first base of sequence is at -32 with respect to the ATG of start site of At1g10010 start site of At1g10010

Plantegenet, Weber et al., 5 sequence alignments for stably heritable ELP and control genes. Sequences represent the Crick strand for the 5 region of the respective genes, i.e. they start with the base closest to the ATG, extending into the 5 regulatory regions; nomenclature: At1g10010-ATG At1g10010-ATG-32 At1g10010-leader At1g10010-leader-23 At1g10010-E At1g10010-L first base of sequence is at -1 with respect to the ATG of At1g10010 first base of sequence is at -32 with respect to the ATG of At1g10010 first base of sequence is at -1 with respect to the transcription start site of At1g10010 first base of sequence is at -23 with respect to the transcription start site of At1g10010 sequence from Eil-0 sequence from Lc-0

ELPs with simple inheritance

At1g05830-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:38 2 Sequences Aligned Alignment Score = 5796 Gaps Inserted = 3 Conserved Identities = 836 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g05830-E.ab1 vs. At1g05830-L.ab1 Aligned Length = 782 Gaps = 2 Identities = 769 (98%) At1g05830-E.ab1 1 TTCAAGGAAGAGAGTAAGAAAGTTGTTGGGTTAATTGAAATTGAAATTGT 50 At1g05830-L.ab1 1 TTCAAGGAAGAGAGTAAGAAAGTTGTTGGGTTAATTGAAATTGAAATTGT 50 At1g05830-E.ab1 51 TAGGTTTTGAAGGATGTCGAGAATTAGGGTTTTAGAGAAAGAGGGATGGT 100 At1g05830-L.ab1 51 TAGGTTTTGAAGGATGTCGAGAATTAGGGTTTTAGAGAAAGAGGGATGGT 100 At1g05830-E.ab1 101 TTTGAGAGAAGAGCTGCTCTTCCTCCAAAAATATCCGTTTTCCCGCCGGC 150 At1g05830-L.ab1 101 TTTGAGAGAAGAGCTGCTCTTCCTCCAAAAATATCCGTTTACCCGCCGGC 150 **************************************** ********* At1g05830-E.ab1 151 TAAAATTAACCAGTAGAGAGTTCTTCTTCTTCTTTCTTCTTCCAGATCTG 200 At1g05830-L.ab1 151 TAAAATTAACCAGTAGAGAGTTCTTCTTCTTCTTTCTTCTTCCAGATCTG 200 At1g05830-E.ab1 201 CTCTTCCCAAACTTTTTAATAACCTCTGTTTATGTGTAAACAAGACACGA 250 At1g05830-L.ab1 201 CTCTTCCCAAACTTTTTAATAACCTCTGTTTATGTGTAAACAAGACACGA 250 At1g05830-E.ab1 251 CGCCGTTTTGCCTGAAGATTCTCTTTTAATCGAATCTGTCTCTTGTTGTC 300 At1g05830-L.ab1 251 CGCCGTTTTGCCTGAAGATTCTCTTTTAATCGAATCTGTCTCTTGTTGTC 300 At1g05830-E.ab1 301 TTAATGATAAGTGTCAGTTCCAGTTCCAGTTCCTAAAAATTATAGTTTGA 350 At1g05830-L.ab1 301 TTAATGATAAGTGTCAGTTCCAGTTC------CTAAAAATTATAGTTTGA 344 ************************** ****************** At1g05830-E.ab1 351 TCCAAATTCTTTCGGTTTATCTATATTTGAACTTGGAAACTTTTCAAATC 400 At1g05830-L.ab1 345 TCCAAATTCTTTCGGTTTATCTATATATGAACTTGGAAACTTTTCAAATC 394 ************************** *********************** At1g05830-E.ab1 401 CTTATTAAAGCTGGTTTTATATTTTTTTGAGGGGAAAAAAAAATTCAAAT 450 At1g05830-L.ab1 395 CTTATTAAAGCTGGTTTTATATTTTTTTGAGGGGAAAAAAAAATTCAAAT 444 At1g05830-E.ab1 451 TCGTATTTGTACAGTATACAAAAACTTGTTCATTTCAGAATCAGAAGTTG 500 At1g05830-L.ab1 445 TCGTATTTGTACAGTATACAAAAACTTGTTCATTTCAGAATCAGAAGTTG 494 At1g05830-E.ab1 501 TTGATTGTGTGTATGTATACATATACATTACATTATATACGTTTTGGTGG 550 At1g05830-L.ab1 495 TTGATTGTGTGTATGTATACATATACATTACATTATATACGTTTTGGTGG 544 At1g05830-E.ab1 551 GCTCGAGACTACATGTGTATGCACAAAAGTGTATATTTCTTATAATTTTT 600 At1g05830-L.ab1 545 GCTCGAGACTACATGTGTATGCACAAAAGTGTATATTTCTTATAATTTTT 594 At1g05830-E.ab1 601 TATGTGCAAAAGAAAAATTGTTTCTGTTTTGATGTTTCTTCTTCTTGTTC 650 At1g05830-L.ab1 595 TATGTGCAAAAGAAAAATTGTTTCTTTTTTGATGTTTCTTCTTCTTGTTC 644

At1g05830-ATG Pairwise Alignments Page 2 Thursday, November 22, 2007 16:38 ************************* ************************ At1g05830-E.ab1 651 TTCAGTCTCCAGAGTTTTGAGTTATGTATGTTGAAGC---TTATGCTTCT 697 At1g05830-L.ab1 645 TTCAGTCTCCAGAGTTTTGAGTTATGTATGTTGAAGCAATTTATGCTTCT 694 ************************************* ********** At1g05830-E.ab1 698 GGAGATGGATTTACTTCTGCAGCTGAAGGCTGTTGAGTCCCGTAGTTCCA 747 At1g05830-L.ab1 695 GGAGATGGATTTACGTCTGCAGCTGAAGGCTGTTGAGTCCCGTAGTTCCA 744 ************** *********************************** At1g05830-E.ab1 748 CAAGTCTCTGAGTTCTTTCCTCACCAACCCTA 779 At1g05830-L.ab1 745 CAAGTCTCTGAGTTCTTTCCTCACCAACCCTA 776 ********************************

At1g07310-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:38 2 Sequences Aligned Alignment Score = 5859 Gaps Inserted = 2 Conserved Identities = 842 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g07310-E.ab1 vs. At1g07310-L.ab1 Aligned Length = 739 Gaps = 0 Identities = 739 (100%) At1g07310-E.ab1 1 GAATACGGTGCGTTTCAAGACGAGACGGTGGCTTACGCGGTGGTCTTAGC 50 At1g07310-L.ab1 1 GAATACGGTGCGTTTCAAGACGAGACGGTGGCTTACGCGGTGGTCTTAGC 50 At1g07310-E.ab1 51 TAACGTGCGCTCGTATCTCAAATATCTGTATCAAAGTCTCAGCTATCATC 100 At1g07310-L.ab1 51 TAACGTGCGCTCGTATCTCAAATATCTGTATCAAAGTCTCAGCTATCATC 100 At1g07310-E.ab1 101 AACTATCATCGTTTTATCACAGAGTTTTATGTCTCAAAAAACCTGCTGGC 150 At1g07310-L.ab1 101 AACTATCATCGTTTTATCACAGAGTTTTATGTCTCAAAAAACCTGCTGGC 150 At1g07310-E.ab1 151 TATATAAGAGGCTTTTGACTTTTGGAGTTTGACTCTTTCTTACTAGCGAC 200 At1g07310-L.ab1 151 TATATAAGAGGCTTTTGACTTTTGGAGTTTGACTCTTTCTTACTAGCGAC 200 At1g07310-E.ab1 201 AGCTGGAGTTATTCATGAACAGGATAGTTATATCCTTATGTCCAAACAGA 250 At1g07310-L.ab1 201 AGCTGGAGTTATTCATGAACAGGATAGTTATATCCTTATGTCCAAACAGA 250 At1g07310-E.ab1 251 TGCATAAATTCTCACCAAGCACAAGATAGGCATTTGAAGAGTGGATAACA 300 At1g07310-L.ab1 251 TGCATAAATTCTCACCAAGCACAAGATAGGCATTTGAAGAGTGGATAACA 300 At1g07310-E.ab1 301 CTTTCTCAGTCTTTCTTCTTCTTCTTCGTTGTGATAGGTCAGGTCAGGGA 350 At1g07310-L.ab1 301 CTTTCTCAGTCTTTCTTCTTCTTCTTCGTTGTGATAGGTCAGGTCAGGGA 350 At1g07310-E.ab1 351 ACAACAATGGCTTCTTCTGCAACAGCACCAAATTCGCTATCTTTCTTCTC 400 At1g07310-L.ab1 351 ACAACAATGGCTTCTTCTGCAACAGCACCAAATTCGCTATCTTTCTTCTC 400 At1g07310-E.ab1 401 ATCTTCTCTCTTTTTATCCTCCTCTCACCAAATCCCTAAAACCTACATTT 450 At1g07310-L.ab1 401 ATCTTCTCTCTTTTTATCCTCCTCTCACCAAATCCCTAAAACCTACATTT 450 At1g07310-E.ab1 451 CCGTTTCAAAACTCGGCTCCGGCAGAGTCTCGAAGCCGCTTTCTGTCTCT 500 At1g07310-L.ab1 451 CCGTTTCAAAACTCGGCTCCGGCAGAGTCTCGAAGCCGCTTTCTGTCTCT 500 At1g07310-E.ab1 501 TCCCAGCTAGCGACTCTACCGATTCTATCATTCGAAGGAGAGAAGGTCGG 550 At1g07310-L.ab1 501 TCCCAGCTAGCGACTCTACCGATTCTATCATTCGAAGGAGAGAAGGTCGG 550 At1g07310-E.ab1 551 AGAGACGTATCTAGACCTCAAAGCGGCGCCGGAGGATACCGCGCGTGCCG 600 At1g07310-L.ab1 551 AGAGACGTATCTAGACCTCAAAGCGGCGCCGGAGGATACCGCGCGTGCCG 600 At1g07310-E.ab1 601 TTGTGCACCGAGCCATCGTGACGGACCTGAATAACAAGCGGCGAGGTACT 650 At1g07310-L.ab1 601 TTGTGCACCGAGCCATCGTGACGGACCTGAATAACAAGCGGCGAGGTACT 650

At1g07310-ATG Pairwise Alignments Page 2 Thursday, November 22, 2007 16:38 At1g07310-E.ab1 651 GCTTCCACACTGACTCGCGGTGAAGTTCGTGGTGGTGGAATTAAACCTTA 700 At1g07310-L.ab1 651 GCTTCCACACTGACTCGCGGTGAAGTTCGTGGTGGTGGAATTAAACCTTA 700 At1g07310-E.ab1 701 CTCACAGAAGAAAACTGGCCACGCGAGGCGTGGATCTCA 739 At1g07310-L.ab1 701 CTCACAGAAGAAAACTGGCCACGCGAGGCGTGGATCTCA 739 ***************************************

