Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001688.1 Corchorus capsularis cultivar CVL-1 contig01688, 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: 4040
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:744 original size:6 final size:6

Alignment explanation


    Indices: 725--774  Score: 57
    Period size: 6  Copynumber: 8.5  Consensus size: 6

        715 TTGACAACGT

                    *        *       *      *                      
        725 AACAAA ATCAAA AACGAA AAC-GA AACAGA AACAAA AACAAA AACAAA
          1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA

               
        772 AAC
          1 AAC

        775 GATACCGAAC


Statistics
Matches: 38,  Mismatches: 5, Indels: 2
        0.84            0.11        0.04

Matches are distributed among these distances:
   5    4  0.11
   6   34  0.89

ACGTcount: A:0.74, C:0.18, G:0.06, T:0.02


Consensus pattern (6 bp):   
AACAAA

Found at i:3019 original size:18 final size:18

Alignment explanation


    Indices: 2996--3056  Score: 59
    Period size: 18  Copynumber: 3.3  Consensus size: 18

       2986 CATATTTTCC

                              
       2996 AATTAATTTTGTATCTAA
          1 AATTAATTTTGTATCTAA

                   * * * *   **
       3014 AATTAAAATATATTTCTTC
          1 AATT-AATTTTGTATCTAA

                              
       3033 AATTAATTTTGTATCTAA
          1 AATTAATTTTGTATCTAA

                  
       3051 AATTAA
          1 AATTAA

       3057 AATCTATTTC


Statistics
Matches: 30,  Mismatches: 12, Indels: 2
        0.68            0.27        0.05

Matches are distributed among these distances:
  18   18  0.60
  19   12  0.40

ACGTcount: A:0.43, C:0.07, G:0.03, T:0.48


Consensus pattern (18 bp):   
AATTAATTTTGTATCTAA

Found at i:3037 original size:37 final size:37

Alignment explanation


    Indices: 2987--3066  Score: 135
    Period size: 37  Copynumber: 2.2  Consensus size: 37

       2977 GACACATACC

                                                 
       2987 ATATTT-TCCAATTAATTTTGTATCTAAAATTAAAAT
          1 ATATTTCTCCAATTAATTTTGTATCTAAAATTAAAAT

                    *                            
       3023 ATATTTCTTCAATTAATTTTGTATCTAAAATTAAAAT
          1 ATATTTCTCCAATTAATTTTGTATCTAAAATTAAAAT

            *      
       3060 CTATTTC
          1 ATATTTC

       3067 CTAAAAAACA


Statistics
Matches: 41,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  36    6  0.15
  37   35  0.85

ACGTcount: A:0.39, C:0.10, G:0.03, T:0.49


Consensus pattern (37 bp):   
ATATTTCTCCAATTAATTTTGTATCTAAAATTAAAAT

Found at i:3958 original size:2 final size:2

Alignment explanation


    Indices: 3942--3995  Score: 65
    Period size: 2  Copynumber: 26.5  Consensus size: 2

       3932 GGTTTGGGGT

                                      **                                    
       3942 TA TA TA TCA TCA TA TA TA GG TA T- TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA T-A T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                            
       3985 TA TA TA TA TA T
          1 TA TA TA TA TA T

       3996 TACTAAATCC


Statistics
Matches: 46,  Mismatches: 4, Indels: 4
        0.85            0.07        0.07

Matches are distributed among these distances:
   1    1  0.02
   2   40  0.87
   3    5  0.11

ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48


Consensus pattern (2 bp):   
TA

Done.