Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019356.1 Corchorus olitorius cultivar O-4 contig19389, 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: 18031
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33


Found at i:1947 original size:18 final size:16

Alignment explanation


    Indices: 1904--1935  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       1894 ATCTTGATTT

                 *          
       1904 TTCAGGGCTTTTCTGC
          1 TTCAGAGCTTTTCTGC

                            
       1920 TTCAGAGCTTTTCTGC
          1 TTCAGAGCTTTTCTGC

       1936 CTTGTAGAGC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.09, C:0.25, G:0.22, T:0.44


Consensus pattern (16 bp):   
TTCAGAGCTTTTCTGC

Found at i:2457 original size:57 final size:57

Alignment explanation


    Indices: 2389--2522  Score: 241
    Period size: 57  Copynumber: 2.4  Consensus size: 57

       2379 TGCTCTAACT

                                                                     
       2389 TTTTCAACTTAGCGAGCTTTTGTGCTATAACTTTTGCCTAAGCCGTCCTTTGCAGGA
          1 TTTTCAACTTAGCGAGCTTTTGTGCTATAACTTTTGCCTAAGCCGTCCTTTGCAGGA

                                      *               *              
       2446 TTTTCAACTTAGCGAGCTTTTGTGCTCTAACTTTTGCCTAAGTCGTCCTTTGCAGGA
          1 TTTTCAACTTAGCGAGCTTTTGTGCTATAACTTTTGCCTAAGCCGTCCTTTGCAGGA

                         *      
       2503 TTTTCAACTTAGCAAGCTTT
          1 TTTTCAACTTAGCGAGCTTT

       2523 GTAAGTAGTT


Statistics
Matches: 74,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  57   74  1.00

ACGTcount: A:0.19, C:0.22, G:0.18, T:0.40


Consensus pattern (57 bp):   
TTTTCAACTTAGCGAGCTTTTGTGCTATAACTTTTGCCTAAGCCGTCCTTTGCAGGA

Found at i:8825 original size:33 final size:33

Alignment explanation


    Indices: 8769--8839  Score: 115
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       8759 AATTCCTTCA

                *        *    *              
       8769 GCTGGCTTGGATTGATCATCTCACTGACCTTTT
          1 GCTGACTTGGATTAATCAGCTCACTGACCTTTT

                                             
       8802 GCTGACTTGGATTAATCAGCTCACTGACCTTTT
          1 GCTGACTTGGATTAATCAGCTCACTGACCTTTT

                 
       8835 GCTGA
          1 GCTGA

       8840 TCAGATGCTT


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  33   35  1.00

ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37


Consensus pattern (33 bp):   
GCTGACTTGGATTAATCAGCTCACTGACCTTTT

Found at i:9902 original size:18 final size:16

Alignment explanation


    Indices: 9859--9890  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       9849 ATCTTGATTT

                 *          
       9859 TTCAGGGCTTTTCTGC
          1 TTCAGAGCTTTTCTGC

                            
       9875 TTCAGAGCTTTTCTGC
          1 TTCAGAGCTTTTCTGC

       9891 CTTGTAGAGC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.09, C:0.25, G:0.22, T:0.44


Consensus pattern (16 bp):   
TTCAGAGCTTTTCTGC

Found at i:13590 original size:33 final size:33

Alignment explanation


    Indices: 13527--13592  Score: 82
    Period size: 33  Copynumber: 2.1  Consensus size: 33

      13517 ATCTAACAAT

                              *** *          
      13527 AAACAGCTATAAACTCATTTTGTAACAAAAAAA
          1 AAACAGCTATAAACTCATACCGCAACAAAAAAA

                                             
      13560 AAACAGCTATAAACTCATACCGC--CAAAAAAA
          1 AAACAGCTATAAACTCATACCGCAACAAAAAAA

              
      13591 AA
          1 AA

      13593 GAGCTCTATA


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  31   10  0.34
  33   19  0.66

ACGTcount: A:0.56, C:0.20, G:0.06, T:0.18


Consensus pattern (33 bp):   
AAACAGCTATAAACTCATACCGCAACAAAAAAA
Done.