Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018002.1 Corchorus olitorius cultivar O-4 contig18035, 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: 32529
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:12588 original size:58 final size:58

Alignment explanation


    Indices: 12523--12681  Score: 291
    Period size: 58  Copynumber: 2.7  Consensus size: 58

      12513 CAGTTTAAAA

                                                     *      *         
      12523 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGATTTTTCAATT
          1 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATT

                                                                      
      12581 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATT
          1 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATT

                                                       
      12639 CAAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGC
          1 CAAAATCTTATCTTG-TTTTAAAATCCTGTTCGAGGTCTCTGC

      12682 AGTGAAACAA


Statistics
Matches: 98,  Mismatches: 2, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
  58   71  0.72
  59   27  0.28

ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43


Consensus pattern (58 bp):   
CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATT

Found at i:24995 original size:116 final size:115

Alignment explanation


    Indices: 24791--25009  Score: 323
    Period size: 116  Copynumber: 1.9  Consensus size: 115

      24781 GAATGAAACC

                                                           *     *           
      24791 AAAATGACCATAATGCCCCTGGATATGCAAAAATGACCAAAATACCATTGGATGTGCAAAAATGA
          1 AAAATGACCATAATGCCCCTGGATATGCAAAAATGACCAAAATACCACTGGATATGCAAAAATGA

                     *       *                                 
      24856 CCAAAATGCTCCTGAATGTGCAAAAATGATAAAAATGCCATGGGATACGTG
         66 CCAAAATGCCCCTGAATATGC-AAAATGATAAAAATGCCATGGGATACGTG

                              *                        *  *                  
      24907 AAAATGACCATAATGCCCTTGGATATGCAAAAATGACCAAAATGCCCCTGGATATGCAAAAATGA
          1 AAAATGACCATAATGCCCCTGGATATGCAAAAATGACCAAAATACCACTGGATATGCAAAAATGA

               *           *              *        
      24972 CCATAATGCCCCTG-GTCATGCAAAATGATCAAAATGCC
         66 CCAAAATGCCCCTGAAT-ATGCAAAATGATAAAAATGCC

      25010 CCTTTAAGTG


Statistics
Matches: 92,  Mismatches: 10, Indels: 3
        0.88            0.10        0.03

Matches are distributed among these distances:
 115   17  0.18
 116   75  0.82

ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21


Consensus pattern (115 bp):   
AAAATGACCATAATGCCCCTGGATATGCAAAAATGACCAAAATACCACTGGATATGCAAAAATGA
CCAAAATGCCCCTGAATATGCAAAATGATAAAAATGCCATGGGATACGTG

Found at i:25007 original size:28 final size:29

Alignment explanation


    Indices: 24791--25012  Score: 243
    Period size: 29  Copynumber: 7.7  Consensus size: 29

      24781 GAATGAAACC

                      *                  
      24791 AAAATGACCATAATGCCCCTGGATATGCA
          1 AAAATGACCAAAATGCCCCTGGATATGCA

                          *  **     *    
      24820 AAAATGACCAAAATACCATTGGATGTGCA
          1 AAAATGACCAAAATGCCCCTGGATATGCA

                            *    *  *    
      24849 AAAATGACCAAAATGCTCCTGAATGTGCA
          1 AAAATGACCAAAATGCCCCTGGATATGCA

                   **         *       * **
      24878 AAAATGATAAAAATG-CCATGGGATACGTG
          1 AAAATGACCAAAATGCCCCT-GGATATGCA

                      *       *          
      24907 AAAATGACCATAATGCCCTTGGATATGCA
          1 AAAATGACCAAAATGCCCCTGGATATGCA

                                         
      24936 AAAATGACCAAAATGCCCCTGGATATGCA
          1 AAAATGACCAAAATGCCCCTGGATATGCA

                      *                   
      24965 AAAATGACCATAATGCCCCTGG-TCATGC-
          1 AAAATGACCAAAATGCCCCTGGAT-ATGCA

                   *            
      24993 AAAATGATCAAAATGCCCCT
          1 AAAATGACCAAAATGCCCCT

      25013 TTAAGTGACC


Statistics
Matches: 159,  Mismatches: 31, Indels: 7
        0.81            0.16        0.04

Matches are distributed among these distances:
  28   21  0.13
  29  135  0.85
  30    3  0.02

ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21


Consensus pattern (29 bp):   
AAAATGACCAAAATGCCCCTGGATATGCA

Found at i:29682 original size:22 final size:22

Alignment explanation


    Indices: 29652--29694  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      29642 AAAGTTTCAG

                *      *    *     
      29652 GGAATTTATCACAATTTCATAA
          1 GGAAATTATCAAAATTCCATAA

                                 
      29674 GGAAATTATCAAAATTCCATA
          1 GGAAATTATCAAAATTCCATA

      29695 GTGTGGTTAT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33


Consensus pattern (22 bp):   
GGAAATTATCAAAATTCCATAA

Found at i:30518 original size:11 final size:11

Alignment explanation


    Indices: 30502--30549  Score: 50
    Period size: 11  Copynumber: 4.7  Consensus size: 11

      30492 GAAGTTCGTG

                       
      30502 TTTGAAGACCA
          1 TTTGAAGACCA

                    ** 
      30513 TTTGAAGATAA
          1 TTTGAAGACCA

                       
      30524 TTTGAAGA-C-
          1 TTTGAAGACCA

                       
      30533 -TTGAAGACCA
          1 TTTGAAGACCA

                    
      30543 -TTGAAGA
          1 TTTGAAGA

      30550 TTTATTTCAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 5
        0.80            0.08        0.12

Matches are distributed among these distances:
   8    7  0.22
   9    1  0.03
  10    7  0.22
  11   17  0.53

ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29


Consensus pattern (11 bp):   
TTTGAAGACCA
Done.