1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
|
GeneMark.hmm (Version 2.2a)
Sequence name: Hvrn.contig8
Sequence length: 50124 bp
G+C content: 44.82%
Matrices file: /home/software/analysis/gene-prediction/genemark/matdir/osativa.mtx (Oryza sativa)
Thu Mar 22 10:25:00 2001
Predicted genes/exons
Gene Exon Strand Exon Exon Range Exon Start/End
# # Type Length Frame
1 1 - Initial 1805 2176 372 3 1
2 5 - Terminal 3108 3229 122 3 2
2 4 - Internal 3869 4501 633 1 2
2 3 - Internal 4820 4888 69 1 2
2 2 - Internal 4981 5061 81 1 2
2 1 - Initial 5296 5656 361 1 1
3 2 - Terminal 7171 7288 118 3 3
3 1 - Initial 7540 7787 248 2 1
4 1 + Single 15431 15757 327 1 3
5 1 + Initial 17526 17696 171 1 3
5 2 + Internal 17772 17887 116 1 2
5 3 + Internal 18005 18074 70 3 3
5 4 + Internal 18456 18539 84 1 3
5 5 + Internal 18628 18714 87 1 3
5 6 + Internal 18807 18870 64 1 1
5 7 + Internal 19944 20038 95 2 3
5 8 + Internal 20139 20293 155 1 2
5 9 + Terminal 20779 20788 10 3 3
6 5 - Terminal 23000 23061 62 3 2
6 4 - Internal 23397 24101 705 1 2
6 3 - Internal 24708 24821 114 1 2
6 2 - Internal 25079 25356 278 1 3
6 1 - Initial 26970 26977 8 2 1
7 3 - Terminal 34218 34310 93 3 1
7 2 - Internal 35900 36301 402 3 1
7 1 - Initial 36392 36448 57 3 1
8 1 + Initial 36531 37064 534 1 3
8 2 + Terminal 37153 37161 9 1 3
9 3 - Terminal 37880 37917 38 3 2
9 2 - Internal 38938 39006 69 1 2
9 1 - Initial 39080 40214 1135 1 1
10 2 - Terminal 41091 41554 464 3 2
10 1 - Initial 41635 41713 79 1 1
11 1 - Single 41744 42061 318 3 1
12 1 + Initial 42171 42212 42 1 3
12 2 + Terminal 42432 42824 393 1 3
13 7 - Terminal 43798 43932 135 3 1
13 6 - Internal 44220 44297 78 3 1
13 5 - Internal 47595 47685 91 3 3
13 4 - Internal 48393 48526 134 2 1
13 3 - Internal 48643 49024 382 3 3
13 2 - Internal 49118 49149 32 2 1
13 1 - Initial 49457 49507 51 3 1
Predicted gene sequence(s):
>Hvrn.contig8|GeneMark.hmm|gene 1|124_aa
MEVAVKGYADASFDTDPDDSKSQTGYVFILNGGAVSWCSSKQSVVADSRCEAEYMAALEA
AKEGVWMKQFMTDLGVVSSALDPLTLLCDNTRAIALAKEPRFHNKTRHIKRRFNLIRDYV
EGED
>Hvrn.contig8|GeneMark.hmm|gene 2|421_aa
MAHAKVTLNFNTFLEKAKLKDDGSNFVDWARNLKLLLQAGKKDYVLNVALGDEPPAAADQ
DAKNAWLACKEDYSVVQCAVLYGLEPGLQRCFERHGAYEMFQELKFIFQKNARIERYETS
ESELRKEHQVLMVNKATSFKRSGKGKKGYGSLEAQLSKYLAGKKAAKEKSENNGCSISMS
NIFYGHAPNVRGLFILNLDSDNTHIHNIETKRVRVNNDSAMFLWHCRLGHIGVKRMKKLH
TDGLLESLDFDSLDTCEPCLMGKMTKTPFSGTMERASDLLEIIHTDVCGPMSAEARGGYR
YFLTFIDDLSRYGYVYLMKHKSETFEKFKQFQSEVENHRNKKIKFLRSDHGGEYLSFEFG
AHLRQCGIVSQLTPLGTPQRNEAMVGPDSNKWLEAMKSEIGSMYGNKVWTLEVLPEGRKA
I
>Hvrn.contig8|GeneMark.hmm|gene 3|121_aa
MVRRQRLIYRMTSFDYRKVFGHYRECTESDEWVPNVHREGPTHPGKPIGPRGGAPALGGL
VGQPKRALCAKDRKSKRKKKRKRSRYFTTTGAPSRCRRTHLLIRLACWIKKAEIIIELYV
C
>Hvrn.contig8|GeneMark.hmm|gene 4|108_aa
