Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016804.1 Corchorus olitorius cultivar O-4 contig16837, 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: 16977
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31


Found at i:809 original size:15 final size:15

Alignment explanation


    Indices: 779--820  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        769 TTACTTTGCT

                            
        779 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
        795 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
        810 TTGCTTTCTGT
          1 TTGTTTTCTGT

        821 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:4861 original size:29 final size:29

Alignment explanation


    Indices: 4806--4861  Score: 78
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       4796 TTGAAGATTT

                                  *      
       4806 ATTGAAGATAATTTCAAGATAGGAAGACC
          1 ATTGAAGATAATTTCAAGATAGCAAGACC

                      *                 
       4835 ATTGAAGAATTATTTCAAGA-AGCAAGA
          1 ATTGAAG-ATAATTTCAAGATAGCAAGA

       4862 ATTGAGGATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  29   13  0.54
  30   11  0.46

ACGTcount: A:0.46, C:0.09, G:0.20, T:0.25


Consensus pattern (29 bp):   
ATTGAAGATAATTTCAAGATAGCAAGACC

Found at i:9571 original size:25 final size:25

Alignment explanation


    Indices: 9530--9577  Score: 78
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       9520 GAAAATCAAT

                                     
       9530 TTTTTTTTTAGAAAAAACGCAGAAA
          1 TTTTTTTTTAGAAAAAACGCAGAAA

                     *  *          
       9555 TTTTTTTTTGGAGAAAACGCAGA
          1 TTTTTTTTTAGAAAAAACGCAGA

       9578 GACTAAGAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  25   21  1.00

ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38


Consensus pattern (25 bp):   
TTTTTTTTTAGAAAAAACGCAGAAA

Found at i:12374 original size:18 final size:18

Alignment explanation


    Indices: 12351--12389  Score: 60
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      12341 GATGGCGTGG

                       *      
      12351 ATTGCCATTTCTGATGCC
          1 ATTGCCATTTCCGATGCC

                         *    
      12369 ATTGCCATTTCCGTTGCC
          1 ATTGCCATTTCCGATGCC

               
      12387 ATT
          1 ATT

      12390 TCTGACATGT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.15, C:0.28, G:0.15, T:0.41


Consensus pattern (18 bp):   
ATTGCCATTTCCGATGCC

Found at i:12945 original size:14 final size:16

Alignment explanation


    Indices: 12928--12965  Score: 62
    Period size: 14  Copynumber: 2.5  Consensus size: 16

      12918 AGACCTTGCA

                            
      12928 AAAAAGAAG-AAAA-T
          1 AAAAAGAAGTAAAAGT

                            
      12942 AAAAAGAAGTAAAAGT
          1 AAAAAGAAGTAAAAGT

                    
      12958 AAAAAGAA
          1 AAAAAGAA

      12966 AACCTTTAAA


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

Matches are distributed among these distances:
  14    9  0.41
  15    4  0.18
  16    9  0.41

ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08


Consensus pattern (16 bp):   
AAAAAGAAGTAAAAGT

Found at i:14922 original size:16 final size:15

Alignment explanation


    Indices: 14884--14925  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      14874 ACAGAGGTTG

                   *       
      14884 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
      14899 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      14914 ACTAGAAAACAA
          1 AC-AGAAAACAA

      14926 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.