Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016318.1 Corchorus olitorius cultivar O-4 contig16351, 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, 978

Length: 1630
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.29


Found at i:1437 original size:35 final size:34

Alignment explanation


    Indices: 1402--1630  Score: 294
    Period size: 35  Copynumber: 6.8  Consensus size: 34

       1392 CGGTCATTCA

                                         *    
       1402 AAGAAGTTTTTATGATCAGAGTTGATCTCGTTTC
          1 AAGAAGTTTTTATGATCAGAGTTGATCTCATTTC

                                                
       1436 AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCC
          1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTT-C

                       *                       
       1472 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
          1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC

                                                
       1507 AAGAAGTTTTTTATGATC--A---GA---CATTTCC
          1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTT-C

                       *                 *     
       1535 AAGAAGTTTTCGATGATCAGAGTTGATCTTATTTC
          1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC

                                          *    
       1570 AAGAAGATTTTTATGATCAGAGTTGATCTCGTTTC
          1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC

                                      
       1605 AAGAAGTTTTTATGATCAGAGTTGAT
          1 AAGAAGTTTTTATGATCAGAGTTGAT


Statistics
Matches: 172,  Mismatches: 8, Indels: 30
        0.82            0.04        0.14

Matches are distributed among these distances:
  27    9  0.05
  28   13  0.08
  30    3  0.02
  33    3  0.02
  34   26  0.15
  35   77  0.45
  36   41  0.24

ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40


Consensus pattern (34 bp):   
AAGAAGTTTTTATGATCAGAGTTGATCTCATTTC

Found at i:1532 original size:27 final size:28

Alignment explanation


    Indices: 1501--1555  Score: 85
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       1491 GAGTTGATCT

                             **         
       1501 CATTT-CAAGAAGTTTTTTATGATCAGA
          1 CATTTCCAAGAAGTTTTCGATGATCAGA

                                        
       1528 CATTTCCAAGAAGTTTTCGATGATCAGA
          1 CATTTCCAAGAAGTTTTCGATGATCAGA

       1556 GTTGATCTTA


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  27    5  0.20
  28   20  0.80

ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Consensus pattern (28 bp):   
CATTTCCAAGAAGTTTTCGATGATCAGA

Found at i:1538 original size:63 final size:63

Alignment explanation


    Indices: 1465--1590  Score: 234
    Period size: 63  Copynumber: 2.0  Consensus size: 63

       1455 GAGTTGATCT

                                                            *              
       1465 CATTTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGA
          1 CATTTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGATTTTTATGATCAGA

                                                *                          
       1528 CATTTCCAAGAAGTTTTCGATGATCAGAGTTGATCTTATTTCAAGAAGATTTTTATGATCAGA
          1 CATTTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGATTTTTATGATCAGA

       1591 GTTGATCTCG


Statistics
Matches: 61,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  63   61  1.00

ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38


Consensus pattern (63 bp):   
CATTTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGATTTTTATGATCAGA

Found at i:1608 original size:98 final size:98

Alignment explanation


    Indices: 1435--1624  Score: 303
    Period size: 99  Copynumber: 1.9  Consensus size: 98

       1425 GATCTCGTTT

                       **                                                    
       1435 CAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCCAAGAAGTTTTCGATGATCAGAGTTGATC
          1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCCAAGAAGTTTTCGATGATCAGAGTTGATC

                                              
       1500 TCATTTCAAGAAGTTTTTTATGATCAGACATTTC
         66 TCATTTCAAGAAG-TTTTTATGATCAGACATTTC

                                          *                  *               
       1534 CAAGAAGTTTTCGATGATCAGAGTTGATCTTATTT-CAAGAAGATTTT-TATGATCAGAGTTGAT
          1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCCAAGAAG-TTTTCGATGATCAGAGTTGAT

               *                        
       1597 CTCGTTTCAAGAAGTTTTTATGATCAGA
         65 CTCATTTCAAGAAGTTTTTATGATCAGA

       1625 GTTGAT


Statistics
Matches: 85,  Mismatches: 5, Indels: 4
        0.90            0.05        0.04

Matches are distributed among these distances:
  97   14  0.16
  98   35  0.41
  99   36  0.42

ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39


Consensus pattern (98 bp):   
CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCCAAGAAGTTTTCGATGATCAGAGTTGATC
TCATTTCAAGAAGTTTTTATGATCAGACATTTC
Done.