Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022352.1 Corchorus olitorius cultivar O-4 contig22385, 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: 27141
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32


Found at i:3166 original size:21 final size:21

Alignment explanation


    Indices: 3125--3197  Score: 76
    Period size: 21  Copynumber: 3.5  Consensus size: 21

       3115 GCCTGGTTAG

                           *      
       3125 GACCGGCCACTACCTTA-CCAA
          1 GACCGGCCACTACC-GAGCCAA

                 *               
       3146 GACCGACCACTACCGAGCCAA
          1 GACCGGCCACTACCGAGCCAA

               *     *     *    *
       3167 GACTGGCCATTACCGTGCCAG
          1 GACCGGCCACTACCGAGCCAA

                      
       3188 GACCGGCCAC
          1 GACCGGCCAC

       3198 CCATGCATCC


Statistics
Matches: 42,  Mismatches: 9, Indels: 2
        0.79            0.17        0.04

Matches are distributed among these distances:
  20    1  0.02
  21   41  0.98

ACGTcount: A:0.26, C:0.41, G:0.22, T:0.11


Consensus pattern (21 bp):   
GACCGGCCACTACCGAGCCAA

Found at i:5179 original size:24 final size:24

Alignment explanation


    Indices: 5152--5209  Score: 107
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       5142 CGCGAAGGAA

                             *      
       5152 TGAAGACATGCTATGGAGAAGTCT
          1 TGAAGACATGCTATGGAAAAGTCT

                                    
       5176 TGAAGACATGCTATGGAAAAGTCT
          1 TGAAGACATGCTATGGAAAAGTCT

                      
       5200 TGAAGACATG
          1 TGAAGACATG

       5210 GAATTATGAA


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  24   33  1.00

ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24


Consensus pattern (24 bp):   
TGAAGACATGCTATGGAAAAGTCT

Found at i:9798 original size:24 final size:25

Alignment explanation


    Indices: 9761--9815  Score: 76
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       9751 CAAAGAAATG

                  *               *  
       9761 TGTAGAGTGG-AAAAGGAATGCCAA
          1 TGTAGAATGGAAAAAGGAATGCAAA

                     *               
       9785 TGTAGAATGTAAAAAGGAATGCAAA
          1 TGTAGAATGGAAAAAGGAATGCAAA

                  
       9810 TGTAGA
          1 TGTAGA

       9816 TTACAGCCAC


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  24    8  0.30
  25   19  0.70

ACGTcount: A:0.45, C:0.05, G:0.29, T:0.20


Consensus pattern (25 bp):   
TGTAGAATGGAAAAAGGAATGCAAA

Found at i:14039 original size:2 final size:2

Alignment explanation


    Indices: 14034--14058  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      14024 AAAGAAAAGA

                                                 
      14034 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

      14059 ACTAATAATA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:26493 original size:85 final size:84

Alignment explanation


    Indices: 26390--26559  Score: 306
    Period size: 85  Copynumber: 2.0  Consensus size: 84

      26380 AGAAAAAGAA

                                                                             
      26390 TAATAACCTTTCTCTCTGTGGGTTCGACCCCTACTTGCCCTAACTATCTTTAGTTACTAATTGTA
          1 TAATAACCTTTCTCTCTGTGGGTTCGACCCCTACTTGCCCTAACTATCTTTAGTTACTAATTGT-

                                 
      26455 T-GGATTTTTATTTTTATGAT
         65 TGGGA-TTTTATTTTTATGAT

                                                                    *        
      26475 TAATAACCTTTCTCTCTGTGGGTTCGACCCCTACTTGCCCTAACTATCTTTAGTTAGTAATTGTT
          1 TAATAACCTTTCTCTCTGTGGGTTCGACCCCTACTTGCCCTAACTATCTTTAGTTACTAATTGTT

                               
      26540 GGGATTTTATTTTTATGAT
         66 GGGATTTTATTTTTATGAT

             
      26559 T
          1 T

      26560 TGCTGACGAC


Statistics
Matches: 83,  Mismatches: 1, Indels: 3
        0.95            0.01        0.03

Matches are distributed among these distances:
  84   17  0.20
  85   66  0.80

ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46


Consensus pattern (84 bp):   
TAATAACCTTTCTCTCTGTGGGTTCGACCCCTACTTGCCCTAACTATCTTTAGTTACTAATTGTT
GGGATTTTATTTTTATGAT
Done.