Basic Local Alignment Search Tool

Transcription

1 NCBI Blast:MARVRSTARVEREGDEAEGAETVPISEAMQRSGLVTSERIPTAETDA... Page 1 of 24 BLAST Basic Local Alignment Search Tool Edit and Resubmit Save Search Strategies Formatting options Download MARVRSTARVEREGDEAEGAETVPISEAMQRSGLVTSERIPTAETDAETEQAAAEAEQGD Results for: lcl 9267 MARVRSTARVEREGDEAEGAETVPISEAMQRSGLVTSERIPTAETDAETEQAAAEAEQGD(63aa) Your BLAST job specified more than one input sequence. This box lets you choose which input sequence to show BLAST results for. Query ID lcl 9267 lcl 9267 Description MARVRSTARVEREGDEAEGAETVPISEAMQRSGLVTSERIPTAETDAETEQAAAEAEQGD Molecule type amino acid Query Length 63 Database Name nr Description All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,environmental samples or phase 0, 1 or 2 HTGS sequences) Program TBLASTN Citation Reference Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25: Other reports: Search Summary [Taxonomy reports] Search Parameters Search parameter name Search parameter value Program tblastn Word size 3 Expect value 10 Hitlist size 100 Gapcosts 11,1 Matrix BLOSUM62 Low Complexity Filter Yes Filter string L; Genetic Code 1 Window Size 40 Threshold 13 Composition-based stats 2 Database Database parameter name Database parameter value Posted date Oct 23, :13 PM Number of letters 33,760,621,945 Number of sequences 13,809,601 Entrez query none Karlin-Altschul statistics Params Ungapped Gapped Lambda K H Results Statistics Results Statistics parameter name Results Statistics parameter value Length adjustment 37

2 NCBI Blast:MARVRSTARVEREGDEAEGAETVPISEAMQRSGLVTSERIPTAETDA... Page 2 of 24 Effective length of query 26 Effective length of database Effective search space Effective search space used Graphic Summary Distribution of 144 Blast Hits on the Query Sequence [?] An overview of the database sequences aligned to the query sequence is shown. The score of each alignment is indicated by one of five different colors, which divides the range of scores into five groups. Multiple alignments on the same database sequence are connected by a striped line. Mousing over a hit sequence causes the definition and score to be shown in the window at the top, clicking on a hit sequence takes the user to the associated alignments. New: This graphic is an overview of database sequences aligned to the query sequence. Alignments are color-coded by score, within one of five score ranges. Multiple alignments on the same database sequence are connected by a dashed line. Mousing over an alignment shows the alignment definition and score in the box at the top. Clicking an alignment displays the alignment detail.

3 NCBI Blast:MARVRSTARVEREGDEAEGAETVPISEAMQRSGLVTSERIPTAETDA... Page 3 of 24 Descriptions Legend for links to other resources: UniGene GEO Gene Structure Map Viewer PubChem BioAssay Sequences producing significant alignments: Accession Description AC Max score Total score Query coverage E Max value ident Zea mays BAC clone CH I20 from chromosome 6, complete sequence % 4e-23 96% EF Zea mays clone FS2_20 chromosome B, genomic sequence % 1e-22 94% AC AC AC AC AC AC AC Zea mays BAC clone CH P8 from chromosome 9, complete sequence % 4e-22 91% Zea mays BAC clone CH B20 from chromosome 10, complete sequence % 3e-21 94% Zea mays BAC clone CH G21 from chromosome 7, complete sequence % 3e-20 85% Zea mays BAC clone CH P15 from chromosome 5, complete sequence % 1e-19 83% Zea mays BAC clone CH201-98J13 from chromosome 5, complete sequence % 1e-19 83% Zea mays BAC clone CH J9 from chromosome 8, complete sequence % 5e-16 75% Zea mays BAC clone CH N10 from chromosome 5, complete sequence % 1e-14 75% GU Zea mays cultivar B73 clone BAC c0171e08 genomic sequence % 2e-14 75% AF AC AC AC AC Contiguous genomic DNA sequence comprising the 19-kDa-zein gene family from Zea mays, complete sequence % 2e-14 73% Zea mays BAC clone CH B12 from chromosome 5, complete sequence % 2e-14 75% Zea mays BAC clone CH O9 from chromosome 5, complete sequence % 2e-14 75% Genomic seqeunce for Zea mays BAC clone ZMMBBb0448F23, complete sequence % 3e-14 75% Zea mays BAC clone CH O5 from chromosome 9, complete sequence % 6e-14 73% AC Zea mays clone ZMMBBb-37E5, complete sequence % 6e-14 73% GQ Zea mays chromosome 4 sequence AGI.478 genomic sequence % 7e-14 79% AY AF AC AC AC AC AC AF Zea mays rust resistance protein rp3-1 (rp3-1) gene, complete cds; and truncated rust resistance protein rp3-2t (rp3-2) gene, complete % 8e-14 79% sequence Zea mays cultivar B73 putative gag protein, putative gag-pol precursor, putative transposase, putative copia-type pol polyprotein, putative copia-like retrotransposon Hopscotch polyprotein, putative gag protein, putative prpol, putative prpol, putative pol protein, putative pol protein, % 8e-14 69% putative gag protein, and teosinte branched1 protein genes, complete cds Zea mays BAC clone CH A17 from chromosome 5, complete sequence % 1e-13 72% Zea mays BAC clone CH G11 from chromosome 10, complete sequence % 2e-13 73% Zea mays BAC clone CH G15 from chromosome 8, complete sequence % 2e-13 71% Zea mays BAC clone CH201-98H14 from chromosome 6, complete sequence % 2e-13 67% Zea mays BAC clone CH M1 from chromosome 5, complete sequence % 3e-13 71% Zea mays putative transposase (Z195D10.1) gene, partial cds; glycyltrna synthetase (Z195D10.2), ornithine carbamoyltransferase (Z195D10.3), putative gag protein (Z195D10.5), putative SET-domain transcriptional regulator (Z195D10.7), putative oxysterol-binding protein (Z195D10.8), putative polyprotein (Z195D10.9), putative oxysterolbinding protein (Z195D10.10), putative gag-pol polyprotein (Z195D10.11), putative phosphatidylinositol-4-phosphate-5-kinase (Z195D10.12), hypothetical protein (Z195D10.15), putative gag-pol polyprotein (Z195D10.16), putative polyprotein (Z195D10.17), putative retrotransposon protein (Z195D10.18), and prpol (Z195D10.19) genes, complete cds; and putative teosinte branched2 (Z195D10.20) gene, partial cds % 3e-13 73% AC Zea mays BAC clone Z418K17, complete sequence % 4e-13 70% Links

