where NOT all, but more than 90% of the small string is included in the bi string

Hm. Your sample does not demonstrate that. The best match is 12.01% (at offset 575).

The simplest (and fastest pure Perl) method is to use bitwise-xor masking at each of the possible offsets and the count the number of nulls (zero-bytes) in the result. Here is code that demonstrates that:

#! perl -slw
use strict;

my $bigstring="MNRIYSLRYSAVARGFIAVSEFARKCVHKSVRRLCFPVLLLIPVLFSAGSLAGTV
+NNELGYQLFRDFAENKGMFRPGATNIAIYNKQGEFVGTLDKAAMPDFSAVDSEIGVATLINPQYIASVK
+HNGGYTNVSFGDGENRYNIVDRNNAPSLDFHAPRLDKLVTEVAPTAVTAQGAVAGAYLDKERYPVFYRL
+GSGTQYIKDSNGQLTKMGGAYSWLTGGTVGSLSSYQNGEMISTSSGLVFDYKLNGAMPIYGEAGDSGSP
+LFAFDTVQNKWVLVGVLTAGNGAGGRGNNWAVIPLDFIGQKFNEDNDAPVTFRTSEGGALEWSFNSSTG
+AGALTQGTTTYAMHGQQGNDLNAGKNLIFQGQNGQINLKDSVSQGAGSLTFRDNYTVTTSNGSTWTGAG
+IVVDNGVSVNWQVNGVKGDNLHKIGEGTLTVQGTGINEGGLKVGDGKVVLNQQADNKGQVQAFSSVNIA
+SGRPTVVLTDERQVNPDTVSWGYRGGTLDVNGNSLTFHQLKAADYGAVLANNVDKRATITLDYALRADK
+VALNGWSESGKGTAGNLYKYNNPYTNTTDYFILKQSTYGYFPTDQSSNATWEFVGHSQGDAQKLVADRF
+NTAGYLFHGQLKGNLNVDNRLPEGVTGALVMDGAADISGTFTQENGRLTLQGHPVIHAYNTQSVADKLA
+ASGDHSVLTQPTSFSQEDWENRSFTFDRLSLKNTDFGLGRNATLNTTIQADNSSVTLGDSRVFIDKNDG
+QGTAFTLEEGTSVATKDADKSVFNGTVNLDNQSVLNINDIFNGGIQANNSTVNISSDSAVLGNSTLTST
+ALNLNKGANALASQSFVSDGPVNISDATLSLNSRPDEVSHTLLPVYDYAGSWNLKGDDARLNVGPYSML
+SGNINVQDKGTVTLGGEGELSPDLTLQNQMLYSLFNGYRNIWSGSLNAPDATVSMTDTQWSMNGNSTAG
+NMKLNRTIVGFNGGTSPFTTLTTDNLDAVQSAFVMRTDLNKADKLVINKSATGHDNSIWVNFLKKPSNK
+DTLDIPLVSAPEATADNLFRASTRVVGFSDVTPILSVRKEDGKKEWVLDGYQVARNDGQGKAAATFMHI
+SYNNFITEVNNLNKRMGDLRDINGEAGTWVRLLNGSGSADGGFTDHYTLLQMGADRKHELGSMDLFTGV
+MATYTDTDASADLYSGKTKSWGGGFYASGLFRSGAYFDVIAKYIHNENKYDLNFAGAGKQNFRSHSLYA
+GAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNWNDSGMDVSMRRNSVNPLVGRTGVVSGKTFSGKDWS
+LTARAGLHYEFDLTDSADVHLKDAAGEHQINGRKDSRMLYGVGLNARFGDNTRLGLEVERSAFGKYNTD
+DAINANIRYSF";
my $smallstring="GTMARNDGQGKAAATFMHISYNNFITEVDNLNKRMGDLRDINGEAGTWVRLLN
+GSGSADGGFTDHYTLLQMGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTKSWGGGFYASGLFRSG
+AYFDVIAKYIHNENKYDLNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNW
+NDSGMDVSMRRNSVNPLVGRTGVVSGKTFSGKDWSLTARAGLHYEFDLTDSADVHLKDAAGEHQINGRK
+DSRMLYGVGLNARFGDNTRLGLEVERSAFGKYNTDDAINANIRYSFLE";
my $lenBig = length $bigstring;
my $lenSmall = length $smallstring;

for my $o ( 0 .. ( $lenBig - $lenSmall + 1 ) ) {
    my $masked = substr( $bigstring, $o, $lenSmall ) ^ $smallstring;
    my $matched = $masked =~ tr[\0][];
    if( ( $matched / $lenSmall ) > 0.10 ) {
        $masked =~ tr[\1-\255][ ];
        $masked =~ tr[\0][*];
        printf "%.2f%% match at offset %u\n", $matched / $lenSmall * 1
+00, $o;
        print substr $bigstring, $o, $lenSmall;
        print $smallstring;
        print $masked;
    }
}
[download]

