Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020218.1 Corchorus olitorius cultivar O-4 contig20251, 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: 5731
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:4118 original size:42 final size:43

Alignment explanation


    Indices: 4071--4156  Score: 147
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       4061 CTCGATGAAA

                         *                     *       
       4071 TGGATTTGAGAG-GAATGGCCGAAGGCTTGTTATTTCTCGTTG
          1 TGGATTTGAGAGAAAATGGCCGAAGGCTTGTTATTCCTCGTTG

                                                       
       4113 TGGATTTGAGAGAAAATGGCCGAAGGCTTGTTATTCCTCGTTG
          1 TGGATTTGAGAGAAAATGGCCGAAGGCTTGTTATTCCTCGTTG

             
       4156 T
          1 T

       4157 CGAATTTGCT


Statistics
Matches: 41,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  42   12  0.29
  43   29  0.71

ACGTcount: A:0.21, C:0.13, G:0.31, T:0.35


Consensus pattern (43 bp):   
TGGATTTGAGAGAAAATGGCCGAAGGCTTGTTATTCCTCGTTG

Found at i:4492 original size:102 final size:102

Alignment explanation


    Indices: 4321--4530  Score: 377
    Period size: 102  Copynumber: 2.1  Consensus size: 102

       4311 GCTTTGTTGT

                                                 *                           
       4321 TGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTTGGTTTGCTTGAGAAGAACTTTGCCTTGCC
          1 TGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGAGAAGAACTTTGCCTTGCC

                         *                       
       4386 TTGCCTTGAATTTGGAGAGATCGCTGGTGGCTTGGAA
         66 TTGCCTTGAATTTAGAGAGATCGCTGGTGGCTTGGAA

                                                                             
       4423 TGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGAGAAGAACTTTGCCTTGCC
          1 TGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGAGAAGAACTTTGCCTTGCC

                                 *            *  
       4488 TTGCCTTGAATTTAGAGAGATTGCTGGTGGCTTGTAA
         66 TTGCCTTGAATTTAGAGAGATCGCTGGTGGCTTGGAA

                   
       4525 T-CTTTG
          1 TGCTTTG

       4531 AGGAGGCTAG


Statistics
Matches: 104,  Mismatches: 4, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
 101    5  0.05
 102   99  0.95

ACGTcount: A:0.20, C:0.15, G:0.28, T:0.38


Consensus pattern (102 bp):   
TGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGAGAAGAACTTTGCCTTGCC
TTGCCTTGAATTTAGAGAGATCGCTGGTGGCTTGGAA
Done.