Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007712.1 Corchorus olitorius cultivar O-4 contig07738, 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: 2157
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34


Found at i:1253 original size:27 final size:26

Alignment explanation


    Indices: 1199--1259  Score: 72
    Period size: 27  Copynumber: 2.3  Consensus size: 26

       1189 CTAAATTTCC

                                        
       1199 ATTATTTTAATAATGGAATAATTAAAAT
          1 ATTA-TTTAATAATGGAAT-ATTAAAAT

                                        
       1227 ATTATTTAATAATGGCAAT-TTAGAAAT
          1 ATTATTTAATAATGG-AATATTA-AAAT

                   
       1254 A-TATTT
          1 ATTATTT

       1260 GAAAAAAAGG


Statistics
Matches: 31,  Mismatches: 0, Indels: 6
        0.84            0.00        0.16

Matches are distributed among these distances:
  26    8  0.26
  27   16  0.52
  28    7  0.23

ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44


Consensus pattern (26 bp):   
ATTATTTAATAATGGAATATTAAAAT

Found at i:1560 original size:21 final size:22

Alignment explanation


    Indices: 1520--1560  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

       1510 GACAAACTCG

                           *      
       1520 TAACCCGAATAACCCGAGAAGA
          1 TAACCCGAATAACCCAAGAAGA

                      *         
       1542 TAACCCG-ATGACCCAAGAA
          1 TAACCCGAATAACCCAAGAA

       1561 TATTATAAAC


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   10  0.59
  22    7  0.41

ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10


Consensus pattern (22 bp):   
TAACCCGAATAACCCAAGAAGA

Found at i:1911 original size:2 final size:2

Alignment explanation


    Indices: 1904--1935  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       1894 ATACACTCCA

                                                           
       1904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1936 TAAACTATCA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.