Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012388.1 Corchorus olitorius cultivar O-4 contig12421, 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: 24498
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31


Found at i:7747 original size:29 final size:30

Alignment explanation


    Indices: 7710--7769  Score: 77
    Period size: 29  Copynumber: 2.0  Consensus size: 30

       7700 CAATTCTTGC

                *        *                
       7710 TCTTGAAATAAATTTTCAAA-GTCTTCAAA
          1 TCTTCAAATAAATCTTCAAAGGTCTTCAAA

                       *                   
       7739 TCTTCAAATAAGTCTTCAAATGGTCTTCAAA
          1 TCTTCAAATAAATCTTCAAA-GGTCTTCAAA

       7770 CACGAACTTC


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29   17  0.65
  31    9  0.35

ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37


Consensus pattern (30 bp):   
TCTTCAAATAAATCTTCAAAGGTCTTCAAA

Found at i:10152 original size:29 final size:29

Alignment explanation


    Indices: 10120--10175  Score: 78
    Period size: 29  Copynumber: 1.9  Consensus size: 29

      10110 ACAAATAATT

                                 *        
      10120 GCAATTC-AATCAATCAATAGCAAGATATG
          1 GCAATTCAAATCAA-CAATAGAAAGATATG

                              *        
      10149 GCAATTCAAATCAACAATTGAAAGATA
          1 GCAATTCAAATCAACAATAGAAAGATA

      10176 GAATAAGCAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  29   18  0.75
  30    6  0.25

ACGTcount: A:0.48, C:0.16, G:0.12, T:0.23


Consensus pattern (29 bp):   
GCAATTCAAATCAACAATAGAAAGATATG

Found at i:15276 original size:22 final size:22

Alignment explanation


    Indices: 15251--15300  Score: 66
    Period size: 22  Copynumber: 2.3  Consensus size: 22

      15241 CTTTCTGACC

                    *              
      15251 ATTATTTACTGA-AATAATAATA
          1 ATTATTTAATGATAA-AATAATA

                      *           
      15273 ATTATTTAATTATAAAATAATA
          1 ATTATTTAATGATAAAATAATA

                  
      15295 ATTATT
          1 ATTATT

      15301 ATTCAATAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  22   23  0.92
  23    2  0.08

ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46


Consensus pattern (22 bp):   
ATTATTTAATGATAAAATAATA

Found at i:16783 original size:86 final size:86

Alignment explanation


    Indices: 16690--16905  Score: 414
    Period size: 86  Copynumber: 2.5  Consensus size: 86

      16680 ATTTCTACAT

                                                          *                  
      16690 CTTCCACAATTTGGCAAGATTTAGAAAATATTATCATTATTATTCATTCTTTATGATTTATTTAT
          1 CTTCCACAATTTGGCAAGATTTAGAAAATATTATCATTATTATTCAATCTTTATGATTTATTTAT

                                 
      16755 TTCTTAAAATATATCCTAAAC
         66 TTCTTAAAATATATCCTAAAC

                                                                             
      16776 CTTCCACAATTTGGCAAGATTTAGAAAATATTATCATTATTATTCAATCTTTATGATTTATTTAT
          1 CTTCCACAATTTGGCAAGATTTAGAAAATATTATCATTATTATTCAATCTTTATGATTTATTTAT

                                 
      16841 TTCTTAAAATATATCCTAAAC
         66 TTCTTAAAATATATCCTAAAC

                                            *           
      16862 CTTCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATT
          1 CTTCCACAATTTGGCAAGATTTAGAAAATATTATCATTATTATT

      16906 TATTGATTAT


Statistics
Matches: 128,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  86  128  1.00

ACGTcount: A:0.35, C:0.14, G:0.06, T:0.44


Consensus pattern (86 bp):   
CTTCCACAATTTGGCAAGATTTAGAAAATATTATCATTATTATTCAATCTTTATGATTTATTTAT
TTCTTAAAATATATCCTAAAC

Found at i:19236 original size:31 final size:31

Alignment explanation


    Indices: 19195--19288  Score: 125
    Period size: 31  Copynumber: 3.0  Consensus size: 31

      19185 GCATGCCACA

                *             *       *    
      19195 TGTCACTTTTTGGTACACATGGTGTGACATG
          1 TGTCGCTTTTTGGTACACGTGGTGTGCCATG

                                  *      **
      19226 TGTCGCTTTTTGGTACACGTGGCGTGCCACA
          1 TGTCGCTTTTTGGTACACGTGGTGTGCCATG

                                   *       
      19257 TGTCGCTTTTTGGTACACGTGGTATGCCATG
          1 TGTCGCTTTTTGGTACACGTGGTGTGCCATG

             
      19288 T
          1 T

      19289 TGGACACCGT


Statistics
Matches: 53,  Mismatches: 10, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  31   53  1.00

ACGTcount: A:0.15, C:0.20, G:0.28, T:0.37


Consensus pattern (31 bp):   
TGTCGCTTTTTGGTACACGTGGTGTGCCATG

Found at i:19258 original size:62 final size:60

Alignment explanation


    Indices: 19165--19288  Score: 167
    Period size: 62  Copynumber: 2.0  Consensus size: 60

      19155 CATGTGGCAC

                         *                                       *      
      19165 GTGTCCTTTTTGTGCACGAGGCATGCCACATGTCACTTTTTGGTACACATGGTGTGACAT
          1 GTGTCCTTTTTGTACACGAGGCATGCCACATGTCACTTTTTGGTACACATGGTATGACAT

                                *   *           *             *       *   
      19225 GTGTCGCTTTTTGGTACACGTGGCGTGCCACATGTCGCTTTTTGGTACACGTGGTATGCCAT
          1 GTGTC-CTTTTT-GTACACGAGGCATGCCACATGTCACTTTTTGGTACACATGGTATGACAT

              
      19287 GT
          1 GT

      19289 TGGACACCGT


Statistics
Matches: 55,  Mismatches: 7, Indels: 2
        0.86            0.11        0.03

Matches are distributed among these distances:
  60    5  0.09
  61    6  0.11
  62   44  0.80

ACGTcount: A:0.15, C:0.22, G:0.27, T:0.35


Consensus pattern (60 bp):   
GTGTCCTTTTTGTACACGAGGCATGCCACATGTCACTTTTTGGTACACATGGTATGACAT
Done.