Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012417.1 Corchorus olitorius cultivar O-4 contig12450, 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: 4440
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34


Found at i:1980 original size:25 final size:25

Alignment explanation


    Indices: 1952--2000  Score: 80
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       1942 ATAAAAAAAT

                                     
       1952 TTTACCGTTAAAAATATGATTTTTG
          1 TTTACCGTTAAAAATATGATTTTTG

                **                  
       1977 TTTATTGTTAAAAATATGATTTTT
          1 TTTACCGTTAAAAATATGATTTTT

       2001 AACTATGATT


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53


Consensus pattern (25 bp):   
TTTACCGTTAAAAATATGATTTTTG

Found at i:2069 original size:20 final size:19

Alignment explanation


    Indices: 2028--2077  Score: 64
    Period size: 20  Copynumber: 2.6  Consensus size: 19

       2018 ACATGTTAAG

                   *        *  
       2028 TTTAATTGATTTATTATAA
          1 TTTAATTAATTTATTAGAA

                              * 
       2047 TTTAATTAATTATATTAGGA
          1 TTTAATTAATT-TATTAGAA

                       
       2067 TTTAATTAATT
          1 TTTAATTAATT

       2078 GATCAAATAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  19   10  0.37
  20   17  0.63

ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56


Consensus pattern (19 bp):   
TTTAATTAATTTATTAGAA

Found at i:2523 original size:37 final size:36

Alignment explanation


    Indices: 2482--2554  Score: 119
    Period size: 37  Copynumber: 2.0  Consensus size: 36

       2472 ATTGAAATCC

                                                 
       2482 AACTTGAAAAGAATCAAGTACTAAAATAAAATTACTT
          1 AACTTGAAAAGAATCAAGTACTAAAA-AAAATTACTT

                                  *    *        
       2519 AACTTGAAAAGAATCAAGTACTGAAAAGAATTACTT
          1 AACTTGAAAAGAATCAAGTACTAAAAAAAATTACTT

       2555 TGGAAACGCA


Statistics
Matches: 34,  Mismatches: 2, Indels: 1
        0.92            0.05        0.03

Matches are distributed among these distances:
  36    9  0.26
  37   25  0.74

ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26


Consensus pattern (36 bp):   
AACTTGAAAAGAATCAAGTACTAAAAAAAATTACTT

Found at i:2545 original size:17 final size:17

Alignment explanation


    Indices: 2486--2549  Score: 56
    Period size: 17  Copynumber: 3.6  Consensus size: 17

       2476 AAATCCAACT

                             
       2486 TGAAAAGAATCAAGTAC
          1 TGAAAAGAATCAAGTAC

             *     *   * **    
       2503 TAAAATAAAATTACTTAAC
          1 TGAAA-AGAATCAAGT-AC

                              
       2522 TTGAAAAGAATCAAGTAC
          1 -TGAAAAGAATCAAGTAC

                      
       2540 TGAAAAGAAT
          1 TGAAAAGAAT

       2550 TACTTTGGAA


Statistics
Matches: 34,  Mismatches: 10, Indels: 6
        0.68            0.20        0.12

Matches are distributed among these distances:
  17   14  0.41
  18    8  0.24
  19    8  0.24
  20    4  0.12

ACGTcount: A:0.55, C:0.09, G:0.12, T:0.23


Consensus pattern (17 bp):   
TGAAAAGAATCAAGTAC
Done.