
    Period size: 29  Copynumber: 4.2  Consensus size: 29

        773 ACTTAATTTG

                  *      *               
        783 CATTTTCGCACATCCAGGGGCATTTTGGT
          1 CATTTTTGCACATTCAGGGGCATTTTGGT

                      *             *    
        812 CATTTTTGCATATTCAGGGGCATTATGGT
          1 CATTTTTGCACATTCAGGGGCATTTTGGT

                      *             *    
        841 CATTTTTGCATATTCAGGGGCATTATGGT
          1 CATTTTTGCACATTCAGGGGCATTTTGGT

                                *        
        870 CATTTTTGCACATTCAGGGGTATTTTGGT
          1 CATTTTTGCACATTCAGGGGCATTTTGGT

                 
        899 CATTT
          1 CATTT

        904 GTACTCCAGG


Statistics
Matches: 85,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  29   85  1.00

ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41


Consensus pattern (29 bp):   
CATTTTTGCACATTCAGGGGCATTTTGGT

Found at i:1160 original size:30 final size:30

Alignment explanation


    Indices: 1124--1187  Score: 128
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       1114 TGTCAATTAT

                                          
       1124 TTGGATTAATTCACATTGTTAAGTATAGAG
          1 TTGGATTAATTCACATTGTTAAGTATAGAG

                                          
       1154 TTGGATTAATTCACATTGTTAAGTATAGAG
          1 TTGGATTAATTCACATTGTTAAGTATAGAG

                
       1184 TTGG
          1 TTGG

       1188 CATTTTAATT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   34  1.00

ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41


Consensus pattern (30 bp):   
TTGGATTAATTCACATTGTTAAGTATAGAG

Found at i:1253 original size:20 final size:21

Alignment explanation


    Indices: 1214--1255  Score: 59
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       1204 GGCATTAACT

                                  
       1214 GTATAAAAAGTCAAAAAAAAAG
          1 GTATAAAAAG-CAAAAAAAAAG

                        *        
       1236 GTATAAAAA-CAGAAAAAAAG
          1 GTATAAAAAGCAAAAAAAAAG

       1256 CACAAAGTTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  20   10  0.53
  22    9  0.47

ACGTcount: A:0.69, C:0.05, G:0.14, T:0.12


Consensus pattern (21 bp):   
GTATAAAAAGCAAAAAAAAAG
Done.