Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013545.1 Corchorus capsularis cultivar CVL-1 contig13566, 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: 21021
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35


Found at i:510 original size:21 final size:20

Alignment explanation


    Indices: 486--550  Score: 87
    Period size: 21  Copynumber: 3.2  Consensus size: 20

        476 GGTATAGTAA

                                 
        486 AATGTAGTCACTATTTGGTGT
          1 AATGTA-TCACTATTTGGTGT

                      *         
        507 AATG-ATCACAATTTGGTGT
          1 AATGTATCACTATTTGGTGT

                        *        
        526 AATGGTATCACTTTTTGGTGT
          1 AAT-GTATCACTATTTGGTGT

                
        547 AATG
          1 AATG

        551 AAAATTATCA


Statistics
Matches: 39,  Mismatches: 3, Indels: 5
        0.83            0.06        0.11

Matches are distributed among these distances:
  19   16  0.41
  20    3  0.08
  21   20  0.51

ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42


Consensus pattern (20 bp):   
AATGTATCACTATTTGGTGT

Found at i:520 original size:19 final size:19

Alignment explanation


    Indices: 493--551  Score: 82
    Period size: 19  Copynumber: 3.0  Consensus size: 19

        483 TAAAATGTAG

                               
        493 TCACTATTTGGTGTAATGA
          1 TCACTATTTGGTGTAATGA

                *                
        512 TCACAATTTGGTGTAATGGTA
          1 TCACTATTTGGTGTAAT-G-A

                 *             
        533 TCACTTTTTGGTGTAATGA
          1 TCACTATTTGGTGTAATGA

        552 AAATTATCAC


Statistics
Matches: 35,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
  19   17  0.49
  20    2  0.06
  21   16  0.46

ACGTcount: A:0.25, C:0.10, G:0.22, T:0.42


Consensus pattern (19 bp):   
TCACTATTTGGTGTAATGA

Found at i:5146 original size:18 final size:19

Alignment explanation


    Indices: 5123--5158  Score: 65
    Period size: 18  Copynumber: 1.9  Consensus size: 19

       5113 TAATCAAATG

                               
       5123 AAAAAAATATAT-TATATC
          1 AAAAAAATATATATATATC

                              
       5141 AAAAAAATATATATATAT
          1 AAAAAAATATATATATAT

       5159 ATAATTCATT


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

Matches are distributed among these distances:
  18   12  0.71
  19    5  0.29

ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33


Consensus pattern (19 bp):   
AAAAAAATATATATATATC

Found at i:20784 original size:14 final size:14

Alignment explanation


    Indices: 20765--20795  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

      20755 ATCTATCTAG

                          
      20765 TTACTATAAAAAAA
          1 TTACTATAAAAAAA

                          
      20779 TTACTATAAAAAAA
          1 TTACTATAAAAAAA

               
      20793 TTA
          1 TTA

      20796 GTAAGTTTGA


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

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32


Consensus pattern (14 bp):   
TTACTATAAAAAAA

Found at i:20853 original size:2 final size:2

Alignment explanation


    Indices: 20846--20878  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      20836 TTTATGTTAG

                                                             
      20846 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      20879 GGTATGAGTT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
TA

Done.