Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023433.1 Corchorus olitorius cultivar O-4 contig23466, 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: 18267
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38


Found at i:288 original size:2 final size:2

Alignment explanation


    Indices: 276--319  Score: 81
    Period size: 2  Copynumber: 22.5  Consensus size: 2

        266 ACTAAAAATA

                                                                          
        276 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                
        317 AT A
          1 AT A

        320 AGAAAACCAG


Statistics
Matches: 41,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.02
   2   40  0.98

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:1405 original size:37 final size:37

Alignment explanation


    Indices: 1343--1439  Score: 133
    Period size: 39  Copynumber: 2.6  Consensus size: 37

       1333 ATAATATCTT

                                               *  
       1343 AAACAGTTTTAAGTATTGTTTTTATGCTG-AAAAAGAA
          1 AAACAGTTTTAAGTATT-TTTTTATGCTGAAAAAAAAA

               *                                   
       1380 AAATAGTTTTAAGTATTTTTCTTATGCTGCAAAAAAAAA
          1 AAACAGTTTTAAGTATTTTT-TTATGCTG-AAAAAAAAA

                     *           
       1419 AAACAGTTTGAAGTATTTTTT
          1 AAACAGTTTTAAGTATTTTTT

       1440 AAGTAAGACA


Statistics
Matches: 53,  Mismatches: 4, Indels: 5
        0.85            0.06        0.08

Matches are distributed among these distances:
  36    3  0.06
  37   24  0.45
  38    1  0.02
  39   25  0.47

ACGTcount: A:0.40, C:0.06, G:0.13, T:0.40


Consensus pattern (37 bp):   
AAACAGTTTTAAGTATTTTTTTATGCTGAAAAAAAAA

Found at i:2955 original size:49 final size:49

Alignment explanation


    Indices: 2898--3004  Score: 214
    Period size: 49  Copynumber: 2.2  Consensus size: 49

       2888 TAAATAGTTC

                                                             
       2898 TAGTCGTGTTGTGTCATGTTTGAGTTACACGCTTATAAAATCGTCGTGT
          1 TAGTCGTGTTGTGTCATGTTTGAGTTACACGCTTATAAAATCGTCGTGT

                                                             
       2947 TAGTCGTGTTGTGTCATGTTTGAGTTACACGCTTATAAAATCGTCGTGT
          1 TAGTCGTGTTGTGTCATGTTTGAGTTACACGCTTATAAAATCGTCGTGT

                     
       2996 TAGTCGTGT
          1 TAGTCGTGT

       3005 CGTATCGTGT


Statistics
Matches: 58,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  49   58  1.00

ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41


Consensus pattern (49 bp):   
TAGTCGTGTTGTGTCATGTTTGAGTTACACGCTTATAAAATCGTCGTGT

Found at i:14590 original size:57 final size:57

Alignment explanation


    Indices: 14521--14636  Score: 205
    Period size: 57  Copynumber: 2.0  Consensus size: 57

      14511 TCAGCTTGCT

                              *                               *      
      14521 GATTGCTTCACAAAGGGTGTTTATTCAACTACATTTGCTTCTTCATTCTCTAAACTG
          1 GATTGCTTCACAAAGGGTCTTTATTCAACTACATTTGCTTCTTCATTCTCCAAACTG

                                  *                                  
      14578 GATTGCTTCACAAAGGGTCTTTCTTCAACTACATTTGCTTCTTCATTCTCCAAACTG
          1 GATTGCTTCACAAAGGGTCTTTATTCAACTACATTTGCTTCTTCATTCTCCAAACTG

              
      14635 GA
          1 GA

      14637 AATATTGAAC


Statistics
Matches: 56,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  57   56  1.00

ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39


Consensus pattern (57 bp):   
GATTGCTTCACAAAGGGTCTTTATTCAACTACATTTGCTTCTTCATTCTCCAAACTG
Done.