At1g13650-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:38 2 Sequences Aligned Alignment Score = 4081 Gaps Inserted = 219 Conserved Identities = 603 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 0.0 Extend Gap Penalty = 0.0 Processing time: 0.3 seconds 1. At1g13650-E.ab1 vs. At1g13650-L.ab1 Aligned Length = 972 Gaps = 215 Identities = 566 (69%) At1g13650-E.ab1 1 TCTCAAGAAATTTTATCCTTTTACCACCACGAAAACACCACCCCTGTATT 50 At1g13650-L.ab1 1 TCTCAAGAAATTTTATCCTTTTACCACCACGAAAACACCACCCCTGTATT 50 At1g13650-E.ab1 51 AGGAAAAACAAGTGGATTAGTTCTAAAAAATCTTCGGAAAACACAATCAA 100 At1g13650-L.ab1 51 AGGAAAAACAAGTGGATTGGTTCTAAAAAATCTTCGGAAAACACAATCAA 100 ****************** ******************************* At1g13650-E.ab1 101 GAATAGAAGGTAATCTAACAAACAAAGAACAAGATTGTCTCAATTTGTAA 150 At1g13650-L.ab1 101 GAATAGAAGGTAATCTAACAAACAAAGAACAAGATTGTCTCAATTTGTAA 150 At1g13650-E.ab1 151 CTTGAAGGTAACCTGAATCTCTTAACT--A--G--TGT-T-TTT--T-TG 189 At1g13650-L.ab1 151 CTTGAAGGTAACCTGAATCTCTTAACTGTAAAGGATGTATATTTGATATA 200 *************************** * * *** * *** * * At1g13650-E.ab1 190 CTCTGGATAGTCAA-G-GTGT-TTCA---CTC-TCTACT-TATAAGGAGT 231 At1g13650-L.ab1 201 -T-T--ATA--CAAAGAG-ATA--CAGAGCTTGTTTA-TATACAAGAAGT 240 * * *** *** * * * ** ** * ** * ** *** *** At1g13650-E.ab1 232 ---C--A--CCTT-C--TT-TAC--C--CT--AAT--C--A---TCA-TG 256 At1g13650-L.ab1 241 AGGCGTAAGCCTCACGATTATGCAATAACTGTAATTTCCTAAACT-AGTG 289 * * *** * ** * * ** *** * * * * ** At1g13650-E.ab1 257 A--TA-AGGT-TCTCCAAGTGCTTC-AATC-CTGATTCTCATTAGGAT-T 299 At1g13650-L.ab1 290 AACTAGAA-TAT-T--GAGTA-T-CGAATCA-T-AT-CTC-TT-G-ATGT 327 * ** * * * * *** * * **** * ** *** ** * ** * At1g13650-E.ab1 300 ACGCC--CCA-A-CTTTTAA-A-ACC-------G-TA-AGA--TT--ATA 330 At1g13650-L.ab1 328 AT-CTAATCATATCTCTTGATACACCCCCTCNAGATGGAGAGGTTGCA-A 375 * * ** * ** ** * * *** * * *** ** * * At1g13650-E.ab1 331 --A-TCCAA-CT-G-CT-T-A-AT---CAAAC-GATACACGTGGAAATAA 367 At1g13650-L.ab1 376 CCACTCCAATCTTGTCTCTGAGATAAATAAACTG-TGCACGTG-A---GA 420 * ***** ** * ** * * ** **** * * ****** * * At1g13650-E.ab1 368 GATAAGATTTT-TGCAATCTGCAGTTCTGC-ACTTGTATGCAAG-GCC-G 413 At1g13650-L.ab1 421 G-C--GGTTTCGT-CAAT--GC-GT-CTGCGA---GT-TG---GT-CCT- 453 * * *** * **** ** ** **** * ** ** * ** At1g13650-E.ab1 414 CATG-ACTGGTATAGAAGGAAAGCA-ACTAA-AACCATC-GATTCGGGCC 459 At1g13650-L.ab1 454 T-TGTATTGACAT-GA-G-AGA-CACGC-AATG-C--TCCGA--CG---- 488 ** * ** ** ** * * * ** * ** * ** ** ** At1g13650-E.ab1 460 TCAAAATTTAGTAATTAAAACCCC-CAAC-TAAA-GATATATTGTGA-AA 505 At1g13650-L.ab1 489 T-GAA-TCT-GT--------CCTCGCA-CG-AAATGGTA-ATC--GACAG 522 * ** * * ** ** * ** * *** * ** ** ** * At1g13650-E.ab1 506 AAACCCCTTAAT-TATTT-ATT--TAA-TGAAAAAATACCTGAAGTTTAA 550 At1g13650-L.ab1 523 ------C--AATGTGCTTCATCCGTGAGTGGAAA---AC-TGGA-TT-G- 557

At1g13650-ATG Pairwise Alignments Page 2 Thursday, November 22, 2007 16:38 * *** * ** ** * * ** *** ** ** * ** At1g13650-E.ab1 551 AATTATTTGTGAA-AAC-CA-CCCGCCGTCTACAGTACTGTCA-AAATAA 596 At1g13650-L.ab1 558 -GC-AC--AT-AAGAACGTAGC--ACCG---ACA-T--TGTCGCAG-TAA 593 * * ** *** * * *** *** * **** * *** At1g13650-E.ab1 597 A--AC-GATGTGT-TTTAA--A-TATAAAAAAATA--ACATGTTTT-TTT 636 At1g13650-L.ab1 594 ACTACCGGTG-GTGT--AGGGAGT-TGA---A-TGCCA-A-GTTCTG--T 631 * ** * ** ** * * * * * * * * * * *** * * At1g13650-E.ab1 637 GCTTAAAACAACACG-AAATAAA-CAAAAAAACAACACGAAGTTCTTATA 684 At1g13650-L.ab1 632 G---AGGATG-T-TGCA--T--ATC-------CAAC-TGA-GTTCT---G 660 * * * * * * * * **** ** ***** At1g13650-E.ab1 685 C--C--TTATTA-TAA-A-CCCCTAAATCCACTTTAGCT-C--TTAAATC 724 At1g13650-L.ab1 661 CGGCGGT-ATTAGCGACAGCCC-TA--T--ACTCT-GCTTCGGTTGAA-- 701 * * * **** * * *** ** * *** * *** * ** ** At1g13650-E.ab1 725 GACGACNTTG--A-A--ATC-GCGAAATTT-T--G-TAG--AC-TGA-AT 760 At1g13650-L.ab1 702 GAC--C-TTGCCACACCATTT-TG---TTTCTTCGCT-GTC-CATGAGAT 742 *** * *** * * ** * *** * * * * * *** ** At1g13650-E.ab1 761 -GCGGCTGGA-G--CTT-G-CAA--GATGTTAAGGTAACT-GT--TACA- 798 At1g13650-L.ab1 743 AG-GG--GGAAGAGCCTAGATAAACGATGT-A-GGCA-TTTGTGG-ACAC 785 * ** *** * * * * ** ***** * ** * * ** *** At1g13650-E.ab1 799 A-GA-CATTC-T-T-ATN 811 At1g13650-L.ab1 786 ACAATCATTTATGTCACCAGCC 807 * * **** * * *

At1g14120-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:39 2 Sequences Aligned Alignment Score = 5606 Gaps Inserted = 4 Conserved Identities = 827 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g14120-E.ab1 vs. At1g14120-L.ab1 Aligned Length = 811 Gaps = 2 Identities = 795 (98%) At1g14120-E.ab1 1 TATCTTCATGAAAAGGCTTTTCTCTAGTCAAGCAATTTGGACAGCTAAAA 50 At1g14120-L.ab1 1 TATCTTCATGAAAAGGCTTTTCTCTAGTCAAGCAATTTGGACAGCTAAAA 50 At1g14120-E.ab1 51 ACAGTCATCAGAGAAAAAAGAATTACATATAAGTCGAAGAAACCCTAGCA 100 At1g14120-L.ab1 51 ACAGTCATCAGAGAAAAAAGAATTACATATAAGTCGAAGAAACCCTAGCA 100 At1g14120-E.ab1 101 ATGATGAGTTTTCAGAAATGGTTTATTTTCTTTATATGATCTACTCAAAG 150 At1g14120-L.ab1 101 ATGATGAGTTTTCAGAAATGGTTTATTTTCTTTATATGATCTACTCAAAG 150 At1g14120-E.ab1 151 AGTTTTCAGAAATCAGAAATAAAGAGTACCTTAATTTCGTCGGGATCCTT 200 At1g14120-L.ab1 151 AGTTTTCAGAAATCAGAAATAAAGAGTACCTTAATTTCGTCGGGATCCTT 200 At1g14120-E.ab1 201 ATTAATTATCTCTAGATTTCTCGAGAAAAACGAAGGAGTAAATGTATTGT 250 At1g14120-L.ab1 201 ATTAATTATCTCTAGATTTCTCGAGAAAAACGAAGGAGTAAATGTATTGT 250 At1g14120-E.ab1 251 AAGATGACTTATCGAAGGCGAGATTATTATATAAAGAAGTCGAAGTATTT 300 At1g14120-L.ab1 251 AAAATGACTTATCGAAGGCGAGATTATTATATAAAGAAGTCGAAGTATTT 300 ** *********************************************** At1g14120-E.ab1 301 TCGACCATGCACAGAAGTCTGCCGTAGTAATTAATAAAATACTCTCCACG 350 At1g14120-L.ab1 301 TCGACCATGCACAGAAGTCTGCCGTAGTAATTAATAAAATACTCTCCACG 350 At1g14120-E.ab1 351 CTTTCCACGTGAATGTGACACTACGGGCATAATGTGGTTCCTTT-----G 395 At1g14120-L.ab1 351 CTTTCCACGTGAATGTGACACTACGGGCATAATGTGGTTCCTTTAATTTG 400 ******************************************** * At1g14120-E.ab1 396 TGTTAACATCATATAGATACATCATACATGCAAATACGAATTTGCATAGG 445 At1g14120-L.ab1 401 TGTTAACATCATATAGATACATCATACATGCAAATACGAATTTGCATAGG 450 At1g14120-E.ab1 446 GATGCAACTATTAGAGTCAACCGGTAAAACAAAAATGAAAGATATTGGTT 495 At1g14120-L.ab1 451 GATGCAACTATTAAAGTCAACCGGTAAAACAAAAATGAAAGATATTGGTT 500 ************* ************************************ At1g14120-E.ab1 496 CCTTTGTTTTTGAAAGATATAAGAAGACAACGCAACGCCACCTCTTAGCG 545 At1g14120-L.ab1 501 CCTTTGTTTTTGAAAGATATAAGAAGACAACGCAACGCCACCTCTTAGCG 550 At1g14120-E.ab1 546 GTTTGAGATACATGTGGCGTCATGGGCCGGATCTAGAGCCACCAAGGAAG 595 At1g14120-L.ab1 551 GTTTGAGATAAATGTGGCGTCATGGGCCGGATCTAGAGCCACCAAGGAAG 600 ********** *************************************** At1g14120-E.ab1 596 GTGCATCTGCCTCCTATGCATTTTAGATATCCAACTACTCTTAAAGCTGC 645 At1g14120-L.ab1 601 GTGCATCTGCCTCCTATGCATTTTAGATATCCAACTACTCTTAAAGCTGC 650

