Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013139.1 Corchorus capsularis cultivar CVL-1 contig13160, 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: 9913
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33


Found at i:282 original size:16 final size:17

Alignment explanation


    Indices: 250--284  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        240 TTTTAAAATT

                             
        250 TTTTCAAAAATTCTTGC
          1 TTTTCAAAAATTCTTGC

                     *       
        267 TTTTCAAAACTT-TTGC
          1 TTTTCAAAAATTCTTGC

              
        283 TT
          1 TT

        285 CTCTGGTTAA


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

Matches are distributed among these distances:
  16    6  0.35
  17   11  0.65

ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51


Consensus pattern (17 bp):   
TTTTCAAAAATTCTTGC

Found at i:6085 original size:2 final size:2

Alignment explanation


    Indices: 6078--6104  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       6068 ATTGCCTAGA

                                                    
       6078 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

       6105 CTAGTTTTTG


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:6417 original size:43 final size:43

Alignment explanation


    Indices: 6356--6442  Score: 165
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       6346 GATCAATTTT

                       *                               
       6356 AATGAGGATCCTTTTTCTTCATTCATCACTCAGATTTTTGTCC
          1 AATGAGGATCCCTTTTCTTCATTCATCACTCAGATTTTTGTCC

                                                       
       6399 AATGAGGATCCCTTTTCTTCATTCATCACTCAGATTTTTGTCC
          1 AATGAGGATCCCTTTTCTTCATTCATCACTCAGATTTTTGTCC

             
       6442 A
          1 A

       6443 TCGGCTTCTG


Statistics
Matches: 43,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  43   43  1.00

ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43


Consensus pattern (43 bp):   
AATGAGGATCCCTTTTCTTCATTCATCACTCAGATTTTTGTCC

Found at i:8420 original size:2 final size:2

Alignment explanation


    Indices: 8413--8447  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       8403 ACCAAATTAG

                                                                
       8413 AT AT AT AT 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 AT AT AT AT A

       8448 AAAGCGAGGT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.