Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006779.1 Corchorus capsularis cultivar CVL-1 contig06800, 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: 17639
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31


Found at i:11845 original size:20 final size:20

Alignment explanation


    Indices: 11822--11869  Score: 60
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      11812 TCTGATTTGA

                    *           
      11822 CTTTTCTTCCTTTTTTATTT
          1 CTTTTCTTACTTTTTTATTT

                **   *          
      11842 CTTTAATTAGTTTTTTATTT
          1 CTTTTCTTACTTTTTTATTT

                    
      11862 CTTTTCTT
          1 CTTTTCTT

      11870 TTTCTTTTCA


Statistics
Matches: 22,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.10, C:0.15, G:0.02, T:0.73


Consensus pattern (20 bp):   
CTTTTCTTACTTTTTTATTT

Found at i:11909 original size:15 final size:15

Alignment explanation


    Indices: 11889--11917  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

      11879 ACTTTTCTGA

                           
      11889 TTTGATGATTTTTTT
          1 TTTGATGATTTTTTT

                          
      11904 TTTGATGATTTTTT
          1 TTTGATGATTTTTT

      11918 GATTATTATT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72


Consensus pattern (15 bp):   
TTTGATGATTTTTTT

Found at i:11956 original size:2 final size:2

Alignment explanation


    Indices: 11949--11975  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      11939 AATAGTAATA

                                                    
      11949 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

      11976 CACTAATTAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:14127 original size:38 final size:38

Alignment explanation


    Indices: 14077--14375  Score: 467
    Period size: 38  Copynumber: 7.8  Consensus size: 38

      14067 CAATCTAGCA

                                                  
      14077 AACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTACC
          1 AACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC

                                     *            
      14114 AACAGTTTAACCCCCTGAGGCACGGATCCACTCTTACC
          1 AACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC

                                                * 
      14152 AACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTATC
          1 AACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC

                                                   
      14190 AATCAGTTTAA-CCCCTGAGGCACGGGTCCACTCTTACC
          1 AA-CAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC

                                *                 
      14228 AACAGTTTAACCCCCTGAGGTACGGGTCCACTCTTACC
          1 AACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC

             *                      *               
      14266 ATCAGTTTAACCCCCTGAGGCACGTGTCCACTCTTATACC
          1 AACAGTTTAACCCCCTGAGGCACGGGTCCACTC-T-TACC

             *         *         *                
      14306 ATCAGTTTAACTCCCTGAGGCGCGGGTCCACTCTTACC
          1 AACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC

             *                   *          
      14344 ATCAGTTTAACCCCCTGAGGCGCGGGTCCACT
          1 AACAGTTTAACCCCCTGAGGCACGGGTCCACT

      14376 ATGCACAGCC


Statistics
Matches: 245,  Mismatches: 12, Indels: 9
        0.92            0.05        0.03

Matches are distributed among these distances:
  37   13  0.05
  38  188  0.77
  39   10  0.04
  40   34  0.14

ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23


Consensus pattern (38 bp):   
AACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC

Found at i:14520 original size:19 final size:19

Alignment explanation


    Indices: 14484--14523  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      14474 CGATTTTACG

                    * *  *     
      14484 AAAACAATGATACTCTTTC
          1 AAAACAATAAAACACTTTC

                               
      14503 AAAACAATAAAACACTTTC
          1 AAAACAATAAAACACTTTC

              
      14522 AA
          1 AA

      14524 TCATTTATAG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.53, C:0.20, G:0.03, T:0.25


Consensus pattern (19 bp):   
AAAACAATAAAACACTTTC

Found at i:15630 original size:12 final size:12

Alignment explanation


    Indices: 15613--15642  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

      15603 AGAACTAACC

                        
      15613 TTAGAGCACCCA
          1 TTAGAGCACCCA

                        
      15625 TTAGAGCACCCA
          1 TTAGAGCACCCA

            *     
      15637 ATAGAG
          1 TTAGAG

      15643 ATGAAAACAA


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

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.37, C:0.27, G:0.20, T:0.17


Consensus pattern (12 bp):   
TTAGAGCACCCA
Done.