At1g14120-ATG Pairwise Alignments Page 2 Thursday, November 22, 2007 16:39 At1g14120-E.ab1 646 ACGCCGATGGTTCTTGCATAATTTGTGCCAACACATACA----CACAATA 691 At1g14120-L.ab1 651 ACGCCGATGGTTCTTGCATAATTTGTGCTAACACATACATGAACACAATA 700 **************************** ********** ******* At1g14120-E.ab1 692 TGCAAAAATTAGTTCTTGTTACTGGCCAAGTAGATCAATCTACCAATGGT 741 At1g14120-L.ab1 701 TGCAAAAATTAGTTCTTGTTACTGGCCAAGTAGATCAATCTACCAATGGT 750 At1g14120-E.ab1 742 TTGGAGATAAGGCTCAGGATCAAGTACAAGTGGCGATTTGGGACCCAACC 791 At1g14120-L.ab1 751 TTGGAGATAAGGCTCAGGATCAAGTACAAGTGGCGATTTGGGACCAAACC 800 ********************************************* **** At1g14120-E.ab1 792 AGGCTGGTTAC 802 At1g14120-L.ab1 801 AGGCTATTTAC 811 ***** ****

At1g24240-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:39 2 Sequences Aligned Alignment Score = 4797 Gaps Inserted = 9 Conserved Identities = 740 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.3 seconds 1. At1g24240-E.ab1 vs. At1g24240-L.ab1 Aligned Length = 560 Gaps = 6 Identities = 481 (89%) At1g24240-E.ab1 1 TTCTCCGCAAAGGAATCGATCTATGCGATCACAAATATCCAAAA-GCTTT 49 At1g24240-L.ab1 1 TTCTCCGCAGCGGAATCGATCTATACGATCACAAATATCCAAAAAGCTTT 50 ********* ************* ******************* ***** At1g24240-E.ab1 50 CAGAGATTTTG--AGA------------AAAACAAATCCCTTGTCATTGC 85 At1g24240-L.ab1 51 CAGAGATTTTGCCGGAGTTTGAACTTACAAAACAAAACCCTTGTCATTGC 100 *********** ** ******** ************* At1g24240-E.ab1 86 TCCTTCAGGTTTCTTTATTTTTGTTTTGGTAATTTGCATATATACCCCTG 135 At1g24240-L.ab1 101 TCCTTCAGGTTTCTTTATTTTTGTTTTGGTAATTTGCATATAAACCCCTG 150 ****************************************** ******* At1g24240-E.ab1 136 ATATTTTTTGCTTTTATCAAATACATCCTTTCTTTTTTCTTTGACATCTT 185 At1g24240-L.ab1 151 ATATTTTTTGCTTTCATCAAATACATCCTTTCTTTTTTCTTTGACTTCTT 200 ************** ****************************** **** At1g24240-E.ab1 186 CTTGCTAGAAAGAGTTTAGTGTGATGCTTATTGTATAGAGAACAGAACAT 235 At1g24240-L.ab1 201 CTTGCTAGAAAGAGTTTAGTGTGATGCTTATT------------------ 232 ******************************** At1g24240-E.ab1 236 CATTACATACATGCACTTACAATAAAACTCTTGTCTATCCATGTAG---- 281 At1g24240-L.ab1 233 ----ACATACATGCACTTACAAAAAAACTCATGTTTATCCATGTAGTCAT 278 ****************** ******* *** *********** At1g24240-E.ab1 282 ----AAATCATAATCTAAAATAATTCAAAACAAAATCGATATGACCTCAT 327 At1g24240-L.ab1 279 GTAGAAATCATAATCCAAAATAATTCAAAACAAAATCGATATGACCTCAT 328 *********** ********************************** At1g24240-E.ab1 328 ATGAAAACCTCAATGTTAACAAAAAAAAAA--CATTGAGGTGAAAAATGA 375 At1g24240-L.ab1 329 ATGAAAACCTCAATGTTAACAAAAAAAAAAAATATCGAGGTGTAAAAGGA 378 ****************************** ** ****** **** ** At1g24240-E.ab1 376 TTGTATTGTTTCATATATTATAGAGATTTGAATTCAGGTCGATTCTTCTT 425 At1g24240-L.ab1 379 TTGTAGGGTTTCATATATAAAAGAGGTTTGAATTCGGGTCGATTCTTCTT 428 ***** *********** * **** ********* ************** At1g24240-E.ab1 426 CTGGCATGTACATATATGATTTTTGGTTTGGGGTCATATTTGTTAGAAAC 475 At1g24240-L.ab1 429 CGGGCAGGAACATATATGATTTTGGGTTGGGGGTCATATTTGTTAAAAAC 478 * **** * ************** **** **************** **** At1g24240-E.ab1 476 CGAGAGGCGAGAGTGTAAGCACTCAAAAGTCAAAGCAGAGTTCAACGTAT 525 At1g24240-L.ab1 479 CGAGAGGCGAGAGTGTAAGCCCTCAAAAGTCAAAGCAAAGTTCAACGTAT 528 ******************** **************** ************ At1g24240-E.ab1 526 AGACGAAAAC 535 At1g24240-L.ab1 529 AGCCAAAAAC 538 ** * *****

At1g27190-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:39 2 Sequences Aligned Alignment Score = 5217 Gaps Inserted = 10 Conserved Identities = 789 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g27190-E.ab1 vs. At1g27190-L.ab1 Aligned Length = 228 Gaps = 0 Identities = 228 (100%) At1g27190-E.ab1 1 GATTAAGGATGGATCTAGTTCTTCTTCTTAGGTTAAAAAGCAGAGAGAGC 50 At1g27190-L.ab1 1 GATTAAGGATGGATCTAGTTCTTCTTCTTAGGTTAAAAAGCAGAGAGAGC 50 At1g27190-E.ab1 51 TTCTATGGCGGAAGAAGAATGGTCATTGACTGTGTGATACTGTTGAGAAA 100 At1g27190-L.ab1 51 TTCTATGGCGGAAGAAGAATGGTCATTGACTGTGTGATACTGTTGAGAAA 100 At1g27190-E.ab1 101 AGATGAGAAACTTTTTTTTTTTGTTGCCCTTTTGACCCTTTTTTTTTTTA 150 At1g27190-L.ab1 101 AGATGAGAAACTTTTTTTTTTTGTTGCCCTTTTGACCCTTTTTTTTTTTA 150 At1g27190-E.ab1 151 AAAACCTTAGGGAAAATTAATTTTTTCCTTTTGTTGGGGAAAAAAAAACC 200 At1g27190-L.ab1 151 AAAACCTTAGGGAAAATTAATTTTTTCCTTTTGTTGGGGAAAAAAAAACC 200 At1g27190-E.ab1 201 TCCTTCCAAACCCCCCCCTTTGGAAAAC 228 At1g27190-L.ab1 201 TCCTTCCAAACCCCCCCCTTTGGAAAAC 228 ****************************

At1g27570-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:39 2 Sequences Aligned Alignment Score = 5088 Gaps Inserted = 9 Conserved Identities = 743 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g27570-E.ab1 vs. At1g27570-L.ab1 Aligned Length = 521 Gaps = 4 Identities = 496 (96%) At1g27570-E.ab1 1 GCTTGCGGGGCCTACTTTTGGGTTTTTCAGGTTGAAGAAGAGAAAAATCT 50 At1g27570-L.ab1 1 GCTTGCGGGGCCTACTTTTGGGTTTTTCAGGTTGAAGAAGAGAAAAATCT 50 At1g27570-E.ab1 51 TGGCGACACAGAAGCAGCGGACAGTGACAGTGACAGTGACAG------AG 94 At1g27570-L.ab1 51 TGGCGACACAGAAGCAGCGGACAGTGACAGTGACAGTGACAGTGACAGAG 100 ****************************************** ** At1g27570-E.ab1 95 CAATTTACGCATAGACAAAATTGCTGGATAAGAGGAAACACTAGGCCTGG 144 At1g27570-L.ab1 101 CAATTTACGCATAGACAAAATTGCTGGATAAGAGGAAACACTAGG----- 145 ********************************************* At1g27570-E.ab1 145 GAGTTCGGTTAAACCGGGTTATTCGGGTCGGGTTATTCGGTTTGGTGGAA 194 At1g27570-L.ab1 146 -AGTTCGGTTAAACCGGGTTATTCGGGTCGGGTTATTCGGTTTGGTGGAA 194 ************************************************* At1g27570-E.ab1 195 ATTCGGTTTTTTAAAAATCTCACCGAATAGACCCGAATTGAAATTCGGTT 244 At1g27570-L.ab1 195 ATTCGGTTTTCTAAAAATCTCACCGAATAGACCCGAATTGAAATTCGGTT 244 ********** *************************************** At1g27570-E.ab1 245 CAGGTCGGTTCGGACGTCGGTTTGTTCGGGTCGGTTATAGCCTAAAAAAT 294 At1g27570-L.ab1 245 CGGGTCGGTTCGGACGTCGGTTTGTTCGGGTCGGTTATAGCCTAAAAAAT 294 * ************************************************ At1g27570-E.ab1 295 ATTTTTCGAATATGAATTAAATTCTTTTTTTT-CTTCGGTTTATCCGGTT 343 At1g27570-L.ab1 295 ATGTTCCGAATATGAACCAAATTCTTTTTTTTTCTTCGGTTTATCCGGTT 344 ** ** ********** ************** ***************** At1g27570-E.ab1 344 TACACATTAAAAAAAAAATTGGTCTATTACAAATACAACAAAATAAAAGC 393 At1g27570-L.ab1 345 TACACATTAAAAAAAAAATTGGTCTATTACAAATCCAACAAATTAAAAGC 394 ********************************** ******* ******* At1g27570-E.ab1 394 CCAATACACTTAACAAAACCCAACATACAATCAATAAGCCCAACCCACAA 443 At1g27570-L.ab1 395 CCAATACCCTTAACAAAACCCAACATACAATCAATAAGCCCAACCCACAA 444 ******* ****************************************** At1g27570-E.ab1 444 TTAATAAGCCCAGACTTGTAAAAATTTTAGGGTTTTGAAAAAGCTGTGTG 493 At1g27570-L.ab1 445 TTAATAAACCCAGACTTGTAAAAATTT-AGGGTTTTGAAAAAGCTGTGTG 493 ******* ******************* ********************** At1g27570-E.ab1 494 TAGTGTGACGGCTGCGACTCC 514 At1g27570-L.ab1 494 TAGTGTGACGGCTGCAACTCC 514 *************** *****

