Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012382.1 Corchorus capsularis cultivar CVL-1 contig12403, 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: 25414
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:101 original size:26 final size:26

Alignment explanation


    Indices: 72--139  Score: 93
    Period size: 26  Copynumber: 2.6  Consensus size: 26

         62 TACTTAGTTT

                                      
         72 ATTAGTTTATGTTTAATTAATATCTA
          1 ATTAGTTTATGTTTAATTAATATCTA

                                *   *  
         98 ATTAGTTTAT-TATTAATTAGTATTTA
          1 ATTAGTTTATGT-TTAATTAATATCTA

                       *    
        124 ATTAGTTTATGATTAA
          1 ATTAGTTTATGTTTAA

        140 AATGAAGGAA


Statistics
Matches: 37,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  25    1  0.03
  26   36  0.97

ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54


Consensus pattern (26 bp):   
ATTAGTTTATGTTTAATTAATATCTA

Found at i:116 original size:15 final size:15

Alignment explanation


    Indices: 96--139  Score: 51
    Period size: 15  Copynumber: 3.2  Consensus size: 15

         86 AATTAATATC

                           
         96 TAATTAGTTTATTAT
          1 TAATTAGTTTATTAT

                           
        111 TAATTAG--TA-T-T
          1 TAATTAGTTTATTAT

                        *  
        122 TAATTAGTTTATGAT
          1 TAATTAGTTTATTAT

               
        137 TAA
          1 TAA

        140 AATGAAGGAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 8
        0.73            0.03        0.24

Matches are distributed among these distances:
  11    8  0.33
  12    1  0.04
  13    4  0.17
  15   11  0.46

ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55


Consensus pattern (15 bp):   
TAATTAGTTTATTAT

Found at i:183 original size:24 final size:25

Alignment explanation


    Indices: 149--206  Score: 93
    Period size: 25  Copynumber: 2.4  Consensus size: 25

        139 AAATGAAGGA

                             *       
        149 AAATGAA-TTTGAAG-ATTTGTTAG
          1 AAATGAAGTTTGAAGAAGTTGTTAG

                                     
        172 AAATGAAGTTTGAAGAAGTTGTTAG
          1 AAATGAAGTTTGAAGAAGTTGTTAG

                      
        197 AAATGAAGTT
          1 AAATGAAGTT

        207 AAGGGTTTGA


Statistics
Matches: 32,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  23    7  0.22
  24    7  0.22
  25   18  0.56

ACGTcount: A:0.41, C:0.00, G:0.24, T:0.34


Consensus pattern (25 bp):   
AAATGAAGTTTGAAGAAGTTGTTAG

Found at i:2819 original size:24 final size:25

Alignment explanation


    Indices: 2777--2829  Score: 81
    Period size: 24  Copynumber: 2.2  Consensus size: 25

       2767 CATGTTCTGA

                                     
       2777 AATTAACAGAAAATATATTAAAATT
          1 AATTAACAGAAAATATATTAAAATT

                  *             *    
       2802 AATTAATAG-AAATATATTATAATT
          1 AATTAACAGAAAATATATTAAAATT

                
       2826 AATT
          1 AATT

       2830 GCTCCATAAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  24   18  0.69
  25    8  0.31

ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38


Consensus pattern (25 bp):   
AATTAACAGAAAATATATTAAAATT

Found at i:19164 original size:113 final size:114

Alignment explanation


    Indices: 18963--19202  Score: 401
    Period size: 113  Copynumber: 2.1  Consensus size: 114

      18953 CAATTGGGGG

                                                    *    *   *    *          
      18963 GTACATATTTCAGTGACTAATAAGACAACACAAGGATATGGAACATAAATTCCATACAGATTCAC
          1 GTACATATTTCAGTGACTAATAAGACAACACAAGGATATGAAACAAAAAATCCACACAGATTCAC

            *                              *              *  
      19028 TAACATAAGTTTTAATATTCAGAAACACACAGCAAAAGCATATTGGTG-
         66 CAACATAAGTTTTAATATTCAGAAACACACAACAAAAGCATATTGGAGA

              *                                                              
      19076 GTGCATATTTCAGTGACTAATAAGACAACACAAGGATATGAAACAAAAAATCCACACAGATTCAC
          1 GTACATATTTCAGTGACTAATAAGACAACACAAGGATATGAAACAAAAAATCCACACAGATTCAC

                                                             
      19141 CAACATAAGTTTTAATATTCAGAAACACACAACAAAAGCATATTGGAGA
         66 CAACATAAGTTTTAATATTCAGAAACACACAACAAAAGCATATTGGAGA

                         
      19190 GTACATATTTCAG
          1 GTACATATTTCAG

      19203 GCAAGATACT


Statistics
Matches: 117,  Mismatches: 9, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
 113  105  0.90
 114   12  0.10

ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24


Consensus pattern (114 bp):   
GTACATATTTCAGTGACTAATAAGACAACACAAGGATATGAAACAAAAAATCCACACAGATTCAC
CAACATAAGTTTTAATATTCAGAAACACACAACAAAAGCATATTGGAGA

Found at i:23031 original size:1 final size:1

Alignment explanation


    Indices: 23025--23056  Score: 64
    Period size: 1  Copynumber: 32.0  Consensus size: 1

      23015 TTTCAAACAG

                                            
      23025 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      23057 GGACAAAATT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   31  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.