Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011582.1 Corchorus capsularis cultivar CVL-1 contig11603, 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: 23106
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:1456 original size:2 final size:2

Alignment explanation


    Indices: 1451--1476  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       1441 TTTTGGGTTA

                                                  
       1451 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       1477 GAACATCACC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:1973 original size:11 final size:11

Alignment explanation


    Indices: 1959--2002  Score: 54
    Period size: 11  Copynumber: 4.0  Consensus size: 11

       1949 GAAGAAGAAA

                       
       1959 TATTTTATTTT
          1 TATTTTATTTT

                       
       1970 TATTTTATTTT
          1 TATTTTATTTT

                   * *  
       1981 TATATTTCTATT
          1 TAT-TTTATTTT

                       
       1993 TATTTT-TTTT
          1 TATTTTATTTT

       2003 AACCCAAATC


Statistics
Matches: 29,  Mismatches: 3, Indels: 3
        0.83            0.09        0.09

Matches are distributed among these distances:
  10    3  0.10
  11   17  0.59
  12    9  0.31

ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80


Consensus pattern (11 bp):   
TATTTTATTTT

Found at i:2000 original size:19 final size:17

Alignment explanation


    Indices: 1961--1999  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       1951 AGAAGAAATA

                             
       1961 TTTTATTTTTATTTTAT
          1 TTTTATTTTTATTTTAT

                               
       1978 TTTTATATTTCTA-TTTAT
          1 TTTTAT-TTT-TATTTTAT

                
       1996 TTTT
          1 TTTT

       2000 TTTAACCCAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  17    6  0.30
  18   12  0.60
  19    2  0.10

ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79


Consensus pattern (17 bp):   
TTTTATTTTTATTTTAT

Found at i:22782 original size:2 final size:2

Alignment explanation


    Indices: 22777--22814  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      22767 AGATATCTTC

                                                                    
      22777 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      22815 CTAATACAAA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.