At1g31335-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:40 2 Sequences Aligned Alignment Score = 4082 Gaps Inserted = 28 Conserved Identities = 620 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.3 seconds 1. At1g31335-E.ab1 vs. At1g31335-L.ab1 Aligned Length = 614 Gaps = 24 Identities = 445 (73%) At1g31335-E.ab1 1 CGCATCTTGACTCTTGAGATCTAGATTCAATCTTCTTTCTGATTGATTTT 50 At1g31335-L.ab1 1 CGCATCTTGACTCTTGAGATCTAGATTCAATCTTCTTTCTGATTGATTTT 50 At1g31335-E.ab1 51 TATTCTTGGACTCTTGTTCTTGCTTTGATTCTACTTCAGATGTATTTATA 100 At1g31335-L.ab1 51 TATTCTTGGACTCTTGGTCTTGCTTTGATTCTACTTCGCATGTATGTATA 100 **************** ******************** ****** **** At1g31335-E.ab1 101 CT-----GTATGAG-TTTGTGGGAGGCTCATGGAAGGATCCGATTCTGTC 144 At1g31335-L.ab1 101 TTTATATGTATGAGATTTGTGGGAGGCTC-TGGAAGGATCCGATTCTGTC 149 * ******* ************** ******************** At1g31335-E.ab1 145 CGCAAACGTTTATGTCTTGAAAAGCTTTGAAGCGTAACGTTTAAATCTCA 194 At1g31335-L.ab1 150 CGCTA-CGTTTATGTCTTGTAAAGCTTGAAAGCTTAACGTTTAAATCTCA 198 *** * ************* ******* **** **************** At1g31335-E.ab1 195 ACGGTCATCTTTTTTTTGTGACGGCCCATCCATACGATTTCTTCTAGCTT 244 At1g31335-L.ab1 199 ACGGTCACCTTTTTTTGGT--CGGCCCATCCATACAATTTCTTCTAATTT 246 ******* ******** ** ************** ********** ** At1g31335-E.ab1 245 ACAGGAACACATTCGACATGTCCCATGAGCCCTTATGAGGGTGTGAACGT 294 At1g31335-L.ab1 247 TTATAGTCACATTAGTCATGTCGCATGTGCTTTTCTG--GCTATGAAAGT 294 * ****** * ****** **** ** ** ** * * **** ** At1g31335-E.ab1 295 ATAGATGAATCCGCCTCT---TTAATA--CCAACTTATATAGGAGA---A 336 At1g31335-L.ab1 295 ATAGA-GAATCAAACTCAAAGTTGACAAGTTAAGTTACTTAGAAAATTAA 343 ***** ***** *** ** * * ** *** *** * * * At1g31335-E.ab1 337 ATTCAAAACAGATAACTCAAATG-ACAA--GTTAAGTT--AC--TTAGAA 379 At1g31335-L.ab1 344 AGTAAAAATTGTTAAATGTGATGGACACTCATTGGATTTGACGATTTGTA 393 * * **** * *** * *** *** ** ** ** ** * * At1g31335-E.ab1 380 A----------ATTAAAGTAAAAATAACT-------TGTTA-------CA 405 At1g31335-L.ab1 394 ACCACTATTTCATTGTAATGCAAATAAATATGGGACTATTGATGGACTCA 443 * *** * * ****** * * ** ** At1g31335-E.ab1 406 TGTGAC--GCA------------CTAATTC-ATTGTA-ATGCAACCAG-- 437 At1g31335-L.ab1 444 TGCAACCAGCAATCTCAATCGGCCTGGTCCGATCTTACACATAGCTCGAT 493 ** ** *** ** * * ** ** * * * * At1g31335-E.ab1 438 --------CAAATGTCTAGCCTCTTTCTTGAATGAAAGATATTCATCATA 479 At1g31335-L.ab1 494 CCTATTTTCACATGTCTAGCCTCTTTCTTGAATGAAAGATATTCATCATA 543 ** *************************************** At1g31335-E.ab1 480 AATAGCTAAATCCCAAATAAATAAGTTTTAAGTATGATTCGATATTTAAA 529 At1g31335-L.ab1 544 AATAGCTAAATCCCAAATAAATATGTTA-AAGTACGATTCGATGTT-AAA 591 *********************** *** ***** ******** ** *** At1g31335-E.ab1 530 AAAAAAAAAAGGAT 543 At1g31335-L.ab1 592 CAAAACAAAATGAT 605

At1g31335-ATG Pairwise Alignments Page 2 Thursday, November 22, 2007 16:40 **** **** ***

At1g33040-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:40 2 Sequences Aligned Alignment Score = 5351 Gaps Inserted = 3 Conserved Identities = 800 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g33040-E.ab1 vs. At1g33040-L.ab1 Aligned Length = 810 Gaps = 2 Identities = 763 (94%) At1g33040-E.ab1 1 CTTTCTTCTTCTTTTCTTTCTTAGCGCAGCGAGACCTTCCTTAACAGTGA 50 At1g33040-L.ab1 1 CTTTCTTCTTCTTTTCTTTCTTAGCGCAGCAAGACCTTCCTTAACAGTGA 50 ****************************** ******************* At1g33040-E.ab1 51 GTGACAGATGAAACAAATAAAGTAGATAAATGATCCTCTGCTCCGCGGTT 100 At1g33040-L.ab1 51 GTGACAGATGAAACAAATAAAGTAGATAAATGATCCTCTGCTCCGCGGTT 100 At1g33040-E.ab1 101 CACTATAAACAAACCCAATGGTCGTCAATTAAAAGCCCATTGGGCCTCAG 150 At1g33040-L.ab1 101 CACTATAAACAAACCCAATGGTCGTCAATTAAAAGCCCATTGGGCCTCAG 150 At1g33040-E.ab1 151 TCTCAAAAACTTTGATTTGTTCTTTAGTTTACTTGGCGAATTTACGTACG 200 At1g33040-L.ab1 151 TCTCAAAAACTTTGATTTGTTCTTTAGTTTACTTGGCGAATTTACGTACG 200 At1g33040-E.ab1 201 TCTCCATGCCAGAATGGTCAAAAAAAAGAGAAGAAACTATTAGTCTAAAG 250 At1g33040-L.ab1 201 TCTCCATGCCAGAATGGTCAAAAAAAAGAGAAGAAACTATTAGTCTAAAG 250 At1g33040-E.ab1 251 AAATGAAGCATTCACAATTTGACCAGAATTGTCAAAAGCTTTTGCTTTGT 300 At1g33040-L.ab1 251 AAATGAAGCATTCACAATTTGACTAGAATTGACAAAAGCTTTTGCTTTGT 300 *********************** ******* ****************** At1g33040-E.ab1 301 TTCAGAGATTCAGGAAGCAAGAAAAATTTAGAAAATGGAAGAACAAAACC 350 At1g33040-L.ab1 301 TTCAGAGATTCAGGAAGCAAGAAAAATTTAGAAAATGGAAGAACAAAACC 350 At1g33040-E.ab1 351 TCTCCTCGTACGCAATGATCTTATCAAGCTCTTCTGTTCTTCCCATGGTT 400 At1g33040-L.ab1 351 TCTCCTCGTACGCAATGATCTTATCAAGCTCTTCTGTTCTTCCCATGGTT 400 At1g33040-E.ab1 401 CTTAAGACAGCCATTGATCTTGGTCTCTTTGACATATTATCTGAATCTGG 450 At1g33040-L.ab1 401 CTTAAGACAGCCATTGATCTTGGTCTCTTTGACATATTAGCTGAATCTGG 450 *************************************** ********** At1g33040-E.ab1 451 TCCTTCATCTGCTTCTCAGATCGTGTCTTTATTGTCTAATCAGACACAGA 500 At1g33040-L.ab1 451 TCCTTCCTCTGCTTCTCAGATCTTTTCTTTGTTGTCTAATGAGACAAAGA 500 ****** *************** * ***** ********* ***** *** At1g33040-E.ab1 501 AACATCATGATTCAAGCTTGGTCAATCGGATTCTTCGATTTCTTGCGAGT 550 At1g33040-L.ab1 501 AACATCATGATTCAAGCTTGGTCAATCGGATTCTGAGATTTCTTGCGAGT 550 ********************************** ************** At1g33040-E.ab1 551 TACTCCATAGTCACATGCTCTGTTTCTACTGACCACGGTGAGCCATTTGC 600 At1g33040-L.ab1 551 TACTCTATACTCACATGCTCTGTTTCTACTGAACACGGTGAGCCATTTGC 600 ***** *** ********************** ***************** At1g33040-E.ab1 601 GGTCTATGGCTTAGCTCCTGTTGCCAAGTACTTCACCAAGAACCAAA--- 647 At1g33040-L.ab1 601 AATCTATGGCTTAGCTCCTGTTGCCAAGTACTTCACCAAGAACCAAAATG 650

At1g33040-ATG Pairwise Alignments Page 2 Thursday, November 22, 2007 16:40 ********************************************* At1g33040-E.ab1 648 ---GTGGCTCCTTGGCTCCGTTGGTGAATTTGTTTCAGGACAAGGTCGTG 694 At1g33040-L.ab1 651 GAGGTGGATCGTTGGCTCCGATGGTGAATCTGTTTCAGGACAAGGTCGTG 700 **** ** ********* ******** ******************** At1g33040-E.ab1 695 ATTGATATGTGGTAACATCATTAACAACATCCTAACTCTTTTGTCTAAAA 744 At1g33040-L.ab1 701 ACTGATATGTGGTAACATCATTAACAACATCCTCACTCTTTCGTCTTAAA 750 * ******************************* ******* **** *** At1g33040-E.ab1 745 ACTTTATTATCTC---------ATGCAATCTGATGTCGTATCTAACTATG 785 At1g33040-L.ab1 751 ACGTTATCATCTTTGACTTGTTATGCAATCTGATGTTGTATTTACCTATA 800 ** **** **** ************** **** ** **** At1g33040-E.ab1 786 AAAAGGTACA 795 At1g33040-L.ab1 801 AAAAGGTACA 810 **********

