Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004981.1 Corchorus capsularis cultivar CVL-1 contig04999, 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: 6070
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37


Found at i:63 original size:2 final size:2

Alignment explanation


    Indices: 56--82  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

         46 CCTAGCCACA

                                                    
         56 AT 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 AT A

         83 AAAGCACGAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:406 original size:154 final size:154

Alignment explanation


    Indices: 236--541  Score: 594
    Period size: 154  Copynumber: 2.0  Consensus size: 154

        226 TATTATTATT

                                                                             
        236 TATCTATACTATATATAAAAGTATGAGTTTTGTAAAACTTTTGAATCGACTATTATACCCTTATT
          1 TATCTATACTATATATAAAAGTATGAGTTTTGTAAAACTTTTGAATCGACTATTATACCCTTATT

                                                                             
        301 TTTCAAAAATATTTCTTAAATGCCATTGATTAACTATTATAGTTTTATTCTACTAAAAACTCTAT
         66 TTTCAAAAATATTTCTTAAATGCCATTGATTAACTATTATAGTTTTATTCTACTAAAAACTCTAT

                                    
        366 TTTTATTCAATTAAATCTAATATC
        131 TTTTATTCAATTAAATCTAATATC

                                                                             
        390 TATCTATACTATATATAAAAGTATGAGTTTTGTAAAACTTTTGAATCGACTATTATACCCTTATT
          1 TATCTATACTATATATAAAAGTATGAGTTTTGTAAAACTTTTGAATCGACTATTATACCCTTATT

                                        *    *                               
        455 TTTCAAAAATATTTCTTAAATGCCATTGCTTAATTATTATAGTTTTATTCTACTAAAAACTCTAT
         66 TTTCAAAAATATTTCTTAAATGCCATTGATTAACTATTATAGTTTTATTCTACTAAAAACTCTAT

                                  
        520 TTTTATTCAATTAAATCTAATA
        131 TTTTATTCAATTAAATCTAATA

        542 ACTTTATAAT


Statistics
Matches: 150,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 154  150  1.00

ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45


Consensus pattern (154 bp):   
TATCTATACTATATATAAAAGTATGAGTTTTGTAAAACTTTTGAATCGACTATTATACCCTTATT
TTTCAAAAATATTTCTTAAATGCCATTGATTAACTATTATAGTTTTATTCTACTAAAAACTCTAT
TTTTATTCAATTAAATCTAATATC

Found at i:4171 original size:17 final size:18

Alignment explanation


    Indices: 4157--4190  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       4147 CACTAGTGGT

                              
       4157 CTAAGATCACCAGTGATG
          1 CTAAGATCACCAGTGATG

                       *     
       4175 C-AAGATCACCGGTGAT
          1 CTAAGATCACCAGTGAT

       4191 CAAAGATTAT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17   14  0.93
  18    1  0.07

ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21


Consensus pattern (18 bp):   
CTAAGATCACCAGTGATG
Done.