Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024030.1 Corchorus olitorius cultivar O-4 contig24063, 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: 8437
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34


Found at i:1100 original size:80 final size:80

Alignment explanation


    Indices: 941--1096  Score: 251
    Period size: 80  Copynumber: 2.0  Consensus size: 80

        931 AAAGTGGTTT

                                                                             
        941 CGGATCTTAGACGACTTTTGAAGATAAGTCGGCTGGAAAACCTATTTTAGGAAGAGAAATAAAAA
          1 CGGATCTTAGACGACTTTTGAAGATAAGTCGGCTGGAAAACCTATTTTAGGAAGAGAAATAAAAA

                           
       1006 CGAGGGGGAGTTGCA
         66 CGAGGGGGAGTTGCA

                                     **  *                  *     *     *    
       1021 CGGATCTTAGACGACTTTTGAAGATGGGTTGGCTGGAAAACCTATTTTGGGAAGGGAAATGAAAA
          1 CGGATCTTAGACGACTTTTGAAGATAAGTCGGCTGGAAAACCTATTTTAGGAAGAGAAATAAAAA

                        
       1086 CGA-GGGGAGTT
         66 CGAGGGGGAGTT

       1097 TGCATAACGA


Statistics
Matches: 70,  Mismatches: 6, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  79    8  0.11
  80   62  0.89

ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24


Consensus pattern (80 bp):   
CGGATCTTAGACGACTTTTGAAGATAAGTCGGCTGGAAAACCTATTTTAGGAAGAGAAATAAAAA
CGAGGGGGAGTTGCA

Found at i:5015 original size:29 final size:31

Alignment explanation


    Indices: 4973--5048  Score: 113
    Period size: 29  Copynumber: 2.5  Consensus size: 31

       4963 ACTTGTAGCG

                                           
       4973 TTTGGACGTTTTGCCCCA-TGAACT-TCAAT
          1 TTTGGACGTTTTGCCCCAGTGAACTCTCAAT

                   *       *               
       5002 TTTGGACATTTTG-CGCAGTGAACTCTCAAT
          1 TTTGGACGTTTTGCCCCAGTGAACTCTCAAT

                             
       5032 TTTGGACGTTTTGCCCC
          1 TTTGGACGTTTTGCCCC

       5049 CTCTCAAACG


Statistics
Matches: 40,  Mismatches: 4, Indels: 4
        0.83            0.08        0.08

Matches are distributed among these distances:
  28    3  0.08
  29   18  0.45
  30   17  0.43
  31    2  0.05

ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38


Consensus pattern (31 bp):   
TTTGGACGTTTTGCCCCAGTGAACTCTCAAT

Found at i:5033 original size:30 final size:28

Alignment explanation


    Indices: 4973--5047  Score: 105
    Period size: 30  Copynumber: 2.6  Consensus size: 28

       4963 ACTTGTAGCG

                                         
       4973 TTTGGACGTTTTGCCCCATGAACTTCAAT
          1 TTTGGACGTTTTG-CCCATGAACTTCAAT

                   *      *               
       5002 TTTGGACATTTTGCGCAGTGAACTCTCAAT
          1 TTTGGACGTTTTGCCCA-TGAACT-TCAAT

                            
       5032 TTTGGACGTTTTGCCC
          1 TTTGGACGTTTTGCCC

       5048 CCTCTCAAAC


Statistics
Matches: 40,  Mismatches: 4, Indels: 3
        0.85            0.09        0.06

Matches are distributed among these distances:
  28    3  0.08
  29   18  0.45
  30   19  0.47

ACGTcount: A:0.19, C:0.23, G:0.20, T:0.39


Consensus pattern (28 bp):   
TTTGGACGTTTTGCCCATGAACTTCAAT

Found at i:5246 original size:29 final size:30

Alignment explanation


    Indices: 5188--5264  Score: 129
    Period size: 29  Copynumber: 2.6  Consensus size: 30

       5178 ATCGTTTGAG

                        *                 
       5188 AGGGGGCAAAACATCCAAAATTGAGAGTTC
          1 AGGGGGCAAAACGTCCAAAATTGAGAGTTC

                       *                  
       5218 AGGGGGCAAAATGTCCAAAATTGA-AGTTC
          1 AGGGGGCAAAACGTCCAAAATTGAGAGTTC

                              
       5247 AGGGGGCAAAACGTCCAA
          1 AGGGGGCAAAACGTCCAA

       5265 CCGCTACAAG


Statistics
Matches: 44,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  29   22  0.50
  30   22  0.50

ACGTcount: A:0.39, C:0.17, G:0.29, T:0.16


Consensus pattern (30 bp):   
AGGGGGCAAAACGTCCAAAATTGAGAGTTC

Found at i:6106 original size:62 final size:64

Alignment explanation


    Indices: 6037--6165  Score: 217
    Period size: 66  Copynumber: 2.0  Consensus size: 64

       6027 ATTAATACCG

                                                       *                    
       6037 GTAATGAAATTGAAATGTTTTCCTT-C-TTCTAATCAAATGGGTGCTAAGTGCCTTATTGACAT
          1 GTAATGAAATTGAAATGTTTTCCTTCCTTTCTAATCAAATGGGCGCTAAGTGCCTTATTGACAT

                                                                             
       6099 GTAATGAAATTGAAATGTTTTCCTTCCTTGTTCTAATCAAATGGGCGCTAAGTGCCTTATTGACA
          1 GTAATGAAATTGAAATGTTTTCCTTCC-T-TTCTAATCAAATGGGCGCTAAGTGCCTTATTGACA

             
       6164 T
         64 T

             
       6165 G
          1 G

       6166 CTTGCTAGTA


Statistics
Matches: 62,  Mismatches: 1, Indels: 4
        0.93            0.01        0.06

Matches are distributed among these distances:
  62   25  0.40
  63    1  0.02
  66   36  0.58

ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38


Consensus pattern (64 bp):   
GTAATGAAATTGAAATGTTTTCCTTCCTTTCTAATCAAATGGGCGCTAAGTGCCTTATTGACAT

Found at i:6847 original size:26 final size:27

Alignment explanation


    Indices: 6772--6847  Score: 73
    Period size: 26  Copynumber: 2.9  Consensus size: 27

       6762 TGTTTTGTTC

                *     *    *           
       6772 TTTGATCATTCGCATGTTCAAGGTCAT
          1 TTTGGTCATTTGCATATTCAAGGTCAT

                       ** * * *        
       6799 TTTGGTCATTTTTACAATAAAGG-CAT
          1 TTTGGTCATTTGCATATTCAAGGTCAT

                                   
       6825 TTTGGTCATTTGCATATTCAAGG
          1 TTTGGTCATTTGCATATTCAAGG

       6848 GCACGTGGGT


Statistics
Matches: 36,  Mismatches: 13, Indels: 1
        0.72            0.26        0.02

Matches are distributed among these distances:
  26   21  0.58
  27   15  0.42

ACGTcount: A:0.25, C:0.14, G:0.18, T:0.42


Consensus pattern (27 bp):   
TTTGGTCATTTGCATATTCAAGGTCAT
Done.