At1g33480-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:40 2 Sequences Aligned Alignment Score = 5230 Gaps Inserted = 14 Conserved Identities = 755 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.3 seconds 1. At1g33480-E.ab1 vs. At1g33480-L.ab1 Aligned Length = 653 Gaps = 9 Identities = 569 (87%) At1g33480-E.ab1 1 CACCACACACAAGACAAAACTAGACAAGCAAAGTCTAAAAACCC-AAAAA 49 At1g33480-L.ab1 1 CACCACACACAAGACAAAACTAGACAAGCAAAGTCTAAAAACCCCAAAAA 50 ******************************************** ***** At1g33480-E.ab1 50 GTCTCCCCCTTTGAATGAAGAAACCAGAGATCCTCAAGATTCAAGATTGG 99 At1g33480-L.ab1 51 GTCTCCTCCTTTGAATGAAGAAACCAGAGATCGTCAAGATTCAAGATTGG 100 ****** ************************* ***************** At1g33480-E.ab1 100 AGTTATAAAAAAAACAATAAT-------GTGTGTGTGTGAGAGAGAAAGA 142 At1g33480-L.ab1 101 AGTTATAAAAAAAACAATAATTGAAATAATGTATGTGTGAGAGAGAAAGA 150 ********************* *** ***************** At1g33480-E.ab1 143 GAGATGTGGCAGAGGAGAGGTTTCAGGTGAAGCATTT-AGCTTTCAGTAT 191 At1g33480-L.ab1 151 GAGATGTGGCAGAGGAGAGGTTTCAGGTGAAGCATTTTAGCTTTCAGTAT 200 ************************************* ************ At1g33480-E.ab1 192 AGGGCAACTGTCTGTTTCCTTGTTATTTTTAAAGAGGAAAATTAAAAAA- 240 At1g33480-L.ab1 201 AGGGCAACTGTCTGTTTCCTTGTTATTTTTAAAGAGGAAAATTAAAAAAA 250 ************************************************* At1g33480-E.ab1 241 GTTCGGGGGCATTAATAATGAATTTGAGAGATTAT-GAAATGTTAGATAA 289 At1g33480-L.ab1 251 GTTAGGGGGCATTAATAATGAATTTGAGAGATTATTGAAATGTTAGATAA 300 *** ******************************* ************** At1g33480-E.ab1 290 CTTTTCCCGTAGATTCTGGCCGAACAAGCAAACAAGAAAACAAGAGGAGG 339 At1g33480-L.ab1 301 CTTTTCCCGTAGATTCTGGCCGAATAAGCAAACAAGAAAACAAGAGGAGG 350 ************************ ************************* At1g33480-E.ab1 340 GGGAACGTTATTACATGCACCGATCATAATCC--------GACGAATCCT 381 At1g33480-L.ab1 351 GGAAACGTTATTACTTGCACCGATCATAATCCATTAAACCGACAAATCCT 400 ** *********** ***************** *** ****** At1g33480-E.ab1 382 TCAT---------------------------------------ATTGTTC 392 At1g33480-L.ab1 401 TCATTTTGTTGGCCATCACCAAGTTGTCAACCTCAAGGTCTTGATTGTTC 450 **** ******* At1g33480-E.ab1 393 TCTTTTGTAAACAAATGGAGACACGTACCAGATTGCTTTTGTTTTTTCTC 442 At1g33480-L.ab1 451 TCTTTTGTAACCAAAGGGAGACACGTACCAGATTGCTTTTGTTTTTTCTC 500 ********** **** ********************************** At1g33480-E.ab1 443 TCTAGATTCATAAAGTA----TCCATAAAGAAGAACTACGACTTGGTTAG 488 At1g33480-L.ab1 501 TCTAGATTCATAAAGTACTTATCCATAAAGAAGAACAAGGACTTGGTTAG 550 ***************** *************** * *********** At1g33480-E.ab1 489 TTCAAGGGTACT---------CTTGAAAACATTCATTTGCCTTTCTCATT 529 At1g33480-L.ab1 551 TTCAAGGGTACTTTTGATTGTCTTGAAAACATTCATTTGCCTTTCTCATT 600 ************ ***************************** At1g33480-E.ab1 530 ATATATTTAGTTGGACATGAATATGAGTACATGACTTATCTTCTATATTT 579 At1g33480-L.ab1 601 ATATATTTAGTTGGACATGAATATGAGTACATGACTTATCTTCTATATTT 650

At1g33480-ATG Pairwise Alignments Page 2 Thursday, November 22, 2007 16:40 At1g33480-E.ab1 580 TCC 582 At1g33480-L.ab1 651 TCC 653 ***

At1g33960-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:40 2 Sequences Aligned Alignment Score = 5059 Gaps Inserted = 12 Conserved Identities = 754 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g33960-E.ab1 vs. At1g33960-L.ab1 Aligned Length = 360 Gaps = 1 Identities = 357 (99%) At1g33960-E.ab1 1 TTGCTGAAATTTCCTTAAACCCTTCATTTTTCACGTAAAATGTTAATTAT 50 At1g33960-L.ab1 1 TTGCTGAAATTTCCTTAAACCCTTCATTTTTCACGTAAAATGTTAATTAT 50 At1g33960-E.ab1 51 TAGCTAATAGATCAACATAAAAACGTTGAAAAAGCTATAAGTGTATGGTT 100 At1g33960-L.ab1 51 TAGCTAATAGATCAACATAAAAACGTTGAAAAAGCTATACGTGTATGGTT 100 *************************************** ********** At1g33960-E.ab1 101 ACGATGTTTGAGAAAAGGAAAATATAATCACATGAAGAAAAACTGGAAAC 150 At1g33960-L.ab1 101 ACGATGTTTGAGAAAAGGAAAATATAATCACATGAAGAAAAACTGGAAAC 150 At1g33960-E.ab1 151 TTAAAGCTTGTAAGTTGTCAATTAAAATCACATGAAATACAGAGAAAGCT 200 At1g33960-L.ab1 151 TTAAAGCTTGTAAGTTGTCAATTAAAATCACATGAAATACAGAGAAAGCT 200 At1g33960-E.ab1 201 TAGAGGGCACGTAATCGTAAACCATACAAATTGATCGATGAGAAATTTAA 250 At1g33960-L.ab1 201 TAGAGGGCACGTAATCGTAAACCATACAAATTGATCGATGAGAAATTTAA 250 At1g33960-E.ab1 251 AAAAAAAAAAAA-GGGGGGGAAAAAGGCCAATTTTTTTTTTCCGGGCCCC 299 At1g33960-L.ab1 251 AAAAAAAAAAAAAGGGGGGGAAAAAGGCCAATTTTTTTTTTCCGGGGCCC 300 ************ ********************************* *** At1g33960-E.ab1 300 CCTAACCAAAGCCGGGGAAAAGGGGTTCCCCCCCCAGCCTGTTTTCCGGT 349 At1g33960-L.ab1 301 CCTAACCAAAGCCGGGGAAAAGGGGTTCCCCCCCCAGCCTGTTTTCCGGT 350 At1g33960-E.ab1 350 TTAAAAAAAA 359 At1g33960-L.ab1 351 TTAAAAAAAA 360 **********

At1g51990-ATG-3 Pairwise Alignments Page 1 Thursday, November 22, 2007 16:40 2 Sequences Aligned Alignment Score = 3778 Gaps Inserted = 56 Conserved Identities = 542 Open Gap Penalty = 10.0 Extend Gap Penalty = 10.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g51990-E.ab1 vs. At1g51990-L.ab1 Aligned Length = 855 Gaps = 51 Identities = 503 (65%) At1g51990-E.ab1 1 GTACTATTGTTTCGGTTGAATAATGTGATTGCAAAATGTGGAGTGTTGGA 50 At1g51990-L.ab1 1 GTACTATTGTTTCGGTTGAATAATGTGATTGCAAAATGTGGAGTGTTGGA 50 At1g51990-E.ab1 51 AAATGAAATTAAGTAATGTTTTTGAAGTGTACTAACAGCCTATGGGGGGC 100 At1g51990-L.ab1 51 AAATGAAATTAAGTAATGTTTTTGAAGTTTACTAACAGCC---------- 90 **************************** *********** At1g51990-E.ab1 101 TACTAACTGCCAGCAGGGTATTAGATGTTTATAAAAGTCTACACCAACTC 150 At1g51990-L.ab1 91 ----AAC-------GGGGTATTAGGTGTTTATAAAAGTCTACACCAACTC 129 *** ********* ************************* At1g51990-E.ab1 151 CCACCTCATTTCTTTTAGAACGAAATT-TAGATTC--------ACTTTTA 191 At1g51990-L.ab1 130 CCATCTCATTTCTTTTAGAAGCATATAATAGACTCCCAAATAAATTTATA 179 *** **************** * ** **** ** * ** ** At1g51990-E.ab1 192 GGGGTAAACCATTTTATT-----CACCTTCTTTTGT---ATTAACCAATA 233 At1g51990-L.ab1 180 TAAG-AAATCATTAAAATGGACACACCAACTGCCGCTAAATTGTTTAA-A 227 * *** **** * * **** ** * *** ** * At1g51990-E.ab1 234 AAAACATGTCATATCAAATCCTATTTAAATTACAT------AATAAATTA 277 At1g51990-L.ab1 228 GAAAAATACCCTAC--AATAGCAATTAAAAAACGTTTTGTGAATAA-TTA 274 *** ** * ** *** * ***** ** * ***** *** At1g51990-E.ab1 278 AA----AT-TATAATTATAATTCAAACTGA--TATATAATCTC------- 313 At1g51990-L.ab1 275 TACCACATATGTAACAATGGTTTCGGTTGAATTATGTGATTGCAATATGT 324 * ** * *** ** ** *** *** * ** * At1g51990-E.ab1 314 -----GTTTAATTACAAAATCTAAACCCTAATTCTCTTTT-GTAAACTCA 357 At1g51990-L.ab1 325 GGAGTGTTGGAAAATGAAAT-TAAG---TAATGTTTTTGAAGTGTACT-- 368 *** * * **** *** **** * ** ** *** At1g51990-E.ab1 358 AACCGCC-AT------TTA--AACT----------CATTTAATCGTAAAA 388 At1g51990-L.ab1 369 AACAGCCTATGGGGGGCTACTAACTGCCAGCAGGGTATTAGATGTTTATA 418 *** *** ** ** **** *** ** * * * At1g51990-E.ab1 389 AAA--CTA----AACCCTAATCGTATTTTTTAAACCCAAACCGATATTTA 432 At1g51990-L.ab1 419 AAAGTCTACACCAACTCCCATCTCATTTCTT----TTAGAACGAAATTTG 464 *** *** *** * *** **** ** * * *** **** At1g51990-E.ab1 433 ACCTCGTTT--AATTGTAAA-------ATCTAAATATGTTTATAC--ACC 471 At1g51990-L.ab1 465 GATTCACTTCTAGGGGTAAACCATTTTATTCACCTTCTTTTGTATTAACC 514 ** ** * ***** ** * * *** ** *** At1g51990-E.ab1 472 --TAAACCTATAT----TTAACTC--GTTTAA-TCATAAAATCTAAACTC 512 At1g51990-L.ab1 515 AATAAAAACATGTCATATCAAATCCTATTTAAATTACATAA--TAAATTA 562 **** ** * * ** ** ***** * * * ** **** * At1g51990-E.ab1 513 TAATCGTACTTTTCTAAATCCAAACCGATATTTAACTTCGTTTAATCACA 562 At1g51990-L.ab1 563 AAGTTATAATTAT---AATTCAAACTGATATATAATCTCGTTTAATTACA 609

