Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009698.1 Corchorus capsularis cultivar CVL-1 contig09719, 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: 46588
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:1099 original size:34 final size:34

Alignment explanation


    Indices: 1033--1101  Score: 84
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       1023 GCAGCTTAAG

                             *      ****      
       1033 CACACTGTCATTACAGGTCAATTATTTGAACAAA
          1 CACACTGTCATTACAGGCCAATTACACAAACAAA

                *                             
       1067 CACATTGTCATTACAGGCCAATTACACAAACAAA
          1 CACACTGTCATTACAGGCCAATTACACAAACAAA

             
       1101 C
          1 C

       1102 CCTAGAAAAT


Statistics
Matches: 29,  Mismatches: 6, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  34   29  1.00

ACGTcount: A:0.41, C:0.25, G:0.10, T:0.25


Consensus pattern (34 bp):   
CACACTGTCATTACAGGCCAATTACACAAACAAA

Found at i:7713 original size:57 final size:57

Alignment explanation


    Indices: 7625--7735  Score: 213
    Period size: 57  Copynumber: 1.9  Consensus size: 57

       7615 TGTCCATAAA

                                     *                               
       7625 CCATAGTTATTTTTTTTAAATCTATGTATATATAGGAGATATTGTGCCCACCCTAAC
          1 CCATAGTTATTTTTTTTAAATCTATATATATATAGGAGATATTGTGCCCACCCTAAC

                                                                  
       7682 CCATAGTTATTTTTTTTAAATCTATATATATATAGGAGATATTGTGCCCACCCT
          1 CCATAGTTATTTTTTTTAAATCTATATATATATAGGAGATATTGTGCCCACCCT

       7736 GACAAATGCT


Statistics
Matches: 53,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  57   53  1.00

ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41


Consensus pattern (57 bp):   
CCATAGTTATTTTTTTTAAATCTATATATATATAGGAGATATTGTGCCCACCCTAAC

Found at i:23614 original size:30 final size:29

Alignment explanation


    Indices: 23578--23634  Score: 78
    Period size: 29  Copynumber: 1.9  Consensus size: 29

      23568 ACGTAGACCC

                               *          
      23578 AAATTGAGAGTTGAAGGGGTAAAATGTCCA
          1 AAATTGA-AGTTGAAGGGGCAAAATGTCCA

                         *        *    
      23608 AAATTGAAGTTGAGGGGGCAAAGTGTC
          1 AAATTGAAGTTGAAGGGGCAAAATGTC

      23635 TAAACCCTAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  29   17  0.71
  30    7  0.29

ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23


Consensus pattern (29 bp):   
AAATTGAAGTTGAAGGGGCAAAATGTCCA

Found at i:24206 original size:18 final size:18

Alignment explanation


    Indices: 24180--24215  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      24170 GTAGGCACAA

                *             
      24180 GACAGTACTGAAGCGTAC
          1 GACAATACTGAAGCGTAC

                              
      24198 GACAATACTGAAGCGTAC
          1 GACAATACTGAAGCGTAC

      24216 ATAAGAAAGT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17


Consensus pattern (18 bp):   
GACAATACTGAAGCGTAC

Found at i:26255 original size:16 final size:16

Alignment explanation


    Indices: 26234--26267  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      26224 TCATTAAAAT

                        *   
      26234 GTGTTAAAATTTTCTA
          1 GTGTTAAAATTTCCTA

                            
      26250 GTGTTAAAATTTCCTA
          1 GTGTTAAAATTTCCTA

              
      26266 GT
          1 GT

      26268 TTTTCATTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47


Consensus pattern (16 bp):   
GTGTTAAAATTTCCTA

Found at i:27453 original size:21 final size:20

Alignment explanation


    Indices: 27415--27456  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 20

      27405 TAACATTGAG

                                
      27415 ACAAATTACATCTAAAAAAA
          1 ACAAATTACATCTAAAAAAA

                                  
      27435 ACAAATTA-ATCTTTAAAAAAA
          1 ACAAATTACATC--TAAAAAAA

             
      27456 A
          1 A

      27457 ACTGAAACAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  19    3  0.15
  20    8  0.40
  21    9  0.45

ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24


Consensus pattern (20 bp):   
ACAAATTACATCTAAAAAAA

Found at i:36834 original size:49 final size:49

Alignment explanation


    Indices: 36777--36873  Score: 185
    Period size: 49  Copynumber: 2.0  Consensus size: 49

      36767 GCGCCTGGTC

                                                             
      36777 GGAGCTAGGGGCGAGGCAAGGGTCGCGACGCTGGGATCATGCGAGCGGT
          1 GGAGCTAGGGGCGAGGCAAGGGTCGCGACGCTGGGATCATGCGAGCGGT

                                                  *         
      36826 GGAGCTAGGGGCGAGGCAAGGGTCGCGACGCTGGGATCGTGCGAGCGG
          1 GGAGCTAGGGGCGAGGCAAGGGTCGCGACGCTGGGATCATGCGAGCGG

      36874 CACGGCTGTG


Statistics
Matches: 47,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  49   47  1.00

ACGTcount: A:0.18, C:0.21, G:0.51, T:0.11


Consensus pattern (49 bp):   
GGAGCTAGGGGCGAGGCAAGGGTCGCGACGCTGGGATCATGCGAGCGGT
Done.