problem with option -n and -l

[mewu3]

Hello,

I understand the behavior of bowtie as aligning from the 5' of reads (the seed region) to references, and by reading the document I understand that option -n number bowtie will tolerate the given number of mismatches in the seed region.

So here the commander line bowtie -x {params.refDB} -f {input[0]} -n 2 -l 7 -a --nofw --sam -p {params.threads} {output} was meant to aligne oligonucleotides (13-mer) to genomes data, i was hoping that the mismatches tolerated would limited to the seed region that would be de 5' of the 13-mers.
Yet by examining the output sam file, especially the MD tags, it seems to me that mismatches are tolerated outside of the seed region.

4749	16	KX810065.1	3712	255	13M	*	0	0	TGTGGTTGGATGA	IIIIIIIIIIIII	XA:i:1	MD:Z:10C2	NM:i:1	XM:i:378
4749	16	MH118060.1	3766	255	13M	*	0	0	TGTGGTTGGATGA	IIIIIIIIIIIII	XA:i:1	MD:Z:10C2	NM:i:1	XM:i:378
4749	16	MF285667.1	3780	255	13M	*	0	0	TGTGGTTGGATGA	IIIIIIIIIIIII	XA:i:1	MD:Z:10C2	NM:i:1	XM:i:378
4749	16	MG957117.1	3653	255	13M	*	0	0	TGTGGTTGGATGA	IIIIIIIIIIIII	XA:i:1	MD:Z:1C8C2	NM:i:2	XM:i:378
4749	16	MH118080.1	3736	255	13M	*	0	0	TGTGGTTGGATGA	IIIIIIIIIIIII	XA:i:1	MD:Z:5C4C2	NM:i:2	XM:i:378
4749	16	MH118053.1	3739	255	13M	*	0	0	TGTGGTTGGATGA	IIIIIIIIIIIII	XA:i:1	MD:Z:5C4C2	NM:i:2	XM:i:378
4749	16	KF958311.1	5364	255	13M	*	0	0	TGTGGTTGGATGA	IIIIIIIIIIIII	XA:i:2	MD:Z:10C0C1	NM:i:2	XM:i:378
4749	16	JF317013.1	5352	255	13M	*	0	0	TGTGGTTGGATGA	IIIIIIIIIIIII	XA:i:2	MD:Z:10C0C1	NM:i:2	XM:i:378

It could be my misunderstanding that leads to this false conclusion.

mewu3