Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024134.1 Corchorus olitorius cultivar O-4 contig24167, 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: 13578
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:1914 original size:30 final size:30

Alignment explanation


    Indices: 1878--1934  Score: 78
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       1868 GTTTGGATAA

                        *    *            
       1878 TCCCAAAAGAAGGTTTTTGAAAATAAAGGT
          1 TCCCAAAAGAAGATTTTGGAAAATAAAGGT

                     *            *    
       1908 TCCCAAAAGGAGATTTTGGAAATTAAA
          1 TCCCAAAAGAAGATTTTGGAAAATAAA

       1935 TGGGTAAGTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  30   23  1.00

ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26


Consensus pattern (30 bp):   
TCCCAAAAGAAGATTTTGGAAAATAAAGGT

Found at i:2538 original size:15 final size:16

Alignment explanation


    Indices: 2512--2541  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       2502 AGATAACAAT

                            
       2512 ATAAACAACTTAAGAA
          1 ATAAACAACTTAAGAA

                           
       2528 ATAAA-AACTTAAGA
          1 ATAAACAACTTAAGA

       2542 TTGGAAGATC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    9  0.64
  16    5  0.36

ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20


Consensus pattern (16 bp):   
ATAAACAACTTAAGAA

Found at i:2675 original size:42 final size:42

Alignment explanation


    Indices: 2616--2718  Score: 206
    Period size: 42  Copynumber: 2.5  Consensus size: 42

       2606 AACTTAAGTA

                                                      
       2616 TGACAACTTCTGGTGTCAAAATTGAATAATAATTTTCTTGTG
          1 TGACAACTTCTGGTGTCAAAATTGAATAATAATTTTCTTGTG

                                                      
       2658 TGACAACTTCTGGTGTCAAAATTGAATAATAATTTTCTTGTG
          1 TGACAACTTCTGGTGTCAAAATTGAATAATAATTTTCTTGTG

                               
       2700 TGACAACTTCTGGTGTCAA
          1 TGACAACTTCTGGTGTCAA

       2719 TTAAATTTAC


Statistics
Matches: 61,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   61  1.00

ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39


Consensus pattern (42 bp):   
TGACAACTTCTGGTGTCAAAATTGAATAATAATTTTCTTGTG

Found at i:3012 original size:11 final size:11

Alignment explanation


    Indices: 2998--3028  Score: 53
    Period size: 11  Copynumber: 2.8  Consensus size: 11

       2988 AATCTACTTA

                       
       2998 AATCTTCAGAT
          1 AATCTTCAGAT

                 *     
       3009 AATCTCCAGAT
          1 AATCTTCAGAT

                     
       3020 AATCTTCAG
          1 AATCTTCAG

       3029 TTGAAATCTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32


Consensus pattern (11 bp):   
AATCTTCAGAT

Found at i:3059 original size:13 final size:13

Alignment explanation


    Indices: 3021--3060  Score: 53
    Period size: 13  Copynumber: 3.1  Consensus size: 13

       3011 TCTCCAGATA

                  *     *
       3021 ATCTTCAGTTGAA
          1 ATCTTCTGTTGAT

                    *    
       3034 ATCTTCTGATGAT
          1 ATCTTCTGTTGAT

                         
       3047 ATCTTCTGTTGAT
          1 ATCTTCTGTTGAT

             
       3060 A
          1 A

       3061 ATATTCTCTG


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  13   23  1.00

ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45


Consensus pattern (13 bp):   
ATCTTCTGTTGAT

Found at i:3417 original size:22 final size:20

Alignment explanation


    Indices: 3369--3417  Score: 55
    Period size: 22  Copynumber: 2.3  Consensus size: 20

       3359 GATTCAACTT

                                
       3369 AAACTTTATACCTTTTGTAC
          1 AAACTTTATACCTTTTGTAC

                                    
       3389 AATACTTT-TACACTTTTATGTAC
          1 AA-ACTTTATAC-C-TTT-TGTAC

                  
       3412 AAACTT
          1 AAACTT

       3418 CTCTTATGTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  20    5  0.20
  21    6  0.24
  22    7  0.28
  23    7  0.28

ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45


Consensus pattern (20 bp):   
AAACTTTATACCTTTTGTAC
Done.