Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006970.1 Corchorus olitorius cultivar O-4 contig06995, 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, 604

Length: 1008
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24


Found at i:746 original size:28 final size:28

Alignment explanation


    Indices: 715--879  Score: 104
    Period size: 27  Copynumber: 5.9  Consensus size: 28

        705 CTAGCAAAAA

                 *                      
        715 GGGGATGACCCCCCTGCCATGCGCAAAG
          1 GGGGACGACCCCCCTGCCATGCGCAAAG

                         *   *    ***   *
        743 GGGG-CGACCCCCTTGCTA-GTAAAAAAA
          1 GGGGACGACCCCCCTGCCATG-CGCAAAG

                 *       *               
        770 GGGGATGACCCCCTTGACCATGCGCAAAG
          1 GGGGACGACCCCCCTG-CCATGCGCAAAG

                         *   *    **    
        799 GGGG-CGACCCCCTTGCTA-GCAAAAAG
          1 GGGGACGACCCCCCTGCCATGCGCAAAG

                 * *              *      
        825 GGGGATGGCCCCCCTGCCATGCTCAAAAG
          1 GGGGACGACCCCCCTGCCATGCGC-AAAG

                *             *       
        854 GGGGGCGACCCCCCCTGCTATGCGCA
          1 GGGGACGA-CCCCCCTGCCATGCGCA

        880 CATAAAAAGA


Statistics
Matches: 101,  Mismatches: 28, Indels: 15
        0.70            0.19        0.10

Matches are distributed among these distances:
  26   11  0.11
  27   30  0.30
  28   26  0.26
  29   19  0.19
  30   15  0.15

ACGTcount: A:0.23, C:0.33, G:0.31, T:0.13


Consensus pattern (28 bp):   
GGGGACGACCCCCCTGCCATGCGCAAAG

Found at i:804 original size:56 final size:54

Alignment explanation


    Indices: 691--866  Score: 237
    Period size: 56  Copynumber: 3.2  Consensus size: 54

        681 ACTGCGCAAT

                *     *        *                                  
        691 GGGCTACCCCTTTGCTAG-CAAAAAGGGGATGACCCCCCTGCCATGCGCAAAGG
          1 GGGCGACCCCCTTGCTAGAAAAAAAGGGGATGACCCCCCTGCCATGCGCAAAGG

                                                   *                
        744 GGGCGACCCCCTTGCTAGTAAAAAAAGGGGATGACCCCCTTGACCATGCGCAAAGG
          1 GGGCGACCCCCTTGCTAG-AAAAAAAGGGGATGACCCCCCTG-CCATGCGCAAAGG

                              *     *       *              *        
        800 GGGCGACCCCCTTGCTAGCAAAAAGGGGGATGGCCCCCCTGCCATGCTCAAAAGGG
          1 GGGCGACCCCCTTGCTAGAAAAAAAGGGGATGACCCCCCTGCCATGCGC-AAA-GG

                       
        856 GGGCGACCCCC
          1 GGGCGACCCCC

        867 CCTGCTATGC


Statistics
Matches: 109,  Mismatches: 9, Indels: 7
        0.87            0.07        0.06

Matches are distributed among these distances:
  53   16  0.15
  54    7  0.06
  55   42  0.39
  56   44  0.40

ACGTcount: A:0.24, C:0.32, G:0.30, T:0.13


Consensus pattern (54 bp):   
GGGCGACCCCCTTGCTAGAAAAAAAGGGGATGACCCCCCTGCCATGCGCAAAGG

Found at i:970 original size:17 final size:16

Alignment explanation


    Indices: 947--995  Score: 75
    Period size: 14  Copynumber: 3.1  Consensus size: 16

        937 AAAAAAAAGG

                            
        947 AATAAAAAAATAAAAT
          1 AATAAAAAAATAAAAT

                            
        963 AAT--AAAAATAAAAT
          1 AATAAAAAAATAAAAT

                             
        977 AATAAAAACAATAAAAT
          1 AATAAAAA-AATAAAAT

              
        994 AA
          1 AA

        996 CGATAGAACA


Statistics
Matches: 30,  Mismatches: 0, Indels: 5
        0.86            0.00        0.14

Matches are distributed among these distances:
  14   14  0.47
  16    6  0.20
  17   10  0.33

ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18


Consensus pattern (16 bp):   
AATAAAAAAATAAAAT

Found at i:973 original size:22 final size:23

Alignment explanation


    Indices: 947--992  Score: 67
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        937 AAAAAAAAGG

                            *      
        947 AATAAAAAAAT-AAAATAATAAA
          1 AATAAAAAAATAAAAACAATAAA

                   *               
        969 AATAAAATAATAAAAACAATAAA
          1 AATAAAAAAATAAAAACAATAAA

             
        992 A
          1 A

        993 TAACGATAGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  22   10  0.48
  23   11  0.52

ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17


Consensus pattern (23 bp):   
AATAAAAAAATAAAAACAATAAA

Found at i:991 original size:9 final size:8

Alignment explanation


    Indices: 947--992  Score: 51
    Period size: 8  Copynumber: 5.9  Consensus size: 8

        937 AAAAAAAAGG

                    
        947 AATAAAAA
          1 AATAAAAA

                   *
        955 AATAAAAT
          1 AATAAAAA

                    
        963 AAT--AAA
          1 AATAAAAA

                   *
        969 AATAAAAT
          1 AATAAAAA

                    
        977 AATAAAAA
          1 AATAAAAA

                    
        985 CAATAAAA
          1 -AATAAAA

        993 TAACGATAGA


Statistics
Matches: 31,  Mismatches: 4, Indels: 5
        0.77            0.10        0.12

Matches are distributed among these distances:
   6    5  0.16
   8   19  0.61
   9    7  0.23

ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17


Consensus pattern (8 bp):   
AATAAAAA

Done.