Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017378.1 Corchorus olitorius cultivar O-4 contig17411, 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: 6611
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32


Found at i:2079 original size:16 final size:15

Alignment explanation


    Indices: 2058--2099  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       2048 TTACTTTGCT

                            
       2058 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                   *       
       2074 TTGTTTTATGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       2089 TTGCTTTCTGT
          1 TTGTTTTCTGT

       2100 CAATCTCTGT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  15   15  0.65
  16    8  0.35

ACGTcount: A:0.14, C:0.07, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:2481 original size:21 final size:22

Alignment explanation


    Indices: 2456--2501  Score: 76
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       2446 TTGTTTTGTG

                               *  
       2456 TTTTGCGTCG-AAAAAAAATAT
          1 TTTTGCGTCGTAAAAAAAAAAT

                                  
       2477 TTTTGCGTCGTAAAAAAAAAAT
          1 TTTTGCGTCGTAAAAAAAAAAT

               
       2499 TTT
          1 TTT

       2502 GTTTCTGCGT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  21   10  0.43
  22   13  0.57

ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37


Consensus pattern (22 bp):   
TTTTGCGTCGTAAAAAAAAAAT

Found at i:2498 original size:24 final size:27

Alignment explanation


    Indices: 2466--2522  Score: 75
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       2456 TTTTGCGTCG

                                   *   
       2466 AAAAAAAA-TAT-TTT-TGCGTCGTAA
          1 AAAAAAAATTATGTTTCTGCGTCATAA

                      *                
       2490 AAAAAAAATTTTGTTTCTGCGTCATAA
          1 AAAAAAAATTATGTTTCTGCGTCATAA

                  
       2517 AAAAAA
          1 AAAAAA

       2523 GTTTTTGCGT


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  24    8  0.29
  25    2  0.07
  26    3  0.11
  27   15  0.54

ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32


Consensus pattern (27 bp):   
AAAAAAAATTATGTTTCTGCGTCATAA

Found at i:2502 original size:21 final size:21

Alignment explanation


    Indices: 2456--2502  Score: 69
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       2446 TTGTTTTGTG

                                *
       2456 TTTTGCGTCGAAAAAAAATAT
          1 TTTTGCGTCGAAAAAAAATAA

                                  
       2477 TTTTGCGTCGTAAAAAAAA-AA
          1 TTTTGCGTCG-AAAAAAAATAA

                 
       2498 TTTTG
          1 TTTTG

       2503 TTTCTGCGTC


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  21   16  0.67
  22    8  0.33

ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36


Consensus pattern (21 bp):   
TTTTGCGTCGAAAAAAAATAA

Found at i:5578 original size:21 final size:21

Alignment explanation


    Indices: 5554--5608  Score: 74
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       5544 CGCCCATTCA

                           **    
       5554 CCGTGCCACCACCGGTTAAGC
          1 CCGTGCCACCACCGGCCAAGC

                              *  
       5575 CCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGCCAAGC

                    *    
       5596 CCGTGCCATCACC
          1 CCGTGCCACCACC

       5609 ATTCCAAGCC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCCAAGC
Done.