Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000941.1 Corchorus capsularis cultivar CVL-1 contig00941, 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: 8044
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34


Found at i:62 original size:29 final size:30

Alignment explanation


    Indices: 1--80  Score: 108
    Period size: 29  Copynumber: 2.7  Consensus size: 30

                 *                        
          1 AAGTTGAGGGGGCAAAACGTCCCAAAATTG
          1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG

                      *      *       *    
         31 AAGTTCAGGGAGCAAAATGT-CCAAGATTG
          1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG

                  *              
         60 AAGTTCGGGGGGCAAAACGTC
          1 AAGTTCAGGGGGCAAAACGTC

         81 TAAACACTAC


Statistics
Matches: 42,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  29   25  0.60
  30   17  0.40

ACGTcount: A:0.35, C:0.16, G:0.31, T:0.17


Consensus pattern (30 bp):   
AAGTTCAGGGGGCAAAACGTCCCAAAATTG

Found at i:2957 original size:17 final size:17

Alignment explanation


    Indices: 2937--2969  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       2927 TAGCATATTT

                              
       2937 AAATATAAAAAA-AAAAG
          1 AAATA-AAAAAATAAAAG

                            
       2954 AAATAAAAAAATAAAA
          1 AAATAAAAAAATAAAA

       2970 AAAGTCAAAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    6  0.40
  17    9  0.60

ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12


Consensus pattern (17 bp):   
AAATAAAAAAATAAAAG

Found at i:7363 original size:2 final size:2

Alignment explanation


    Indices: 7356--7394  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       7346 AATTCATTGA

                                                                      
       7356 AT AT 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 AT AT A

       7395 GGATCATTTC


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

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


Consensus pattern (2 bp):   
AT

Done.