The output:

C:\test>1070240.pl
10.06% match at offset 50
LAGTVNNELGYQLFRDFAENKGMFRPGATNIAIYNKQGEFVGTLDKAAMPDFSAVDSEIGVATLINPQYI
+ASVKHNGGYTNVSFGDGENRYNIVDRNNAPSLDFHAPRLDKLVTEVAPTAVTAQGAVAGAYLDKERYPV
+FYRLGSGTQYIKDSNGQLTKMGGAYSWLTGGTVGSLSSYQNGEMISTSSGLVFDYKLNGAMPIYGEAGD
+SGSPLFAFDTVQNKWVLVGVLTAGNGAGGRGNNWAVIPLDFIGQKFNEDNDAPVTFRTSEGGALEWSFN
+SSTGAGALTQGTTTYAMHGQQGNDLNAGKNL
GTMARNDGQGKAAATFMHISYNNFITEVDNLNKRMGDLRDINGEAGTWVRLLNGSGSADGGFTDHYTLLQ
+MGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTKSWGGGFYASGLFRSGAYFDVIAKYIHNENKYD
+LNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNWNDSGMDVSMRRNSVNPL
+VGRTGVVSGKTFSGKDWSLTARAGLHYEFDLTDSADVHLKDAAGEHQINGRKDSRMLYGVGLNARFGDN
+TRLGLEVERSAFGKYNTDDAINANIRYSFLE
     *   *             *     *                          *  *  *       
+                *           *                       *   *   *   *    
+    * * *             *    **  *                     *      *        
+ *                    **          *   *                     *       *
+   *          *
10.06% match at offset 143
VDRNNAPSLDFHAPRLDKLVTEVAPTAVTAQGAVAGAYLDKERYPVFYRLGSGTQYIKDSNGQLTKMGGA
+YSWLTGGTVGSLSSYQNGEMISTSSGLVFDYKLNGAMPIYGEAGDSGSPLFAFDTVQNKWVLVGVLTAG
+NGAGGRGNNWAVIPLDFIGQKFNEDNDAPVTFRTSEGGALEWSFNSSTGAGALTQGTTTYAMHGQQGND
+LNAGKNLIFQGQNGQINLKDSVSQGAGSLTFRDNYTVTTSNGSTWTGAGIVVDNGVSVNWQVNGVKGDN
+LHKIGEGTLTVQGTGINEGGLKVGDGKVVLN
GTMARNDGQGKAAATFMHISYNNFITEVDNLNKRMGDLRDINGEAGTWVRLLNGSGSADGGFTDHYTLLQ
+MGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTKSWGGGFYASGLFRSGAYFDVIAKYIHNENKYD
+LNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNWNDSGMDVSMRRNSVNPL
+VGRTGVVSGKTFSGKDWSLTARAGLHYEFDLTDSADVHLKDAAGEHQINGRKDSRMLYGVGLNARFGDN
+TRLGLEVERSAFGKYNTDDAINANIRYSFLE
            *            * *       *   *                  *           
+         **           *      *          *    **                      
+    * *           *           *        * *             *             
+             *                  *   *               *         *   ***
+     *      *                *
10.71% match at offset 211
GAYSWLTGGTVGSLSSYQNGEMISTSSGLVFDYKLNGAMPIYGEAGDSGSPLFAFDTVQNKWVLVGVLTA
+GNGAGGRGNNWAVIPLDFIGQKFNEDNDAPVTFRTSEGGALEWSFNSSTGAGALTQGTTTYAMHGQQGN
+DLNAGKNLIFQGQNGQINLKDSVSQGAGSLTFRDNYTVTTSNGSTWTGAGIVVDNGVSVNWQVNGVKGD
+NLHKIGEGTLTVQGTGINEGGLKVGDGKVVLNQQADNKGQVQAFSSVNIASGRPTVVLTDERQVNPDTV
+SWGYRGGTLDVNGNSLTFHQLKAADYGAVLA
GTMARNDGQGKAAATFMHISYNNFITEVDNLNKRMGDLRDINGEAGTWVRLLNGSGSADGGFTDHYTLLQ
+MGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTKSWGGGFYASGLFRSGAYFDVIAKYIHNENKYD
+LNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNWNDSGMDVSMRRNSVNPL
+VGRTGVVSGKTFSGKDWSLTARAGLHYEFDLTDSADVHLKDAAGEHQINGRKDSRMLYGVGLNARFGDN
+TRLGLEVERSAFGKYNTDDAINANIRYSFLE
*      *                                * ****     *               *  
