Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019389.1 Corchorus olitorius cultivar O-4 contig19422, 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: 7318
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--41  Score: 73
    Period size: 2  Copynumber: 20.5  Consensus size: 2

                                                               *         
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

         42 AATCAGAATG


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
AT

Found at i:374 original size:79 final size:78

Alignment explanation


    Indices: 272--428  Score: 260
    Period size: 79  Copynumber: 2.0  Consensus size: 78

        262 AAGAAGAAAG

                        *                                                    
        272 GGAGCAGATGCCCACCACAGGGAAATCGAGGAAAACCAGGGGAGTGGGTGGGAATGGAAGCGAGT
          1 GGAGCAGATGCCAACCACAGGGAAATCGAGGAAAACCAGGGGAGTGGGTGGGAATGGAAGCGAGT

              *          
        337 AGTGGGCAAGCAA
         66 AGCGGGCAAGCAA

                   *                            *                        *   
        350 GGAGCAGGTGGCCAACCACAGGGAAATCGAGGAAAATCAGGGGAGTGGGTGGGAATGGAAGGGAG
          1 GGAGCAGAT-GCCAACCACAGGGAAATCGAGGAAAACCAGGGGAGTGGGTGGGAATGGAAGCGAG

                          
        415 TAGCGGGCAAGCAA
         65 TAGCGGGCAAGCAA

        429 TCGAAAATCT


Statistics
Matches: 73,  Mismatches: 5, Indels: 1
        0.92            0.06        0.01

Matches are distributed among these distances:
  78    8  0.11
  79   65  0.89

ACGTcount: A:0.33, C:0.15, G:0.43, T:0.09


Consensus pattern (78 bp):   
GGAGCAGATGCCAACCACAGGGAAATCGAGGAAAACCAGGGGAGTGGGTGGGAATGGAAGCGAGT
AGCGGGCAAGCAA

Found at i:4992 original size:23 final size:22

Alignment explanation


    Indices: 4961--5043  Score: 78
    Period size: 23  Copynumber: 3.6  Consensus size: 22

       4951 CCATTTAGTA

                *                  
       4961 ATATTTATAATTAAATACATATT
          1 ATATATATAATTAAATA-ATATT

                        *          
       4984 ATATATATATATAAAATAATATT
          1 ATATATATA-ATTAAATAATATT

                           *       *
       5007 AGATATATATAATTACAT-ATATA
          1 --ATATATATAATTAAATAATATT

                          
       5030 ATAATATATAATTA
          1 AT-ATATATAATTA

       5044 TTAAACGGTT


Statistics
Matches: 51,  Mismatches: 5, Indels: 9
        0.78            0.08        0.14

Matches are distributed among these distances:
  21    2  0.04
  22   11  0.22
  23   17  0.33
  24   12  0.24
  25    9  0.18

ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43


Consensus pattern (22 bp):   
ATATATATAATTAAATAATATT

Found at i:5038 original size:10 final size:10

Alignment explanation


    Indices: 4983--5041  Score: 52
    Period size: 10  Copynumber: 5.8  Consensus size: 10

       4973 AAATACATAT

                       
       4983 TATAT-ATATA
          1 TATATAATA-A

                *     
       4993 TATAAAATAA
          1 TATATAATAA

                       
       5003 TAT-TAGAT-A
          1 TATATA-ATAA

                        
       5012 TATATAATTACA
          1 TATATAA-TA-A

                      
       5024 TATATAATAA
          1 TATATAATAA

                    
       5034 TATATAAT
          1 TATATAAT

       5042 TATTAAACGG


Statistics
Matches: 41,  Mismatches: 2, Indels: 12
        0.75            0.04        0.22

Matches are distributed among these distances:
   9    6  0.15
  10   22  0.54
  11    5  0.12
  12    8  0.20

ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42


Consensus pattern (10 bp):   
TATATAATAA
Done.