Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012770.1 Corchorus capsularis cultivar CVL-1 contig12791, 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: 19348
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:12097 original size:38 final size:38

Alignment explanation


    Indices: 12052--12129  Score: 147
    Period size: 38  Copynumber: 2.1  Consensus size: 38

      12042 AGGTCGATCC

                                *                 
      12052 AAAATGGAAACATCAAAGGATCCATAATAGGCCCAAAT
          1 AAAATGGAAACATCAAAGGACCCATAATAGGCCCAAAT

                                                  
      12090 AAAATGGAAACATCAAAGGACCCATAATAGGCCCAAAT
          1 AAAATGGAAACATCAAAGGACCCATAATAGGCCCAAAT

              
      12128 AA
          1 AA

      12130 CCAAATAATC


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  38   39  1.00

ACGTcount: A:0.51, C:0.19, G:0.15, T:0.14


Consensus pattern (38 bp):   
AAAATGGAAACATCAAAGGACCCATAATAGGCCCAAAT

Found at i:14452 original size:16 final size:17

Alignment explanation


    Indices: 14412--14456  Score: 56
    Period size: 18  Copynumber: 2.6  Consensus size: 17

      14402 AAAAATCCAT

                              
      14412 CAATTAAAATGTCTAAAC
          1 CAATTAAAATGTCT-AAC

            *      *         
      14430 AAATTAAGATGTCT-AC
          1 CAATTAAAATGTCTAAC

                       
      14446 CAATTAAAATG
          1 CAATTAAAATG

      14457 GATGTGCTAT


Statistics
Matches: 23,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  16   11  0.48
  18   12  0.52

ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29


Consensus pattern (17 bp):   
CAATTAAAATGTCTAAC

Found at i:15046 original size:71 final size:72

Alignment explanation


    Indices: 14963--15097  Score: 166
    Period size: 72  Copynumber: 1.9  Consensus size: 72

      14953 AAGAATGACT

                   *           *                                             
      14963 ACCCTCGGTCA-TTCCGACGCAAACCGAAG-AAAGACCACCCTGGGTCAACTGAAATAAACTGAA
          1 ACCCTCGATCATTTCCGA-ACAAACCGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAA

                    
      15026 AAACAACC
         65 AAACAACC

                           *   *   **               *        *      *       
      15034 ACCCTCGATCATTTCGGAATAAATTGAAGAAAAGACCACCTTGGGTCAATTGAAATTAACTGAA
          1 ACCCTCGATCATTTCCGAACAAACCGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAA

      15098 GAAAAATCGC


Statistics
Matches: 53,  Mismatches: 9, Indels: 3
        0.82            0.14        0.05

Matches are distributed among these distances:
  71   17  0.32
  72   36  0.68

ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19


Consensus pattern (72 bp):   
ACCCTCGATCATTTCCGAACAAACCGAAGAAAAGACCACCCTGGGTCAACTGAAATAAACTGAAA
AACAACC

Found at i:15099 original size:36 final size:36

Alignment explanation


    Indices: 14983--15102  Score: 120
    Period size: 36  Copynumber: 3.4  Consensus size: 36

      14973 ATTCCGACGC

                *                        *      
      14983 AAACCGAAG-AAAGACCACCCTGGGTCAACTGAAAT
          1 AAACTGAAGAAAAGACCACCCTGGGTCAATTGAAAT

                                   * *   *    *   
      15018 AAACTGAA-AAACA-ACCACCCTCGATCATTTCGGAAT
          1 AAACTGAAGAAA-AGACCACCCTGGGTCAATT-GAAAT

               *                *               
      15054 AAATTGAAGAAAAGACCACCTTGGGTCAATTGAAAT
          1 AAACTGAAGAAAAGACCACCCTGGGTCAATTGAAAT

            *            
      15090 TAACTGAAGAAAA
          1 AAACTGAAGAAAA

      15103 ATCGCCCTGG


Statistics
Matches: 66,  Mismatches: 14, Indels: 9
        0.74            0.16        0.10

Matches are distributed among these distances:
  35   22  0.33
  36   28  0.42
  37   16  0.24

ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17


Consensus pattern (36 bp):   
AAACTGAAGAAAAGACCACCCTGGGTCAATTGAAAT

Found at i:16722 original size:13 final size:13

Alignment explanation


    Indices: 16704--16746  Score: 52
    Period size: 13  Copynumber: 3.3  Consensus size: 13

      16694 GTATCATAAT

                  *      
      16704 CAAAGTTATAAAC
          1 CAAAGTAATAAAC

                         
      16717 CAAAGTAATAAAC
          1 CAAAGTAATAAAC

                      *   
      16730 CAGAA-TAATCAAC
          1 CA-AAGTAATAAAC

                
      16743 CAAA
          1 CAAA

      16747 ACAGTCAGAC


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  12    2  0.07
  13   23  0.85
  14    2  0.07

ACGTcount: A:0.58, C:0.19, G:0.07, T:0.16


Consensus pattern (13 bp):   
CAAAGTAATAAAC
Done.