Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022300.1 Corchorus olitorius cultivar O-4 contig22333, 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: 2843
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:744 original size:63 final size:63

Alignment explanation


    Indices: 677--831  Score: 199
    Period size: 63  Copynumber: 2.4  Consensus size: 63

        667 TTTCATTTCA

                     **                                                    
        677 TTTTTTTTTGGAGGTGGAAACTTTTTTTT-TTGGGTTTCTGGAAAGTGGGAAAAAGCAAAT-C
          1 TTTTTTTTTCAAGGTGGAAACTTTTTTTTGTTGGGTTTCTGGAAAGTGGGAAAAAGCAAATCC

                                  *                 *                        
        738 -TTTTTTTTCAAGGTGGAAGCATTTTTTTTTGTTGGGTTTTTGGAAAGTGGGAAAAAGCAAATCT
          1 TTTTTTTTTCAAGGTGGAA--ACTTTTTTTTGTTGGGTTTCTGGAAAGTGGGAAAAAGCAAATC-

              
        802 TC
         63 -C

                               * *      
        804 TTTTTTTTTCAAGGTGGAAGCATTTTTT
          1 TTTTTTTTTCAAGGTGGAAACTTTTTTT

        832 CTGGGTTGGG


Statistics
Matches: 80,  Mismatches: 7, Indels: 10
        0.82            0.07        0.10

Matches are distributed among these distances:
  60   16  0.20
  62    9  0.11
  63   30  0.38
  65    6  0.08
  66    1  0.01
  67   18  0.22

ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46


Consensus pattern (63 bp):   
TTTTTTTTTCAAGGTGGAAACTTTTTTTTGTTGGGTTTCTGGAAAGTGGGAAAAAGCAAATCC

Found at i:2214 original size:43 final size:42

Alignment explanation


    Indices: 2167--2260  Score: 136
    Period size: 43  Copynumber: 2.2  Consensus size: 42

       2157 CAGACCTCTA

                                   *                    
       2167 AAAATTGACAAGAAGACAATTC-GGAAATCAACATAGATCTCCG
          1 AAAATTGACAAGAAGACAATTCAAG-AATCAACATAGAT-TCCG

                  *                                  *
       2210 AAAATTAACAAGAAGACAATTCAAGAATCAACATAGATTCCT
          1 AAAATTGACAAGAAGACAATTCAAGAATCAACATAGATTCCG

                     
       2252 AAAATTGAC
          1 AAAATTGAC

       2261 TGAAAGGCCA


Statistics
Matches: 46,  Mismatches: 4, Indels: 3
        0.87            0.08        0.06

Matches are distributed among these distances:
  42   11  0.24
  43   34  0.74
  44    1  0.02

ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20


Consensus pattern (42 bp):   
AAAATTGACAAGAAGACAATTCAAGAATCAACATAGATTCCG

Found at i:2656 original size:70 final size:70

Alignment explanation


    Indices: 2552--2693  Score: 182
    Period size: 70  Copynumber: 2.0  Consensus size: 70

       2542 AAACCTCATT

                                      *        *  *               * *        
       2552 GAACTTTGCTTATGGAAAAGCCCTCTTGTGCTTGGGTGGAACC-AAGACTTAAAGTGACTCATAT
          1 GAACTTTGCTTATGGAAAAGCCCTCTAGTGCTTGGATGAAACCGAAG-CTTAAACTAACTCATAT

                  
       2616 GGAAAC
         65 GGAAAC

                                                                          *  
       2622 GAACTTTGGCTTATGGAAAAG-CCTC-AGATGCTTGGATGAAACCGAAGCTTAAACTAACTCGTA
          1 GAACTTT-GCTTATGGAAAAGCCCTCTAG-TGCTTGGATGAAACCGAAGCTTAAACTAACTCATA

                   
       2685 TGGAAAC
         64 TGGAAAC

              
       2692 GA
          1 GA

       2694 GTTTGCTCTT


Statistics
Matches: 63,  Mismatches: 6, Indels: 6
        0.84            0.08        0.08

Matches are distributed among these distances:
  69    1  0.02
  70   46  0.73
  71   16  0.25

ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25


Consensus pattern (70 bp):   
GAACTTTGCTTATGGAAAAGCCCTCTAGTGCTTGGATGAAACCGAAGCTTAAACTAACTCATATG
GAAAC
Done.