An Improved Scoring Matrix for Multiple Sequence Alignment

Table 5

Ambiguities in sequence alignment using the window size of 5 bases.

No.	Names	Sequences	Window position	Ambiguity positions
2	DMSPARC	ATGCGCTCCCTTTGGCTGCTG; CTCGGCTTGGGCCTGCTGGC; TGTGAGCCACGTCCAGGCCT	18	0, 3
4	RATSC1	ATGAAGGCCGTGCTTCTCCT; CCTGTATGCCTTGGGGATCG; CTGCTGCAGTCCCG	18	0, 3
5	MOUSESC1	ATGAAGGCTGTGCTTCTCCTC; CTGTGCGCCTTGGGAACCGC; TGTGGCAATCCCG	18	0, 3
6	HUMANHEVIN	ATGAAGACTGGGCCTTTTTTCCTAT; GTCTCTTGGGAACTGCAGCTGCAAT; CCCG	11	−5, −4
7	BOVINAMEX	ATGGGGACCTGGATTTTGTTTGCCT; GCCTCCTGGGAGCAGCCTTCTCTAT; GCCT	20	−4, 0
10	XENOPUS2AM	ATGAGGCCATTGGTAATGCTAACA; GCTCTCATTGGAGCAGCCTTTTCTCT; TCCT	7	−1, 0
12	MOUSEAMEX	ATGGGGACCTGGATTTTGTTTGCCT; GCCTCCTGGGAGCAGCTTTTGCTAT; GCCC	20	−4, 0
13	RATAMEX	ATGGGGACCTGGATTTTGTTTGCCT; GCCTCCTGGGAGCAGCTTTTGCTAT; GCCC	20	−4,0
16	HUMANAMEY	ATGGGGACCTGGATTTTGTTTGCCT; GCCTTGTGGGAGCAGCTTTTGCCAT; GCCT	20	−4, 0
17	HUMAMAMEX	ATGGGGACCTGGATTTTATTTGCCT; GCCTCCTGGGAGCAGCTTTTGCCAT; GCCT	20	−4, 0
18	CAVIAAMEX	ATGGGAACCTGGATTTTGTTTGCCT; GCCTCTTGGGAACAGCCTTTGCTAT; GCCT	20	−4, 0
23	CHICKENSPA	ATGAGAACCTGGATTTTCTTCTTCCT; CTGCCTGGCAGGCAAAGCCCTGGC; AGCTCCG	16	−3, 0
24	QUAILSPARC	ATGAGAGCCTGGATTTTCTTCCTCCT; CTGCCTGGCAGGCAAAGCCCTGGC; AGCCCCG	19	−3, 0
25	ZEBRAFSPAR	ATGAGGGTTTGGATCTTCTTCCTGT; TCTGCCTCGCTGGCAAGACTCTGGC; AGCTCCA	16	0, 3
26	TROUTSPARC	ATGAGGGTGTGGATTGTCTTCCTCC; TGTGCCTAGCTGGTCAGGCATTCAC; CGCTTCC	7	−4, 5
27	XENOPUSSPA	ATGAGGGTCTGGGTCTTCTTCGTCT; TGTGCCTGGCTGGCAAAGCACTAG; CTGCCCCT	16	0, 3