At1g51990-ATG-3 Pairwise Alignments Page 2 Thursday, November 22, 2007 16:40 * * ** ** * *** ***** ***** *** ********* *** At1g51990-E.ab1 563 AAATCTAAACCCTGACATTTTCTAATAAACCCAAACCGATACATCATTT- 611 At1g51990-L.ab1 610 AAATCTAAACCCTAATTCTCTTTTGTAAACTCAAACCG---C--CATTTA 654 ************* * * * * ***** ******* * ***** At1g51990-E.ab1 612 CGTTTTAGTAGCAAATTAAATTTTATAATTAAATTAATATTTATTATTGT 661 At1g51990-L.ab1 655 CACTC---------ATTTAATCGTAAAA--AAACTAAACCCTA--ATCGT 691 * * *** *** ** ** *** *** ** ** ** At1g51990-E.ab1 662 TATTAGGTGTCAGATTTTAATTGACTAAAATAAAAGAGGTGAATATAAGG 711 At1g51990-L.ab1 692 -ATT----------TTTTAA---ACCCAAACCGAT-ATTTAAATAT---- 722 *** ****** ** *** * * * ***** At1g51990-E.ab1 712 GTTTA--CCCCTAGTAGTGAACCCAAATATTTTTCTTTCTTTTAAAAGCA 759 At1g51990-L.ab1 723 GTTTATACACCTA------AACC--AATATTTAACT--CGTTTAAT---- 758 ***** * **** **** ******* ** * ***** At1g51990-E.ab1 760 TATAA 764 At1g51990-L.ab1 759 CATAA 763 ****

At1g55310-ATG-33 Pairwise Alignments Page 1 Thursday, November 22, 2007 16:41 2 Sequences Aligned Alignment Score = 5594 Gaps Inserted = 1 Conserved Identities = 832 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g55310-E.ab1 vs. At1g55310-L.ab1 Aligned Length = 827 Gaps = 1 Identities = 825 (99%) At1g55310-E.ab1 1 GTCACCAACTAGATTAGAAATACACCAAAAGAGGTTGGATATTTAAGAGA 50 At1g55310-L.ab1 1 GTCACCAACTAGATTAGAAATACACCAAAAGAGGTTGGATATTTAAGAGA 50 At1g55310-E.ab1 51 GAAGAGACCACAAACACAAGAGCTATAACACCAGCGTCTAAGAGAACTTT 100 At1g55310-L.ab1 51 GAAGAGACCACAAACACAAGAGCTATAACACCAGCGTCTAAGAGAACTTT 100 At1g55310-E.ab1 101 AAAGAAGCAATCAATCTAGAAAGATCATATTTTCTAATTGAATAGTAAAT 150 At1g55310-L.ab1 101 AAAGAAGCAATCAATCTAGAAAGATCATATTTTCCAATTGAATAGTAAAT 150 ********************************** *************** At1g55310-E.ab1 151 TATATCAAAATAAGATCACATGCAATTCAGGTAGAGATCGAATCAGCTCA 200 At1g55310-L.ab1 151 TATATCAAAATAAGATCACATGCAATTCAGGTAGAGATCGAATCAGCTCA 200 At1g55310-E.ab1 201 ATTTCAAAAGATAGGAGCTAAGAAACGTTATATGTGAATAGGCACAAAAG 250 At1g55310-L.ab1 201 ATTTCAAAAGATAGGAGCTAAGAAACGTTATATGTGAATAGGCACAAAAG 250 At1g55310-E.ab1 251 ATCACAACTTTCGTCAAACTTACTTAAGATGAACGATTCAATCCTTTATA 300 At1g55310-L.ab1 251 ATCACAACTTTCGTCAAACTTACTTAAGATGAACGATTCAATCCTTTATA 300 At1g55310-E.ab1 301 TCGATGTATAGACATAATAATTGCCTGATCTACAGTTTTTTCCGTCACGG 350 At1g55310-L.ab1 301 TCGATGTATAGACATAATAATTGCCTGATCTACAGTTTTTTCCGTCACGG 350 At1g55310-E.ab1 351 GATCTTTCACCGGACTCAAAAAGTTGTACGGGCAACGAAGTTGTTTACAA 400 At1g55310-L.ab1 351 GATCTTTCACCGGACTCAAAAAGTTGTACGGGCAACGAAGTTGTTTACAA 400 At1g55310-E.ab1 401 TTGAAGGAATCGAAGTCGGAAAAGCCAAGTTTATTCGACAGAGAAAGAAG 450 At1g55310-L.ab1 401 TTGAAGGAATCGAAGTCGGAAAAGCCAAGTTTATTCGACAGAGAAAGAAG 450 At1g55310-E.ab1 451 AAGATACGGGTATATACGGTTGGGAAGAAGAGCAAAATATCAGGGATAAG 500 At1g55310-L.ab1 451 AAGATACGGGTATATACGGTTGGGAAGAAGAGCAAAATATCAGGGATAAG 500 At1g55310-E.ab1 501 ACTTACCGGTGAACGAATCTCGGTGGTGAGGAACGACGGAGAAGTGATGC 550 At1g55310-L.ab1 501 ACTTACCGGTGAACGAATCTCGGTGGTGAGGAACGACGGAGAAGTGATGC 550 At1g55310-E.ab1 551 TGCAAGAATTGGAGAAGATTGATCAATGAACGACTTATTTATTAGGGTTT 600 At1g55310-L.ab1 551 TGCAAGAATTGGAGAAGATTGATCAATGAACGACTTATTTATTAGGGTTT 600 At1g55310-E.ab1 601 CTTTATATTATTTACGTTTTACATTTAACCCCCTCAAAATTATTTTAAAG 650 At1g55310-L.ab1 601 CTTTATATTATTTACGTTTTACATTTAACCCCCTCAAAATTATTTTAAAG 650

At1g55310-ATG-33 Pairwise Alignments Page 2 Thursday, November 22, 2007 16:41 At1g55310-E.ab1 651 TATTAAAATCCCCTTAAAGTTTTCTATTTGATAGATGCTCCATTCCAATT 700 At1g55310-L.ab1 651 TATTAAAATCCCCTTAAAGTTTTCTATTTGATAGATGCTCCATTCCAATT 700 At1g55310-E.ab1 701 TCTGGTAATTAAATTATCTTCCTTTTTATTATCATTATACATTTATACTT 750 At1g55310-L.ab1 701 TCTGGTAATTAAATTATCTTCCTTTTTATTATCATTATACATTTATACTT 750 At1g55310-E.ab1 751 AGTGAGATCAATTATCTAAGAGGAACTAAAAATGTAAAATTCAATAGAAT 800 At1g55310-L.ab1 751 AGTGAGATCAATTATCTAAGAGGAACTAAAAATGTAAAATTCAATAGAAT 800 At1g55310-E.ab1 801 TAAATAGCAAATTGGTGATTTTTCACC 827 At1g55310-L.ab1 801 TAA-TAGCAAATTGGTGATTTTTCACC 826 *** ***********************

At1g56510-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:41 2 Sequences Aligned Alignment Score = 5831 Gaps Inserted = 1 Conserved Identities = 842 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g56510-E.ab1 vs. At1g56510-L.ab1 Aligned Length = 834 Gaps = 1 Identities = 833 (99%) At1g56510-E.ab1 1 GAGAGATGATTCACAAAGACTTTGAGTTAGGATACGAAATGGGAAAATAG 50 At1g56510-L.ab1 1 GAGAGATGATTCACAAAGACTTTGAGTTAGGATACGAAATGGGAAAATAG 50 At1g56510-E.ab1 51 TGTTCACTTTATATATTTCAAAACAGTTAAATGAAGAGAAAAGTCAAAAT 100 At1g56510-L.ab1 51 TGTTCACTTTATATATTTCAAAACAGTTAAATGAAGAGAAAAGTCAAAAT 100 At1g56510-E.ab1 101 GTGATTTTTGGAAACAAGTTATGCAGAAACGCGTAATGAAGCGTACATAA 150 At1g56510-L.ab1 101 GTGATTTTTGGAAACAAGTTATGCAGAAACGCGTAATGAAGCGTACATAA 150 At1g56510-E.ab1 151 GAAG-TTGTATACTGTTCATTCTCGGCCAGAGGTGTTTAGGATAAGTCTT 199 At1g56510-L.ab1 151 GAAGATTGTATACTGTTCATTCTCGGCCAGAGGTGTTTAGGATAAGTCTT 200 **** ********************************************* At1g56510-E.ab1 200 TTATGGAGGAGAAAATAGCAAAGCTGTTTCTTCACTTATTGGTGAGAGAG 249 At1g56510-L.ab1 201 TTATGGAGGAGAAAATAGCAAAGCTGTTTCTTCACTTATTGGTGAGAGAG 250 At1g56510-E.ab1 250 ACGTGGGAAGTTTCTTTGCACTGTAAACGAAATTTCAAAAGAGTTAAATG 299 At1g56510-L.ab1 251 ACGTGGGAAGTTTCTTTGCACTGTAAACGAAATTTCAAAAGAGTTAAATG 300 At1g56510-E.ab1 300 TGTTTTTGGAAAACAAGTGGGTTCCAATAGAAACGCCTAATGCGAGAAGA 349 At1g56510-L.ab1 301 TGTTTTTGGAAAACAAGTGGGTTCCAATAGAAACGCCTAATGCGAGAAGA 350 At1g56510-E.ab1 350 AAGTTATTATTGTTAACTTCTTAAATGGGTTGAAAATGTTTTTGTTTTCT 399 At1g56510-L.ab1 351 AAGTTATTATTGTTAACTTCTTAAATGGGTTGAAAATGTTTTTGTTTTCT 400 At1g56510-E.ab1 400 TCCCAAAGTTTTTTTTAAGTATGTTAGAAACATTAATACAAGTGTGGAAG 449 At1g56510-L.ab1 401 TCCCAAAGTTTTTTTTAAGTATGTTAGAAACATTAATACAAGTGTGGAAG 450 At1g56510-E.ab1 450 CTATCTTGGTGAAGTTTTTCAAGCACACCAATGAATAGATCACACAGAAT 499 At1g56510-L.ab1 451 CTATCTTGGTGAAGTTTTTCAAGCACACCAATGAATAGATCACACAGAAT 500 At1g56510-E.ab1 500 TTAAATATGTTGGTTATAAACTTTTAGCTTTCTGAGTTTGTTTGATCAAA 549 At1g56510-L.ab1 501 TTAAATATGTTGGTTATAAACTTTTAGCTTTCTGAGTTTGTTTGATCAAA 550 At1g56510-E.ab1 550 TCCTCCACATAATACAAATATATGTTGATGGATCGTATTCATATATACCT 599 At1g56510-L.ab1 551 TCCTCCACATAATACAAATATATGTTGATGGATCGTATTCATATATACCT 600 At1g56510-E.ab1 600 GTGGTTTTTAATCATACCACGGTCATGCGGTTCAGCGAGTACCTTGAAGC 649 At1g56510-L.ab1 601 GTGGTTTTTAATCATACCACGGTCATGCGGTTCAGCGAGTACCTTGAAGC 650