4 NCBI Blast:MARVRSTARVEREGDEAEGAETVPISEAMQRSGLVTSERIPTAETDA... Page 4 of 24 AY Zea mays BAC clone c573f08, complete sequence % 8e-13 76% AC Zea mays clone ZMMBBb-272P17, complete sequence % 1e-12 69% AY Zea mays cultivar B73 locus 9008, complete sequence % 2e-12 64% AF Zea mays retrotransposon Cinful % 2e-12 64% AF AC AC AC Zea mays alcohol dehydrogenase 1 (adh1) gene, adh1-f allele, complete cds % 2e-12 64% Zea mays BAC clone CH N23 from chromosome 5, complete sequence % 3e-12 69% Zea mays BAC clone ZMMBBb-223D21 from chromosome 5, complete sequence % 3e-12 69% Zea mays BAC clone CH O17 from chromosome unknown, complete sequence % 3e-12 70% AY Zea mays cultivar Mo17 locus 9008, complete sequence % 4e-12 62% AY AC AC AC AC Zea mays putative growth-regulating factor 1 (Z214A02.12), putative 40S ribosomal protein S8 (Z214A02.25), and putative casein kinase I (Z214A02.27) genes, complete cds % 5e-12 69% Zea mays BAC clone CH201-53J11 from chromosome 5, complete sequence % 7e-12 71% Zea mays BAC clone CH N20 from chromosome 4, complete sequence % 9e-12 69% Zea mays BAC clone ZMMBBb-334D6 from chromosome 5, complete sequence % 1e-11 72% Zea mays BAC clone CH201-73M20 from chromosome 5, complete sequence % 1e-11 72% AY Zea mays cultivar B73 locus 9002, complete sequence % 1e-11 61% AC AC Zea mays BAC clone CH201-65L11 from chromosome 5, complete sequence % 2e-11 72% Zea mays BAC clone CH A2 from chromosome 8, complete sequence % 5e-11 70% AC Zea mays genomic clone ZM15C05 sequence, complete sequence % 3e-10 74% AC Zea mays clone CH E16, complete sequence % 5e-10 64% AC Zea mays BAC clone CH N8 from chromosome 5, complete sequence % 7e-10 73% EU Zea mays clone mrna sequence % 2e-09 71% AC AC AY Zea mays BAC clone CH I12 from chromosome 1, complete sequence % 2e-07 65% Zea mays BAC clone CH N3 from chromosome 3, complete sequence % 5e-04 47% Zea mays alcohol dehydrogenase 1 (adh1a) gene, complete cds; Fourf copia_ltr and Huck gypsy_ltr retrotransposons, complete sequence; Opie2 copia_ltr retrotransposon Zeon gypsy_ltr and Opie1 copia_ltr retrotransposons, complete sequence; Ji copia_ltr 48.9 retrotransposon, complete sequence; and unknown protein (adh1b), % 6e-04 50% cyclin H-1 (adh1c), unknown protein (adh1d), hypothetical protein (adh1e), and unknown protein (adh1f) genes, complete cds AY Zea mays cultivar Mo17 locus 9002, complete sequence % 6e-04 54% AC Zea mays BAC clone CH M12 from chromosome 8, complete sequence % 8e-04 55% AF Zea mays cultivar McC bz locus region % % AY Zea mays BAC clone Z013I05, complete sequence % % AC AC AC AC AC AC DQ AY AF Zea mays BAC clone CH C16 from chromosome 5, complete sequence % % Zea mays BAC clone CH G5 from chromosome 10, complete sequence % % Zea mays BAC clone CH201-26J18 from chromosome 6, complete sequence % % Zea mays BAC clone CH M22 from chromosome 5, complete sequence % % Zea mays BAC clone CH201-70P8 from chromosome 5, complete sequence % % Zea mays BAC clone CH201-87B9 from chromosome 5, complete sequence % % Zea mays B73 serine/threonine kinase protein, expressed protein, and RNA-dependent RNA polymerase (mop1) genes, complete cds % % Zea mays B transcriptional activator (b1) gene, b1-b' allele, exons 1 through 3 and partial cds % % Contiguous genomic DNA sequence comprising the 19-kDa-zein gene family from Zea mays, complete sequence % %

5 NCBI Blast:MARVRSTARVEREGDEAEGAETVPISEAMQRSGLVTSERIPTAETDA... Page 5 of 24 EF EF Zea mays clone pbk118-7 LL repeat sequence and retrotransposon zeon1, complete sequence % % Zea mays clone pbk118-1 LL repeat sequence and retrotransposon zeon1, complete sequence % % AC Zea mays clone ZMMBBb-125O19, complete sequence % % AC Zea mays clone ZMMBBb-7C14, complete sequence % % AF Zea mays 22 kda alpha zein gene cluster, complete sequence % % EF Zea mays clone FS2_19 chromosome B, genomic sequence % % EU Zea mays clone pbs-3 chromosome B genomic sequence % % EF Zea mays clone FS3_49 chromosome B, genomic sequence % % EU Zea mays cultivar W22 bz gene locus, complete sequence % % DQ Zea mays copia retrotransposon opie1, gypsy retrotransposon grande1, xilon1 retrotransposon, helitron B73_14578, gypsy retrotransposon huck1 and ruda retrotransposon, complete sequence % % AC Zea mays clone ZMMBBb-188L18, complete sequence % % FJ Zea mays cultivar B73 p cluster, complete sequence % % AC Zea mays clone ZMMBBb-177G21, complete sequence % % AC AC AC Zea mays BAC clone CH D18 from chromosome 1, complete sequence % % Zea mays BAC clone CH F5 from chromosome 5, complete sequence % % Zea mays BAC clone CH M20 from chromosome 10, complete sequence % % EU Zea mays clone mrna sequence % % AC AC Zea mays BAC clone CH201-52A17 from chromosome 5, complete sequence % % Zea mays BAC clone CH C23 from chromosome 5, complete sequence % % AC Zea mays clone ZMMBBb-151F20, complete sequence % % AC Genomic sequence for Zea mays clone ZMMBBb0614J24, from chromosome 8, complete sequence % % EU Zea mays clone mrna sequence % % DQ Zea mays clone weo116 retrotransposon Zeon, partial sequence % % EU Zea mays clone mrna sequence % % AY Zea mays clone BAC 276N12-123C01, partial sequence % % AC Zea mays BAC clone ZMMBBb-225M3 from chromosome 5, complete sequence % % Alignments Select All Get selected sequences Distance tree of results Multiple alignment >gb AC Length= Zea mays BAC clone CH I20 from chromosome 6, complete sequence Score = 112 bits (280), Expect = 4e-23, Method: Compositional matrix adjust. Identities = 54/56 (97%), Positives = 54/56 (97%), Gaps = 0/56 (0%) EDQLMT AFGTRPKRRLNRVLDAIGFEYADYGRL GDAGGPKRKRIASAADEEVAK Sbjct EDQLMTAAFGTRPKRRLNRVLDAIGFEYADYGRLGGDAGGPKRKRIASAADEEVAK Score = 51.2 bits (121), Expect = 1e-04, Method: Compositional matrix adjust. Identities = 32/57 (57%), Positives = 36/57 (64%), Gaps = 2/57 (3%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAA-DEEVAK 63 ED ++ AFG R K+RLNRV DAIGF Y DY R + G KRK ASA DE AK Sbjct EDNALSTAFGGRVKKRLNRVFDAIGFVYPDY-RCPL*SQGKKRKTAASATLDEPAAK >gb EF Length=39210 Zea mays clone FS2_20 chromosome B, genomic sequence Score = 111 bits (277), Expect = 1e-22, Method: Compositional matrix adjust. Identities = 53/56 (95%), Positives = 53/56 (95%), Gaps = 0/56 (0%)

