Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022350.1 Corchorus olitorius cultivar O-4 contig22383, 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: 36904
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:3085 original size:13 final size:13

Alignment explanation


    Indices: 3067--3092  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       3057 AAGGTAGCAA

                         
       3067 CAAAAATCATCAC
          1 CAAAAATCATCAC

                         
       3080 CAAAAATCATCAC
          1 CAAAAATCATCAC

       3093 TCATGCCAAG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15


Consensus pattern (13 bp):   
CAAAAATCATCAC

Found at i:4676 original size:22 final size:22

Alignment explanation


    Indices: 4629--4676  Score: 53
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       4619 ATATTACCAC

                       *   **     
       4629 AATTATTTTTGGCAGCCATAAT
          1 AATTATTTTTGCCAGAAATAAT

                                   
       4651 AATTATTTTTGCCAAGAAATAA-
          1 AATTATTTTTGCC-AGAAATAAT

                
       4673 AATT
          1 AATT

       4677 GGGTAATAAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  22   16  0.73
  23    6  0.27

ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40


Consensus pattern (22 bp):   
AATTATTTTTGCCAGAAATAAT

Found at i:5676 original size:16 final size:16

Alignment explanation


    Indices: 5655--5689  Score: 70
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       5645 TAACCTCGTC

                            
       5655 ACTCGGTGTTATGGTG
          1 ACTCGGTGTTATGGTG

                            
       5671 ACTCGGTGTTATGGTG
          1 ACTCGGTGTTATGGTG

               
       5687 ACT
          1 ACT

       5690 TATATGGAGG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.14, C:0.14, G:0.34, T:0.37


Consensus pattern (16 bp):   
ACTCGGTGTTATGGTG

Found at i:28450 original size:21 final size:20

Alignment explanation


    Indices: 28425--28471  Score: 58
    Period size: 21  Copynumber: 2.3  Consensus size: 20

      28415 AATTTAAATT

                     *      *    
      28425 AATTAATGCTAATTAATACTA
          1 AATTAATGCAAATTAAAAC-A

                 *              
      28446 AATTATTGCAAATTAAAACA
          1 AATTAATGCAAATTAAAACA

                  
      28466 AATTAA
          1 AATTAA

      28472 GCATTAAATT


Statistics
Matches: 22,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  20    6  0.27
  21   16  0.73

ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34


Consensus pattern (20 bp):   
AATTAATGCAAATTAAAACA

Found at i:28489 original size:31 final size:31

Alignment explanation


    Indices: 28454--28525  Score: 83
    Period size: 31  Copynumber: 2.3  Consensus size: 31

      28444 TAAATTATTG

                            *               
      28454 CAAATTAAAACAAAT-TAAGCATTAAATTAAA
          1 CAAATTAAAA-AAATGAAAGCATTAAATTAAA

                 * **           *          
      28485 CAAATCATTAAAATGAAAGCCTTAAATTAAA
          1 CAAATTAAAAAAATGAAAGCATTAAATTAAA

                      
      28516 CAAATTAAAA
          1 CAAATTAAAA

      28526 GCTGATAGAC


Statistics
Matches: 32,  Mismatches: 8, Indels: 2
        0.76            0.19        0.05

Matches are distributed among these distances:
  30    4  0.12
  31   28  0.88

ACGTcount: A:0.60, C:0.11, G:0.04, T:0.25


Consensus pattern (31 bp):   
CAAATTAAAAAAATGAAAGCATTAAATTAAA

Found at i:35425 original size:24 final size:24

Alignment explanation


    Indices: 35391--35442  Score: 77
    Period size: 24  Copynumber: 2.2  Consensus size: 24

      35381 GAGTACAAAC

                       **           
      35391 CAAAGGCATACTGTAAACACCCAT
          1 CAAAGGCATACCATAAACACCCAT

                  *                 
      35415 CAAAGGTATACCATAAACACCCAT
          1 CAAAGGCATACCATAAACACCCAT

                
      35439 CAAA
          1 CAAA

      35443 TATTATACCC


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.46, C:0.29, G:0.10, T:0.15


Consensus pattern (24 bp):   
CAAAGGCATACCATAAACACCCAT
Done.