Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010413.1 Corchorus capsularis cultivar CVL-1 contig10434, 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: 8063
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:332 original size:11 final size:11

Alignment explanation


    Indices: 316--431  Score: 58
    Period size: 11  Copynumber: 9.7  Consensus size: 11

        306 GAAAATAAAT

                       
        316 TTAAGAAAAAA
          1 TTAAGAAAAAA

                         
        327 TTAAGAAAAGGAA
          1 TTAAGAAAA--AA

             *           
        340 -AAAGAAAAAAAA
          1 TTAAG--AAAAAA

                       
        352 TTAAGAAAAAA
          1 TTAAGAAAAAA

                 ***   
        363 --AAGGTGAAA
          1 TTAAGAAAAAA

                       *
        372 TTAAGAAAAATT
          1 TTAAGAAAAA-A

                       
        384 TTAAGAAAAAA
          1 TTAAGAAAAAA

                             
        395 TATACAACGTATAAAAA
          1 T-T--AA-G-A-AAAAA

                        
        412 CTTAAGAAAAAA
          1 -TTAAGAAAAAA

                    
        424 TTAAGAAA
          1 TTAAGAAA

        432 TTGGGGAAGA


Statistics
Matches: 80,  Mismatches: 10, Indels: 30
        0.67            0.08        0.25

Matches are distributed among these distances:
   9    6  0.08
  11   29  0.36
  12   21  0.26
  13    6  0.08
  14    7  0.09
  15    3  0.04
  16    1  0.01
  17    6  0.08
  18    1  0.01

ACGTcount: A:0.67, C:0.03, G:0.12, T:0.18


Consensus pattern (11 bp):   
TTAAGAAAAAA

Found at i:486 original size:21 final size:21

Alignment explanation


    Indices: 459--531  Score: 60
    Period size: 21  Copynumber: 3.3  Consensus size: 21

        449 GAAAAAATTT

                                 
        459 AAGAAAAGAAATTGATAAAAG
          1 AAGAAAAGAAATTGATAAAAG

            *                 *       
        480 TAGAAAACGGAGAA--GAAAAGGAAG
          1 AAGAAAA--GA-AATTGATAA--AAG

                                 
        504 AAGAAAAGAAATTGATAAAAG
          1 AAGAAAAGAAATTGATAAAAG

            *      
        525 CAGAAAA
          1 AAGAAAA

        532 CGGAGCAGAA


Statistics
Matches: 40,  Mismatches: 5, Indels: 14
        0.68            0.08        0.24

Matches are distributed among these distances:
  21   17  0.43
  22    6  0.15
  23    6  0.15
  24   11  0.28

ACGTcount: A:0.64, C:0.03, G:0.23, T:0.10


Consensus pattern (21 bp):   
AAGAAAAGAAATTGATAAAAG

Found at i:508 original size:45 final size:45

Alignment explanation


    Indices: 459--554  Score: 174
    Period size: 45  Copynumber: 2.1  Consensus size: 45

        449 GAAAAAATTT

                                 *                       
        459 AAGAAAAGAAATTGATAAAAGTAGAAAACGGAGAAGAAAAGGAAG
          1 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG

                                             *           
        504 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGCAGAAAAGGAAG
          1 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG

                  
        549 AAGAAA
          1 AAGAAA

        555 TTGGAGAAAA


Statistics
Matches: 49,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  45   49  1.00

ACGTcount: A:0.62, C:0.04, G:0.26, T:0.07


Consensus pattern (45 bp):   
AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG

Found at i:6693 original size:15 final size:14

Alignment explanation


    Indices: 6673--6720  Score: 78
    Period size: 15  Copynumber: 3.3  Consensus size: 14

       6663 GGCTGATGAT

                           
       6673 TGTTGGGCAGTGGGG
          1 TGTTGGGCAGT-GGG

                           
       6688 TGTTGGGCAGTAGGG
          1 TGTTGGGCAGT-GGG

                          
       6703 TGTTGGGCAGTGGG
          1 TGTTGGGCAGTGGG

                
       6717 TGTT
          1 TGTT

       6721 TCTTGTACTT


Statistics
Matches: 32,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  14    7  0.22
  15   25  0.78

ACGTcount: A:0.08, C:0.06, G:0.54, T:0.31


Consensus pattern (14 bp):   
TGTTGGGCAGTGGG
Done.