Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012540.1 Corchorus capsularis cultivar CVL-1 contig12561, 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: 5839
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--40  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

                                                                       
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         41 ATTGAATATA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:1519 original size:28 final size:29

Alignment explanation


    Indices: 1486--1545  Score: 104
    Period size: 28  Copynumber: 2.1  Consensus size: 29

       1476 GTGCCATGCT

                                         
       1486 AAACTATGGGATTTTTT-GTGCCAAAAAA
          1 AAACTATGGGATTTTTTGGTGCCAAAAAA

                                 *       
       1514 AAACTATGGGATTTTTTGGTGTCAAAAAA
          1 AAACTATGGGATTTTTTGGTGCCAAAAAA

               
       1543 AAA
          1 AAA

       1546 AAAAAAACTA


Statistics
Matches: 30,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  28   17  0.57
  29   13  0.43

ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32


Consensus pattern (29 bp):   
AAACTATGGGATTTTTTGGTGCCAAAAAA

Found at i:5101 original size:2 final size:2

Alignment explanation


    Indices: 5094--5153  Score: 57
    Period size: 2  Copynumber: 29.5  Consensus size: 2

       5084 GTTTAATCTG

                                                   *     *     *     *  * 
       5094 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT CT AT CT AT CT TT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

            *                         
       5136 CT AT AT AT ACT AT AT AT A
          1 AT AT AT AT A-T AT AT AT A

       5154 AAAGTACGAG


Statistics
Matches: 47,  Mismatches: 10, Indels: 2
        0.80            0.17        0.03

Matches are distributed among these distances:
   2   45  0.96
   3    2  0.04

ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:5340 original size:65 final size:65

Alignment explanation


    Indices: 5256--5386  Score: 253
    Period size: 65  Copynumber: 2.0  Consensus size: 65

       5246 TTCTTAAATG

                                                                             
       5256 TCATTACTTAACTATTATAGTTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATCTAATA
          1 TCATTACTTAACTATTATAGTTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATCTAATA

                                                              *              
       5321 TCATTACTTAACTATTATAGTTTTATTCTACTAAAAACTCTATTTTTATTTAATTAAATCTAATA
          1 TCATTACTTAACTATTATAGTTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATCTAATA

             
       5386 T
          1 T

       5387 ATTTATATTT


Statistics
Matches: 65,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  65   65  1.00

ACGTcount: A:0.37, C:0.13, G:0.02, T:0.49


Consensus pattern (65 bp):   
TCATTACTTAACTATTATAGTTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATCTAATA

Done.