Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016885.1 Corchorus olitorius cultivar O-4 contig16918, 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: 3199
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34


Found at i:2824 original size:38 final size:38

Alignment explanation


    Indices: 2778--2887  Score: 148
    Period size: 38  Copynumber: 2.9  Consensus size: 38

       2768 TATTTTTCAA

                            *                     
       2778 TTCTGTGTTGAAGTTTTTGTTTTACTTTTCAATTGCAT
          1 TTCTGTGTTGAAGTTTCTGTTTTACTTTTCAATTGCAT

              *                        * ***      
       2816 TTTTGTGTTGAAGTTTCTGTTTTACTTCTGTTTTGCAT
          1 TTCTGTGTTGAAGTTTCTGTTTTACTTTTCAATTGCAT

                                   * *        
       2854 TTCTGTGTTGAAGTTTCTGTTTTGCATTTCAATT
          1 TTCTGTGTTGAAGTTTCTGTTTTACTTTTCAATT

       2888 TTGTTTAGTG


Statistics
Matches: 59,  Mismatches: 13, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  38   59  1.00

ACGTcount: A:0.14, C:0.11, G:0.17, T:0.58


Consensus pattern (38 bp):   
TTCTGTGTTGAAGTTTCTGTTTTACTTTTCAATTGCAT

Found at i:2859 original size:13 final size:13

Alignment explanation


    Indices: 2810--2883  Score: 62
    Period size: 13  Copynumber: 5.7  Consensus size: 13

       2800 TACTTTTCAA

                    *   *
       2810 TTGCATTTTTGTG
          1 TTGCATTTCTGTT

               *          
       2823 TTGAAGTTTCTGTT
          1 TTGCA-TTTCTGTT

                 *       
       2837 TT--ACTTCTGTT
          1 TTGCATTTCTGTT

                        *
       2848 TTGCATTTCTGTG
          1 TTGCATTTCTGTT

               *          
       2861 TTGAAGTTTCTGTT
          1 TTGCA-TTTCTGTT

                     
       2875 TTGCATTTC
          1 TTGCATTTC

       2884 AATTTTGTTT


Statistics
Matches: 48,  Mismatches: 9, Indels: 8
        0.74            0.14        0.12

Matches are distributed among these distances:
  11    9  0.19
  12    1  0.02
  13   19  0.40
  14   19  0.40

ACGTcount: A:0.11, C:0.12, G:0.19, T:0.58


Consensus pattern (13 bp):   
TTGCATTTCTGTT

Found at i:2919 original size:27 final size:25

Alignment explanation


    Indices: 2871--2920  Score: 73
    Period size: 27  Copynumber: 1.9  Consensus size: 25

       2861 TTGAAGTTTC

                             *       
       2871 TGTTTTGCATTTCAATTTTGTTTAG
          1 TGTTTTGCATTTCAATTCTGTTTAG

                                     
       2896 TGTTTTGCATTTTTCAATTCTGTTT
          1 TGTTTTGCA--TTTCAATTCTGTTT

       2921 TTCAATTCTG


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  25    9  0.41
  27   13  0.59

ACGTcount: A:0.14, C:0.10, G:0.14, T:0.62


Consensus pattern (25 bp):   
TGTTTTGCATTTCAATTCTGTTTAG

Found at i:2923 original size:13 final size:13

Alignment explanation


    Indices: 2905--2934  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       2895 GTGTTTTGCA

                         
       2905 TTTTTCAATTCTG
          1 TTTTTCAATTCTG

                         
       2918 TTTTTCAATTCTG
          1 TTTTTCAATTCTG

                
       2931 TTTT
          1 TTTT

       2935 GCATTTTTCA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67


Consensus pattern (13 bp):   
TTTTTCAATTCTG

Found at i:2960 original size:32 final size:33

Alignment explanation


    Indices: 2896--2972  Score: 129
    Period size: 32  Copynumber: 2.4  Consensus size: 33

       2886 TTTTGTTTAG

                                *            
       2896 TGTTTTGCATTTTTCAATTCTGTTTTTCAATTC
          1 TGTTTTGCATTTTTCAATTCAGTTTTTCAATTC

                                       *     
       2929 TGTTTTGCATTTTTCAATT-AGTTTTTGAATTC
          1 TGTTTTGCATTTTTCAATTCAGTTTTTCAATTC

                        
       2961 TGTTTTGCATTT
          1 TGTTTTGCATTT

       2973 AACTCACTTA


Statistics
Matches: 42,  Mismatches: 2, Indels: 1
        0.93            0.04        0.02

Matches are distributed among these distances:
  32   23  0.55
  33   19  0.45

ACGTcount: A:0.16, C:0.12, G:0.12, T:0.61


Consensus pattern (33 bp):   
TGTTTTGCATTTTTCAATTCAGTTTTTCAATTC
Done.