Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011210.1 Corchorus capsularis cultivar CVL-1 contig11231, 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: 5323
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:2138 original size:15 final size:15

Alignment explanation


    Indices: 2118--2154  Score: 65
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       2108 ATCTGAAATA

                           
       2118 CTTCAGATATTGATT
          1 CTTCAGATATTGATT

                    *      
       2133 CTTCAGATCTTGATT
          1 CTTCAGATATTGATT

                   
       2148 CTTCAGA
          1 CTTCAGA

       2155 GTTTTCTGCT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  15   21  1.00

ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43


Consensus pattern (15 bp):   
CTTCAGATATTGATT

Found at i:2166 original size:15 final size:16

Alignment explanation


    Indices: 2148--2179  Score: 57
    Period size: 15  Copynumber: 2.1  Consensus size: 16

       2138 GATCTTGATT

                            
       2148 CTTCAGAG-TTTTCTG
          1 CTTCAGAGCTTTTCTG

                            
       2163 CTTCAGAGCTTTTCTG
          1 CTTCAGAGCTTTTCTG

             
       2179 C
          1 C

       2180 CTTCTGCATT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    8  0.50
  16    8  0.50

ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44


Consensus pattern (16 bp):   
CTTCAGAGCTTTTCTG

Found at i:5110 original size:3 final size:3

Alignment explanation


    Indices: 5098--5141  Score: 81
    Period size: 3  Copynumber: 15.0  Consensus size: 3

       5088 TTTATTTATG

                                                                       
       5098 ACA A-A ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
          1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA

       5142 TTCAGAAATT


Statistics
Matches: 40,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2    2  0.05
   3   38  0.95

ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00


Consensus pattern (3 bp):   
ACA

Done.