Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022102.1 Corchorus olitorius cultivar O-4 contig22135, 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: 4831
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28


Found at i:522 original size:21 final size:21

Alignment explanation


    Indices: 489--528  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        479 GCGTTTTATT

                                 
        489 CTTGTCAACTCTTT-AACTTC
          1 CTTGTCAACTCTTTCAACTTC

                    *           
        509 CTTGTTCATCTCTTTCAACT
          1 CTTG-TCAACTCTTTCAACT

        529 CAAACGATTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    4  0.24
  21    9  0.53
  22    4  0.24

ACGTcount: A:0.17, C:0.30, G:0.05, T:0.47


Consensus pattern (21 bp):   
CTTGTCAACTCTTTCAACTTC

Found at i:2978 original size:15 final size:15

Alignment explanation


    Indices: 2920--2979  Score: 57
    Period size: 15  Copynumber: 4.0  Consensus size: 15

       2910 GGGTTGGTAT

                       *   
       2920 GGCATAGGTGGCAAC
          1 GGCATAGGTGGAAAC

                  * *   *  
       2935 GGCATACGCGGATAC
          1 GGCATAGGTGGAAAC

                *    *     
       2950 GGCAAAGGTTGAAAC
          1 GGCATAGGTGGAAAC

             *             
       2965 GCCATAGGTGGAAAC
          1 GGCATAGGTGGAAAC

       2980 ATCATTGGCG


Statistics
Matches: 33,  Mismatches: 12, Indels: 0
        0.73            0.27        0.00

Matches are distributed among these distances:
  15   33  1.00

ACGTcount: A:0.32, C:0.20, G:0.35, T:0.13


Consensus pattern (15 bp):   
GGCATAGGTGGAAAC

Found at i:4444 original size:11 final size:11

Alignment explanation


    Indices: 4414--4469  Score: 67
    Period size: 11  Copynumber: 4.8  Consensus size: 11

       4404 TTATGCACCC

                        
       4414 AAAACATTTATT
          1 AAAACATTTA-T

                       
       4426 AAAACATTTAT
          1 AAAACATTTAT

               *       
       4437 AAAGCATTTAT
          1 AAAACATTTAT

                    *    
       4448 ATAAAGCAGTTAT
          1 A-AAA-CATTTAT

                     
       4461 AAAACATTT
          1 AAAACATTT

       4470 CCTCAACGGG


Statistics
Matches: 38,  Mismatches: 4, Indels: 5
        0.81            0.09        0.11

Matches are distributed among these distances:
  11   16  0.42
  12   15  0.39
  13    7  0.18

ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36


Consensus pattern (11 bp):   
AAAACATTTAT

Found at i:4452 original size:13 final size:13

Alignment explanation


    Indices: 4418--4469  Score: 51
    Period size: 13  Copynumber: 4.4  Consensus size: 13

       4408 GCACCCAAAA

                        *
       4418 CATTTAT-TAAAA
          1 CATTTATATAAAG

                         
       4430 CA-TT-TATAAAG
          1 CATTTATATAAAG

                         
       4441 CATTTATATAAAG
          1 CATTTATATAAAG

              *          
       4454 CAGTTATA-AAA-
          1 CATTTATATAAAG

                 
       4465 CATTT
          1 CATTT

       4470 CCTCAACGGG


Statistics
Matches: 34,  Mismatches: 3, Indels: 7
        0.77            0.07        0.16

Matches are distributed among these distances:
  10    1  0.03
  11   12  0.35
  12    7  0.21
  13   14  0.41

ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38


Consensus pattern (13 bp):   
CATTTATATAAAG

Found at i:4460 original size:24 final size:23

Alignment explanation


    Indices: 4414--4469  Score: 76
    Period size: 24  Copynumber: 2.4  Consensus size: 23

       4404 TTATGCACCC

                              *    
       4414 AAAACATTTATTAAAACATTTAT
          1 AAAACATTTATTAAAACAGTTAT

               *            *       
       4437 AAAGCATTTATATAAAGCAGTTAT
          1 AAAACATTTAT-TAAAACAGTTAT

                     
       4461 AAAACATTT
          1 AAAACATTT

       4470 CCTCAACGGG


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  23   10  0.36
  24   18  0.64

ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36


Consensus pattern (23 bp):   
AAAACATTTATTAAAACAGTTAT
Done.