Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021596.1 Corchorus olitorius cultivar O-4 contig21629, 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: 4599
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28


Found at i:858 original size:17 final size:17

Alignment explanation


    Indices: 836--868  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        826 TATTTAATGA

                             
        836 CGTTTCCGTACAAAAGG
          1 CGTTTCCGTACAAAAGG

                            
        853 CGTTTCCGTACAAAAG
          1 CGTTTCCGTACAAAAG

        869 CGTGGCGTCT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24


Consensus pattern (17 bp):   
CGTTTCCGTACAAAAGG

Found at i:883 original size:70 final size:70

Alignment explanation


    Indices: 800--940  Score: 273
    Period size: 70  Copynumber: 2.0  Consensus size: 70

        790 CCACTAAATA

                                                                             
        800 GTGGCATCTTTTTACGGAAACGCCGTTATTTAATGACGTTTCCGTACAAAAGGCGTTTCCGTACA
          1 GTGGCATCTTTTTACGGAAACGCCGTTATTTAATGACGTTTCCGTACAAAAGGCGTTTCCGTACA

                 
        865 AAAGC
         66 AAAGC

                 *                                                           
        870 GTGGCGTCTTTTTACGGAAACGCCGTTATTTAATGACGTTTCCGTACAAAAGGCGTTTCCGTACA
          1 GTGGCATCTTTTTACGGAAACGCCGTTATTTAATGACGTTTCCGTACAAAAGGCGTTTCCGTACA

                 
        935 AAAGC
         66 AAAGC

             
        940 G
          1 G

        941 CCACTATATA


Statistics
Matches: 70,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  70   70  1.00

ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30


Consensus pattern (70 bp):   
GTGGCATCTTTTTACGGAAACGCCGTTATTTAATGACGTTTCCGTACAAAAGGCGTTTCCGTACA
AAAGC

Found at i:928 original size:17 final size:17

Alignment explanation


    Indices: 906--938  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        896 TATTTAATGA

                             
        906 CGTTTCCGTACAAAAGG
          1 CGTTTCCGTACAAAAGG

                            
        923 CGTTTCCGTACAAAAG
          1 CGTTTCCGTACAAAAG

        939 CGCCACTATA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24


Consensus pattern (17 bp):   
CGTTTCCGTACAAAAGG

Found at i:994 original size:33 final size:32

Alignment explanation


    Indices: 921--1014  Score: 107
    Period size: 33  Copynumber: 2.9  Consensus size: 32

        911 CCGTACAAAA

                             *         *    
        921 GGCGTTTCCGTACAAAAGCGCCACTATATAGT
          1 GGCGTTTCCGTACAAAAACGCCACTATTTAGT

               *         *                   
        953 GGCATTTCCGTAAAAAAAACGCCACTATTTAGT
          1 GGCGTTTCCGT-ACAAAAACGCCACTATTTAGT

             **           *       *      
        986 GTTGTTTCCGTACAGAAACGCCGCTATTT
          1 GGCGTTTCCGTACAAAAACGCCACTATTT

       1015 TGGCTTCTTT


Statistics
Matches: 51,  Mismatches: 10, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  32   25  0.49
  33   26  0.51

ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29


Consensus pattern (32 bp):   
GGCGTTTCCGTACAAAAACGCCACTATTTAGT

Found at i:1013 original size:32 final size:31

Alignment explanation


    Indices: 921--1014  Score: 98
    Period size: 32  Copynumber: 2.9  Consensus size: 31

        911 CCGTACAAAA

                                       *    
        921 GGCGTTTCCGTACAAAAGCGCCACTATATAGT
          1 GGCGTTTCCGTACAAAA-CGCCACTATTTAGT

               *          *                  
        953 GGCATTTCCGTAAAAAAAACGCCACTATTTAGT
          1 GGCGTTTCCGT--ACAAAACGCCACTATTTAGT

             **                   *      
        986 GTTGTTTCCGTACAGAAACGCCGCTATTT
          1 GGCGTTTCCGTACA-AAACGCCACTATTT

       1015 TGGCTTCTTT


Statistics
Matches: 51,  Mismatches: 8, Indels: 6
        0.78            0.12        0.09

Matches are distributed among these distances:
  31    2  0.04
  32   23  0.45
  33   21  0.41
  34    5  0.10

ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29


Consensus pattern (31 bp):   
GGCGTTTCCGTACAAAACGCCACTATTTAGT

Found at i:1396 original size:17 final size:17

Alignment explanation


    Indices: 1376--1408  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       1366 ACCATAGGAG

                             
       1376 ATTAAGTTTAATTACAT
          1 ATTAAGTTTAATTACAT

                            
       1393 ATTAAGTTTAATTACA
          1 ATTAAGTTTAATTACA

       1409 AAATATGACA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45


Consensus pattern (17 bp):   
ATTAAGTTTAATTACAT

Found at i:1532 original size:14 final size:14

Alignment explanation


    Indices: 1513--1540  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       1503 ACCGAATTCC

                          
       1513 ACCCAATAAAATAA
          1 ACCCAATAAAATAA

                          
       1527 ACCCAATAAAATAA
          1 ACCCAATAAAATAA

       1541 GTCTTAATTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.64, C:0.21, G:0.00, T:0.14


Consensus pattern (14 bp):   
ACCCAATAAAATAA
Done.