MFTTPKAGGGMYLCLSVGWGIVGRRRVMSGCGQGSEMGLVGLRTRRHWAKTGRGGAAGGA
ASIGDGPRRAADKATLGEDGPGRGVGRGGVGRRRVASGGGDREEDEWS
>Hvrn.contig8|GeneMark.hmm|gene 5|283_aa
MDAAVQEAKLLRQVNALIVAHLRDQNLTQAAAAVAAATMTPKADASLPNHLLRLVAKGLA
AEREEAARGGGAPPAFDSAGGGGLARPLGTSAVDFSVQNVRGPSKTFPKHETRHISDHKN
VARCAKFSPDGKHFATGSGDTSIKFFEVSKIKQTMLGDSKEGPGRPVVRTFYDHVQLLTQ
LLVHSTDKVSSFVTNIPGTDHPVAHLYDVNTFTCFLSANPQDSSAAINQVRYSGTGSMYV
TASKDGSLRIWDGVSAECVRPIIGAHGSVEATSAIFTKDESGF
>Hvrn.contig8|GeneMark.hmm|gene 6|388_aa
MGSVVFLEGSEGNLQALKDTLQAYQVASAQKVNLQKSSILDGKGCRDEDKGTLKQTIGID
SEALSERYSGLPTVVGRLKDGSFEYVRERSKGKVSGSVGKASVALQFPSSLCARVLKARY
FKECTIMNTTCPNAMFWKVLSSEKWVPVAIPPVSEGPHGELASWLLRWFAEVGDPERELM
VHAVYGLWLARNEARDGKRIVDPRVVEENVYQHIIEWNAIHMKKPRSTTPTLAVRWSPPE
QGWLKANSDGALAKLRDRGGGGVVLRDHDGAYRGGACYVFRDVSDPEVVEILACRKAVHL
AVQTGATRVHVEVDSKGMAAMLNDQAKNLSAAGPIVEEIKLLGRTLQGFIVSRVRRSGNH
GAHLLAREVRSVYTHVILKQPLFDTCRL
>Hvrn.contig8|GeneMark.hmm|gene 7|183_aa
MVLTEKEAKGFVFSGPVEEAWGLHHDAQFRDLGNNLFLVHFGGEGDWKHSRNNGPWQFDF
MILKGYDGKTRPSEMVFDSVEAWVRVEDLPLDRRTREFGEALGNWLGEVVKVDVERDGFA
KGKYLRVRAKIFVYEPVVRYFNLKESVDDEVETAEGQAGPLEAEAEARRGASVSAHSFGR
WGK
>Hvrn.contig8|GeneMark.hmm|gene 8|180_aa
MASTVSPWSETPQDILGLVIDRLHSSPDHEEPRLSAAWSRFLLAVPVAAANRRGFQRARR
TRHSAAADRARFRAVCRSWHLAMRQHVSTPRVLPWIILSDGYFFTPSDNGCRAPRRLPSL
PKNARCIGSTDGWLALDCTDARNVHTYLLHNPFSDTTVPLPELDPIIANVSEFFAVRKAA
>Hvrn.contig8|GeneMark.hmm|gene 9|413_aa
MPLKFWDETFSTAVYLINRVPSRVIHNQTPLERLFGLTPNYTFLRIFGCAVWPNLRPFNK
HKLEYRSKQCVFIGYNYLHKGYKCLDVSTGRVYVSQDVIFDEHIFPFASLHPNAGAQLRA
ELVLLPPTLLNLSSPLTPSAAPNDPMAISTIYAPTSANSVQDSAGISHDFMQPNVSTDLV
ATENPGLHASESATAAPGAGDPPLQASGSAAAAPGSSPGFVHQPAASVGRSPASTSDPAR
QPDASAARPPVSDPVRPTTVATALFPASDLVRSPQEIRLQRRAPPTAPWIGRGLPRVVGP
PCLLPWTREISLDVVTRYRLLRLRPMQRRRCPMQRPPRLLFLLVCHLIRYLLTLRCPVVS
STICNPCNQHLHPLGLILGEPENLKEAIADPKWKAAMDEEFDWAGCPDDRRST
>Hvrn.contig8|GeneMark.hmm|gene 10|180_aa
MAAAGKPLDDDELVSYILQGLDSDYNPEARIDAQNGSNTNSFSINLASKGGSRNNNDTRP
SGPGGGNPAAYRGAGGGFFPNTLVAPPPSGGRDETCQICKRQGHATWHCFKRYDKNFNPP
PKRQGGGGGNNSGGGGNSSGGNTKSANTVPAAYDVDTNWYLDTGAMDHVTGELEKLAMHD
>Hvrn.contig8|GeneMark.hmm|gene 11|105_aa
MGYLDGTMAEPPAVLTTETDVAGKKEISSTPNPAHVLWYTQDQQVLTFLLASLSRDVLLQ
VHSLASATGVWTAIQQMFASHSRARHIQLRGQLGNTKKGDSPVAI
>Hvrn.contig8|GeneMark.hmm|gene 12|144_aa
MVELEEEDDMSMEEVALMTNNSNYLIILIRPGKGVWLPKPDTAPFNLFIDIVFLQGKLYG
ITQAEDLASVSIDFDDCGMPTVTTVERLIKHPPLESCEFDVWSDAGEKLEADGDMGDEDQ
VENGGEDHDEALNEVDARIQKENR
>Hvrn.contig8|GeneMark.hmm|gene 13|300_aa
MSTATSLWDKAALMMREELAVAAVVAGCLDMTKLYVVGAGMFSCVTVALYPVSVIKTRMQ
VASGEAMRRNALATFKNILKVDGVPGLYRGFGTVITGAIPARIIFLTALEKTKATSLKLV
EPLQLSESMEAALANGLGGLTASLCSQAVFVPIDVVSQKLMVQGYSGHVRYKGGIDVVQK
IMKADGPRGLYRGFGLSVMTALGRLDDKEDTPSQLKIVGVQATGGMVAGATSLEDNPLSD
NVPQFAETSSAGSPLEKERVRQRASATISVTRDCQCSRRPTIGGVRQLGRSLPMRRDGAT
|