6 NCBI Blast:MARVRSTARVEREGDEAEGAETVPISEAMQRSGLVTSERIPTAETDA... Page 6 of 24 EDQLMT AF TRPKRRLNRVLDAIGFEYADYGRLSGD GGPKRKRIASAADEEVAK Sbjct EDQLMTAAFSTRPKRRLNRVLDAIGFEYADYGRLSGDVGGPKRKRIASAADEEVAK >gb AC Length= Zea mays BAC clone CH P8 from chromosome 9, complete sequence Score = 109 bits (272), Expect = 4e-22, Method: Compositional matrix adjust. Identities = 51/56 (92%), Positives = 51/56 (92%), Gaps = 0/56 (0%) EDQLMT AFGTRPKRRLNRVLDAIGFEYADYGRL GDAGGPKRKRIAS DEEV K Sbjct EDQLMTAAFGTRPKRRLNRVLDAIGFEYADYGRLGGDAGGPKRKRIASTTDEEVTK >gb AC sequence Length= Zea mays BAC clone CH B20 from chromosome 10, complete Score = 106 bits (264), Expect = 3e-21, Method: Compositional matrix adjust. Identities = 50/53 (95%), Positives = 50/53 (95%), Gaps = 0/53 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEE 60 EDQLMT AFGTRPKRRLNRVLDAIGFEYADYGRL GD GGPKRKRIASAADEE Sbjct EDQLMTAAFGTRPKRRLNRVLDAIGFEYADYGRLGGDVGGPKRKRIASAADEE Score = 70.5 bits (171), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 34/51 (67%), Positives = 38/51 (75%), Gaps = 0/51 (0%) EDQLMT AFGTRPKRR+NRVLDA+ FEY D+ RL G KRKRI S + Sbjct EDQLMTAAFGTRPKRRINRVLDALNFEYPDFERLDEGVG*AKRKRIVSILN >gb AC Length= Zea mays BAC clone CH G21 from chromosome 7, complete sequence Score = 103 bits (256), Expect = 3e-20, Method: Compositional matrix adjust. Identities = 48/56 (86%), Positives = 49/56 (88%), Gaps = 0/56 (0%) EDQLMT AFGTRPKRRLNRVLDAIGFEY DYGRL GDAGGPKRKRI +A DEE K Sbjct 7814 EDQLMTAAFGTRPKRRLNRVLDAIGFEYPDYGRLGGDAGGPKRKRIVNAVDEESTK 7647 Score = 80.1 bits (196), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 38/52 (74%), Positives = 41/52 (79%), Gaps = 0/52 (0%) EDQLMT AFGTRPKRRLNRVLDA+GFEY DY L+ A G KRKR+ A DE Sbjct EDQLMTAAFGTRPKRRLNRVLDALGFEYPDYEDLNKGARGQKRKRVTEALDE Score = 75.1 bits (183), Expect = 7e-12, Method: Composition-based stats. Identities = 34/56 (61%), Positives = 40/56 (72%), Gaps = 0/56 (0%) EDQLMT AFG+RPKRRLNRV+DA+ FEY DY RL+ G KRKR+ S A+ Sbjct EDQLMTAAFGSRPKRRLNRVMDALHFEYPDYERLNKGTEGQKRKRVVSVVGRHAAR Score = 35.4 bits (80), Expect = 7.0, Method: Compositional matrix adjust. Identities = 22/42 (53%), Positives = 25/42 (60%), Gaps = 1/42 (2%) Query 21 KRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEEVA 62 K+RLNRV +AIGF Y D R G KRK ASA +E A Sbjct KKRLNRVFNAIGFVYPD-*RYPLRGRGKKRKTAASATPDEPA >gb AC Length= Zea mays BAC clone CH P15 from chromosome 5, complete sequence Score = 100 bits (250), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 47/56 (84%), Positives = 50/56 (90%), Gaps = 0/56 (0%) ED+LMT AFGT+PKRRLNRVLDAIGFEY DYGRL GDAGGPK+KRIASA DEE K Sbjct EDRLMTAAFGTQPKRRLNRVLDAIGFEYPDYGRLGGDAGGPKKKRIASAVDEESTK

7 NCBI Blast:MARVRSTARVEREGDEAEGAETVPISEAMQRSGLVTSERIPTAETDA... Page 7 of 24 >gb AC Length= Zea mays BAC clone CH201-98J13 from chromosome 5, complete sequence Score = 100 bits (250), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 47/56 (84%), Positives = 50/56 (90%), Gaps = 0/56 (0%) ED+LMT AFGT+PKRRLNRVLDAIGFEY DYGRL GDAGGPK+KRIASA DEE K Sbjct EDRLMTAAFGTQPKRRLNRVLDAIGFEYPDYGRLGGDAGGPKKKRIASAVDEESTK Score = 78.2 bits (191), Expect = 9e-13, Method: Compositional matrix adjust. Identities = 36/51 (71%), Positives = 41/51 (81%), Gaps = 0/51 (0%) EDQLMT AFGTRPKRRLNRVLDA+GFEY DY +L+ A G +RKR A A + Sbjct EDQLMTAAFGTRPKRRLNRVLDALGFEYPDYAQLNKGAEGQRRKRTAEALN Score = 45.8 bits (107), Expect = 0.006, Method: Compositional matrix adjust. Identities = 27/58 (47%), Positives = 33/58 (57%), Gaps = 3/58 (5%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADY---GRLSGDAGGPKRKRIASAADEEVA 62 ED ++ AF + K+RLNRV DAIGF Y DY + G RK +ASAA E A Sbjct EDNALSAAFES*KKKRLNRVFDAIGFMYPDYRYPPQGQKRKSGTSRKDVASAASSEPA >gb AC Length= Zea mays BAC clone CH J9 from chromosome 8, complete sequence Score = 89.0 bits (219), Expect = 5e-16, Method: Compositional matrix adjust. Identities = 42/56 (75%), Positives = 46/56 (83%), Gaps = 0/56 (0%) EDQLMT AFGTRPKRRLNRVLDA+ F+Y DY +L GDA GPKRKRI SA D+E K Sbjct EDQLMTAAFGTRPKRRLNRVLDALNFDYPDYEQLGGDAEGPKRKRIVSALDKEGTK >gb AC Length= Zea mays BAC clone CH N10 from chromosome 5, complete sequence Score = 84.3 bits (207), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 39/52 (75%), Positives = 42/52 (81%), Gaps = 0/52 (0%) EDQLMT AFGTRPKRRLNRVLDA+GFEY DY L+ AGG KRKR+ A DE Sbjct EDQLMTAAFGTRPKRRLNRVLDALGFEYPDYENLNKGAGGQKRKRVTEALDE >gb GU Length= Zea mays cultivar B73 clone BAC c0171e08 genomic sequence Score = 83.6 bits (205), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 39/52 (75%), Positives = 42/52 (81%), Gaps = 0/52 (0%) EDQLMT AFGTRPKRRLNRVLDA+GFEY DY L+ AGG KRKRI A +E Sbjct EDQLMTAAFGTRPKRRLNRVLDALGFEYPDYKNLNKGAGGQKRKRITEALNE >gb AF Contiguous genomic DNA sequence comprising the 19-kDa-zein gene family from Zea mays, complete sequence Length= Score = 83.6 bits (205), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 39/53 (74%), Positives = 43/53 (82%), Gaps = 0/53 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEE 60 EDQLMT AFGTRPKRRLNRVLDA+GF+Y DY L+ AGG KRKRI A +EE Sbjct 3908 EDQLMTAAFGTRPKRRLNRVLDALGFDYPDYENLNKGAGGQKRKRITEAMNEE 3750 Score = 75.9 bits (185), Expect = 4e-12, Method: Composition-based stats. Identities = 38/56 (68%), Positives = 43/56 (77%), Gaps = 0/56 (0%) EDQLMT AFGTRPK+RLN VLDA+ F+Y DY +L G A G KRKRI SA D+E K

8 NCBI Blast:MARVRSTARVEREGDEAEGAETVPISEAMQRSGLVTSERIPTAETDA... Page 8 of 24 Sbjct EDQLMTAAFGTRPKQRLNHVLDALNFDYPDYEQLVGGAEGQKRKRIVSALDKEGTK Score = 48.9 bits (115), Expect = 5e-04, Method: Compositional matrix adjust. Identities = 29/58 (50%), Positives = 33/58 (57%), Gaps = 3/58 (5%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYG---RLSGDAGGPKRKRIASAADEEVA 62 ED ++ AFG R K+RLNRV DAIGF Y DY R G K +ASAA E A Sbjct EDTALSAAFGGRKKKRLNRVFDAIGFVYPDYCYPIRGQKRKGTASVKEVASAAPSEPA Score = 47.0 bits (110), Expect = 0.002, Method: Compositional matrix adjust. Identities = 21/31 (68%), Positives = 24/31 (78%), Gaps = 0/31 (0%) ED ++VAFG R K+RLNRV DAIGF Y DY Sbjct EDTALSVAFGGRKKKRLNRVFDAIGFVYPDY Score = 47.0 bits (110), Expect = 0.003, Method: Compositional matrix adjust. Identities = 28/59 (48%), Positives = 33/59 (56%), Gaps = 3/59 (5%) Query 7 DEDQLMTVAFGTRPKRRLNRVLDAIGFEYADY---GRLSGDAGGPKRKRIASAADEEVA 62 ED ++ AFG+R K+RLNRV DAIGF Y Y R G K ASAA E+A Sbjct SEDNALSTAFGSRKKKRLNRVFDAIGFVYPVYRYPPRGQKRKGATSGKVAASAAPSELA Score = 45.1 bits (105), Expect = 0.008, Method: Compositional matrix adjust. Identities = 27/57 (48%), Positives = 32/57 (57%), Gaps = 2/57 (3%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKR-IASAADEEVAK 63 ED ++ AFG K+RLNRV D+IGF Y DY R G KRK + DE V K Sbjct EDNALSTAFGGWGKKRLNRVFDSIGFVYPDY-RYPLRGHGKKRKTATPTTPDEPVPK >gb AC Length= Zea mays BAC clone CH B12 from chromosome 5, complete sequence Score = 83.6 bits (205), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 39/52 (75%), Positives = 42/52 (81%), Gaps = 0/52 (0%) EDQLMT AFGTRPKRRLNRVLDA+GFEY DY L+ AGG KRKRI A +E Sbjct EDQLMTAAFGTRPKRRLNRVLDALGFEYPDYENLNKGAGGQKRKRITEALNE >gb AC Length= Zea mays BAC clone CH O9 from chromosome 5, complete sequence Score = 83.6 bits (205), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 39/52 (75%), Positives = 42/52 (81%), Gaps = 0/52 (0%) EDQLMT AFGTRPKRRLNRVLDA+GFEY DY L+ AGG KRKRI A +E Sbjct EDQLMTAAFGTRPKRRLNRVLDALGFEYPDYENLNKGAGGQKRKRITEALNE >gb AC sequence Length= Genomic seqeunce for Zea mays BAC clone ZMMBBb0448F23, complete Score = 83.2 bits (204), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 39/52 (75%), Positives = 42/52 (81%), Gaps = 0/52 (0%) EDQLMT AFGTRPKRRLNRVLDA+GFEY DY L+ AGG KRKRI A +E Sbjct EDQLMTAAFGTRPKRRLNRVLDALGFEYPDYENLNKGAGGQKRKRITEALNE Score = 44.3 bits (103), Expect = 0.014, Method: Compositional matrix adjust. Identities = 19/31 (62%), Positives = 22/31 (71%), Gaps = 0/31 (0%) ED ++ AFG K+RLNRV DAIGF Y DY Sbjct EDNALSAAFGGWKKKRLNRVFDAIGFMYPDY >gb AC Length= Zea mays BAC clone CH O5 from chromosome 9, complete sequence