At1g56510-ATG Pairwise Alignments Page 2 Thursday, November 22, 2007 16:41 At1g56510-E.ab1 650 TGTAACCCACCAGCATCGGGTGCTCTCGGTTTAACCGTGAATGTGATTGT 699 At1g56510-L.ab1 651 TGTAACCCACCAGCATCGGGTGCTCTCGGTTTAACCGTGAATGTGATTGT 700 At1g56510-E.ab1 700 CCGAGAAGCAGATGATTCTGATTCCACCTTGAAAGGGACCTCAAACTGTA 749 At1g56510-L.ab1 701 CCGAGAAGCAGATGATTCTGATTCCACCTTGAAAGGGACCTCAAACTGTA 750 At1g56510-E.ab1 750 CAGACTGATACAAGCAAACCTCGTCTTCTTTGCAATAATACACCTGCAAT 799 At1g56510-L.ab1 751 CAGACTGATACAAGCAAACCTCGTCTTCTTTGCAATAATACACCTGCAAT 800 At1g56510-E.ab1 800 TACCATTTTCATAAAATACTTGTGCAAGACGTAA 833 At1g56510-L.ab1 801 TACCATTTTCATAAAATACTTGTGCAAGACGTAA 834 **********************************

At1g59900-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:41 2 Sequences Aligned Alignment Score = 5406 Gaps Inserted = 1 Conserved Identities = 810 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g59900-E.ab1 vs. At1g59900-L.ab1 Aligned Length = 622 Gaps = 0 Identities = 610 (98%) At1g59900-E.ab1 1 TTCTCCGCCGTTGATTCGAAGATTCTCCGGCGAATCTGATTGAGAACTTC 50 At1g59900-L.ab1 1 TTCTCCGCCGTTGATTCGAAGATTCTCCGGCGAATCTGATTGAAGACTTC 50 ******************************************* ***** At1g59900-E.ab1 51 GCGTAGGAACTGAGAGGACAATTTCCGTGAAGCAGTAGATAGCGATCCTA 100 At1g59900-L.ab1 51 GCGTAGGAACTGAGAGGACAATTTCCGTGAAGCAGTAGATAGCGATCCTA 100 At1g59900-E.ab1 101 ATATAAGAGACTCTGAGAGGATAAGAAGGTTTTCCGTACACAGCCTCACG 150 At1g59900-L.ab1 101 ATATAAGAGACTCTGAGAGGATAAGAAGGTTTTCCGTACACAGCCTCACG 150 At1g59900-E.ab1 151 TGAGTCACGTGACACCTGTGATAAAAGAGTCAATATATATTCATATTCTC 200 At1g59900-L.ab1 151 TGAGTCACGTGACACCTGTGATAAAAGAGTCAATATATATTCATATTCTC 200 At1g59900-E.ab1 201 TTAAAATCATATTATATAATCAAACTCAAATGTGATTAAAGATAAATAAC 250 At1g59900-L.ab1 201 TTAAAATCATATTATATAATCAAACTCAAATGTGATTAAAGATAAATAAC 250 At1g59900-E.ab1 251 CAAATGGATAAACCAAAATAAATAAATAAAACATGTGATTAAAGAGATTA 300 At1g59900-L.ab1 251 CAAATGGATAAACCAAAATAAATAAATAAAACATGTGATTAAAGAGATTA 300 At1g59900-E.ab1 301 TTAATTTGAAAGAGAATTTAACATTAGAAGGAAAATTCAATAATTGTTCA 350 At1g59900-L.ab1 301 TTAATTTGAAAGAGAATTTAACATTAGAAGGAAAATTCAATAATTGTTCA 350 At1g59900-E.ab1 351 ATGAATGAATTAAAAATATCCAATTTTAGCATCATCCTTAAAAAAAAAAA 400 At1g59900-L.ab1 351 ATGAATGAATTAAAAATATCCAATTTTAGCATCATCCTTAAAAAAAGAAA 400 ********************************************** *** At1g59900-E.ab1 401 AGATTTTCTAACACTATACAGCAAAACTGGCGGCTCCCGCTGCAGTGTAA 450 At1g59900-L.ab1 401 AGATATTCTAACACTATACAGCAAAACTGGCGGCTCCAGCTGCAGTGTAG 450 **** ******************************** *********** At1g59900-E.ab1 451 ACGGTAAAAAATAAAAACTATGGTTGTTGCCATGTGAATCTCTTTGAGCC 500 At1g59900-L.ab1 451 ACTGTAGAAGATAAAAACTATGGTTGTTGCCATGTGAATCTCTTTGAGCC 500 ** *** ** **************************************** At1g59900-E.ab1 501 TAAAATGATGCAAGAATCTTTGTCAAAGACAGTTATTCTCTAGTCTCTCT 550 At1g59900-L.ab1 501 TAAAATGATGCAAGAATCTTTGTCAAAGACAGTTATTCTCTAGTCTCTCT 550 At1g59900-E.ab1 551 CTACTACTACTCATTCTTGCATATCTCATTCTCAGCAAAGAACTTCACCC 600 At1g59900-L.ab1 551 CTACTACTACTCATTCTTGCATATCTCATTCTCAGCAAAGAACTTCACAC 600 ************************************************ * At1g59900-E.ab1 601 CTGCACAATTTATCGGGGGTTA 622 At1g59900-L.ab1 601 CTGCACAATTTATCGTGAGTTA 622

At1g59900-ATG Pairwise Alignments Page 2 Thursday, November 22, 2007 16:41 *************** * ****

At1g60530-ATG-42 Pairwise Alignments Page 1 Thursday, November 22, 2007 16:41 2 Sequences Aligned Alignment Score = 5420 Gaps Inserted = 7 Conserved Identities = 801 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g60530-E.ab1 vs. At1g60530-L.ab1 Aligned Length = 728 Gaps = 2 Identities = 712 (97%) At1g60530-E.ab1 1 AAGGATTAGATGCAGAGAAGAAAAGTTTTTAGTGAGTGAAGAGACTCATG 50 At1g60530-L.ab1 1 AAGGATTAGATGCAGAGAAGAAAAGTTTTTAGTGAGTGAAGAGACTCATG 50 At1g60530-E.ab1 51 TTGGTGGTGACATTTATAGATTGGCTTGTGGTGACCTTTGGTGTTTTAAC 100 At1g60530-L.ab1 51 TTGGTGGTGACATTTATAGATTGGCTTGTGGTGACCTTTGGTGTTTTAAC 100 At1g60530-E.ab1 101 TTTTACAAAGAAGAAGTTTGAAAGTTTTTTTTTTGGTCTAACTGTAGAAG 150 At1g60530-L.ab1 101 TTTTACAAAGAAGAAGTTTGAAAGTTTTTTTTTTGGT-TAAATGTAGAAG 149 ************************************* *** ******** At1g60530-E.ab1 151 TTTGAAAGTTCTTCATTGTTTTAAGAACAAGAGATAGATGTAAATGTTGA 200 At1g60530-L.ab1 150 TTTGAAAGTTCTTCATTGTTTTAAGAACAAGAGATAGATGTAAATGTTGA 199 At1g60530-E.ab1 201 CATCCGAGGTTTGTAACTTTTACGGAGTACAAGAGATAAATTTAACTGTT 250 At1g60530-L.ab1 200 CATCTGAGGTTTGTAACTTTTACGGAGTACAAGAGATAAATTTAACTGTT 249 **** ********************************************* At1g60530-E.ab1 251 AAACTACTATTTTCTATCTTTGATTTTTTAGCCGTCAAGGACTTTGTAGT 300 At1g60530-L.ab1 250 AAACTACTATTTTCTATCTTTGATTTTTTAGCCGTCAAGGACTTTGTAGT 299 At1g60530-E.ab1 301 TTGAACCCCGATAGATTGCAAGTTTGTGATATGAAATTTCATCCCATTAC 350 At1g60530-L.ab1 300 TTGAACCACGATAGATTGCAAGTTTGTGATATGAAATTTCATCCCATTAC 349 ******* ****************************************** At1g60530-E.ab1 351 CTCGTTATTCTCCATAGTTTCGAGAACAAGTTTTTTTTTTGTCGAGTACA 400 At1g60530-L.ab1 350 CTCGTTATTCTCCATAGTTTCGAGAACAAGTTTTTTTTTTGTCGAGTACA 399 At1g60530-E.ab1 401 ATTTAAATTGGGAAAAAATTTTAATTTAACTTTAATATTTCCTCAAATTA 450 At1g60530-L.ab1 400 ATTTAAATTGGTAAAAAATTTTAATTTAACTTTAATATTTCATCAAATTA 449 *********** ***************************** ******** At1g60530-E.ab1 451 GAGAATGCCATAAAAAACTTTTCTTTTTTTAATTTATAAAACTAGAACAC 500 At1g60530-L.ab1 450 GAGAATGCAATAAAAAACTTTTCTTTTTTTAATTTATAAAACTAGAACAC 499 ******** ***************************************** At1g60530-E.ab1 501 TATATAACGTCCAGCGTATAAGAAAACAACCACCAAGAGATCCCCAAAGT 550 At1g60530-L.ab1 500 TATATAACGTCCAGCGTATAAGAAAACAACCACCAAGAGATCCCCAAAGT 549 At1g60530-E.ab1 551 TCCCAACTTTGAAAAATAAACCTTTAGGCAAGACCCAAAAACACGATCTT 600 At1g60530-L.ab1 550 TCCCAACTTTGAAAAATAAACATTTAGGCAAGACCTAAAAACACGATCTT 599 ********************* ************* ************** At1g60530-E.ab1 601 TCTTCACCAAAGCTTGGGTAAAAAGCAATCGATTAACGATCTCCGTACCC 650 At1g60530-L.ab1 600 TCTTCACCAAAGCTTGGGAAAGAAGCAATCGATTAACGATCTCCGTACCC 649

