Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001033.1 Corchorus capsularis cultivar CVL-1 contig01033, 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: 6569
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32


Found at i:10 original size:2 final size:2

Alignment explanation


    Indices: 4--34  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

          1 GAA

                                                          
          4 AT AT AT AT AT 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 A

         35 GTACAAATAC


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


Consensus pattern (2 bp):   
AT

Found at i:3941 original size:23 final size:23

Alignment explanation


    Indices: 3915--3960  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       3905 AATCAGAATT

                                    
       3915 TATAATATATATAA-ATTATAAAA
          1 TATAATATATA-AATATTATAAAA

                * *                
       3938 TATATTTTATAAATATTATAAAA
          1 TATAATATATAAATATTATAAAA

       3961 GGTCATCGGT


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

Matches are distributed among these distances:
  22    2  0.10
  23   18  0.90

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (23 bp):   
TATAATATATAAATATTATAAAA

Found at i:4807 original size:56 final size:56

Alignment explanation


    Indices: 4717--4827  Score: 161
    Period size: 56  Copynumber: 2.0  Consensus size: 56

       4707 CGTTAAATCT

                      *                  *                           
       4717 CAAAAAATGATAAAAATATCTCATATTATTTCTTTTTTTACT-CTCAAAACTCGAAA
          1 CAAAAAATGAGAAAAATATCTCATATTATCTCTTTTTTT-CTCCTCAAAACTCGAAA

                 *       *                         *               
       4773 CAAAACATGAGAATAATATCTCATATTATCTCTTTTTTTTTCCTCAAAACTCGAA
          1 CAAAAAATGAGAAAAATATCTCATATTATCTCTTTTTTTCTCCTCAAAACTCGAA

       4828 CCCTATATGT


Statistics
Matches: 49,  Mismatches: 5, Indels: 2
        0.88            0.09        0.04

Matches are distributed among these distances:
  55    1  0.02
  56   48  0.98

ACGTcount: A:0.40, C:0.18, G:0.05, T:0.38


Consensus pattern (56 bp):   
CAAAAAATGAGAAAAATATCTCATATTATCTCTTTTTTTCTCCTCAAAACTCGAAA
Done.