Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012759.1 Corchorus capsularis cultivar CVL-1 contig12780, 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: 8608
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33


Found at i:2356 original size:12 final size:13

Alignment explanation


    Indices: 2305--2355  Score: 66
    Period size: 13  Copynumber: 3.9  Consensus size: 13

       2295 AAAGATCGTC

                 *    *  
       2305 ATTATTATTTATT
          1 ATTATCATTTTTT

            *    *       
       2318 GTTATTATTTTTT
          1 ATTATCATTTTTT

                         
       2331 ATTATCATTTTTT
          1 ATTATCATTTTTT

                        
       2344 ATTATCATTTTT
          1 ATTATCATTTTT

       2356 AAATGTAATG


Statistics
Matches: 34,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  13   34  1.00

ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71


Consensus pattern (13 bp):   
ATTATCATTTTTT

Found at i:6271 original size:13 final size:13

Alignment explanation


    Indices: 6225--6272  Score: 53
    Period size: 13  Copynumber: 3.6  Consensus size: 13

       6215 TCATTTTTTT

                         
       6225 TCTCTTTTCTTAC
          1 TCTCTTTTCTTAC

                       * *
       6238 TCT-TTTTACTAAT
          1 TCTCTTTT-CTTAC

                          
       6251 TACTCTTTTCTTAC
          1 T-CTCTTTTCTTAC

                    
       6265 TCTCTTTT
          1 TCTCTTTT

       6273 ATTTCTTACC


Statistics
Matches: 28,  Mismatches: 4, Indels: 6
        0.74            0.11        0.16

Matches are distributed among these distances:
  12    4  0.14
  13   14  0.50
  14    6  0.21
  15    4  0.14

ACGTcount: A:0.12, C:0.25, G:0.00, T:0.62


Consensus pattern (13 bp):   
TCTCTTTTCTTAC

Found at i:6385 original size:21 final size:21

Alignment explanation


    Indices: 6346--6427  Score: 103
    Period size: 21  Copynumber: 3.9  Consensus size: 21

       6336 CTGATCACCC

                                  
       6346 TTTTACTCTTTACTGATTATTA
          1 TTTTACTC-TTACTGATTATTA

                                * 
       6368 TTTTACTCTTAC-GAATTATCA
          1 TTTTACTCTTACTG-ATTATTA

            *   *               *
       6389 CTTTGCTCTTACTGATTATTG
          1 TTTTACTCTTACTGATTATTA

                              
       6410 TTTTACTCTTACTGATTA
          1 TTTTACTCTTACTGATTA

       6428 CCTTTTACTG


Statistics
Matches: 51,  Mismatches: 7, Indels: 5
        0.81            0.11        0.08

Matches are distributed among these distances:
  20    1  0.02
  21   41  0.80
  22    9  0.18

ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54


Consensus pattern (21 bp):   
TTTTACTCTTACTGATTATTA

Found at i:6443 original size:42 final size:42

Alignment explanation


    Indices: 6333--6443  Score: 111
    Period size: 42  Copynumber: 2.6  Consensus size: 42

       6323 ACTCTTTGAA

                    *            *                     
       6333 TTACTGATCACCCTTTTACTCTTTACTGATTATTATTTTACTC
          1 TTACTGATTACCCTTTTACT-ATTACTGATTATTATTTTACTC

                         *     *  *            *        
       6376 TTAC-GAATTATCAC-TTTGCTCTTACTGATTATTGTTTTACTC
          1 TTACTG-ATTA-CCCTTTTACTATTACTGATTATTATTTTACTC

                                       
       6418 TTACTGATTA-CCTTTTACTGATTACT
          1 TTACTGATTACCCTTTTACT-ATTACT

       6444 ATTTTACTCT


Statistics
Matches: 55,  Mismatches: 8, Indels: 11
        0.74            0.11        0.15

Matches are distributed among these distances:
  40    1  0.02
  41    5  0.09
  42   34  0.62
  43   13  0.24
  44    2  0.04

ACGTcount: A:0.22, C:0.21, G:0.07, T:0.50


Consensus pattern (42 bp):   
TTACTGATTACCCTTTTACTATTACTGATTATTATTTTACTC

Found at i:6537 original size:16 final size:16

Alignment explanation


    Indices: 6507--6547  Score: 57
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       6497 CTCTCATTGA

                            
       6507 TTACC-TTTTTACTCT
          1 TTACCATTTTTACTCT

                       *    
       6522 TTACCATTTTTGCTCT
          1 TTACCATTTTTACTCT

                      
       6538 TTACCGATTT
          1 TTACC-ATTT

       6548 ACTGATTACT


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15    5  0.22
  16   14  0.61
  17    4  0.17

ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56


Consensus pattern (16 bp):   
TTACCATTTTTACTCT

Found at i:6614 original size:40 final size:39

Alignment explanation


    Indices: 6539--6649  Score: 123
    Period size: 40  Copynumber: 2.7  Consensus size: 39

       6529 TTTTGCTCTT

                *                        *          
       6539 TACCGATTTACTGATTACTTCTTTTACTCCTACTCTTAAA
          1 TACCAATTTACTGATTACTTCTTTTACT-TTACTCTTAAA

                 *                                 *
       6579 TACCATTTTACTGATTACTTCTTTTACTTTGACTCTTAAT
          1 TACCAATTTACTGATTACTTCTTTTACTTT-ACTCTTAAA

              *   *          *             
       6619 TATCAAATTACTGATTAATCTCTTTTTACTT
          1 TACCAATTTACTGATTACT-TC-TTTTACTT

       6650 AATTACTGAT


Statistics
Matches: 60,  Mismatches: 8, Indels: 4
        0.83            0.11        0.06

Matches are distributed among these distances:
  39    1  0.02
  40   49  0.82
  41    2  0.03
  42    8  0.13

ACGTcount: A:0.25, C:0.21, G:0.05, T:0.50


Consensus pattern (39 bp):   
TACCAATTTACTGATTACTTCTTTTACTTTACTCTTAAA
Done.