+                         *  *                      **       *        
+   **                         *           *          * *  *    * *   
+          *  *                *   **      *                          
+            *   *     *      *
11.04% match at offset 227
YQNGEMISTSSGLVFDYKLNGAMPIYGEAGDSGSPLFAFDTVQNKWVLVGVLTAGNGAGGRGNNWAVIPL
+DFIGQKFNEDNDAPVTFRTSEGGALEWSFNSSTGAGALTQGTTTYAMHGQQGNDLNAGKNLIFQGQNGQ
+INLKDSVSQGAGSLTFRDNYTVTTSNGSTWTGAGIVVDNGVSVNWQVNGVKGDNLHKIGEGTLTVQGTG
+INEGGLKVGDGKVVLNQQADNKGQVQAFSSVNIASGRPTVVLTDERQVNPDTVSWGYRGGTLDVNGNSL
+TFHQLKAADYGAVLANNVDKRATITLDYALR
GTMARNDGQGKAAATFMHISYNNFITEVDNLNKRMGDLRDINGEAGTWVRLLNGSGSADGGFTDHYTLLQ
+MGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTKSWGGGFYASGLFRSGAYFDVIAKYIHNENKYD
+LNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNWNDSGMDVSMRRNSVNPL
+VGRTGVVSGKTFSGKDWSLTARAGLHYEFDLTDSADVHLKDAAGEHQINGRKDSRMLYGVGLNARFGDN
+TRLGLEVERSAFGKYNTDDAINANIRYSFLE
                        *              *        *  *     * *          
+     *         *           *     *      *          *         *       
+ *      *   *        *      * *         *    *                       
+    *   *                                   * * *    *    *  *       
+*   *          *  *          *
11.69% match at offset 276
GVLTAGNGAGGRGNNWAVIPLDFIGQKFNEDNDAPVTFRTSEGGALEWSFNSSTGAGALTQGTTTYAMHG
+QQGNDLNAGKNLIFQGQNGQINLKDSVSQGAGSLTFRDNYTVTTSNGSTWTGAGIVVDNGVSVNWQVNG
+VKGDNLHKIGEGTLTVQGTGINEGGLKVGDGKVVLNQQADNKGQVQAFSSVNIASGRPTVVLTDERQVN
+PDTVSWGYRGGTLDVNGNSLTFHQLKAADYGAVLANNVDKRATITLDYALRADKVALNGWSESGKGTAG
+NLYKYNNPYTNTTDYFILKQSTYGYFPTDQS
GTMARNDGQGKAAATFMHISYNNFITEVDNLNKRMGDLRDINGEAGTWVRLLNGSGSADGGFTDHYTLLQ
+MGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTKSWGGGFYASGLFRSGAYFDVIAKYIHNENKYD
+LNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNWNDSGMDVSMRRNSVNPL
+VGRTGVVSGKTFSGKDWSLTARAGLHYEFDLTDSADVHLKDAAGEHQINGRKDSRMLYGVGLNARFGDN
+TRLGLEVERSAFGKYNTDDAINANIRYSFLE
*      * *        *            *      *   * *  *         *    *  *    
+                           *    *             *    **   *      *     
+       *                     *   *  *     *  *        **             
+                        *         *    * *        * *   * *          
+              *
11.04% match at offset 310
PVTFRTSEGGALEWSFNSSTGAGALTQGTTTYAMHGQQGNDLNAGKNLIFQGQNGQINLKDSVSQGAGSL
+TFRDNYTVTTSNGSTWTGAGIVVDNGVSVNWQVNGVKGDNLHKIGEGTLTVQGTGINEGGLKVGDGKVV
+LNQQADNKGQVQAFSSVNIASGRPTVVLTDERQVNPDTVSWGYRGGTLDVNGNSLTFHQLKAADYGAVL
+ANNVDKRATITLDYALRADKVALNGWSESGKGTAGNLYKYNNPYTNTTDYFILKQSTYGYFPTDQSSNA
+TWEFVGHSQGDAQKLVADRFNTAGYLFHGQL
GTMARNDGQGKAAATFMHISYNNFITEVDNLNKRMGDLRDINGEAGTWVRLLNGSGSADGGFTDHYTLLQ
+MGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTKSWGGGFYASGLFRSGAYFDVIAKYIHNENKYD
+LNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNWNDSGMDVSMRRNSVNPL
+VGRTGVVSGKTFSGKDWSLTARAGLHYEFDLTDSADVHLKDAAGEHQINGRKDSRMLYGVGLNARFGDN
+TRLGLEVERSAFGKYNTDDAINANIRYSFLE
    *    *     *         *         *                                  
+   *      *            *   *        *         *                   *  
+**     *      *    *       ***   * *       *      * *               *
+          *                *                             **          
+*            *   *    *
10.06% match at offset 536
DKVALNGWSESGKGTAGNLYKYNNPYTNTTDYFILKQSTYGYFPTDQSSNATWEFVGHSQGDAQKLVADR
+FNTAGYLFHGQLKGNLNVDNRLPEGVTGALVMDGAADISGTFTQENGRLTLQGHPVIHAYNTQSVADKL
+AASGDHSVLTQPTSFSQEDWENRSFTFDRLSLKNTDFGLGRNATLNTTIQADNSSVTLGDSRVFIDKND
+GQGTAFTLEEGTSVATKDADKSVFNGTVNLDNQSVLNINDIFNGGIQANNSTVNISSDSAVLGNSTLTS
+TALNLNKGANALASQSFVSDGPVNISDATLS
GTMARNDGQGKAAATFMHISYNNFITEVDNLNKRMGDLRDINGEAGTWVRLLNGSGSADGGFTDHYTLLQ
+MGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTKSWGGGFYASGLFRSGAYFDVIAKYIHNENKYD
+LNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNWNDSGMDVSMRRNSVNPL
+VGRTGVVSGKTFSGKDWSLTARAGLHYEFDLTDSADVHLKDAAGEHQINGRKDSRMLYGVGLNARFGDN
+TRLGLEVERSAFGKYNTDDAINANIRYSFLE
   * *        *       *                                     *         
+         *       *          *    *     *      *           *          
+                    *                       *       * *      *       
+   *        *                    *         *  * *            *       
+* * *     *            **    *
12.01% match at offset 575
YGYFPTDQSSNATWEFVGHSQGDAQKLVADRFNTAGYLFHGQLKGNLNVDNRLPEGVTGALVMDGAADIS
+GTFTQENGRLTLQGHPVIHAYNTQSVADKLAASGDHSVLTQPTSFSQEDWENRSFTFDRLSLKNTDFGL
+GRNATLNTTIQADNSSVTLGDSRVFIDKNDGQGTAFTLEEGTSVATKDADKSVFNGTVNLDNQSVLNIN
+DIFNGGIQANNSTVNISSDSAVLGNSTLTSTALNLNKGANALASQSFVSDGPVNISDATLSLNSRPDEV
+SHTLLPVYDYAGSWNLKGDDARLNVGPYSML
GTMARNDGQGKAAATFMHISYNNFITEVDNLNKRMGDLRDINGEAGTWVRLLNGSGSADGGFTDHYTLLQ
+MGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTKSWGGGFYASGLFRSGAYFDVIAKYIHNENKYD
+LNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNWNDSGMDVSMRRNSVNPL
+VGRTGVVSGKTFSGKDWSLTARAGLHYEFDLTDSADVHLKDAAGEHQINGRKDSRMLYGVGLNARFGDN
+TRLGLEVERSAFGKYNTDDAINANIRYSFLE
      *    *   *   *       *       * *          *      *       *      
+                   *  *   *     **           *        *        *     
+   *          *              *        *                *          *  
+    *            *  *  *                  *                  ** *    
+    * *   *       *    *
10.06% match at offset 813
TALNLNKGANALASQSFVSDGPVNISDATLSLNSRPDEVSHTLLPVYDYAGSWNLKGDDARLNVGPYSML
+SGNINVQDKGTVTLGGEGELSPDLTLQNQMLYSLFNGYRNIWSGSLNAPDATVSMTDTQWSMNGNSTAG
+NMKLNRTIVGFNGGTSPFTTLTTDNLDAVQSAFVMRTDLNKADKLVINKSATGHDNSIWVNFLKKPSNK
+DTLDIPLVSAPEATADNLFRASTRVVGFSDVTPILSVRKEDGKKEWVLDGYQVARNDGQGKAAATFMHI
