Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002293.1 Corchorus olitorius cultivar O-4 contig02293, 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, 844

Length: 1407
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.37


Found at i:381 original size:15 final size:15

Alignment explanation


    Indices: 351--392  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        341 TTACTTTGTT

                            
        351 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
        367 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

                       
        382 TTGTTTTCTGT
          1 TTGTTTTCTGT

        393 CAACCTCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:766 original size:26 final size:25

Alignment explanation


    Indices: 721--791  Score: 81
    Period size: 25  Copynumber: 2.7  Consensus size: 25

        711 CGTCGTTTTG

                                *       
        721 AAAAAAAAAAGTTTTGTGTTGCGTCGAA
          1 AAAAAAAAAAG-TTT-TGTTACGTC-AA

                                    *
        749 AAAAAAAAAAGTTTTGTTACGTCAT
          1 AAAAAAAAAAGTTTTGTTACGTCAA

                               
        774 AAAAAAAAAA-TTCTTGTT
          1 AAAAAAAAAAGTT-TTGTT

        792 CTTGCGTTTT


Statistics
Matches: 40,  Mismatches: 2, Indels: 5
        0.85            0.04        0.11

Matches are distributed among these distances:
  24    2  0.05
  25   16  0.40
  26    8  0.20
  27    3  0.08
  28   11  0.28

ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31


Consensus pattern (25 bp):   
AAAAAAAAAAGTTTTGTTACGTCAA

Found at i:778 original size:28 final size:28

Alignment explanation


    Indices: 721--783  Score: 85
    Period size: 26  Copynumber: 2.3  Consensus size: 28

        711 CGTCGTTTTG

                                *    *  
        721 AAAAAAAAAAGTTTTGTGTTGCGTCGAA
          1 AAAAAAAAAAGTTTTGTGTTACGTCAAA

                                      * 
        749 AAAAAAAAAAG-TTT-TGTTACGTCATA
          1 AAAAAAAAAAGTTTTGTGTTACGTCAAA

                     
        775 AAAAAAAAA
          1 AAAAAAAAA

        784 TTCTTGTTCT


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  26   18  0.56
  27    3  0.09
  28   11  0.34

ACGTcount: A:0.54, C:0.06, G:0.14, T:0.25


Consensus pattern (28 bp):   
AAAAAAAAAAGTTTTGTGTTACGTCAAA
Done.