At1g60530-ATG-42 Pairwise Alignments Page 2 Thursday, November 22, 2007 16:41 ****************** ** **************************** At1g60530-E.ab1 651 AGAATCCTGATCAACAATGGGCTGCCACAACATCCTTGGCAATCGCTTAA 700 At1g60530-L.ab1 650 AGAATCCTGATCAACAATGG-CTGCCACAACATCCTTGGCAATCGCTTAA 698 ******************** ***************************** At1g60530-E.ab1 701 AACCTAACAAGGGGTCCAACCTTGTTTC 728 At1g60530-L.ab1 699 AACCTAACAAGTGTTCATACCTTGTTTC 726 *********** * ** **********

At1g60750-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:41 2 Sequences Aligned Alignment Score = 3741 Gaps Inserted = 54 Conserved Identities = 531 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g60750-E.ab1 vs. At1g60750-L.ab1 Aligned Length = 756 Gaps = 42 Identities = 452 (63%) At1g60750-E.ab1 1 TGATGTATCAATCTTTAGAAGATAAAAAAAAA--GAAATACAAAGACT-- 46 At1g60750-L.ab1 1 TGATGTATCA-TCTTTAGAAGATAAAAAAAAAAAGAAATCCAAAGACTAT 49 ********** ********************* ***** ******** At1g60750-E.ab1 47 GTGTTTTTGTGAAATCAGAAACAGATTCGAGTGGGATTTATAGGAGTGGA 96 At1g60750-L.ab1 50 GTGTTTTTGTGAAACCAGAAACAGATTCGAGGGGGATTTATAGGAGGGGA 99 ************** **************** ************** *** At1g60750-E.ab1 97 ----------AGATAAAGCAATTAATGATCACCGCCTCGCCATTAGTGAC 136 At1g60750-L.ab1 100 GTTGAGGGGAAAATAAAGCAATTAAGGATCCCCGCCCCGCCTTTAGGGAC 149 * ************* **** ***** **** **** *** At1g60750-E.ab1 137 AATGTTCTAGAGTGTTTTTTATAATTAAGAGGACAAAAACAAAATTGTAG 186 At1g60750-L.ab1 150 AAGGTTCTAAAGGGTTTTTTATAATTAAGAGGACAAAACCAAAATTGTAG 199 ** ****** ** ************************* *********** At1g60750-E.ab1 187 TCTTCTTCATTTGTTAGTATTACTTCAAA--TGTT----------TGAAA 224 At1g60750-L.ab1 200 CCTTCTTCAGTTGTTAGTATTACTTCAAAATTGTTATTATATGACCGAAA 249 ******** ******************* **** **** At1g60750-E.ab1 225 TGTTT-TGCTTTTTCCATCAAATGTT----TTGCTTTTTCCAAATACTAA 269 At1g60750-L.ab1 250 AGAATATATAAGTTCTAT-AAACTTTGACGCCGCCTTTGATGATTTCATA 298 * * * *** ** *** ** ** *** * * * * At1g60750-E.ab1 270 TTAATATTCA--ATCGGATGAAAGAAA------TAAAGAATGATAGTGTT 311 At1g60750-L.ab1 299 TCACCATTCATCATTTGATTTCCAAAACCTTTTTAGAGTATGGGAAT-TT 347 * * ***** ** *** *** ** ** *** * * ** At1g60750-E.ab1 312 TGAAATTAACCAAAACTACTACATGAGTTAAGTTGTTTGAACAGATGATA 361 At1g60750-L.ab1 348 TAAATTTCGCC----CCCTTGCAAGA---AAATT-CTAAAAAAGACTTTA 389 * ** ** ** * * ** ** ** ** * ** *** ** At1g60750-E.ab1 362 TCTT---CACCATAAAGGCTAATCAAACGAGGTTTAGAGATGTTAAAAGG 408 At1g60750-L.ab1 390 GTTGGAATACCATTTAA--TAATAATATAAAATTT---GTTGTTTTTATA 434 * ***** * **** * * * *** * **** * At1g60750-E.ab1 409 GATAAGTTAGGCTTACTTGATCTTCAAGTCATCCATCTTTCAAGAACTTT 458 At1g60750-L.ab1 435 GAAAAGT-A----TACTT----CTAAAAT-ACCC-CCTTGCAAGAAGATT 473 ** **** * ***** * ** * * ** *** ****** ** At1g60750-E.ab1 459 TTCTAAC---CATTATTC------CCTTATTAATA------------TGG 487 At1g60750-L.ab1 474 CTAAAAAAGACGGTAGTTGGAATACCCAATTAATAACAGTATAAAATTCG 523 * ** * ** * ** ******* * * At1g60750-E.ab1 488 TTCCCCTTAAGAAAACAATATATGCTGCTGGGTCA--TGTGTGTCGTATC 535 At1g60750-L.ab1 524 TTGTTTTTTATAGAATAGTATA--CTTCTAAAATAACTAGATAAGGTGAA 571 ** ** * * ** * **** ** ** * * * ** At1g60750-E.ab1 536 TCACATCCTAAAATGGGATAACCTCGGACCACAATATGTCTAAGTGAGAC 585 At1g60750-L.ab1 572 TCCGATCATCAAATGTTTTGCTTTTT--CCA-AATA---CTAATTAATAT 615

At1g60750-ATG Pairwise Alignments Page 2 Thursday, November 22, 2007 16:41 ** *** * ***** * * *** **** **** * * * At1g60750-E.ab1 586 T-AACC---TAAACGACTTGACGTTGTTAT-ATAGGCTTCTCAATTAGTC 630 At1g60750-L.ab1 616 TCAATCGGATGAAAGAAATAAAAA----ATGATAGGGTTTGAAATTAA-C 660 * ** * * ** ** * * ** ***** ** ***** * At1g60750-E.ab1 631 TCTTATATATTTCTTGAGTTTTCGTTTTTGTTTATCTCTGATATATACAT 680 At1g60750-L.ab1 661 CCAAAC-TACTACCTGGGTTAA-GT---TGTTTGAA-CAGATG-ATATCT 703 * * ** * * ** *** ** ***** * *** *** * At1g60750-E.ab1 681 TGTTAT 686 At1g60750-L.ab1 704 TCCC-C 708 *

At1g63540-ATG Pairwise Alignments Page 1 Thursday, November 22, 2007 16:42 2 Sequences Aligned Alignment Score = 5595 Gaps Inserted = 3 Conserved Identities = 835 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Open Gap Penalty = 5.0 Extend Gap Penalty = 0.0 Processing time: 0.4 seconds 1. At1g63540-E.ab1 vs. At1g63540-L.ab1 Aligned Length = 809 Gaps = 0 Identities = 804 (99%) At1g63540-E.ab1 1 TCTTCTTTTGATCTTTCAACTGTTAACCACACAAAAATAAGAAAGGACTC 50 At1g63540-L.ab1 1 TCTTCTTTTGATCTTTCAACTGTTAACCACACAAAAATAAGAAAGGACGC 50 ************************************************ * At1g63540-E.ab1 51 AAATTTGTTTTGGATTAGAGGATAACTTTCAGAAACTAATTCGTATTGCA 100 At1g63540-L.ab1 51 AAATTTGTTTTGGATTAGAGGATAACTTTCAGAAACTAATTCGTATTGCA 100 At1g63540-E.ab1 101 GAAACTAAGTAACAAAAACCCTAAATCCAGATCCGTTAAGATAGTAATTT 150 At1g63540-L.ab1 101 GAAACTAAGTAACAAAAACCCTAAATCCAGATCCGTTAAGATAGTAATTT 150 At1g63540-E.ab1 151 CCACTCAAATTTGGGGGTTATACATCAGAAAGTAACGATTTTTATTCAGT 200 At1g63540-L.ab1 151 CCACTCAAATTTGGGGGTTATACATCAGAAAGTAACGATTTTTATTCAGT 200 At1g63540-E.ab1 201 AATCAGTACAAATGACTAATTGCAGGATCATTGAATCGATAGTTCCAACC 250 At1g63540-L.ab1 201 AATCAGTACAAATGAGTAATTGCAGGATCATTGAATCGATAGTTCCAACC 250 *************** ********************************** At1g63540-E.ab1 251 GATAACAGAGCACTGTTCTCGAATCCACAGAGGAAACAGTATGTAGAAAG 300 At1g63540-L.ab1 251 GATAACAGAGCACTGTTCTCGAATCCACAGAGGAAACAGTATGTAGAAAG 300 At1g63540-E.ab1 301 CGTGGAAAAGAAGCAACAAAAGAACCCTAATTACAAAGAGAAAACATGAT 350 At1g63540-L.ab1 301 CGTGGAAAAGAAGCAACAAAAGAACCCTAATTACAAAGAGAAAACATGAT 350 At1g63540-E.ab1 351 CTAACCCAAATCAAGCAAAACAAAGACATAAAAGATCAAGAGATACTGAT 400 At1g63540-L.ab1 351 CTAACCCAAATCAAGCAAAACAAAGACATAGAAGATCAAGAGATACTGAT 400 ****************************** ******************* At1g63540-E.ab1 401 CGGCAATTCACAATTGTTGCAAGTATTAAAATCGCCCAAAATCGTCAGAG 450 At1g63540-L.ab1 401 CGGCAATTCACAATTGTTGCAAGTATTAAAATCGCCCAAAATCGTCAGAG 450 At1g63540-E.ab1 451 TTTAATAAAAATTGAACCTTTATCAAAGTAGGAAGCAGGGCACCGACCAA 500 At1g63540-L.ab1 451 TTTAATAAAAATTGAACCTTTATCAAAGTAGGAAGCAGGGCACCGACCAA 500 At1g63540-E.ab1 501 GTGATTGAAGGAGAAGCTTACGGAGACAACAACAATGGTGCGGTTTCCGA 550 At1g63540-L.ab1 501 GTGATTGAAGGAGAAGCTTACGGAGACAACAACAATGGTGCGGTTTCCGA 550 At1g63540-E.ab1 551 GTCTGATGATGAAATCAAAGTTAGGGTTAGTGTGAAGAAGAAGAAAAAAG 600 At1g63540-L.ab1 551 GTCTGATGATGAAATCAAAGTTAGGGTTAGTGTGAAGAAGAAGAAAAAAG 600 At1g63540-E.ab1 601 AGTTAACTTTGTGGTTTCAATTTATAGGAAACGATTTCTTCAATTTGCCT 650 At1g63540-L.ab1 601 AGTTAACTTTGTGGTTTCAATTTATAGGAAACGATTTCTTCAATTTGCCT 650