BISMA results:

Reference sequence (original) : ATGAGGATGCCACTGTGGCTCAGTGATGGCGCCGAGACACAGGTGAACACTGTAAAATGTGGATGCCTGGAGGCAGCCCACACCCTGGGCCTTGGCTGGGGGAAAGGTTCCAGAAACGTCATCACAACGATGCATTTCATCAGAACTGAGCACATGAATGGGGAGGGGCAGGACTTCCTGAATGTCCCAACCCCACTGTCCCACCCTCTGTGTCAATATGAGGCTGCCTTATAAAGCACCAAGAGGCTGCCAGTGGGACATTTTCTCGGCCCTGCCAGCCCCCAGGAGGAAGGTG
Reference sequence (converted): ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAACGTTATTATAACGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTCGGTTTTGTTAGTTTTTAGGAGGAAGGTG
Number CpG in Reference sequence: 5

Parameters used:

Alignment mode: pairwise alignment of reference sequence and experimental sequences
Lower threshold conversion rate: 95%
Lower threshold sequence identity: 90%
Upper threshold of N-sites at cytosine positions: 20%
Upper threshold insertions/deletions: 20%

Final sequence alignment of the sequences included:

		

			

			

			
                                                                                                                                                                                                                                                                                                           
		
			

			

			

			
                                                                                                   1                   1                   1                   1                   1                   2                   2                   2                   2                   2                   
		
			

			

			

			
                   2                   4                   6                   8                   0                   2                   4                   6                   8                   0                   2                   4                   6                   8                   
		
			

			
Number
			
Sequence_id
			
                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   
		
			

			

			
Reference
			
ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAACGTTATTATAACGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTCGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
		
		
1
02KP-S100P2R2selection
ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAACGTTATTATAACGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
		
2
04KP-S100P2R4selection
ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAACGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
		
3
05KP-S100P2R5selection
ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAACGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
		
4
01KP-S100P2R1selection
ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
		
5
03KP-S100P2R3selection
ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
		
6
08KP-S100P2R8selection
ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
		
7
10KP-S100P2R10selection
ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTTAGGAGGAAGGTG
		
8
30KP-S100P2R9bselection
ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
		
9
06KP-S100P2R6selection
ATGAGGATGTTATTGTGGTTTAGTGATGGTGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
		
10
07KP-S100P2R7selection
ATGAGGATGTTATTGTGGTTTAGTGATGGTGTTGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTT-AGGAGGAAGGTG
	
	Legend:
		methylated CpG position
		unmethylated CpG position
		unconverted cytosine
		cytosine at unexpected position