Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022321.1 Corchorus olitorius cultivar O-4 contig22354, 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: 3965
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34


Found at i:1836 original size:21 final size:22

Alignment explanation


    Indices: 1770--1854  Score: 163
    Period size: 22  Copynumber: 3.9  Consensus size: 22

       1760 AGTTCTGAGG

                                  
       1770 CTACCCGGCCCCGGGTACCCCC
          1 CTACCCGGCCCCGGGTACCCCC

                                  
       1792 CTACCCGGCCCCGGGTACCCCC
          1 CTACCCGGCCCCGGGTACCCCC

                                  
       1814 CTACCCGGCCCCGGGTA-CCCC
          1 CTACCCGGCCCCGGGTACCCCC

                                
       1835 CTACCCGGCCCCGGGTACCC
          1 CTACCCGGCCCCGGGTACCC

       1855 TCAGGAACGT


Statistics
Matches: 62,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
  21   21  0.34
  22   41  0.66

ACGTcount: A:0.09, C:0.58, G:0.24, T:0.09


Consensus pattern (22 bp):   
CTACCCGGCCCCGGGTACCCCC

Found at i:1849 original size:43 final size:44

Alignment explanation


    Indices: 1770--1854  Score: 163
    Period size: 43  Copynumber: 2.0  Consensus size: 44

       1760 AGTTCTGAGG

                                                        
       1770 CTACCCGGCCCCGGGTACCCCCCTACCCGGCCCCGGGTACCCCC
          1 CTACCCGGCCCCGGGTACCCCCCTACCCGGCCCCGGGTACCCCC

                                                      
       1814 CTACCCGGCCCCGGGTA-CCCCCTACCCGGCCCCGGGTACCC
          1 CTACCCGGCCCCGGGTACCCCCCTACCCGGCCCCGGGTACCC

       1855 TCAGGAACGT


Statistics
Matches: 41,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  43   24  0.59
  44   17  0.41

ACGTcount: A:0.09, C:0.58, G:0.24, T:0.09


Consensus pattern (44 bp):   
CTACCCGGCCCCGGGTACCCCCCTACCCGGCCCCGGGTACCCCC

Found at i:2315 original size:27 final size:28

Alignment explanation


    Indices: 2285--2337  Score: 74
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       2275 TAATCTGGTT

                                         
       2285 ATTTAT-TTT-GGTATTTTATGATTTCAG
          1 ATTTATCTTTAGGT-TTTTATGATTTCAG

                       *              
       2312 ATTTATCTTTATGTTTTTATGATTTC
          1 ATTTATCTTTAGGTTTTTATGATTTC

       2338 TAATTGATTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  27    6  0.26
  28   15  0.65
  29    2  0.09

ACGTcount: A:0.21, C:0.06, G:0.11, T:0.62


Consensus pattern (28 bp):   
ATTTATCTTTAGGTTTTTATGATTTCAG
Done.