Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003814.1 Corchorus capsularis cultivar CVL-1 contig03822, 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, 757

Length: 1263
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34


Found at i:384 original size:21 final size:20

Alignment explanation


    Indices: 347--385  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        337 TTTAGAAGCA

                       *        
        347 ATTAATTAAAAGCATTAAAC
          1 ATTAATTAAAAACATTAAAC

                               
        367 ATTAATTAAAAACAATTAA
          1 ATTAATTAAAAAC-ATTAA

        386 GGAAGGGAGA


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

Matches are distributed among these distances:
  20   12  0.71
  21    5  0.29

ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31


Consensus pattern (20 bp):   
ATTAATTAAAAACATTAAAC

Found at i:469 original size:95 final size:95

Alignment explanation


    Indices: 306--500  Score: 383
    Period size: 95  Copynumber: 2.1  Consensus size: 95

        296 AGCGAGAGAA

                                                                             
        306 ACATTAATTAAAAGTAATTAAGGGTTTAGAGTTTAGAAGCAATTAATTAAAAGCATTAAACATTA
          1 ACATTAATTAAAAGTAATTAAGGGTTTAGAGTTTAGAAGCAATTAATTAAAAGCATTAAACATTA

                                          
        371 ATTAAAAACAATTAAGGAAGGGAGATGTGT
         66 ATTAAAAACAATTAAGGAAGGGAGATGTGT

                                                                             
        401 ACATTAATTAAAAGTAATTAAGGGTTTAGAGTTTAGAAGCAATTAATTAAAAGCATTAAACATTA
          1 ACATTAATTAAAAGTAATTAAGGGTTTAGAGTTTAGAAGCAATTAATTAAAAGCATTAAACATTA

                                          
        466 ATTAAAAACAATTAAGGAAGGGAGATGTGT
         66 ATTAAAAACAATTAAGGAAGGGAGATGTGT

                  
        496 A-ATTA
          1 ACATTA

        501 CGAAAAAGGG


Statistics
Matches: 100,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  94    4  0.04
  95   96  0.96

ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30


Consensus pattern (95 bp):   
ACATTAATTAAAAGTAATTAAGGGTTTAGAGTTTAGAAGCAATTAATTAAAAGCATTAAACATTA
ATTAAAAACAATTAAGGAAGGGAGATGTGT

Found at i:479 original size:21 final size:20

Alignment explanation


    Indices: 442--480  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        432 TTTAGAAGCA

                       *        
        442 ATTAATTAAAAGCATTAAAC
          1 ATTAATTAAAAACATTAAAC

                               
        462 ATTAATTAAAAACAATTAA
          1 ATTAATTAAAAAC-ATTAA

        481 GGAAGGGAGA


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

Matches are distributed among these distances:
  20   12  0.71
  21    5  0.29

ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31


Consensus pattern (20 bp):   
ATTAATTAAAAACATTAAAC

Found at i:1153 original size:13 final size:14

Alignment explanation


    Indices: 1124--1158  Score: 54
    Period size: 13  Copynumber: 2.6  Consensus size: 14

       1114 AGTAAATGAA

                  *       
       1124 TTTAGAGTTTAAAG
          1 TTTAGACTTTAAAG

                          
       1138 TTTAGACTTT-AAG
          1 TTTAGACTTTAAAG

                    
       1151 TTTAGACT
          1 TTTAGACT

       1159 ATGGAGGCTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  13   11  0.55
  14    9  0.45

ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46


Consensus pattern (14 bp):   
TTTAGACTTTAAAG
Done.