Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017905.1 Corchorus olitorius cultivar O-4 contig17938, 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: 31282
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33


Found at i:54 original size:21 final size:20

Alignment explanation


    Indices: 26--68  Score: 68
    Period size: 21  Copynumber: 2.1  Consensus size: 20

         16 TCCAATTCTG

                           *    
         26 TGATTCCGATGTCCGTTGTC
          1 TGATTCCGATGTCCGCTGTC

                                 
         46 TGATGTCCGATGTCCGCTGTC
          1 TGAT-TCCGATGTCCGCTGTC

              
         67 TG
          1 TG

         69 TTTCTGAATC


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  20    4  0.19
  21   17  0.81

ACGTcount: A:0.09, C:0.26, G:0.28, T:0.37


Consensus pattern (20 bp):   
TGATTCCGATGTCCGCTGTC

Found at i:7899 original size:16 final size:15

Alignment explanation


    Indices: 7854--7901  Score: 51
    Period size: 16  Copynumber: 3.1  Consensus size: 15

       7844 TCAAAATAAA

                 *         
       7854 TTTCTGATTTTTATT
          1 TTTCTAATTTTTATT

               *  *         
       7869 TTTTTATTTTATTATT
          1 TTTCTAATTT-TTATT

                            
       7885 TCTTCTAATTTTTATT
          1 T-TTCTAATTTTTATT

             
       7901 T
          1 T

       7902 ATTTAAATAA


Statistics
Matches: 26,  Mismatches: 5, Indels: 3
        0.76            0.15        0.09

Matches are distributed among these distances:
  15    7  0.27
  16   12  0.46
  17    7  0.27

ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75


Consensus pattern (15 bp):   
TTTCTAATTTTTATT

Found at i:23913 original size:29 final size:29

Alignment explanation


    Indices: 23829--23913  Score: 116
    Period size: 29  Copynumber: 2.9  Consensus size: 29

      23819 ACGGTCAAAG

                                      *  *
      23829 TCAACAGGATGACATGGCAGGTTGACCCGG
          1 TCAAC-GGATGACATGGCAGGTTGACTCGA

                  *                      
      23859 TCAACGAATGACATGGCAGGTTGACTCGA
          1 TCAACGGATGACATGGCAGGTTGACTCGA

                        *   *         
      23888 TCAACGGATGACGTGGTAGGTTGACT
          1 TCAACGGATGACATGGCAGGTTGACT

      23914 TAGTCAACAG


Statistics
Matches: 49,  Mismatches: 6, Indels: 1
        0.88            0.11        0.02

Matches are distributed among these distances:
  29   44  0.90
  30    5  0.10

ACGTcount: A:0.27, C:0.20, G:0.32, T:0.21


Consensus pattern (29 bp):   
TCAACGGATGACATGGCAGGTTGACTCGA

Found at i:23920 original size:29 final size:28

Alignment explanation


    Indices: 23827--23926  Score: 101
    Period size: 29  Copynumber: 3.4  Consensus size: 28

      23817 CAACGGTCAA

                                         *
      23827 AGTCAACAGGATGACATGGCAGGTTGACCC
          1 AGTCAAC-GGATGACATGGCAGGTTGA-CT

            *       *                   
      23857 GGTCAACGAATGACATGGCAGGTTGACT
          1 AGTCAACGGATGACATGGCAGGTTGACT

            *              *   *          
      23885 CGATCAACGGATGACGTGGTAGGTTGACTT
          1 AG-TCAACGGATGACATGGCAGGTTGAC-T

                   *    
      23915 AGTCAACAGATG
          1 AGTCAACGGATG

      23927 CCGCGGCAAC


Statistics
Matches: 59,  Mismatches: 9, Indels: 5
        0.81            0.12        0.07

Matches are distributed among these distances:
  28    2  0.03
  29   49  0.83
  30    8  0.14

ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21


Consensus pattern (28 bp):   
AGTCAACGGATGACATGGCAGGTTGACT

Found at i:25242 original size:9 final size:9

Alignment explanation


    Indices: 25228--25253  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

      25218 CACTATCAAA

                     
      25228 GGGAATCAG
          1 GGGAATCAG

                     
      25237 GGGAATCAG
          1 GGGAATCAG

                    
      25246 GGGAATCA
          1 GGGAATCA

      25254 TACGTATAAG


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

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.35, C:0.12, G:0.42, T:0.12


Consensus pattern (9 bp):   
GGGAATCAG
Done.