Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009478.1 Corchorus capsularis cultivar CVL-1 contig09499, 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: 23475
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:6 original size:1 final size:1

Alignment explanation


    Indices: 1--26  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

                                      
          1 TTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTT

         27 GCGATAGGGG


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

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:5258 original size:31 final size:30

Alignment explanation


    Indices: 5223--5295  Score: 105
    Period size: 28  Copynumber: 2.5  Consensus size: 30

       5213 TCTAAATTAG

                                           
       5223 CCCCTTAACTATTTATTTTGGGACAAATTGA
          1 CCCCTTAACT-TTTATTTTGGGACAAATTGA

                                         *
       5254 CCCCTTAAC-TTT-TTTTGGGACAAATTGG
          1 CCCCTTAACTTTTATTTTGGGACAAATTGA

              *           
       5282 CCTCTTAACTTTTA
          1 CCCCTTAACTTTTA

       5296 AAAACGAGAC


Statistics
Matches: 38,  Mismatches: 2, Indels: 5
        0.84            0.04        0.11

Matches are distributed among these distances:
  28   23  0.61
  29    6  0.16
  31    9  0.24

ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41


Consensus pattern (30 bp):   
CCCCTTAACTTTTATTTTGGGACAAATTGA

Found at i:6021 original size:29 final size:29

Alignment explanation


    Indices: 5988--6045  Score: 107
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       5978 TCTCGTTTTT

                                         
       5988 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
          1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA

                         *               
       6017 AAAAGTTAAGGGGTCAATTTGTCCCAAAA
          1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA

       6046 TGGATAGTTA


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

Matches are distributed among these distances:
  29   28  1.00

ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22


Consensus pattern (29 bp):   
AAAAGTTAAGGGGCCAATTTGTCCCAAAA

Found at i:8254 original size:20 final size:20

Alignment explanation


    Indices: 8225--8263  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       8215 TGTTTGGTTT

                                
       8225 GAGGAATTTGAAGGAGTGGG
          1 GAGGAATTTGAAGGAGTGGG

                 *        *    
       8245 GAGGAGTTTGAAGGGGTGG
          1 GAGGAATTTGAAGGAGTGG

       8264 AGACTTGTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.26, C:0.00, G:0.54, T:0.21


Consensus pattern (20 bp):   
GAGGAATTTGAAGGAGTGGG

Found at i:23281 original size:2 final size:2

Alignment explanation


    Indices: 23274--23312  Score: 69
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      23264 GATGACAATA

                                     *                                
      23274 AT AT AT AT AT AT AT AT AC 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 AT AT AT AT AT AT A

      23313 CTCGAACAAA


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46


Consensus pattern (2 bp):   
AT

Done.