Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017924.1 Corchorus olitorius cultivar O-4 contig17957, 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: 11031
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32


Found at i:9426 original size:16 final size:16

Alignment explanation


    Indices: 9386--9423  Score: 60
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       9376 TTTGTTTGTT

                            
       9386 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
       9402 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

                   
       9417 TTGTTTT
          1 TTGTTTT

       9424 TCTTTCAACC


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  15   12  0.57
  16    9  0.43

ACGTcount: A:0.16, C:0.05, G:0.13, T:0.66


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:9869 original size:25 final size:24

Alignment explanation


    Indices: 9837--9913  Score: 84
    Period size: 24  Copynumber: 3.1  Consensus size: 24

       9827 TTGTTTTGTG

                                     
       9837 TTTTGCGTCGAAAAAAAAAATATTT
          1 TTTTGCGTC-AAAAAAAAAATATTT

                      *           * 
       9862 TTTTGCGTCATAAAAAAAAT-TGT
          1 TTTTGCGTCAAAAAAAAAATATTT

              *                  *    
       9885 TTCTGCGTCATAAAAAAAGAAAATTT
          1 TTTTGCGTCA-AAAAAAA-AATATTT

               
       9911 TTT
          1 TTT

       9914 GTGTCTGCGT


Statistics
Matches: 42,  Mismatches: 7, Indels: 5
        0.78            0.13        0.09

Matches are distributed among these distances:
  23   11  0.26
  24   16  0.38
  25   11  0.26
  26    4  0.10

ACGTcount: A:0.42, C:0.09, G:0.12, T:0.38


Consensus pattern (24 bp):   
TTTTGCGTCAAAAAAAAAATATTT

Found at i:9876 original size:22 final size:23

Alignment explanation


    Indices: 9835--9902  Score: 84
    Period size: 23  Copynumber: 2.9  Consensus size: 23

       9825 CCTTGTTTTG

                          *         
       9835 TGTTT-TGCGTCGAAAAAAAAAAT
          1 TGTTTCTGCGTC-ATAAAAAAAAT

              *   *                 
       9858 ATTTTTTTGCGTCATAAAAAAAAT
          1 -TGTTTCTGCGTCATAAAAAAAAT

                                 
       9882 TGTTTCTGCGTCATAAAAAAA
          1 TGTTTCTGCGTCATAAAAAAA

       9903 GAAAATTTTT


Statistics
Matches: 39,  Mismatches: 4, Indels: 3
        0.85            0.09        0.07

Matches are distributed among these distances:
  23   19  0.49
  24   14  0.36
  25    6  0.15

ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35


Consensus pattern (23 bp):   
TGTTTCTGCGTCATAAAAAAAAT
Done.