Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017705.1 Corchorus olitorius cultivar O-4 contig17738, 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: 10267
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:4600 original size:30 final size:30

Alignment explanation


    Indices: 4566--4628  Score: 126
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       4556 CAATTGCTTA

                                          
       4566 ATTATGTTTGTACATGAATCTACTTATTGC
          1 ATTATGTTTGTACATGAATCTACTTATTGC

                                          
       4596 ATTATGTTTGTACATGAATCTACTTATTGC
          1 ATTATGTTTGTACATGAATCTACTTATTGC

               
       4626 ATT
          1 ATT

       4629 GCAATTGCTT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   33  1.00

ACGTcount: A:0.27, C:0.13, G:0.13, T:0.48


Consensus pattern (30 bp):   
ATTATGTTTGTACATGAATCTACTTATTGC

Found at i:6284 original size:2 final size:2

Alignment explanation


    Indices: 6277--6302  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       6267 AAACTCAAGA

                                                  
       6277 AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG

       6303 CACAAGGAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:8225 original size:18 final size:18

Alignment explanation


    Indices: 8202--8238  Score: 65
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       8192 ACCAAATCGA

                              
       8202 GGAGCCTCATTCCCCTGT
          1 GGAGCCTCATTCCCCTGT

                       *      
       8220 GGAGCCTCATTTCCCTGT
          1 GGAGCCTCATTCCCCTGT

             
       8238 G
          1 G

       8239 CTCTAATTAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.11, C:0.35, G:0.24, T:0.30


Consensus pattern (18 bp):   
GGAGCCTCATTCCCCTGT

Found at i:9274 original size:15 final size:14

Alignment explanation


    Indices: 9233--9274  Score: 50
    Period size: 15  Copynumber: 2.9  Consensus size: 14

       9223 TGAACCAAAC

                          
       9233 AAACACAAGGAAAA
          1 AAACACAAGGAAAA

               *            
       9247 AAAAAC-AGAGAAAGA
          1 AAACACAAG-GAAA-A

                         
       9262 AAACACAAGGAAA
          1 AAACACAAGGAAA

       9275 TTCGTTGAAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 5
        0.77            0.07        0.17

Matches are distributed among these distances:
  13    2  0.09
  14    9  0.39
  15   10  0.43
  16    2  0.09

ACGTcount: A:0.71, C:0.12, G:0.17, T:0.00


Consensus pattern (14 bp):   
AAACACAAGGAAAA

Found at i:9866 original size:9 final size:9

Alignment explanation


    Indices: 9849--9883  Score: 52
    Period size: 9  Copynumber: 3.9  Consensus size: 9

       9839 GGGTCTGTTT

                *    
       9849 GGTTTGGGG
          1 GGTTGGGGG

                     
       9858 GGTTGGGGG
          1 GGTTGGGGG

                   * 
       9867 GGTTGGGAG
          1 GGTTGGGGG

                    
       9876 GGTTGGGG
          1 GGTTGGGG

       9884 TGGGGAGTTG


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   9   23  1.00

ACGTcount: A:0.03, C:0.00, G:0.71, T:0.26


Consensus pattern (9 bp):   
GGTTGGGGG
Done.