Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008804.1 Corchorus capsularis cultivar CVL-1 contig08825, 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: 20711
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34


Found at i:5351 original size:38 final size:38

Alignment explanation


    Indices: 5295--5370  Score: 134
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       5285 AGGTTGTTTT

                         *                        
       5295 AATGATGTTGCTTCTGTTTTTATGTACTTTGCTTAAAG
          1 AATGATGTTGCTTATGTTTTTATGTACTTTGCTTAAAG

                                           *      
       5333 AATGATGTTGCTTATGTTTTTATGTACTTTGTTTAAAG
          1 AATGATGTTGCTTATGTTTTTATGTACTTTGCTTAAAG

       5371 GCAGTAACTG


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  38   36  1.00

ACGTcount: A:0.22, C:0.08, G:0.18, T:0.51


Consensus pattern (38 bp):   
AATGATGTTGCTTATGTTTTTATGTACTTTGCTTAAAG

Found at i:5729 original size:13 final size:13

Alignment explanation


    Indices: 5711--5740  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       5701 CACACAAGAA

                         
       5711 AACAACAAATTAG
          1 AACAACAAATTAG

                         
       5724 AACAACAAATTAG
          1 AACAACAAATTAG

                
       5737 AACA
          1 AACA

       5741 CATGTATATG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.63, C:0.17, G:0.07, T:0.13


Consensus pattern (13 bp):   
AACAACAAATTAG

Found at i:6431 original size:31 final size:31

Alignment explanation


    Indices: 6395--6496  Score: 86
    Period size: 31  Copynumber: 3.4  Consensus size: 31

       6385 TCTACGTTTT

                            *              
       6395 TCCTGAATTGACACAAAAGGATAACGTTATA
          1 TCCTGAATTGACACAATAGGATAACGTTATA

                   * *     * **         *  
       6426 TCCTGAAATCACAC-TTTCG-TAACGTTGTA
          1 TCCTGAATTGACACAATAGGATAACGTTATA

                            *                
       6455 TCCTGAATTGA-ACATCTAGGCA-AACGTTATA
          1 TCCTGAATTGACACA-ATAGG-ATAACGTTATA

                       
       6486 TCCTGAATTGA
          1 TCCTGAATTGA

       6497 GTATTTAGCC


Statistics
Matches: 54,  Mismatches: 13, Indels: 8
        0.72            0.17        0.11

Matches are distributed among these distances:
  28    2  0.04
  29   18  0.33
  30    3  0.06
  31   31  0.57

ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30


Consensus pattern (31 bp):   
TCCTGAATTGACACAATAGGATAACGTTATA

Found at i:10470 original size:33 final size:33

Alignment explanation


    Indices: 10412--10474  Score: 90
    Period size: 33  Copynumber: 1.9  Consensus size: 33

      10402 GAGAAGAAAA

                *       *                    
      10412 TCTAGGAGCTCGTGAGACGAGGAAGAAAATTTC
          1 TCTACGAGCTCGAGAGACGAGGAAGAAAATTTC

                             *  *         
      10445 TCTACGAGCTCGAGAGAGGATGAAGAAAAT
          1 TCTACGAGCTCGAGAGACGAGGAAGAAAAT

      10475 GAAAAATGAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  33   26  1.00

ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19


Consensus pattern (33 bp):   
TCTACGAGCTCGAGAGACGAGGAAGAAAATTTC

Found at i:13921 original size:17 final size:17

Alignment explanation


    Indices: 13899--13944  Score: 60
    Period size: 17  Copynumber: 2.7  Consensus size: 17

      13889 TCGGGTATTT

                              
      13899 TCGGGTTCGGG-CTC-GG
          1 TCGGGTTCGGGTC-CAGG

                              
      13915 ATCGGGTTCGGGTCCAGG
          1 -TCGGGTTCGGGTCCAGG

                        
      13933 TCGGGTTCGGGT
          1 TCGGGTTCGGGT

      13945 TCACTTTCGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  17   24  0.89
  18    3  0.11

ACGTcount: A:0.04, C:0.22, G:0.48, T:0.26


Consensus pattern (17 bp):   
TCGGGTTCGGGTCCAGG

Found at i:14759 original size:16 final size:16

Alignment explanation


    Indices: 14740--14782  Score: 77
    Period size: 16  Copynumber: 2.7  Consensus size: 16

      14730 TCGGATTGTC

                         *  
      14740 TCGGGTTCGGGTATTT
          1 TCGGGTTCGGGTAATT

                            
      14756 TCGGGTTCGGGTAATT
          1 TCGGGTTCGGGTAATT

                       
      14772 TCGGGTTCGGG
          1 TCGGGTTCGGG

      14783 CGGGTTCGGG


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  16   26  1.00

ACGTcount: A:0.07, C:0.14, G:0.42, T:0.37


Consensus pattern (16 bp):   
TCGGGTTCGGGTAATT

Found at i:14786 original size:26 final size:26

Alignment explanation


    Indices: 14712--14792  Score: 72
    Period size: 26  Copynumber: 2.9  Consensus size: 26

      14702 CTCGGGTCGG

                                  * **
      14712 TTTCGGGTTCGGGCGGGTTCGGATTG
          1 TTTCGGGTTCGGGCGGGTTCGGGTAA

             *                              
      14738 TCTCGGGTTCGGGTATTTTCGGGTTCGGGTAA
          1 TTTCGGGTTCGGG------CGGGTTCGGGTAA

                                   
      14770 TTTCGGGTTCGGGCGGGTTCGGG
          1 TTTCGGGTTCGGGCGGGTTCGGG

      14793 ACGTTGACTT


Statistics
Matches: 44,  Mismatches: 5, Indels: 12
        0.72            0.08        0.20

Matches are distributed among these distances:
  26   22  0.50
  32   22  0.50

ACGTcount: A:0.05, C:0.16, G:0.44, T:0.35


Consensus pattern (26 bp):   
TTTCGGGTTCGGGCGGGTTCGGGTAA
Done.