Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012250.1 Corchorus capsularis cultivar CVL-1 contig12271, 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: 3515
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27


Found at i:2512 original size:2 final size:2

Alignment explanation


    Indices: 2492--2540  Score: 53
    Period size: 2  Copynumber: 24.5  Consensus size: 2

       2482 TTTTGCTTTT

                     *     *     *         *  *                           
       2492 TA TA TA CA TA CA TA CA TA TA TG TG 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 TA

                      
       2534 TA TA TA T
          1 TA TA TA T

       2541 TTTCCACTGT


Statistics
Matches: 39,  Mismatches: 8, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45


Consensus pattern (2 bp):   
TA

Found at i:2933 original size:19 final size:19

Alignment explanation


    Indices: 2911--2952  Score: 50
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       2901 TGGAAAAATG

                                
       2911 GAAAA-AAAAAATGAAAAAA
          1 GAAAAGAAAAAA-GAAAAAA

                    *        * 
       2930 GAAAAGAAGAAAGAAAAGA
          1 GAAAAGAAAAAAGAAAAAA

                
       2949 GAAA
          1 GAAA

       2953 GAGCAACGAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  19   15  0.75
  20    5  0.25

ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02


Consensus pattern (19 bp):   
GAAAAGAAAAAAGAAAAAA

Found at i:3010 original size:45 final size:45

Alignment explanation


    Indices: 2961--3104  Score: 170
    Period size: 44  Copynumber: 3.2  Consensus size: 45

       2951 AAGAGCAACG

                                        *          *     
       2961 ATGGTTTTCAAAAAATAGTCATGGTTTTTAAAAGGTTTTAATAAA
          1 ATGGTTTTCAAAAAATAGTCATGGTTTTCAAAAGGTTTTGATAAA

                           *                             
       3006 ATGGTTTTC-AAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
          1 ATGGTTTTCAAAAAATAGTCATGGTTTTCAAAAGGTTTTGATAAA

                *                               *            
       3050 ATGTTTTTTCAAGAAGAAT--T-ATGGTTTTCAAGAGGGTTTTGATAAA
          1 ATG-GTTTTCAA-AA-AATAGTCATGGTTTTCAA-AAGGTTTTGATAAA

             *       
       3096 AGGGTTTTC
          1 ATGGTTTTC

       3105 CAAAGTTGCA


Statistics
Matches: 86,  Mismatches: 8, Indels: 10
        0.83            0.08        0.10

Matches are distributed among these distances:
  44   35  0.41
  45   30  0.35
  46   17  0.20
  47    2  0.02
  48    2  0.02

ACGTcount: A:0.35, C:0.06, G:0.20, T:0.40


Consensus pattern (45 bp):   
ATGGTTTTCAAAAAATAGTCATGGTTTTCAAAAGGTTTTGATAAA

Found at i:3029 original size:44 final size:44

Alignment explanation


    Indices: 2961--3104  Score: 180
    Period size: 45  Copynumber: 3.2  Consensus size: 44

       2951 AAGAGCAACG

                           *            *          *     
       2961 ATGGTTTTCAAAAAATAGTCATGGTTTTTAAAAGGTTTTAATAAA
          1 ATGGTTTTC-AAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA

                                                        
       3006 ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
          1 ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA

                *       *    * *             *            
       3050 ATGTTTTTTCAAGAAGAATTATGGTTTTCAAGAGGGTTTTGATAAA
          1 ATG-GTTTTCAAAAAGAGTCATGGTTTTCAA-AAGGTTTTGATAAA

             *       
       3096 AGGGTTTTC
          1 ATGGTTTTC

       3105 CAAAGTTGCA


Statistics
Matches: 87,  Mismatches: 10, Indels: 4
        0.86            0.10        0.04

Matches are distributed among these distances:
  44   35  0.40
  45   37  0.43
  46   15  0.17

ACGTcount: A:0.35, C:0.06, G:0.20, T:0.40


Consensus pattern (44 bp):   
ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
Done.