Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021327.1 Corchorus olitorius cultivar O-4 contig21360, 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: 11439
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:7799 original size:15 final size:15

Alignment explanation


    Indices: 7779--7807  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       7769 AACTTTAAGT

                           
       7779 ACCCGAATCCAAACG
          1 ACCCGAATCCAAACG

                          
       7794 ACCCGAATCCAAAC
          1 ACCCGAATCCAAAC

       7808 CCAAACCCAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.41, C:0.41, G:0.10, T:0.07


Consensus pattern (15 bp):   
ACCCGAATCCAAACG

Found at i:8501 original size:105 final size:102

Alignment explanation


    Indices: 8358--8566  Score: 305
    Period size: 105  Copynumber: 2.0  Consensus size: 102

       8348 TTGCTTAAAT

                                                   *       *                 
       8358 TTTTATAGTCTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATGTAATATCCTAATAAGTA
          1 TTTTATAGTCTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCT--T-A-TA

                                      *            *  
       8423 -CTATTTTATTTTTACCATTTTACT-CTTTTAATTAAAATAC
         62 CCTATTTTATTTTTACCATTTTACTGATTTT-ATTAAAAAAC

                     *                                                       
       8463 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
          1 TTTTATAGTCTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA

                       *                         
       8528 TTTTATTTTTATCATTTTACTGATTTTATTAAAAAAC
         66 TTTTATTTTTACCATTTTACTGATTTTATTAAAAAAC

              
       8565 TT
          1 TT

       8567 AGATATATTA


Statistics
Matches: 96,  Mismatches: 6, Indels: 7
        0.88            0.06        0.06

Matches are distributed among these distances:
 101    2  0.02
 102   35  0.36
 103    5  0.05
 105   54  0.56

ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50


Consensus pattern (102 bp):   
TTTTATAGTCTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
TTTTATTTTTACCATTTTACTGATTTTATTAAAAAAC

Found at i:8540 original size:23 final size:23

Alignment explanation


    Indices: 8514--8557  Score: 54
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       8504 TTAAATCTAA

                *                   
       8514 TATCCTTATACCT-ATTTTATTTT
          1 TATCATTATA-CTGATTTTATTTT

                   *             
       8537 TATCATTTTACTGATTTTATT
          1 TATCATTATACTGATTTTATT

       8558 AAAAAACTTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  22    2  0.11
  23   16  0.89

ACGTcount: A:0.23, C:0.14, G:0.02, T:0.61


Consensus pattern (23 bp):   
TATCATTATACTGATTTTATTTT
Done.