Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022792.1 Corchorus olitorius cultivar O-4 contig22825, 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: 8144
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34


Found at i:4365 original size:28 final size:28

Alignment explanation


    Indices: 4325--4378  Score: 99
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       4315 AGTTTGCCTT

                               *        
       4325 AAATCTCAAATAAGGGTCCGAACTTTAA
          1 AAATCTCAAATAAGGGTCCCAACTTTAA

                                      
       4353 AAATCTCAAATAAGGGTCCCAACTTT
          1 AAATCTCAAATAAGGGTCCCAACTTT

       4379 TTGGGAAGGC


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  28   25  1.00

ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26


Consensus pattern (28 bp):   
AAATCTCAAATAAGGGTCCCAACTTTAA

Found at i:6440 original size:101 final size:103

Alignment explanation


    Indices: 6335--6593  Score: 373
    Period size: 101  Copynumber: 2.5  Consensus size: 103

       6325 TAAAAGTATA

                                    *                                        
       6335 TTAATTTGGGACTAAACTTAGTGATATTAGTTTTATATTTTAATTCTAAAACCCTATAACAATAA
          1 TTAATTTGGG-CTAAACTTAGTGACATTAGTTTTATATTTTAATTCTAAAACCCTATAACAATAA

                                                   
       6400 ATTAATAATTTTAGAATTTACCCTT-A-AAATT-AAATT
         65 ATTAATAATTTTAGAATTTACCCTTAATAAATTAAAATT

                                         *                                   
       6436 TTAATTTGGGGCTAAACTTAGTGACATTAATTTTATATTTTAATTCTAAAACCCTATAACAATAA
          1 TTAATTT-GGGCTAAACTTAGTGACATTAGTTTTATATTTTAATTCTAAAACCCTATAACAATAA

                *       *                             
       6501 ATTATTAATTTTGGAATTTACCCTTAAATTTAAATTAAAATT
         65 ATTAATAATTTTAGAATTTACCCTT-AA--TAAATTAAAATT

                             *  *                               
       6543 TTAATTTAGGGCTAAACATAATGACATTAGTTTTATA-TTTAATTTCTAAAA
          1 TTAATTT-GGGCTAAACTTAGTGACATTAGTTTTATATTTTAA-TTCTAAAA

       6594 AGAATAAAAA


Statistics
Matches: 142,  Mismatches: 8, Indels: 10
        0.89            0.05        0.06

Matches are distributed among these distances:
 101   82  0.58
 102    3  0.02
 103    1  0.01
 106   10  0.07
 107   46  0.32

ACGTcount: A:0.40, C:0.10, G:0.08, T:0.43


Consensus pattern (103 bp):   
TTAATTTGGGCTAAACTTAGTGACATTAGTTTTATATTTTAATTCTAAAACCCTATAACAATAAA
TTAATAATTTTAGAATTTACCCTTAATAAATTAAAATT

Found at i:7249 original size:18 final size:19

Alignment explanation


    Indices: 7215--7251  Score: 58
    Period size: 18  Copynumber: 2.0  Consensus size: 19

       7205 GTTAAATTTC

                               
       7215 ATTATATGAAAAATAAATA
          1 ATTATATGAAAAATAAATA

                      *        
       7234 ATTATAT-AAGAATAAATA
          1 ATTATATGAAAAATAAATA

       7252 CTAAATCAGT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18   10  0.59
  19    7  0.41

ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32


Consensus pattern (19 bp):   
ATTATATGAAAAATAAATA

Found at i:8069 original size:4 final size:4

Alignment explanation


    Indices: 8060--8111  Score: 104
    Period size: 4  Copynumber: 13.0  Consensus size: 4

       8050 TTACAAAACT

                                                                       
       8060 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
          1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA

                
       8108 CATA
          1 CATA

       8112 TATATATATA


Statistics
Matches: 48,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   48  1.00

ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25


Consensus pattern (4 bp):   
CATA

Found at i:8116 original size:2 final size:2

Alignment explanation


    Indices: 8109--8144  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       8099 ACATACATAC

                                                                 
       8109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.