9 NCBI Blast:MARVRSTARVEREGDEAEGAETVPISEAMQRSGLVTSERIPTAETDA... Page 9 of 24 Score = 82.0 bits (201), Expect = 6e-14, Method: Compositional matrix adjust. Identities = 38/52 (74%), Positives = 41/52 (79%), Gaps = 0/52 (0%) EDQLMT AFGTRPKRRLNRVLDA+GFEY DY L+ GG KRKRI A +E Sbjct EDQLMTAAFGTRPKRRLNRVLDALGFEYPDYENLNKGVGGQKRKRITEALNE Score = 79.7 bits (195), Expect = 3e-13, Method: Compositional matrix adjust. Identities = 39/55 (71%), Positives = 43/55 (79%), Gaps = 2/55 (3%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIAS--AADEE 60 EDQLMT AFGTRPKRRLNRV DA+GFEY DY +L+ AGG KRKR+A DEE Sbjct EDQLMTAAFGTRPKRRLNRVFDALGFEYPDYEQLNKGAGGHKRKRVAEILTKDEE Score = 44.3 bits (103), Expect = 0.014, Method: Compositional matrix adjust. Identities = 25/51 (50%), Positives = 30/51 (59%), Gaps = 3/51 (5%) ED ++ AFG K+RLNRV DAIGF Y DY G KRK +SA + Sbjct EDTALSAAFGG*KKKRLNRVFDAIGFVYPDY---RYPTRGQKRKNTSSAKE >gb AC Length= Zea mays clone ZMMBBb-37E5, complete sequence Score = 82.0 bits (201), Expect = 6e-14, Method: Compositional matrix adjust. Identities = 38/52 (74%), Positives = 41/52 (79%), Gaps = 0/52 (0%) EDQLMT AFGTRPKRRLNRVLDA+GFEY DY L+ GG KRKRI A +E Sbjct 6394 EDQLMTAAFGTRPKRRLNRVLDALGFEYPDYENLNKGVGGQKRKRITEALNE 6549 Score = 65.1 bits (157), Expect = 8e-09, Method: Compositional matrix adjust. Identities = 30/49 (62%), Positives = 37/49 (76%), Gaps = 0/49 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASA 56 ED LMT FGTR K RL+R++DA+GFEY +Y RL +AGG KRKR+ S Sbjct ED*LMTATFGTREKWRLDRLMDALGFEYPNYKRLDDEAGGLKRKRVVSV Score = 59.7 bits (143), Expect = 3e-07, Method: Compositional matrix adjust. Identities = 30/45 (67%), Positives = 34/45 (76%), Gaps = 3/45 (6%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKR 52 EDQLMT AFGTRPKRRLNRV+DA+ FEY D +S A PK +R Sbjct EDQLMTAAFGTRPKRRLNRVMDALNFEYPD---MSDSARVPKGQR Score = 51.2 bits (121), Expect = 1e-04, Method: Compositional matrix adjust. Identities = 28/53 (53%), Positives = 34/53 (65%), Gaps = 1/53 (1%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEE 60 ED ++ AFG++ K+RLNRV DAIGF+Y DY R G KRK A AA E Sbjct EDNALSTAFGSQGKKRLNRVFDAIGFDYPDY-RYPLRGQGKKRKATALAASAE Score = 48.5 bits (114), Expect = 8e-04, Method: Compositional matrix adjust. Identities = 28/49 (58%), Positives = 30/49 (62%), Gaps = 1/49 (2%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASA 56 ED MT+AF R K+RLNRV D IGF Y DY LS G KRK SA Sbjct EDDAMTLAFVGRGKKRLNRVFDVIGFVYPDYCYLSRKQGK-KRKDATSA Score = 47.8 bits (112), Expect = 0.001, Method: Compositional matrix adjust. Identities = 30/56 (54%), Positives = 35/56 (63%), Gaps = 3/56 (5%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYG-RLSGDAGGPKRKRIASAADEEVA 62 ED ++ +FG R K+RLNRV DAIGF Y DY L G G KRK ASA +E A Sbjct EDNALSASFGGRGKKRLNRVFDAIGFVYPDYCYPLRGR--GKKRKTAASATLDEPA >gb GQ Length=27503 Zea mays chromosome 4 sequence AGI.478 genomic sequence Score = 81.6 bits (200), Expect = 7e-14, Method: Compositional matrix adjust. Identities = 39/49 (80%), Positives = 40/49 (82%), Gaps = 0/49 (0%)

