Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005779.1 Corchorus capsularis cultivar CVL-1 contig05797, 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: 2711
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32


Found at i:24 original size:16 final size:16

Alignment explanation


    Indices: 1--49  Score: 73
    Period size: 16  Copynumber: 3.1  Consensus size: 16

                            
          1 AACTAGGGTTTTTGAA
          1 AACTAGGGTTTTTGAA

             *        *     
         17 ATCTAGGGTTCTTGAA
          1 AACTAGGGTTTTTGAA

                            
         33 AACTAGGG-TTTTGAA
          1 AACTAGGGTTTTTGAA

              
         48 AA
          1 AA

         50 AAGCAGTGGA


Statistics
Matches: 29,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  15    8  0.28
  16   21  0.72

ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35


Consensus pattern (16 bp):   
AACTAGGGTTTTTGAA

Found at i:1481 original size:55 final size:55

Alignment explanation


    Indices: 1422--2141  Score: 1095
    Period size: 55  Copynumber: 13.2  Consensus size: 55

       1412 CAATCCGAAC

                               * *                                  
       1422 AGTAATCAGTAAATCAGTAATTAAGTGAA-AAGAGATTAATCAGAGTCAAGGTAAT
          1 AGTAATCAGTAAATCAGTAGTCAAGT-AAGAAGAGATTAATCAGAGTCAAGGTAAT

                          *                                        
       1477 AGTAATCAGTAAATTAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAA-G----
          1 AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT

                                        *     *                    
       1527 -GTAAT-AGT-AATCAGTAGTCAAGTAAAAAGAGGTTAATCAGAGTCAAGGTAAT
          1 AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT

                    *          * *                            *     
       1579 AGTAATCAATAAATCAGTAATTAAGTGAA-AAGAGATTAATCAGAGTCAAAGTAAT
          1 AGTAATCAGTAAATCAGTAGTCAAGT-AAGAAGAGATTAATCAGAGTCAAGGTAAT

                *         *                                        
       1634 AGTAGTCAGTAAATAAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT
          1 AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT

                                        *                          
       1689 AGTAATCAGTAAATCAGTAGTCAAGTAAAAAGAGATTAATCAGAGTCAAGGTAAT
          1 AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT

                                    *                              
       1744 AGTAATCAGTAAATCAGTAGTCAATTAAGAAGAGATTAATCAGAGTCAAGGTAAT
          1 AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT

                               * *                           *     
       1799 AGTAATCAGTAAATCAGTAATTAAGTAAGAAGAGATTAATCAGAGTCAAAGTAAT
          1 AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT

                               * *                            *     
       1854 AGTAATCAGTAAATCAGTAATTAAGTGAA-AAGAGATTAATCAGAGTCAAAGTAAT
          1 AGTAATCAGTAAATCAGTAGTCAAGT-AAGAAGAGATTAATCAGAGTCAAGGTAAT

                               * *                            *     
       1909 AGTAATCAGTAAATCAGTAATTAAGTGAA-AAGAGATTAATCAGAGTCAAAGTAAT
          1 AGTAATCAGTAAATCAGTAGTCAAGT-AAGAAGAGATTAATCAGAGTCAAGGTAAT

                     *    *        *                               
       1964 AGTAATCAGCAAATAAGTAGTCATGTAAGAAGAGATTAATCAGAGTCAAGGTAAT
          1 AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT

                                                                   
       2019 AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT
          1 AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT

                                                                   
       2074 AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT
          1 AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT

                         
       2129 AGTAATCAGTAAA
          1 AGTAATCAGTAAA

       2142 AAGAGATTAA


Statistics
Matches: 617,  Mismatches: 35, Indels: 26
        0.91            0.05        0.04

Matches are distributed among these distances:
  47   35  0.06
  48    4  0.01
  49    5  0.01
  53    5  0.01
  54    9  0.01
  55  555  0.90
  56    4  0.01

ACGTcount: A:0.47, C:0.08, G:0.20, T:0.25


Consensus pattern (55 bp):   
AGTAATCAGTAAATCAGTAGTCAAGTAAGAAGAGATTAATCAGAGTCAAGGTAAT

Found at i:1539 original size:21 final size:21

Alignment explanation


    Indices: 1513--1586  Score: 78
    Period size: 21  Copynumber: 3.3  Consensus size: 21

       1503 AAGAAGAGAT

                                 
       1513 TAATCAGAGTCAAGGTAATAG
          1 TAATCAGAGTCAAGGTAATAG

                                  *   
       1534 TAATCAGTAGTCAA-GTAAAAAGAGG
          1 TAATCAG-AGTCAAGGT---AATA-G

                                  
       1559 TTAATCAGAGTCAAGGTAATAG
          1 -TAATCAGAGTCAAGGTAATAG

                  
       1581 TAATCA
          1 TAATCA

       1587 ATAAATCAGT


Statistics
Matches: 44,  Mismatches: 2, Indels: 14
        0.73            0.03        0.23

Matches are distributed among these distances:
  21   15  0.34
  22    7  0.16
  23    3  0.07
  24    3  0.07
  25    7  0.16
  26    9  0.20

ACGTcount: A:0.45, C:0.09, G:0.22, T:0.24


Consensus pattern (21 bp):   
TAATCAGAGTCAAGGTAATAG

Done.