+SYNNFITEVNNLNKRMGDLRDINGEAGTWVR
GTMARNDGQGKAAATFMHISYNNFITEVDNLNKRMGDLRDINGEAGTWVRLLNGSGSADGGFTDHYTLLQ
+MGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTKSWGGGFYASGLFRSGAYFDVIAKYIHNENKYD
+LNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNWNDSGMDVSMRRNSVNPL
+VGRTGVVSGKTFSGKDWSLTARAGLHYEFDLTDSADVHLKDAAGEHQINGRKDSRMLYGVGLNARFGDN
+TRLGLEVERSAFGKYNTDDAINANIRYSFLE
     * *    *           *           *                     *           
+ *       *   *          *     ***                                    
+          *                     **          *                        
+               *    *        * *    *   *   *    *    *        * *   
+       *     *   *
11.69% match at offset 970
TTLTTDNLDAVQSAFVMRTDLNKADKLVINKSATGHDNSIWVNFLKKPSNKDTLDIPLVSAPEATADNLF
+RASTRVVGFSDVTPILSVRKEDGKKEWVLDGYQVARNDGQGKAAATFMHISYNNFITEVNNLNKRMGDL
+RDINGEAGTWVRLLNGSGSADGGFTDHYTLLQMGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTK
+SWGGGFYASGLFRSGAYFDVIAKYIHNENKYDLNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQ
+AELVWGRLQGQTFNWNDSGMDVSMRRNSVNP
GTMARNDGQGKAAATFMHISYNNFITEVDNLNKRMGDLRDINGEAGTWVRLLNGSGSADGGFTDHYTLLQ
+MGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTKSWGGGFYASGLFRSGAYFDVIAKYIHNENKYD
+LNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNWNDSGMDVSMRRNSVNPL
+VGRTGVVSGKTFSGKDWSLTARAGLHYEFDLTDSADVHLKDAAGEHQINGRKDSRMLYGVGLNARFGDN
+TRLGLEVERSAFGKYNTDDAINANIRYSFLE
 *           *  *    *     * *      *                               * 
+    *            *           * *        *   *     *   *              
+    *      *       *  *   * *                            * *    *    
+    *      *             * *           *     *           *           
+  *            *         * *
10.06% match at offset 1054
ILSVRKEDGKKEWVLDGYQVARNDGQGKAAATFMHISYNNFITEVNNLNKRMGDLRDINGEAGTWVRLLN
+GSGSADGGFTDHYTLLQMGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTKSWGGGFYASGLFRSG
+AYFDVIAKYIHNENKYDLNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNW
+NDSGMDVSMRRNSVNPLVGRTGVVSGKTFSGKDWSLTARAGLHYEFDLTDSADVHLKDAAGEHQINGRK
+DSRMLYGVGLNARFGDNTRLGLEVERSAFGK
GTMARNDGQGKAAATFMHISYNNFITEVDNLNKRMGDLRDINGEAGTWVRLLNGSGSADGGFTDHYTLLQ
+MGADRKHELGSMDLFTGVMATYTDTDASADLYSGKTKSWGGGFYASGLFRSGAYFDVIAKYIHNENKYD
+LNFAGAGKQNFRSHSLYAGAEVGYRYHLTDTTFVEPQAELVWGRLQGQTFNWNDSGMDVSMRRNSVNPL
+VGRTGVVSGKTFSGKDWSLTARAGLHYEFDLTDSADVHLKDAAGEHQINGRKDSRMLYGVGLNARFGDN
+TRLGLEVERSAFGKYNTDDAINANIRYSFLE
    *     *           *                    *               *       ** 
+                   *       * **  *             *            *        
+  *    *                                    *   **                   
+      **    *               *   *           *       *       *     *  
+    *                    *  *
[download]