10 Page 10 of 24 Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASA 56 EDQLMT AFGTRPKRRLNRVLDAIGFEY DY RL A G KRKR+A A Sbjct EDQLMTAAFGTRPKRRLNRVLDAIGFEYPDYERLDKGAEGQKRKRVAGA Score = 73.9 bits (180), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 35/56 (63%), Positives = 42/56 (75%), Gaps = 0/56 (0%) EDQLMT AFGTRPKRRLN V+DA+ FEY DY +L+ A G KRKRI S + + A+ Sbjct EDQLMTAAFGTRPKRRLNWVMDALKFEYPDYEQLNKGAEGSKRKRIVSILNRQAAR Score = 45.8 bits (107), Expect = 0.005, Method: Compositional matrix adjust. Identities = 25/51 (50%), Positives = 31/51 (61%), Gaps = 3/51 (5%) ED ++ AFG R ++RLNRV DAIGF Y DY G KRK +SA + Sbjct 4900 EDTALSAAFGGRKRKRLNRVFDAIGFVYPDY---RYPVRGEKRKNTSSAKE 5043 >gb AY Zea mays rust resistance protein rp3-1 (rp3-1) gene, complete cds; and truncated rust resistance protein rp3-2t (rp3-2) gene, complete sequence Length= bp at 5' side: rust resistance protein rp3-1 Score = 81.6 bits (200), Expect = 8e-14, Method: Compositional matrix adjust. Identities = 39/49 (80%), Positives = 40/49 (82%), Gaps = 0/49 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASA 56 EDQLMT AFGTRPKRRLNRVLDAIGFEY DY RL A G KRKR+AS Sbjct EDQLMTAAFGTRPKRRLNRVLDAIGFEYPDYERLDKGAEGQKRKRVAST bp at 3' side: rust resistance protein rp3-1 Score = 65.5 bits (158), Expect = 6e-09, Method: Composition-based stats. Identities = 31/43 (73%), Positives = 33/43 (77%), Gaps = 0/43 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKR 50 EDQLMT FGTRPKRRLNRV+DA+ FEY DY RL A G KR Sbjct EDQLMTATFGTRPKRRLNRVMDALNFEYPDYERLDRGAEGQKR bp at 5' side: rust resistance protein rp3-1 Score = 47.4 bits (111), Expect = 0.002, Method: Compositional matrix adjust. Identities = 28/53 (53%), Positives = 31/53 (59%), Gaps = 1/53 (1%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEE 60 ED + AFG R ++RLNRV DAIGF Y DY R G KRK ASA E Sbjct EDNALFAAFGGRGRKRLNRVFDAIGFVYPDY-RYPLRGQGKKRKTAASATPVE >gb AF Zea mays cultivar B73 putative gag protein, putative gag-pol precursor, putative transposase, putative copia-type pol polyprotein, putative copia-like retrotransposon Hopscotch polyprotein, putative gag protein, putative prpol, putative prpol, putative pol protein, putative pol protein, putative gag protein, and teosinte branched1 protein genes, complete cds Length= Score = 81.6 bits (200), Expect = 8e-14, Method: Composition-based stats. Identities = 39/56 (70%), Positives = 44/56 (79%), Gaps = 0/56 (0%) EDQLMT AFGTRPKRRLNRV+DA+ FEY DY RL DA G KRKR+A A ++E K Sbjct EDQLMTAAFGTRPKRRLNRVMDALDFEYPDYERLDKDAEGQKRKRVAGALNKEATK Score = 46.6 bits (109), Expect = 0.003, Method: Compositional matrix adjust. Identities = 21/31 (68%), Positives = 23/31 (75%), Gaps = 0/31 (0%) ED+ MTVAFG R KRRLNRV + IGF Y Y

11 Page 11 of 24 Sbjct EDEAMTVAFGARGKRRLNRVFNVIGFVYPHY >gb AC Length= Zea mays BAC clone CH A17 from chromosome 5, complete sequence Score = 81.3 bits (199), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 40/55 (73%), Positives = 44/55 (80%), Gaps = 2/55 (3%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIAS--AADEE 60 EDQLMT AFGTRPKRRLNRV DA+GFEY DY +L+ AGG KRKR+A A DEE Sbjct EDQLMTAAFGTRPKRRLNRVFDALGFEYPDYEQLNKGAGGHKRKRVAEILAKDEE Score = 77.8 bits (190), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 38/53 (72%), Positives = 40/53 (76%), Gaps = 0/53 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEE 60 EDQLMT AFGTRPKRRLNRVLDAIGFEY DY RL G K KR+A A +E Sbjct EDQLMTAAFGTRPKRRLNRVLDAIGFEYPDYERLDKGVEGQKMKRVAGALIKE Score = 48.5 bits (114), Expect = 9e-04, Method: Compositional matrix adjust. Identities = 28/55 (51%), Positives = 31/55 (57%), Gaps = 3/55 (5%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEEVA 62 ED M+ AFG R K+RLNRV DAIGF Y DY KRK SA +E A Sbjct EDTAMSAAFGGRKKKRLNRVFDAIGFVYPDY---CYPIRRQKRKNTTSAKEETAA >gb AC sequence Length= Zea mays BAC clone CH G11 from chromosome 10, complete Score = 80.5 bits (197), Expect = 2e-13, Method: Composition-based stats. Identities = 39/53 (74%), Positives = 43/53 (82%), Gaps = 0/53 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEE 60 EDQLMT AFGTRPKRRLNRVLDA+GF+Y DY L+ AGG KRKRI A +EE Sbjct EDQLMTAAFGTRPKRRLNRVLDALGFDYPDYENLNKGAGGQKRKRITEAMNEE Score = 72.4 bits (176), Expect = 5e-11, Method: Compositional matrix adjust. Identities = 35/56 (63%), Positives = 41/56 (74%), Gaps = 0/56 (0%) EDQLMT AFGTR KR LN+V+DA+ F+Y DY RLS A GPKRKR S +VA+ Sbjct EDQLMTAAFGTRLKRMLNQVMDALKFDYPDYERLSKGAEGPKRKRAVSIIQRQVAR Score = 71.6 bits (174), Expect = 8e-11, Method: Compositional matrix adjust. Identities = 34/48 (71%), Positives = 39/48 (82%), Gaps = 0/48 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIAS 55 EDQLMT A GTR KRRLNRV+DA+GF+Y DY RL +AGG KRKR+ S Sbjct EDQLMTDAIGTREKRRLNRVMDALGFKYPDYERLDDEAGGLKRKRVVS Score = 66.2 bits (160), Expect = 4e-09, Method: Composition-based stats. Identities = 31/48 (65%), Positives = 36/48 (75%), Gaps = 0/48 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIAS 55 EDQLM AFGTRPKRRLNRV+D + F+Y DY RL A G KRKR+ + Sbjct EDQLMIAAFGTRPKRRLNRVMDVLNFKYPDYERLDEGARGAKRKRVVN Score = 42.4 bits (98), Expect = 0.052, Method: Compositional matrix adjust. Identities = 25/56 (45%), Positives = 33/56 (59%), Gaps = 2/56 (3%) ED ++ AFG R K+RLNRV +AIGF Y DY G K+++ A+ A V K Sbjct EDDALSSAFGGRGKKRLNRVFEAIGFIYPDYCYPLRRQG--KKRKTAALAISAVPK >gb AC Length= Zea mays BAC clone CH G15 from chromosome 8, complete sequence Score = 80.1 bits (196), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 37/52 (72%), Positives = 42/52 (81%), Gaps = 0/52 (0%)

12 Page 12 of 24 EDQLMT AFGTRPKRRLNRVLDA+GFEY DY +L+ G KRKR+A A +E Sbjct EDQLMTAAFGTRPKRRLNRVLDALGFEYPDYEQLNKIVEGRKRKRVAKALNE >gb AC Length= Zea mays BAC clone CH201-98H14 from chromosome 6, complete sequence Score = 80.1 bits (196), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 38/56 (68%), Positives = 43/56 (77%), Gaps = 0/56 (0%) EDQLMT AFGTRPKR LNRV+DA+ FEY DY RL DA G KRKR+A A ++E K Sbjct EDQLMTAAFGTRPKRMLNRVMDALDFEYPDYERLDKDAEGQKRKRVAGALNKEATK Score = 48.5 bits (114), Expect = 8e-04, Method: Compositional matrix adjust. Identities = 28/55 (51%), Positives = 31/55 (57%), Gaps = 3/55 (5%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEEVA 62 ED M+ AFG R K+RLNRV DAIGF Y DY KRK SA +E A Sbjct EDTAMSAAFGGRKKKRLNRVFDAIGFVYPDY---CYPIRRQKRKNTTSAKEETAA Score = 44.3 bits (103), Expect = 0.013, Method: Compositional matrix adjust. Identities = 24/51 (48%), Positives = 29/51 (57%), Gaps = 3/51 (5%) ED ++ AF R K+RLNRV D IGF Y DY G KRK +SA + Sbjct EDTALSAAFRGRKKKRLNRVFDTIGFVYPDYHY---PVQGQKRKNTSSAKE >gb AC Length= Zea mays BAC clone CH M1 from chromosome 5, complete sequence Score = 79.7 bits (195), Expect = 3e-13, Method: Composition-based stats. Identities = 38/53 (72%), Positives = 43/53 (82%), Gaps = 0/53 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEE 60 EDQLMT AFGTRPK+RLNRVLDA+GFEY DY L+ AGG KRKRI A +E+ Sbjct EDQLMTAAFGTRPKQRLNRVLDALGFEYPDYENLNKGAGGQKRKRITEALNED Score = 46.2 bits (108), Expect = 0.004, Method: Compositional matrix adjust. Identities = 28/58 (49%), Positives = 32/58 (56%), Gaps = 3/58 (5%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADY---GRLSGDAGGPKRKRIASAADEEVA 62 ED ++ AFG R K+RLNRV DAIG+ Y DY R G K ASAA E A Sbjct EDTALSAAFGGRKKKRLNRVFDAIGYVYPDYRYPARGQKRKGTTSAKETASAAPSEPA >gb AF Zea mays putative transposase (Z195D10.1) gene, partial cds; glycyl-trna synthetase (Z195D10.2), ornithine carbamoyltransferase (Z195D10.3), putative gag protein (Z195D10.5), putative SET-domain transcriptional regulator (Z195D10.7), putative oxysterol-binding protein (Z195D10.8), putative polyprotein (Z195D10.9), putative oxysterol-binding protein (Z195D10.10), putative gag-pol polyprotein (Z195D10.11), putative phosphatidylinositol-4-phosphate-5-kinase (Z195D10.12), hypothetical protein (Z195D10.15), putative gag-pol polyprotein (Z195D10.16), putative polyprotein (Z195D10.17), putative retrotransposon protein (Z195D10.18), and prpol (Z195D10.19) genes, complete cds; and putative teosinte branched2 (Z195D10.20) gene, partial cds Length= Score = 79.7 bits (195), Expect = 3e-13, Method: Compositional matrix adjust. Identities = 38/52 (74%), Positives = 41/52 (79%), Gaps = 0/52 (0%) EDQLMT AFGTRPK+RLNRVLDA+GFEY DY L+ AGG KRKR A DE Sbjct EDQLMTAAFGTRPKQRLNRVLDALGFEYPDYENLNKGAGGQKRKRGTEALDE Score = 45.8 bits (107), Expect = 0.005, Method: Composition-based stats. Identities = 27/52 (52%), Positives = 30/52 (58%), Gaps = 3/52 (5%)

