Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022221.1 Corchorus olitorius cultivar O-4 contig22254, 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: 34296
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:6580 original size:148 final size:149

Alignment explanation


    Indices: 6308--6603  Score: 459
    Period size: 148  Copynumber: 2.0  Consensus size: 149

       6298 TATGCTCCCG

                                                            *                
       6308 AAGAAAAGTGTTCGGAAAAGGGGGGCAGAGGGGGTCTACAATGACAAATAACTCTTCCATTTCCA
          1 AAGAAAAGTGTTCGGAAAAGGGGGGCAGAGGGGGTCTACAATGACAAACAACTCTTCCATTTCCA

                                                      *           *          
       6373 TTTCTGGATTGGCGTGTCCACAGAGGAGCAAGCAAATTGGATTGAAATTTGAAGTCTCTGCAAAC
         66 TTTCTGGATTGGCGTGTCCACAGAGGAGCAAGCAAATTGGATGGAAATTTGAAGCCTCTGCAAAC

                               
       6438 TAAAAATAGAAATGAAGTA
        131 TAAAAATAGAAATGAAGTA

                 *      *     *                *   *          *     *        
       6457 AAGAAGAGTGTTGGGAAAGGGGGGGCAGAGGGGGTTTA-TATGACAAACAGCTCTTTCATTTCCA
          1 AAGAAAAGTGTTCGGAAAAGGGGGGCAGAGGGGGTCTACAATGACAAACAACTCTTCCATTTCCA

                                                                            *
       6521 TTTCTGGATTGGCGTGTCCACAGAGGAGCAAGCAAATTGGATGGAAATTTGAAGCCTCTGCAAAT
         66 TTTCTGGATTGGCGTGTCCACAGAGGAGCAAGCAAATTGGATGGAAATTTGAAGCCTCTGCAAAC

             *   *   *        
       6586 TGAAAGTAGCAATGAAGT
        131 TAAAAATAGAAATGAAGT

       6604 CACTGGCAAT


Statistics
Matches: 133,  Mismatches: 14, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
 148   99  0.74
 149   34  0.26

ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24


Consensus pattern (149 bp):   
AAGAAAAGTGTTCGGAAAAGGGGGGCAGAGGGGGTCTACAATGACAAACAACTCTTCCATTTCCA
TTTCTGGATTGGCGTGTCCACAGAGGAGCAAGCAAATTGGATGGAAATTTGAAGCCTCTGCAAAC
TAAAAATAGAAATGAAGTA

Found at i:6626 original size:30 final size:30

Alignment explanation


    Indices: 6590--6650  Score: 113
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       6580 GCAAATTGAA

                        *                 
       6590 AGTAGCAATGAAGTCACTGGCAATTTCCTT
          1 AGTAGCAATGAACTCACTGGCAATTTCCTT

                                          
       6620 AGTAGCAATGAACTCACTGGCAATTTCCTT
          1 AGTAGCAATGAACTCACTGGCAATTTCCTT

             
       6650 A
          1 A

       6651 ATATTCATTT


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   30  1.00

ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30


Consensus pattern (30 bp):   
AGTAGCAATGAACTCACTGGCAATTTCCTT

Found at i:13655 original size:14 final size:14

Alignment explanation


    Indices: 13617--13659  Score: 59
    Period size: 14  Copynumber: 3.1  Consensus size: 14

      13607 CTTCTCCTTT

                          
      13617 AATCGGTAATTTCC
          1 AATCGGTAATTTCC

               ** *       
      13631 AATATGCAATTTCC
          1 AATCGGTAATTTCC

                          
      13645 AATCGGTAATTTCC
          1 AATCGGTAATTTCC

             
      13659 A
          1 A

      13660 GGTATTTGTG


Statistics
Matches: 23,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  14   23  1.00

ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35


Consensus pattern (14 bp):   
AATCGGTAATTTCC

Found at i:23376 original size:13 final size:13

Alignment explanation


    Indices: 23358--23383  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      23348 TTTTAGTGCC

                         
      23358 ATACAAATTAATT
          1 ATACAAATTAATT

                         
      23371 ATACAAATTAATT
          1 ATACAAATTAATT

      23384 CCAAAGACAG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38


Consensus pattern (13 bp):   
ATACAAATTAATT

Found at i:31613 original size:57 final size:57

Alignment explanation


    Indices: 31505--31618  Score: 158
    Period size: 57  Copynumber: 2.0  Consensus size: 57

      31495 ATTAATCAAA

                                                          *           
      31505 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGGCT
          1 TATCAAGTGACATGTTCTTTATTAGATGCAT-AAAAAAGACGTTTTAGGACCAAGGCT

                *            *            *                     *    
      31563 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAGACGTTTTAGGACCGAGGC
          1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGC

      31619 ATGATGCTAT


Statistics
Matches: 50,  Mismatches: 5, Indels: 3
        0.86            0.09        0.05

Matches are distributed among these distances:
  57   22  0.44
  58   13  0.26
  59   15  0.30

ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32


Consensus pattern (57 bp):   
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCT

Found at i:32929 original size:32 final size:32

Alignment explanation


    Indices: 32886--32946  Score: 95
    Period size: 32  Copynumber: 1.9  Consensus size: 32

      32876 TTCAATAACC

                         *      *           
      32886 TTACATCTTTTGTGATTTTGGTTATCATATTA
          1 TTACATCTTTTGTAATTTTGATTATCATATTA

                  *                      
      32918 TTACATTTTTTGTAATTTTGATTATCATA
          1 TTACATCTTTTGTAATTTTGATTATCATA

      32947 CAAAATCTCA


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  32   26  1.00

ACGTcount: A:0.25, C:0.08, G:0.10, T:0.57


Consensus pattern (32 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTA
Done.