Output of the program for detecting near duplicates.  The numbers at right are the global alignment scores.

(2_Shigella_boydii_Sb227, 1_Escherichia_coli_K12) = 234
(3_Shigella_flexneri_2a_str._2457T, 1_Escherichia_coli_K12) = 234
(3_Shigella_flexneri_2a_str._2457T, 2_Shigella_boydii_Sb227) = 234
(4_Shigella_dysenteriae_Sd197, 1_Escherichia_coli_K12) = 230
(4_Shigella_dysenteriae_Sd197, 2_Shigella_boydii_Sb227) = 230
(4_Shigella_dysenteriae_Sd197, 3_Shigella_flexneri_2a_str._2457T) = 230
(5_Salmonella_enterica_subsp._enterica_serovar_Typhi_Ty2, 1_Escherichia_coli_K12) = 184
(5_Salmonella_enterica_subsp._enterica_serovar_Typhi_Ty2, 2_Shigella_boydii_Sb227) = 184
(5_Salmonella_enterica_subsp._enterica_serovar_Typhi_Ty2, 3_Shigella_flexneri_2a_str._2457T) = 184
(5_Salmonella_enterica_subsp._enterica_serovar_Typhi_Ty2, 4_Shigella_dysenteriae_Sd197) = 182
(6_Salmonella_typhimurium_LT2, 1_Escherichia_coli_K12) = 183
(6_Salmonella_typhimurium_LT2, 2_Shigella_boydii_Sb227) = 183
(6_Salmonella_typhimurium_LT2, 3_Shigella_flexneri_2a_str._2457T) = 183
(6_Salmonella_typhimurium_LT2, 4_Shigella_dysenteriae_Sd197) = 181
(6_Salmonella_typhimurium_LT2, 5_Salmonella_enterica_subsp._enterica_serovar_Typhi_Ty2) = 222
(9_Yersinia_pestis_biovar_Medievalis_str._91001, 8_Yersinia_pseudotuberculosis_IP_32953) = 92

ClustalW alignment of sequences 1-6.  You can see that retaining any of sequences 1-4 and discarding the remainder would not have much of an impact on motif discovery.

1_Escherichia_coli_K12              AAAGTAACTCCGCGGTTCGACCACTTTTTTATCCAAAGTTTCGGGCTGTT 50
2_Shigella_boydii_Sb227             AAAGTAACTCCGCGGTTCGACCACTTTTTTATCCAAAGTTTCGGGCTGTT 50
3_Shigella_flexneri_2a_str._24      AAAGTAACTCCGCGGTTCGACCACTTTTTTATCCAAAGTTTCGGGCTGTT 50
4_Shigella_dysenteriae_Sd197        AAAGTAACTCTGCGGTTCGACCACTTTTTTATCCAAAGTTTCGGGCTGTT 50
5_Salmonella_enterica_subsp._e      AAAGTAACTCAGCGGTTCGACCACTTTTTTATCCAAAGTTTCGGGCTGTT 50
6_Salmonella_typhimurium_LT2        AAAGTAACTCAGCGGTTCGACCACTTTTTTATCCAAAGTTTCGGGCTGTT 50
                                    ********** ***************************************

1_Escherichia_coli_K12              ATGTTTTAATGTGCAACATTCATGGTCTGTTGGGGGCAAAAATGGCATTA 100
2_Shigella_boydii_Sb227             ATGTTTTAATGTGCAACATTCATGGTCTGTTGGGGGCAAAAATGGCATTA 100
3_Shigella_flexneri_2a_str._24      ATGTTTTAATGTGCAACATTCATGGTCTGTTGGGGGCAAAAATGGCATTA 100
4_Shigella_dysenteriae_Sd197        ATGTTTTAATGTGCAACATTCATGGTCTGTTGGGGGCAAAAATGGCATTA 100
5_Salmonella_enterica_subsp._e      ATGTTTTAATGTGCAACATTCATGGTCTGTTGGGGGCAAAAATGGCATTA 100
6_Salmonella_typhimurium_LT2        ATGTTTTAATGTGCAACATTCATGGTCTGTTGGGGGCAAAAATGGCATTA 100
                                    **************************************************

1_Escherichia_coli_K12              TGCGTCCCCAAAGATAAAACTGGCATCGAACCAGGTTCAGACAGAAAGGT 150
2_Shigella_boydii_Sb227             TGCGTCCCCAAAGATAAAACTGGCATCGAACCAGGTTCAGACAGAAAGGT 150
3_Shigella_flexneri_2a_str._24      TGCGTCCCCAAAGATAAAACTGGCATCGAACCAGGTTCAGACAGAAAGGT 150
4_Shigella_dysenteriae_Sd197        TGCCTCCCCAAAGATAAAACTGGCATCGAACCAGGTTCAGACAGAAAGGT 150
5_Salmonella_enterica_subsp._e      TGCGCCCCTTATAATAAAGCTGAC------TAAGGTTCAGGCAGAAAGGT 144
6_Salmonella_typhimurium_LT2        TGCGCCCCTTATAATAAAGCTGAC------TAAGGTTCAGGCAGAAAGGT 144
                                    ***  ***  *  ***** *** *        ******** *********

1_Escherichia_coli_K12              CCCTANNNNNNNNNNTAACTGATAAGGGCAGGGCCACTGGCTCTGCCCTT 200
2_Shigella_boydii_Sb227             CCCTANNNNNNNNNNTAACTGATAAGGGCAGGGCCACTGGCTCTGCCCTT 200
3_Shigella_flexneri_2a_str._24      CCCTANNNNNNNNNNTAACTGATAAGGGCAGGGCCACTGGCTCTGCCCTT 200
4_Shigella_dysenteriae_Sd197        CCCTANNNNNNNNNNTAACTGATAAGGGCAGGGCCACTGGCTCTGCCCTT 200
5_Salmonella_enterica_subsp._e      CACCANNNNNNNNNNTAACTGAAAAGGGCAGGGCCGCAGGCTCTGCCCTT 194
6_Salmonella_typhimurium_LT2        CACCANNNNNNNNNNTAACTGAAAAGGGCAGGGCCGCAGGCTCTGCCCTT 194
                                    * * ****************** ************ * ************

1_Escherichia_coli_K12              TTGCTATTCTCACCGTAACGAATCAGCGGATACC 234
2_Shigella_boydii_Sb227             TTGCTATTCTCACCGTAACGAATCAGCGGATACC 234
3_Shigella_flexneri_2a_str._24      TTGCTATTCTCACCGTAACGAATCAGCGGATACC 234
4_Shigella_dysenteriae_Sd197        TTGCTATTCTCACCGTAACGAATCAGCGGATACC 234
5_Salmonella_enterica_subsp._e      TTGCT--TTTCACCGTAAAGAAGCAGCGGAATCA 226
6_Salmonella_typhimurium_LT2        TTGCT--TTTCACCGTAAAGAAGCAGCGTAAACA 226
                                    *****  * ********* *** ***** *  *