13 Page 13 of 24 ED M+ AFG R K+RLNRV DAIGF Y DY KRK SA +E Sbjct EDTAMSAAFGGRKKKRLNRVFDAIGFVYPDY---CYPIRRQKRKNTTSAKEE >gb AC Length= Zea mays BAC clone Z418K17, complete sequence Score = 79.3 bits (194), Expect = 4e-13, Method: Compositional matrix adjust. Identities = 36/51 (71%), Positives = 41/51 (81%), Gaps = 0/51 (0%) EDQLMT AFGTRPKRRLNRVLDA+GFEY DY L+ G KRKR+A A++ Sbjct EDQLMTAAFGTRPKRRLNRVLDALGFEYPDYENLNKSVEGRKRKRVAEASN >gb AY Length= Zea mays BAC clone c573f08, complete sequence Score = 78.6 bits (192), Expect = 8e-13, Method: Compositional matrix adjust. Identities = 35/46 (77%), Positives = 38/46 (83%), Gaps = 0/46 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRI 53 EDQLMT AFGTRPKRRLNRV+DA+ FEY DY RL DA G KRKR+ Sbjct EDQLMTAAFGTRPKRRLNRVMDALDFEYPDYERLDKDAKGQKRKRV Score = 48.9 bits (115), Expect = 6e-04, Method: Compositional matrix adjust. Identities = 20/32 (63%), Positives = 24/32 (75%), Gaps = 0/32 (0%) Query 7 DEDQLMTVAFGTRPKRRLNRVLDAIGFEYADY 38 ED ++ AFG+R K+RLNRV DAIGF Y DY Sbjct SEDNALSAAFGSRKKKRLNRVFDAIGFVYPDY Score = 36.6 bits (83), Expect = 3.2, Method: Compositional matrix adjust. Identities = 17/39 (44%), Positives = 25/39 (65%), Gaps = 0/39 (0%) Query 25 NRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEEVAK 63 NRV++A+ F+Y DY +L A KRKRI S + + A+ Sbjct NRVMNALNFDYPDYEKLDEGAERIKRKRIVSILNRQAAR >gb AC Length= Zea mays clone ZMMBBb-272P17, complete sequence Score = 77.8 bits (190), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 39/56 (70%), Positives = 44/56 (79%), Gaps = 2/56 (3%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAA--DEEV 61 EDQLMT AFG RPKRRLNRVLDA+GFEY DY +L+ A G KRKR+A A DEE+ Sbjct 1468 EDQLMTAAFGARPKRRLNRVLDALGFEYPDYEQLNKGAEGLKRKRVAEALIRDEEI 1635 >gb AY Length= Zea mays cultivar B73 locus 9008, complete sequence bp at 5' side: unknown 9213 bp at 3' side: unknown Score = 77.4 bits (189), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 36/56 (65%), Positives = 41/56 (74%), Gaps = 0/56 (0%) EDQLMT AFGTRPKRRLNRV+D + FEY DY RL+ A G KRKRI S + A+ Sbjct EDQLMTAAFGTRPKRRLNRVMDVLNFEYPDYERLNKGAEGQKRKRIVSVLSRQAAR bp at 5' side: unknown bp at 3' side: unknown Score = 44.3 bits (103), Expect = 0.013, Method: Compositional matrix adjust. Identities = 19/31 (62%), Positives = 23/31 (75%), Gaps = 0/31 (0%) E+ ++ AFG R K+RLNRV DAIGF Y DY Sbjct ENTALSAAFGGRKKKRLNRVFDAIGFFYPDY 40876

14 Page 14 of 24 >gb AF Zea mays retrotransposon Cinful-2 Length=8458 Score = 76.6 bits (187), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 36/56 (65%), Positives = 40/56 (72%), Gaps = 0/56 (0%) EDQLMT AFGTRPKRRLNRV+D + FEY DY RL A G KRKRI S + A+ Sbjct 7566 EDQLMTTAFGTRPKRRLNRVMDTLNFEYPDYKRLDKGAEGVKRKRIVSILSRQAAR 7399 >gb AF complete cds Length= Zea mays alcohol dehydrogenase 1 (adh1) gene, adh1-f allele, Score = 76.6 bits (187), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 36/56 (65%), Positives = 40/56 (72%), Gaps = 0/56 (0%) EDQLMT AFGTRPKRRLNRV+D + FEY DY RL A G KRKRI S + A+ Sbjct 8793 EDQLMTTAFGTRPKRRLNRVMDTLNFEYPDYKRLDKGAEGVKRKRIVSILSRQAAR 8960 >gb AC Length= Zea mays BAC clone CH N23 from chromosome 5, complete sequence Score = 76.6 bits (187), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 38/55 (70%), Positives = 42/55 (77%), Gaps = 2/55 (3%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIAS--AADEE 60 EDQLMT AFGTRPKRRLNRV DA+GFEY DY +L+ A G KRKR+A DEE Sbjct EDQLMTAAFGTRPKRRLNRVFDALGFEYPDYEQLNKGAEGHKRKRVAEILTKDEE >gb AC sequence Length= Zea mays BAC clone ZMMBBb-223D21 from chromosome 5, complete Score = 76.6 bits (187), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 38/55 (70%), Positives = 42/55 (77%), Gaps = 2/55 (3%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIAS--AADEE 60 EDQLMT AFGTRPKRRLNRV DA+GFEY DY +L+ A G KRKR+A DEE Sbjct EDQLMTAAFGTRPKRRLNRVFDALGFEYPDYEQLNKGAEGHKRKRVAEILTKDEE >gb AC sequence Length= Zea mays BAC clone CH O17 from chromosome unknown, complete Score = 76.3 bits (186), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 39/55 (71%), Positives = 42/55 (77%), Gaps = 2/55 (3%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASA--ADEE 60 EDQLMT AFG RPKRRLNRVLDA+GFEY DY +L+ A G KRKRIA DEE Sbjct EDQLMTAAFGARPKRRLNRVLDALGFEYPDYEQLNKGAEGLKRKRIAETPITDEE Score = 48.1 bits (113), Expect = 0.001, Method: Compositional matrix adjust. Identities = 20/32 (63%), Positives = 24/32 (75%), Gaps = 0/32 (0%) Query 7 DEDQLMTVAFGTRPKRRLNRVLDAIGFEYADY 38 ED ++ AFG+R K+RLNRV DAIGF Y DY Sbjct SEDNALSAAFGSRKKKRLNRVFDAIGFVYPDY >gb AY Length= Zea mays cultivar Mo17 locus 9008, complete sequence bp at 5' side: unknown 9648 bp at 3' side: unknown Score = 75.9 bits (185), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 35/56 (63%), Positives = 41/56 (74%), Gaps = 0/56 (0%) EDQLMT AFGTRPK+RLNRV+D + FEY DY RL+ A G KRKRI S + A+ Sbjct EDQLMTAAFGTRPKQRLNRVMDVLNFEYPDYERLNKGAEGQKRKRIVSVLSRQAAR >gb AY Zea mays putative growth-regulating factor 1 (Z214A02.12), putative

