Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024223.1 Corchorus olitorius cultivar O-4 contig24256, 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: 13654
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31


Found at i:4705 original size:26 final size:26

Alignment explanation


    Indices: 4664--4717  Score: 83
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       4654 AAGCTAGTAA

                               *      
       4664 TGAAGTACGAAAGACCAAAGTGCCCC
          1 TGAAGTACGAAAGACCAAAATGCCCC

                                       
       4690 TGAAGTAC-AAATGACCAAAATGCCCC
          1 TGAAGTACGAAA-GACCAAAATGCCCC

              
       4716 TG
          1 TG

       4718 GACTTTGAAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  25    3  0.12
  26   23  0.88

ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15


Consensus pattern (26 bp):   
TGAAGTACGAAAGACCAAAATGCCCC

Found at i:7146 original size:16 final size:15

Alignment explanation


    Indices: 7108--7149  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       7098 ACAGAGATTG

                   *       
       7108 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       7123 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       7138 ACTAGAAAACAA
          1 AC-AGAAAACAA

       7150 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

Found at i:7925 original size:11 final size:11

Alignment explanation


    Indices: 7909--7934  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       7899 CCTTTGCCTA

                       
       7909 AAAACTAGAAG
          1 AAAACTAGAAG

                       
       7920 AAAACTAGAAG
          1 AAAACTAGAAG

                
       7931 AAAA
          1 AAAA

       7935 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG

Found at i:10451 original size:21 final size:21

Alignment explanation


    Indices: 10427--10488  Score: 70
    Period size: 21  Copynumber: 2.9  Consensus size: 21

      10417 GGAGTCGTGA

                                 
      10427 TGGCACGGGCATGGCCGGTGG
          1 TGGCACGGGCATGGCCGGTGG

                      * **       
      10448 TGGCACGGGCTTAACCGGTGG
          1 TGGCACGGGCATGGCCGGTGG

              *       *         
      10469 TGTCACGGTGAATGGCCGGT
          1 TGGCACGG-GCATGGCCGGT

      10489 AATGGCTTGG


Statistics
Matches: 32,  Mismatches: 8, Indels: 1
        0.78            0.20        0.02

Matches are distributed among these distances:
  21   25  0.78
  22    7  0.22

ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19


Consensus pattern (21 bp):   
TGGCACGGGCATGGCCGGTGG
Done.