Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009513.1 Corchorus capsularis cultivar CVL-1 contig09534, 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: 11872
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:975 original size:31 final size:31

Alignment explanation


    Indices: 932--1082  Score: 151
    Period size: 31  Copynumber: 4.9  Consensus size: 31

        922 GATGTGGCAT

                *         *        **  *   
        932 GCCATGTGTACCAATAAGTGACATGTGACAC
          1 GCCACGTGTACCAAAAAGTGACACATGTCAC

                   *                       
        963 GCCACGTATACCAAAAAGTGACACATGTCAC
          1 GCCACGTGTACCAAAAAGTGACACATGTCAC

             *  *                          
        994 GTCAGGTGTACCAAAAAGTGACACATGTCAC
          1 GCCACGTGTACCAAAAAGTGACACATGTCAC

                                    **  *  *
       1025 GCCACGTGTACC-AAAAGCTGACATGTGGCAT
          1 GCCACGTGTACCAAAAAG-TGACACATGTCAC

                 *   **                
       1056 GCCACATGTTTCAAAAAGTGACACATG
          1 GCCACGTGTACCAAAAAGTGACACATG

       1083 ACATGCCATG


Statistics
Matches: 98,  Mismatches: 20, Indels: 4
        0.80            0.16        0.03

Matches are distributed among these distances:
  30    5  0.05
  31   88  0.90
  32    5  0.05

ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20


Consensus pattern (31 bp):   
GCCACGTGTACCAAAAAGTGACACATGTCAC

Found at i:3366 original size:14 final size:14

Alignment explanation


    Indices: 3347--3400  Score: 54
    Period size: 14  Copynumber: 3.6  Consensus size: 14

       3337 GTAAAAGAAC

                          
       3347 AAACATTTAACAAT
          1 AAACATTTAACAAT

                          *  *
       3361 AAACATTTCACCAAGAAC
          1 AAACATTT----AACAAT

                          
       3379 AAACATTTAACAAT
          1 AAACATTTAACAAT

                    
       3393 AAACATTT
          1 AAACATTT

       3401 CACACACCAT


Statistics
Matches: 32,  Mismatches: 4, Indels: 8
        0.73            0.09        0.18

Matches are distributed among these distances:
  14   20  0.62
  18   12  0.38

ACGTcount: A:0.54, C:0.19, G:0.02, T:0.26


Consensus pattern (14 bp):   
AAACATTTAACAAT

Found at i:3382 original size:32 final size:32

Alignment explanation


    Indices: 3341--3403  Score: 126
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       3331 GTGGTTGTAA

                                            
       3341 AAGAACAAACATTTAACAATAAACATTTCACC
          1 AAGAACAAACATTTAACAATAAACATTTCACC

                                           
       3373 AAGAACAAACATTTAACAATAAACATTTCAC
          1 AAGAACAAACATTTAACAATAAACATTTCAC

       3404 ACACCATGAC


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   31  1.00

ACGTcount: A:0.54, C:0.21, G:0.03, T:0.22


Consensus pattern (32 bp):   
AAGAACAAACATTTAACAATAAACATTTCACC

Found at i:4832 original size:21 final size:22

Alignment explanation


    Indices: 4806--4850  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 22

       4796 TCAATCTGGA

                       *          
       4806 TTGCTAAACACTGTCCCAT-TT
          1 TTGCTAAACACCGTCCCATCTT

                  **              
       4827 TTGCTATTCACCGTCCCATCTT
          1 TTGCTAAACACCGTCCCATCTT

              
       4849 TT
          1 TT

       4851 ACGTTTTTTT


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  21   16  0.80
  22    4  0.20

ACGTcount: A:0.18, C:0.31, G:0.09, T:0.42


Consensus pattern (22 bp):   
TTGCTAAACACCGTCCCATCTT

Found at i:8462 original size:23 final size:23

Alignment explanation


    Indices: 8406--8462  Score: 80
    Period size: 24  Copynumber: 2.4  Consensus size: 23

       8396 CTAGCTTTTG

                                   
       8406 AACTTTAATTGTTGCAAAGTACT
          1 AACTTTAATTGTTGCAAAGTACT

                  *                 
       8429 AACTCTCAATTGTTGCAAAGTAC-
          1 AACT-TTAATTGTTGCAAAGTACT

                       
       8452 AACTATTAATT
          1 AACT-TTAATT

       8463 TTATTCAGTT


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  23   13  0.43
  24   17  0.57

ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37


Consensus pattern (23 bp):   
AACTTTAATTGTTGCAAAGTACT
Done.