15 Page 15 of 24 40S ribosomal protein S8 (Z214A02.25), and putative casein kinase I (Z214A02.27) genes, complete cds Length= Score = 75.9 bits (185), Expect = 5e-12, Method: Compositional matrix adjust. Identities = 38/55 (70%), Positives = 42/55 (77%), Gaps = 2/55 (3%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRI--ASAADEE 60 EDQLMT AFGTRPKRRLNRVLDA+ FEY DY L+ + G KRKR+ AS DEE Sbjct EDQLMTAAFGTRPKRRLNRVLDALEFEYPDYENLNKNVEGQKRKRMTEASNKDEE >gb AC Length= Zea mays BAC clone CH201-53J11 from chromosome 5, complete sequence Score = 75.1 bits (183), Expect = 7e-12, Method: Compositional matrix adjust. Identities = 37/52 (72%), Positives = 41/52 (79%), Gaps = 0/52 (0%) EDQLMT AFGTR KRRLN V+DAIGFEY DY RL A G KRKR+ASA ++ Sbjct EDQLMTAAFGTRSKRRLN*VMDAIGFEYPDYERLDKGAEGQKRKRVASALNK >gb AC Length= Zea mays BAC clone CH N20 from chromosome 4, complete sequence Score = 75.1 bits (183), Expect = 9e-12, Method: Composition-based stats. Identities = 35/56 (63%), Positives = 40/56 (72%), Gaps = 0/56 (0%) EDQLMT FGTRPK RLNRV+DA+ FEY DY RLS GPKRKR+ S + A+ Sbjct EDQLMTATFGTRPK*RLNRVMDALNFEYPDYERLSKGVEGPKRKRVVSVLSRQAAR Score = 74.3 bits (181), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 34/49 (70%), Positives = 37/49 (76%), Gaps = 0/49 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASA 56 EDQLM FGTRPK RLNRV+DA+ FEY DY RL DA G KRKR+A A Sbjct EDQLMIATFGTRPKWRLNRVMDALDFEYPDYERLDKDAEGQKRKRVAGA >gb AC Length= Zea mays BAC clone ZMMBBb-334D6 from chromosome 5, complete sequence Score = 74.7 bits (182), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 34/47 (73%), Positives = 39/47 (83%), Gaps = 0/47 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIA 54 EDQLMT AFG RPKRRLNRV DA+GFEY+DY +L+ A G KRKR+A Sbjct EDQLMTAAFGARPKRRLNRVFDALGFEYSDYEQLNKGAEGHKRKRVA >gb AC Length= Zea mays BAC clone CH201-73M20 from chromosome 5, complete sequence Score = 74.7 bits (182), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 34/47 (73%), Positives = 39/47 (83%), Gaps = 0/47 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIA 54 EDQLMT AFG RPKRRLNRV DA+GFEY+DY +L+ A G KRKR+A Sbjct EDQLMTAAFGARPKRRLNRVFDALGFEYSDYEQLNKGAEGHKRKRVA >gb AY Length= Zea mays cultivar B73 locus 9002, complete sequence bp at 5' side: putative integral membrane protein bp at 3' side: bronze-2 protein Score = 74.3 bits (181), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 34/56 (61%), Positives = 41/56 (74%), Gaps = 0/56 (0%) +DQLMT AFGTRPKRRLNRV+D + FEY DY RL+ A G KRKR+ S + A+ Sbjct KDQLMTAAFGTRPKRRLNRVMDVLNFEYPDYERLNKGAEGVKRKRVVSVLSRQAAR

16 Page 16 of bp at 5' side: hypothetical protein Score = 48.9 bits (115), Expect = 6e-04, Method: Compositional matrix adjust. Identities = 26/50 (52%), Positives = 33/50 (66%), Gaps = 2/50 (4%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAA 57 ED MT+AFG R KRRLN+V D IGF Y DY S G K+++ A++A Sbjct EDGAMTLAFGGRGKRRLNKVFDVIGFVYPDYCYPSRKQG--KKRKAATSA bp at 5' side: hypothetical protein bp at 3' side: hypothetical protein Score = 45.4 bits (106), Expect = 0.007, Method: Compositional matrix adjust. Identities = 19/31 (62%), Positives = 23/31 (75%), Gaps = 0/31 (0%) ED ++ FG+R K+RLNRV DAIGF Y DY Sbjct EDNALSATFGSRKKKRLNRVFDAIGFVYPDY >gb AC Length= Zea mays BAC clone CH201-65L11 from chromosome 5, complete sequence Score = 73.9 bits (180), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 34/47 (73%), Positives = 38/47 (81%), Gaps = 0/47 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIA 54 EDQLMT AFGTRPKRRLNRV DA+G EY DY +L+ A G KRKR+A Sbjct EDQLMTAAFGTRPKRRLNRVFDALGLEYPDYEQLNKGAEGHKRKRVA >gb AC Length= Zea mays BAC clone CH A2 from chromosome 8, complete sequence Score = 72.4 bits (176), Expect = 5e-11, Method: Compositional matrix adjust. Identities = 34/48 (71%), Positives = 38/48 (80%), Gaps = 0/48 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIAS 55 +DQLMT AFGT PKRRLNRV+DA+ FEY +Y RL AGG KRKRI S Sbjct KDQLMTAAFGTHPKRRLNRVMDALNFEYPNYERLDEGAGGVKRKRIVS Score = 66.6 bits (161), Expect = 3e-09, Method: Compositional matrix adjust. Identities = 32/53 (61%), Positives = 37/53 (70%), Gaps = 0/53 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEE 60 EDQ MT AFGTR K RLNRV+DA+ FEY DY RL G G KRKR+ S + + Sbjct EDQQMTAAFGTRQK*RLNRVMDALNFEYQDYERLDGGIIGAKRKRVVSILNRQ Score = 49.3 bits (116), Expect = 5e-04, Method: Compositional matrix adjust. Identities = 28/59 (48%), Positives = 35/59 (60%), Gaps = 3/59 (5%) Query 7 DEDQLMTVAFGTRPKRRLNRVLDAIGFEYADY---GRLSGDAGGPKRKRIASAADEEVA 62 ED ++VAFG++ K+RLN V DAIGF Y DY + G RK +ASAA E A Sbjct SEDNALSVAFGSQKKKRLNIVFDAIGFVYPDYRYPPQGQKRKGATSRKVVASAAPSEPA Score = 47.8 bits (112), Expect = 0.001, Method: Compositional matrix adjust. Identities = 26/45 (58%), Positives = 26/45 (58%), Gaps = 9/45 (20%) Query 3 EADSDE DQLMTVAFGTRPKRRLNRVLDAIGFEYADY 38 EA SDE D MT AFG R KRRLNRV D IGF Y DY Sbjct EASSDELLGAYSKAKDDAMTTAFGARGKRRLNRVFDVIGFIYPDY Score = 47.4 bits (111), Expect = 0.002, Method: Compositional matrix adjust. Identities = 28/58 (49%), Positives = 32/58 (56%), Gaps = 3/58 (5%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADY---GRLSGDAGGPKRKRIASAADEEVA 62 ED ++ AFG+R K+RLNRV DAIGF Y DY R G K ASA E A Sbjct EDNALSAAFGSRKKKRLNRVFDAIGFVYLDYRYPPRGQKSKGATSGKTAASAVSSEPA >gb AC Length=99606 Zea mays genomic clone ZM15C05 sequence, complete sequence Score = 69.7 bits (169), Expect = 3e-10, Method: Composition-based stats.

