
A.

Alignment of the sequences corresponding to the putative bidirectional transcription initiation site (TIS) from the strand switch regions (SSR) of L. major chromosome 1 and H. muscarum scaffold 40. These regions share 57.8% identity.


L. major Chr1 SSR TIS	----------------------------------GGCTGCA----------------------------TGACGAACCGCCCATCCCCCCCCCCTCTTGCC-------------------
H. muscarum Scaf40 SSR	AACCATGACAGGGTCGTGGTAAGCAGGGGGGGGGGGCTGTACCTCTTGCGCGCTGGGGCAAGCAGCTGTCCACAACTTCCCCCCCCCCCCCCCCCCCCCCCCCAAACAACAAAAGCAGGC
                                                  	  *****.*                            . **.* .. *** .********** *.. **                   

L. major Chr1 SSR	--------AACAGCCCCCCCCCTCCAGGTACAGGT------------------------------------------------------------TGCCTCCGAGATCGGTCACAGAAG-
H. muscarum Scaf40 SSR	ACAGCAAGAACGGCGAATCCCGCCCACGTATGCATGCCTATGTAAAGGGGAAAAGCTCGCCAACATCTCTGCAGTGGTCGCTGATGCTCATTGTGTGTTTTTGTGCCCAGGCCCAGCAA-
                        	***.**   .*** .*** ***.. .*                                                            **..*..* * .*.* * *** *.                        





B.

Alignment of the whole strand-switch region from L. major and H. muscarum shows 47.43% identity. The transcription initiation site from L. major is included for reference.

L. major Chr1 SSR 	catatgaag--------------------------------cctgctctgaagtgctatg
L. major Chr1 SSR TIS	------------------------------------------------------------
H. muscarum Scaf40 SSR	AAAGTGTTGGAATCGGATATCGTAAACCTTTGAAATATTCCGCTTTTCCAATACACTCGC
                                                                            

L. major Chr1 SSR 	gaatcgccccttgtgagtggtgacgcttgtaaga---gcggagaagagacagcgaggcaa
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	CAACTACTTATTCTTTGTCAGATCGCTTTTCGAGTGTATTTAAAGGAGACAGCAATAAAG
                                                                            

L. major Chr1 SSR 	agtgaacagcatgtagaaggtaaatggtgaggggcaatcagtgcattgtattctctccag
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	CGTTGGAGGCACAAAAATGGCGAGGAGTAATGAGTCAAACTTTCTTTGCTGGAACGGGAG
                                                                            

L. major Chr1 SSR 	agcgggggatcacatgga---cgcagtcgcatcagtagatctgcgtcgtagtggga----
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	GGGGGGGGACCAACCGGAGAGCGCAGACAT-TCATTAGAACAGCGACAATGCTGGATGCC
                                                                            

L. major Chr1 SSR 	-------------aaaagaaaaactcaggcagacttctcagcctacaggtac--------
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	CAGGGACTATCAGCACGGAAAAAACATAGTAGTTGTCAGAGCGTCACAGTACTTCTGGTA
                                                                            

L. major Chr1 SSR 	--ctgcgccggtttctgtgaaaaacggcaagaatggctgca-------------------
L. major Chr1 SSR TIS 	----------------------------------GGCTGCA-------------------
H. muscarum Scaf40 SSR 	AACCATGACAGGGTCGTGGTAAGCAGGGGGGGGGGGCTGTACCTCTTGCGCGCTGGGGCA
                       		                          *****.*                   

L. major Chr1 SSR 	---------tgacgaaccgcccatcccccccccc-cttgcc-------------------
L. major Chr1 SSR TIS 	---------TGACGAACCGCCCATCCCCCCCCCCTCTTGCC-------------------
H. muscarum Scaf40 SSR 	AGCAGCTGTCCACAACTTCCCCCCCCCCCCCCCCCCCCCCCCCAAACAACAAAAGCAGGC
                       		 . **.* .. *** .********** *.. **                   

