Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015870.1 Corchorus capsularis cultivar CVL-1 contig15891, 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: 8193
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29


Found at i:6970 original size:3 final size:3

Alignment explanation


    Indices: 6957--6986  Score: 51
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       6947 AATTGCATTG

                 *                                 
       6957 AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

       6987 TGGATAAAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:7676 original size:10 final size:10

Alignment explanation


    Indices: 7656--7716  Score: 70
    Period size: 10  Copynumber: 5.9  Consensus size: 10

       7646 CCCAGGAAAA

                       
       7656 AAAAGAAGAAG
          1 AAAA-AAGAAG

                      
       7667 AAAAAAGAAG
          1 AAAAAAGAAG

                       
       7677 AGAAAAAG-AG
          1 A-AAAAAGAAG

               *      
       7687 AAAGAAGAAG
          1 AAAAAAGAAG

                     * 
       7697 AATAAAAGAGG
          1 AA-AAAAGAAG

                     
       7708 AAAAAAGAA
          1 AAAAAAGAA

       7717 AAAGAGCAGA


Statistics
Matches: 43,  Mismatches: 4, Indels: 7
        0.80            0.07        0.13

Matches are distributed among these distances:
   9    5  0.12
  10   20  0.47
  11   18  0.42

ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02


Consensus pattern (10 bp):   
AAAAAAGAAG

Found at i:7693 original size:30 final size:30

Alignment explanation


    Indices: 7655--7721  Score: 100
    Period size: 30  Copynumber: 2.2  Consensus size: 30

       7645 TCCCAGGAAA

                                           
       7655 AAAAAGAAGAAGAA-AAAAGAAGAGAAAAAG
          1 AAAAAGAAGAAGAATAAAAGAAGA-AAAAAG

             *                   *        
       7685 AGAAAGAAGAAGAATAAAAGAGGAAAAAAG
          1 AAAAAGAAGAAGAATAAAAGAAGAAAAAAG

                   
       7715 AAAAAGA
          1 AAAAAGA

       7722 GCAGAAGCAA


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  30   25  0.76
  31    8  0.24

ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01


Consensus pattern (30 bp):   
AAAAAGAAGAAGAATAAAAGAAGAAAAAAG

Found at i:7859 original size:48 final size:47

Alignment explanation


    Indices: 7743--7883  Score: 196
    Period size: 45  Copynumber: 3.0  Consensus size: 47

       7733 GATGGTTTTC

                 *        *                                
       7743 AAAAAGAGTCATGGATTTCAAAAGGTGTTAATAAAATGGTTTTTC--
          1 AAAAAAAGTCATGGTTTTCAAAAGGTGTTAATAAAATGGTTTTTCAA

                         *             *                   
       7788 AAAAAAAGTCATGATTTTCAAAAGGTGATAATAAAATGGTTTTTCAA
          1 AAAAAAAGTCATGGTTTTCAAAAGGTGTTAATAAAATGGTTTTTCAA

                                       *         *      *   
       7835 AAAAAATAGTCATGGTTTTCAAAAGGTTTTAATAAAAGGGTTTTCCAA
          1 AAAAAA-AGTCATGGTTTTCAAAAGGTGTTAATAAAATGGTTTTTCAA

             
       7883 A
          1 A

       7884 GTTGCATTTT


Statistics
Matches: 84,  Mismatches: 9, Indels: 3
        0.88            0.09        0.03

Matches are distributed among these distances:
  45   41  0.49
  47    6  0.07
  48   37  0.44

ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33


Consensus pattern (47 bp):   
AAAAAAAGTCATGGTTTTCAAAAGGTGTTAATAAAATGGTTTTTCAA
Done.