17 Page 17 of 24 Identities = 35/47 (75%), Positives = 37/47 (79%), Gaps = 0/47 (0%) Query 9 DQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIAS 55 DQLMT AFGTRPKRRLN+VLD IGFEY DY RL A G KRK +AS Sbjct DQLMTAAFGTRPKRRLNKVLDVIGFEYPDYERLDKGAEG*KRKIVAS Score = 48.1 bits (113), Expect = 0.001, Method: Compositional matrix adjust. Identities = 28/49 (58%), Positives = 31/49 (64%), Gaps = 1/49 (2%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASA 56 +D MT+AFG R K+RLNRV D IGF Y DY S G KRK ASA Sbjct KDDAMTLAFGGRGKKRLNRVFDVIGFVYPDYCYPSRKQ-GKKRKATASA Score = 45.8 bits (107), Expect = 0.005, Method: Compositional matrix adjust. Identities = 26/51 (51%), Positives = 31/51 (61%), Gaps = 3/51 (5%) ED ++ AFG R K+RLNRV AIGF Y DY A G KRK +SA + Sbjct EDTALSAAFGGRKKKRLNRVFYAIGFVYPDY---RYPARGEKRKNTSSAKE >gb AC Length= Zea mays clone CH E16, complete sequence Score = 68.9 bits (167), Expect = 5e-10, Method: Compositional matrix adjust. Identities = 32/50 (64%), Positives = 38/50 (76%), Gaps = 0/50 (0%) Query 7 DEDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASA 56 +EDQLMT AFGTRPK RL+RV+DA+ FEY DY RL+ A G +RK I S Sbjct NEDQLMTAAFGTRPK*RLDRVMDALNFEYPDYERLNKGAKGQERKMIVSV >gb AC Length= Zea mays BAC clone CH N8 from chromosome 5, complete sequence Score = 68.6 bits (166), Expect = 7e-10, Method: Composition-based stats. Identities = 33/55 (60%), Positives = 39/55 (71%), Gaps = 0/55 (0%) Query 9 DQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEEVAK 63 DQLMT AFG RPKRRLNRV+DA+ FEY DY +L+ G KRKRI S + A+ Sbjct DQLMTAAFGARPKRRLNRVMDALNFEYPDYEQLNKGTEGQKRKRIVSVVGRQAAR Score = 67.0 bits (162), Expect = 2e-09, Method: Composition-based stats. Identities = 33/45 (74%), Positives = 35/45 (78%), Gaps = 0/45 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKR 52 EDQLMT AF TRPK RLNRV+DAIGFEY DY RL A G KRK+ Sbjct EDQLMTAAFNTRPK*RLNRVMDAIGFEYPDYERLDKGAEGQKRKK Score = 48.1 bits (113), Expect = 0.001, Method: Compositional matrix adjust. Identities = 28/55 (51%), Positives = 31/55 (57%), Gaps = 3/55 (5%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEEVA 62 ED M+ AFG R K+RLNRV DAIGF Y DY KRK SA +E A Sbjct EDNAMSAAFGGRKKKRLNRVYDAIGFVYPDYCYPIRRQ---KRKNTTSAKEESAA >gb EU Length=985 Zea mays clone mrna sequence Score = 67.0 bits (162), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 32/45 (72%), Positives = 37/45 (83%), Gaps = 0/45 (0%) Query 16 FGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEE 60 FGTRPKRRLNRV+DAIGFEY DY RL A G KRKR+ASA +++ Sbjct 534 FGTRPKRRLNRVMDAIGFEYPDYERLDKGAEGQKRKRVASALNKD 668 >gb AC Length= Zea mays BAC clone CH I12 from chromosome 1, complete sequence Score = 60.8 bits (146), Expect = 2e-07, Method: Composition-based stats. Identities = 29/44 (66%), Positives = 32/44 (73%), Gaps = 0/44 (0%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRK 51 EDQLM AFGTRPKRRLNRV+DA+ FEY DY RL+ K K Sbjct EDQLMIAAFGTRPKRRLNRVMDALKFEYPDYERLNKGVKEQKEK 72154

18 Page 18 of 24 >gb AC Length= Zea mays BAC clone CH N3 from chromosome 3, complete sequence Score = 49.3 bits (116), Expect = 5e-04, Method: Compositional matrix adjust. Identities = 28/59 (48%), Positives = 34/59 (58%), Gaps = 3/59 (5%) Query 7 DEDQLMTVAFGTRPKRRLNRVLDAIGFEYADY---GRLSGDAGGPKRKRIASAADEEVA 62 ED ++VAF ++ K+RLNRV DAIGF Y DY R G K +ASAA E A Sbjct SEDNALSVAFESQKKKRLNRVFDAIGFMYPDYRYPSRGQKRKGATSWKDVASAASSEPA >gb AY Zea mays alcohol dehydrogenase 1 (adh1a) gene, complete cds; Fourf copia_ltr and Huck gypsy_ltr retrotransposons, complete sequence; Opie2 copia_ltr retrotransposon Zeon gypsy_ltr and Opie1 copia_ltr retrotransposons, complete sequence; Ji copia_ltr retrotransposon, complete sequence; and unknown protein (adh1b), cyclin H-1 (adh1c), unknown protein (adh1d), hypothetical protein (adh1e), and unknown protein (adh1f) genes, complete cds Length= Score = 48.9 bits (115), Expect = 6e-04, Method: Compositional matrix adjust. Identities = 28/55 (51%), Positives = 31/55 (57%), Gaps = 3/55 (5%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAADEEVA 62 ED M+ AFG R K+RLNRV DAIGF Y DY KRK SA +E A Sbjct EDTAMSAAFGGRKKKRLNRVFDAIGFVYPDY---CYPIRRQKRKNTTSAKEETTA >gb AY Length= Zea mays cultivar Mo17 locus 9002, complete sequence bp at 5' side: hypothetical protein Score = 48.9 bits (115), Expect = 6e-04, Method: Compositional matrix adjust. Identities = 27/50 (54%), Positives = 33/50 (66%), Gaps = 2/50 (4%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYGRLSGDAGGPKRKRIASAA 57 ED MT+AFG R KRRLNRV D IGF Y DY S G K+++ A++A Sbjct EDDAMTLAFGGRGKRRLNRVFDVIGFVYPDYCYPS*KQG--KKRKAATSA >gb AC Length= Zea mays BAC clone CH M12 from chromosome 8, complete sequence Score = 48.5 bits (114), Expect = 8e-04, Method: Compositional matrix adjust. Identities = 30/54 (56%), Positives = 33/54 (62%), Gaps = 3/54 (5%) Query 8 EDQLMTVAFGTRPKRRLNRVLDAIGFEYADYG-RLSGDAGGPKRKRIASAADEE 60 ED ++ AFG R K+RLNRV DAIGF Y DY L G G KRK ASA E Sbjct EDNALSAAFGGRNKKRLNRVFDAIGFVYLDYCYPLRGQ--GIKRKIAASATTAE >gb AF Length= Zea mays cultivar McC bz locus region 3044 bp at 5' side: Zeon1 gag protein bp at 3' side: serine threonine kinase 1 Score = 48.1 bits (113), Expect = 0.001, Method: Compositional matrix adjust. Identities = 21/31 (68%), Positives = 23/31 (75%), Gaps = 0/31 (0%) ED M+ AFG R K+RLNRV DAIGF Y DY Sbjct EDTAMSAAFGGRKKKRLNRVFDAIGFVYPDY >gb AY Length= Zea mays BAC clone Z013I05, complete sequence Score = 48.1 bits (113), Expect = 0.001, Method: Compositional matrix adjust. Identities = 21/31 (68%), Positives = 23/31 (75%), Gaps = 0/31 (0%) ED M+ AFG R K+RLNRV DAIGF Y DY Sbjct EDNAMSAAFGGRKKKRLNRVFDAIGFVYPDY Score = 45.8 bits (107), Expect = 0.005, Method: Compositional matrix adjust. Identities = 29/49 (60%), Positives = 30/49 (62%), Gaps = 1/49 (2%)