Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018975.1 Corchorus olitorius cultivar O-4 contig19008, 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: 8604
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29


Found at i:2793 original size:31 final size:31

Alignment explanation


    Indices: 2755--2817  Score: 108
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       2745 TATGACCGTA

                                           
       2755 GGTATTAGCCTTCGTTGGTAAACGACAGTTT
          1 GGTATTAGCCTTCGTTGGTAAACGACAGTTT

                        *         *        
       2786 GGTATTAGCCTTTGTTGGTAAATGACAGTTT
          1 GGTATTAGCCTTCGTTGGTAAACGACAGTTT

             
       2817 G
          1 G

       2818 TTTGTAGCGG


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   30  1.00

ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38


Consensus pattern (31 bp):   
GGTATTAGCCTTCGTTGGTAAACGACAGTTT

Found at i:2916 original size:38 final size:40

Alignment explanation


    Indices: 2842--2918  Score: 104
    Period size: 42  Copynumber: 1.9  Consensus size: 40

       2832 AAAAAAAAAA

                *       *                             
       2842 GACAGTTTGTTTGTAGGTATTAGCCTTCCTTTGTTGGTAAAT
          1 GACAATTTGTTTCTAGGTATTAGCCTTCC--TGTTGGTAAAT

                                                 
       2884 GACAATTTGTTTCTAGGTATTAGCCTT-C-GTTGGTA
          1 GACAATTTGTTTCTAGGTATTAGCCTTCCTGTTGGTA

       2919 TTAGCCTTTG


Statistics
Matches: 33,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  38    7  0.21
  41    1  0.03
  42   25  0.76

ACGTcount: A:0.19, C:0.13, G:0.23, T:0.44


Consensus pattern (40 bp):   
GACAATTTGTTTCTAGGTATTAGCCTTCCTGTTGGTAAAT

Found at i:2920 original size:16 final size:16

Alignment explanation


    Indices: 2899--2934  Score: 63
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       2889 TTTGTTTCTA

                            
       2899 GGTATTAGCCTTCGTT
          1 GGTATTAGCCTTCGTT

                        *   
       2915 GGTATTAGCCTTTGTT
          1 GGTATTAGCCTTCGTT

                
       2931 GGTA
          1 GGTA

       2935 AATGACAGTG


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.14, C:0.14, G:0.28, T:0.44


Consensus pattern (16 bp):   
GGTATTAGCCTTCGTT

Found at i:2979 original size:42 final size:41

Alignment explanation


    Indices: 2920--3002  Score: 157
    Period size: 42  Copynumber: 2.0  Consensus size: 41

       2910 TCGTTGGTAT

                                                      
       2920 TAGCCTTTGTTGGTAAATGACAGTGTTTGTAGGGGTCTCTTA
          1 TAGCCTTTGTTGGTAAATGACAGTGTTTGTA-GGGTCTCTTA

                                                     
       2962 TAGCCTTTGTTGGTAAATGACAGTGTTTGTAGGGTCTCTTA
          1 TAGCCTTTGTTGGTAAATGACAGTGTTTGTAGGGTCTCTTA

       3003 GTAAGAATTT


Statistics
Matches: 41,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  41   10  0.24
  42   31  0.76

ACGTcount: A:0.19, C:0.12, G:0.28, T:0.41


Consensus pattern (41 bp):   
TAGCCTTTGTTGGTAAATGACAGTGTTTGTAGGGTCTCTTA
Done.