L. major Chr1 SSR 	--------aacagccccccccctccaggtacaggt-------------------------
L. major Chr1 SSR TIS 	--------AACAGCCCCCCCCCTCCAGGTACAGGT-------------------------
H. muscarum Scaf40 SSR 	ACAGCAAGAACGGCGAATCCCGCCCACGTATGCATGCCTATGTAAAGGGGAAAAGCTCGC
                     		***.**   .*** .*** ***.. .*                         

L. major Chr1 SSR 	-----------------------------------tgcctccgagatcggtcacagaagg
L. major Chr1 SSR TIS 	-----------------------------------TGCCTCCGAGATCGGTCACAGAAG-
H. muscarum Scaf40 SSR 	CAACATCTCTGCAGTGGTCGCTGATGCTCATTGTGTGTTTTTGTGCCCAGGCCCAGCAA-
                            		                   **..*..* * .*.* * *** *. 

L. major Chr1 SSR 	tgtgcgacacactttgtcggctgcgggaca-----------------------ccacgtg
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR	-ACACAGAGTCATTTTCCAACTAAAAGACAAATATTGATGATGAGCAGAAAGTCATAGTG
                                                                            

L. major Chr1 SSR 	agaagaactgtctgtgcagcgaaccggataaagccagcaag----------ctgtattct
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	ACAACCACTTGTCATACGAAAGAAGAGATCTGGCCATGAAGACTGGCGGCACTGCGATGC
                                                                            

L. major Chr1 SSR 	tctgcgagcaggaaaccgcagcatttt----------------cactgtttcagcgccga
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	GTCGTAGTAAAGGTGCACCAATAGTTTGGTATGGGTCACAAGACACTCATTTGGCACTCC
                                                                            

L. major Chr1 SSR 	a---catgagacccaca----agcgaaaaaaaaagcagataaaaacacaaagtattgcag
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	ACCCCACAAAACACACGTTCTGCCCAATAAAACGACCAGCCGGGGTCCAGAGCTGCCTAA
                                                                            

L. major Chr1 SSR 	cttaaccttctttcgatgtgacgtcattttac----------------------------
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	CTCACCTTCTGTTCCAAATCACCGCCGCCCCCCCCCCCCCCACACCCCCCACCCCCACTC
                                                                            

L. major Chr1 SSR 	-------------------------------------------------tgtcgcgggta
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	CCCCAGACGGGAGCATTGGCGACTTGTAAATGTGTGTGGCGAGGATGCATGCCGTGCAAG
                                                                            

L. major Chr1 SSR 	gaagctgac-----tacattctttgttaaaaatacgatggcgcttttttatgtatgaaga
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	GGGGTTGACATTTATAAATCCTCCACTAACGCCAAAATGGCACCGATACATGGTTCATTT
                                                                            

L. major Chr1 SSR 	gtctccttgatcaccaatgcaaaaaaacaaattcgttgaacgtggtgccgacgagcagac
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	GAGTCCATCGCCATCCCCAAGACTGGGAACATTTACTAGTGATG--GACGAATAGCTTTA
                                                                            

L. major Chr1 SSR 	tagcttcgcacctcaatcgactccagtccctttaattttctcgagccctccctttctttt
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	TGGAAAAGCACCGCCACCATCACCTGAAAATATAATAAGCATGATACCAGCTTTATTGTT
                                                                            

L. major Chr1 SSR	-----------cggaccctatttcggc----aaaatcacagcacgcata-----------
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	GCCTCAAAATGTAGAGCCTAATTAACTTCCAACAACTGCCATACGCCTAACCTCTTTCTC
                                                                            

L. major Chr1 SSR 	----cacgcacacaaat-----gaaagatagggtttacaaaagccctgttcg--------
L. major Chr1 SSR TIS 	------------------------------------------------------------
H. muscarum Scaf40 SSR 	ACCCCGTATATATTAACCTGTGAAGAAATATCTTTTTTAGGAAAATTGATTACCGATTGA
                                                                            

L. major Chr1 SSR 	------tcttttccaattatagaattccgagtgctgtt
L. major Chr1 SSR TIS 	--------------------------------------
H. muscarum Scaf40 SSR 	TTCTATTCTCTTCCACACTCAAAACACGA---------