Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020633.1 Corchorus olitorius cultivar O-4 contig20666, 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: 7538
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:2779 original size:21 final size:21

Alignment explanation


    Indices: 2717--2772  Score: 71
    Period size: 21  Copynumber: 2.7  Consensus size: 21

       2707 ATTTCACTTC

                            *   *
       2717 TAAAAAA-CTTATAAAGTTAC
          1 TAAAAAATCTTATAAACTTAT

                                  
       2737 TAAAAAATC-TACTAAACTTAT
          1 TAAAAAATCTTA-TAAACTTAT

                           
       2758 TAAAAAATCTTATAA
          1 TAAAAAATCTTATAA

       2773 GATTATTTTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
  20    9  0.29
  21   20  0.65
  22    2  0.06

ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32


Consensus pattern (21 bp):   
TAAAAAATCTTATAAACTTAT

Found at i:3289 original size:21 final size:21

Alignment explanation


    Indices: 3256--3295  Score: 55
    Period size: 22  Copynumber: 1.9  Consensus size: 21

       3246 ACTTTATACT

                 *                
       3256 AAAAATACTTATACAGTTTATA
          1 AAAAAAACTTATACA-TTTATA

                               
       3278 AAAAAAAC-TATACATTTA
          1 AAAAAAACTTATACATTTA

       3296 CAAACAAATT


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

Matches are distributed among these distances:
  20    4  0.24
  21    6  0.35
  22    7  0.41

ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33


Consensus pattern (21 bp):   
AAAAAAACTTATACATTTATA

Found at i:4123 original size:29 final size:30

Alignment explanation


    Indices: 4073--4137  Score: 105
    Period size: 29  Copynumber: 2.2  Consensus size: 30

       4063 AAAAAGGGCC

                                        * 
       4073 TATTTGGCCAAAATAAGAAGTTGAGGGGTT
          1 TATTTGGCCAAAATAAGAAGTTGAGGGGAT

                                  *       
       4103 TATTTGGCCAAAATAA-AAGTTTAGGGGAT
          1 TATTTGGCCAAAATAAGAAGTTGAGGGGAT

                  
       4132 TATTTG
          1 TATTTG

       4138 ACCGTTGTGC


Statistics
Matches: 33,  Mismatches: 2, Indels: 1
        0.92            0.06        0.03

Matches are distributed among these distances:
  29   17  0.52
  30   16  0.48

ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34


Consensus pattern (30 bp):   
TATTTGGCCAAAATAAGAAGTTGAGGGGAT

Found at i:4912 original size:28 final size:30

Alignment explanation


    Indices: 4869--4935  Score: 86
    Period size: 31  Copynumber: 2.3  Consensus size: 30

       4859 TGAGTTCAGA

                                    *     
       4869 GGGGCAAACGTCCAAAAT-TA-AAGTTTAG
          1 GGGGCAAACGTCCAAAATCTAGAAATTTAG

                                            
       4897 GGGGCAAATCGT-CAAAATCGTAGAAATTTAG
          1 GGGGCAAA-CGTCCAAAATC-TAGAAATTTAG

                    
       4928 GGGGCAAA
          1 GGGGCAAA

       4936 AAGGGCATTA


Statistics
Matches: 34,  Mismatches: 1, Indels: 5
        0.85            0.03        0.12

Matches are distributed among these distances:
  28   14  0.41
  29    3  0.09
  30    2  0.06
  31   15  0.44

ACGTcount: A:0.39, C:0.13, G:0.28, T:0.19


Consensus pattern (30 bp):   
GGGGCAAACGTCCAAAATCTAGAAATTTAG

Found at i:6252 original size:27 final size:27

Alignment explanation


    Indices: 6222--6320  Score: 144
    Period size: 27  Copynumber: 3.7  Consensus size: 27

       6212 GGTCATCTAT

                      *           * *  
       6222 GGGGCATTTTTGTCATTTGCACGTCCA
          1 GGGGCATTTTGGTCATTTGCACATTCA

                      *                
       6249 GGGGCATTTTTGTCATTTGCACATTCA
          1 GGGGCATTTTGGTCATTTGCACATTCA

            *                 *        
       6276 AGGGCATTTTGGTCATTTACACATTCA
          1 GGGGCATTTTGGTCATTTGCACATTCA

                              
       6303 GGGGCATTTTGGTCATTT
          1 GGGGCATTTTGGTCATTT

       6321 TAAGCTCACT


Statistics
Matches: 66,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   66  1.00

ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39


Consensus pattern (27 bp):   
GGGGCATTTTGGTCATTTGCACATTCA
Done.