Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015637.1 Corchorus olitorius cultivar O-4 contig15670, 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: 7237
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:14 original size:2 final size:2

Alignment explanation


    Indices: 8--52  Score: 90
    Period size: 2  Copynumber: 22.5  Consensus size: 2

          1 AACCTAC

                                                                          
          8 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                
         50 TA T
          1 TA T

         53 TTTTAGCTTT


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   43  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:157 original size:21 final size:22

Alignment explanation


    Indices: 113--191  Score: 88
    Period size: 22  Copynumber: 3.6  Consensus size: 22

        103 TTTTTTTATG

                                  
        113 AAATTTTGATAACCACCATATA
          1 AAATTTTGATAACCACCATATA

                        **        
        135 AAATTTTGATAATTACC-TATA
          1 AAATTTTGATAACCACCATATA

                 *      * *      *
        156 AAATTGTGATAAACTCCATATG
          1 AAATTTTGATAACCACCATATA

               *          
        178 AAACTTTGATAACC
          1 AAATTTTGATAACC

        192 TAACTATGAA


Statistics
Matches: 46,  Mismatches: 10, Indels: 2
        0.79            0.17        0.03

Matches are distributed among these distances:
  21   17  0.37
  22   29  0.63

ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34


Consensus pattern (22 bp):   
AAATTTTGATAACCACCATATA

Found at i:2545 original size:14 final size:15

Alignment explanation


    Indices: 2526--2561  Score: 56
    Period size: 14  Copynumber: 2.5  Consensus size: 15

       2516 AAGAGTGTAC

                  *        
       2526 TACAAATTACAA-AG
          1 TACAAAATACAATAG

                           
       2540 TACAAAATACAATAG
          1 TACAAAATACAATAG

                   
       2555 TACAAAA
          1 TACAAAA

       2562 CGTGTCCATA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  14   11  0.55
  15    9  0.45

ACGTcount: A:0.61, C:0.14, G:0.06, T:0.19


Consensus pattern (15 bp):   
TACAAAATACAATAG

Found at i:4720 original size:22 final size:22

Alignment explanation


    Indices: 4668--4720  Score: 54
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       4658 TGTGCTAGCC

                   *     *   *    
       4668 TCTCCTGAGCATTGTGTTGGCA
          1 TCTCCTGGGCATTATGTGGGCA

                 *                 
       4690 TCGT-GTGGGCATTATGTGGGCA
          1 TC-TCCTGGGCATTATGTGGGCA

                     
       4712 TCTCCTGGG
          1 TCTCCTGGG

       4721 TCTCCTCTTT


Statistics
Matches: 24,  Mismatches: 5, Indels: 4
        0.73            0.15        0.12

Matches are distributed among these distances:
  21    1  0.04
  22   22  0.92
  23    1  0.04

ACGTcount: A:0.11, C:0.21, G:0.34, T:0.34


Consensus pattern (22 bp):   
TCTCCTGGGCATTATGTGGGCA

Found at i:5806 original size:41 final size:41

Alignment explanation


    Indices: 5761--5889  Score: 215
    Period size: 41  Copynumber: 3.1  Consensus size: 41

       5751 TCTGTTTATA

                                                     
       5761 GACTTTGATATAGATGCCTCTTTGTTATAAATGTGCTTGAG
          1 GACTTTGATATAGATGCCTCTTTGTTATAAATGTGCTTGAG

                                    *                 
       5802 GACTTTGATATAGATGCCT-TTGTATTATAAATGTGCTTGAG
          1 GACTTTGATATAGATGCCTCTT-TGTTATAAATGTGCTTGAG

                                 *   *               
       5843 GACTTTGATATAGATGCCTCTGTGTAATAAATGTGCTTGAG
          1 GACTTTGATATAGATGCCTCTTTGTTATAAATGTGCTTGAG

                  
       5884 GACTTT
          1 GACTTT

       5890 TAGAGAGAGA


Statistics
Matches: 82,  Mismatches: 4, Indels: 4
        0.91            0.04        0.04

Matches are distributed among these distances:
  40    2  0.02
  41   79  0.96
  42    1  0.01

ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40


Consensus pattern (41 bp):   
GACTTTGATATAGATGCCTCTTTGTTATAAATGTGCTTGAG
Done.