Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019081.1 Corchorus olitorius cultivar O-4 contig19114, 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: 47437
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:4027 original size:19 final size:19

Alignment explanation


    Indices: 4003--4055  Score: 106
    Period size: 19  Copynumber: 2.8  Consensus size: 19

       3993 TCCCATAAAA

                               
       4003 TTTGCTGACGTGGCAAACG
          1 TTTGCTGACGTGGCAAACG

                               
       4022 TTTGCTGACGTGGCAAACG
          1 TTTGCTGACGTGGCAAACG

                           
       4041 TTTGCTGACGTGGCA
          1 TTTGCTGACGTGGCA

       4056 CTTCCACATC


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   34  1.00

ACGTcount: A:0.19, C:0.21, G:0.32, T:0.28


Consensus pattern (19 bp):   
TTTGCTGACGTGGCAAACG

Found at i:11243 original size:64 final size:64

Alignment explanation


    Indices: 11142--11273  Score: 255
    Period size: 64  Copynumber: 2.1  Consensus size: 64

      11132 AACAGGTATT

                              *                                             
      11142 ATTAGTTTGAAATTATTCGTTATTTCGAATGAAGAAGTTACAATCCTTGATCTGATCACATCTA
          1 ATTAGTTTGAAATTATTCATTATTTCGAATGAAGAAGTTACAATCCTTGATCTGATCACATCTA

                                                                            
      11206 ATTAGTTTGAAATTATTCATTATTTCGAATGAAGAAGTTACAATCCTTGATCTGATCACATCTA
          1 ATTAGTTTGAAATTATTCATTATTTCGAATGAAGAAGTTACAATCCTTGATCTGATCACATCTA

                
      11270 ATTA
          1 ATTA

      11274 AGACTAATCG


Statistics
Matches: 67,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  64   67  1.00

ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39


Consensus pattern (64 bp):   
ATTAGTTTGAAATTATTCATTATTTCGAATGAAGAAGTTACAATCCTTGATCTGATCACATCTA

Found at i:12134 original size:60 final size:61

Alignment explanation


    Indices: 12032--12149  Score: 168
    Period size: 60  Copynumber: 2.0  Consensus size: 61

      12022 TTTTTCGCCA

                                 *           *                           
      12032 TGAACTTTTAATTTGAAACTTTCACCTCCTAAATTATCAAAATCAAGACAATTTCCCCTAT
          1 TGAACTTTTAATTTGAAACTTGCACCTCCTAAACTATCAAAATCAAGACAATTTCCCCTAT

                                                        ***            
      12093 TGAACTTTTAATTTGGAAA-TTGCACC-CCTAAACTATCAAAATGGGGACAATTTCCCC
          1 TGAACTTTTAATTT-GAAACTTGCACCTCCTAAACTATCAAAATCAAGACAATTTCCCC

      12150 CATTAAGTGG


Statistics
Matches: 51,  Mismatches: 5, Indels: 3
        0.86            0.08        0.05

Matches are distributed among these distances:
  60   27  0.53
  61   20  0.39
  62    4  0.08

ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33


Consensus pattern (61 bp):   
TGAACTTTTAATTTGAAACTTGCACCTCCTAAACTATCAAAATCAAGACAATTTCCCCTAT

Found at i:26643 original size:21 final size:21

Alignment explanation


    Indices: 26618--26678  Score: 104
    Period size: 21  Copynumber: 2.9  Consensus size: 21

      26608 GTTAACATTT

                         *       
      26618 AAGAAACAGGGGATAATGAAG
          1 AAGAAACAGGGGAAAATGAAG

                       *         
      26639 AAGAAACAGGGAAAAATGAAG
          1 AAGAAACAGGGGAAAATGAAG

                               
      26660 AAGAAACAGGGGAAAATGA
          1 AAGAAACAGGGGAAAATGA

      26679 GAAAAAAGAA


Statistics
Matches: 37,  Mismatches: 3, Indels: 0
        0.93            0.08        0.00

Matches are distributed among these distances:
  21   37  1.00

ACGTcount: A:0.57, C:0.05, G:0.31, T:0.07


Consensus pattern (21 bp):   
AAGAAACAGGGGAAAATGAAG

Found at i:44671 original size:42 final size:42

Alignment explanation


    Indices: 44622--44706  Score: 161
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      44612 ATGAAATGTA

                                                      
      44622 CATATCCTTGTATTGAATAAAGTTATCTCTGCAAAAATGCAG
          1 CATATCCTTGTATTGAATAAAGTTATCTCTGCAAAAATGCAG

                       *                              
      44664 CATATCCTTGTGTTGAATAAAGTTATCTCTGCAAAAATGCAG
          1 CATATCCTTGTATTGAATAAAGTTATCTCTGCAAAAATGCAG

             
      44706 C
          1 C

      44707 CCAAATTGTC


Statistics
Matches: 42,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   42  1.00

ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33


Consensus pattern (42 bp):   
CATATCCTTGTATTGAATAAAGTTATCTCTGCAAAAATGCAG
Done.