Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006126.1 Corchorus capsularis cultivar CVL-1 contig06144, 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: 16809
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:6515 original size:27 final size:27

Alignment explanation


    Indices: 6479--6534  Score: 103
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       6469 TCTCGTTTTT

                                       
       6479 AAAAATTAAGGAGTCAATTTGTCCCAA
          1 AAAAATTAAGGAGTCAATTTGTCCCAA

                       *               
       6506 AAAAATTAAGGGGTCAATTTGTCCCAA
          1 AAAAATTAAGGAGTCAATTTGTCCCAA

              
       6533 AA
          1 AA

       6535 TGGATAGTTA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25


Consensus pattern (27 bp):   
AAAAATTAAGGAGTCAATTTGTCCCAA

Found at i:7212 original size:16 final size:16

Alignment explanation


    Indices: 7181--7235  Score: 60
    Period size: 16  Copynumber: 3.4  Consensus size: 16

       7171 CTCAAATGTC

                      *     
       7181 GGGTCA-TTTAGGTTT
          1 GGGTCATTTTTGGTTT

                            
       7196 GGGTCATTTTTGGTTT
          1 GGGTCATTTTTGGTTT

                 *            
       7212 GGGT-GTTTTTCGGTTTT
          1 GGGTCATTTTT-GG-TTT

                   
       7229 GGGTCAT
          1 GGGTCAT

       7236 ATGGTTCCAA


Statistics
Matches: 33,  Mismatches: 3, Indels: 5
        0.80            0.07        0.12

Matches are distributed among these distances:
  15   11  0.33
  16   14  0.42
  17    7  0.21
  18    1  0.03

ACGTcount: A:0.07, C:0.07, G:0.35, T:0.51


Consensus pattern (16 bp):   
GGGTCATTTTTGGTTT

Found at i:7623 original size:12 final size:11

Alignment explanation


    Indices: 7589--7627  Score: 51
    Period size: 11  Copynumber: 3.4  Consensus size: 11

       7579 CGTAGGAAAG

                       
       7589 AAATCATTAAA
          1 AAATCATTAAA

                *       
       7600 AAATTATATAAA
          1 AAATCAT-TAAA

                        
       7612 GAAATCATTAAA
          1 -AAATCATTAAA

                
       7624 AAAT
          1 AAAT

       7628 TAAACATAAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 4
        0.80            0.07        0.13

Matches are distributed among these distances:
  11   10  0.42
  12    8  0.33
  13    6  0.25

ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28


Consensus pattern (11 bp):   
AAATCATTAAA

Found at i:13189 original size:15 final size:16

Alignment explanation


    Indices: 13169--13199  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

      13159 TCTGCTTTTA

                            
      13169 TAATTT-AATTGCTTT
          1 TAATTTAAATTGCTTT

                            
      13184 TAATTTAAATTGCTTT
          1 TAATTTAAATTGCTTT

      13200 GACCACTCTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    6  0.40
  16    9  0.60

ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58


Consensus pattern (16 bp):   
TAATTTAAATTGCTTT

Done.