Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001224.1 Corchorus capsularis cultivar CVL-1 contig01224, 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: 13532
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34


Found at i:2278 original size:33 final size:33

Alignment explanation


    Indices: 2227--2292  Score: 114
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       2217 CATGGGATAA

                         *                   
       2227 AACGTTGGGTTAATAAGGTTAATTAACGTGATT
          1 AACGTTGGGTTAACAAGGTTAATTAACGTGATT

                    *                        
       2260 AACGTTGGTTTAACAAGGTTAATTAACGTGATT
          1 AACGTTGGGTTAACAAGGTTAATTAACGTGATT

       2293 TTAACGTGAG


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   31  1.00

ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36


Consensus pattern (33 bp):   
AACGTTGGGTTAACAAGGTTAATTAACGTGATT

Found at i:5487 original size:2 final size:2

Alignment explanation


    Indices: 5482--5512  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       5472 TTTTTTCTTG

                                                          
       5482 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 T

       5513 CTTATAAATT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:6050 original size:26 final size:27

Alignment explanation


    Indices: 6019--6070  Score: 88
    Period size: 26  Copynumber: 1.9  Consensus size: 27

       6009 TGTAATTTTG

                                       
       6019 TTTGGAAAAATATT-TTTTTTTGGCCA
          1 TTTGGAAAAATATTCTTTTTTTGGCCA

                                      
       6045 TTTGGAAAAATATTGCTTTTTTTGGC
          1 TTTGGAAAAATATT-CTTTTTTTGGC

       6071 GAGAGGAAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  26   14  0.58
  28   10  0.42

ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50


Consensus pattern (27 bp):   
TTTGGAAAAATATTCTTTTTTTGGCCA

Found at i:6078 original size:27 final size:27

Alignment explanation


    Indices: 6022--6088  Score: 84
    Period size: 26  Copynumber: 2.5  Consensus size: 27

       6012 AATTTTGTTT

                                     **
       6022 GGAAAAATATT-TTTTTTTGGCCATTT
          1 GGAAAAATATTGTTTTTTTGGCCATGA

                                   *    
       6048 GGAAAAATATTGCTTTTTTTGGCGA-GA
          1 GGAAAAATATTG-TTTTTTTGGCCATGA

                          
       6075 GGAAAAATATTGTT
          1 GGAAAAATATTGTT

       6089 AGAAATGCAA


Statistics
Matches: 36,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  26   13  0.36
  27   12  0.33
  28   11  0.31

ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42


Consensus pattern (27 bp):   
GGAAAAATATTGTTTTTTTGGCCATGA
Done.