Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01003250.1 Corchorus olitorius cultivar O-4 contig03256, 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, 647

Length: 1079
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32


Found at i:317 original size:27 final size:27

Alignment explanation


    Indices: 287--367  Score: 67
    Period size: 27  Copynumber: 3.0  Consensus size: 27

        277 AAATAAATTT

                                       
        287 AAGAAATTTAAAACACTTAGAAATGAA
          1 AAGAAATTTAAAACACTTAGAAATGAA

                 *         *  **       **
        314 AAGAAGTTTAGAAATGA-AAAGAAAT-TT
          1 AAGAAATTTA-AAA-CACTTAGAAATGAA

                                       
        341 AAGAAATTTTAAAACACTTAGAAATGA
          1 AAGAAA-TTTAAAACACTTAGAAATGA

        368 GACGGATAAG


Statistics
Matches: 38,  Mismatches: 11, Indels: 9
        0.66            0.19        0.16

Matches are distributed among these distances:
  26    1  0.03
  27   23  0.61
  28   13  0.34
  29    1  0.03

ACGTcount: A:0.57, C:0.05, G:0.14, T:0.25


Consensus pattern (27 bp):   
AAGAAATTTAAAACACTTAGAAATGAA

Found at i:347 original size:19 final size:18

Alignment explanation


    Indices: 303--347  Score: 72
    Period size: 18  Copynumber: 2.4  Consensus size: 18

        293 TTTAAAACAC

                            * 
        303 TTAGAAATGAAAAGAAGT
          1 TTAGAAATGAAAAGAAAT

                              
        321 TTAGAAATGAAAAGAAAT
          1 TTAGAAATGAAAAGAAAT

                     
        339 TTAAGAAAT
          1 TT-AGAAAT

        348 TTTAAAACAC


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  18   19  0.76
  19    6  0.24

ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24


Consensus pattern (18 bp):   
TTAGAAATGAAAAGAAAT

Found at i:730 original size:15 final size:15

Alignment explanation


    Indices: 710--740  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        700 TAGTTAACAT

                           
        710 TAACATTAACTATGA
          1 TAACATTAACTATGA

                           
        725 TAACATTAACTATGA
          1 TAACATTAACTATGA

             
        740 T
          1 T

        741 CATTGTAATT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35


Consensus pattern (15 bp):   
TAACATTAACTATGA
Done.