Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011270.1 Corchorus capsularis cultivar CVL-1 contig11291, 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: 17137
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:2222 original size:6 final size:6

Alignment explanation


    Indices: 2211--2235  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

       2201 CAAACCCACC

                                         
       2211 ACCAGT ACCAGT ACCAGT ACCAGT A
          1 ACCAGT ACCAGT ACCAGT ACCAGT A

       2236 GCACTCAAAG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16


Consensus pattern (6 bp):   
ACCAGT

Found at i:2748 original size:12 final size:12

Alignment explanation


    Indices: 2731--2769  Score: 53
    Period size: 12  Copynumber: 3.2  Consensus size: 12

       2721 GGAAGCGGTG

                        
       2731 AAGCGAAAGGGA
          1 AAGCGAAAGGGA

                       * 
       2743 AAGCGAAAGGCAA
          1 AAGCGAAAGG-GA

                        
       2756 AAG-GAAAGGGA
          1 AAGCGAAAGGGA

               
       2767 AAG
          1 AAG

       2770 GGGGTTTCTG


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  11    4  0.17
  12   16  0.67
  13    4  0.17

ACGTcount: A:0.54, C:0.08, G:0.38, T:0.00


Consensus pattern (12 bp):   
AAGCGAAAGGGA

Found at i:3330 original size:14 final size:14

Alignment explanation


    Indices: 3311--3343  Score: 66
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       3301 CCATAAAAGG

                          
       3311 CAATCTAAATGCTT
          1 CAATCTAAATGCTT

                          
       3325 CAATCTAAATGCTT
          1 CAATCTAAATGCTT

                 
       3339 CAATC
          1 CAATC

       3344 ATTTTGATGT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33


Consensus pattern (14 bp):   
CAATCTAAATGCTT

Found at i:5543 original size:3 final size:3

Alignment explanation


    Indices: 5530--5558  Score: 51
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       5520 TCCTTTCATA

                                                   
       5530 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

       5559 CCTGATCTCA


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2    2  0.08
   3   23  0.92

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (3 bp):   
AAT

Found at i:6852 original size:7 final size:7

Alignment explanation


    Indices: 6840--6870  Score: 62
    Period size: 7  Copynumber: 4.4  Consensus size: 7

       6830 CCACTACCAC

                   
       6840 CAACTCA
          1 CAACTCA

                   
       6847 CAACTCA
          1 CAACTCA

                   
       6854 CAACTCA
          1 CAACTCA

                   
       6861 CAACTCA
          1 CAACTCA

               
       6868 CAA
          1 CAA

       6871 GCGATCAAGC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   24  1.00

ACGTcount: A:0.45, C:0.42, G:0.00, T:0.13


Consensus pattern (7 bp):   
CAACTCA

Done.