Origin IGS: gacgattgaggggcaaatattatactgtggccgtaacctgtttagaagatctttatggacttgatagccatattcgatacatcaactgtccggcgtgagcaatgataggcaaagattagacaatgtgcaagacaaaacggaacgacgagagaagaatacgaatctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagattcgtattcttctctcgtcgttccgttttgtcttgcacattgtctaatctttgcctatcattgctcacgccggacagttgatgtatcgaatatggctatcaagtccataaagatcttctaaacaggttacggccacagtataatatttgcccctcaatcgtc Mask Tandem Repeat Region ================================================ gacgattgaggggcaaatattatactgtggccgtaacctgtttagaagatctttatggacttgatagccatattcgatacatcaactgtccggcgtgagcaatgataggcaaagattagacaatgtgcaagacaaaacggaacgacgagagaagaatacgaatctc Find is-nt database================================================ Query_seq: PG0918:PG0919|PG0918:PG0919:hypothetical protein:dihydroorotase:<-<-:978909..979074 166 gacgattgaggggcaaatattatactgtggccgtaacctgtttagaagatctttatggacttgatagccatattcgatacatcaactgtccggcgtgagcaatgataggcaaagattagacaatgtgcaagacaaaacggaacgacgagagaagaatacgaatctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0918:PG0919|PG0918:PG0919:hypothetical protein:dihydroorotase:<-<-:978909..979074 166 gacgattgaggggcaaatattatactgtggccgtaacctgtttagaagatctttatggacttgatagccatattcgatacatcaactgtccggcgtgagcaatgataggcaaagattagacaatgtgcaagacaaaacggaacgacgagagaagaatacgaatctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0918:PG0919|PG0918:PG0919:hypothetical protein:dihydroorotase:<-<-:978909..979074 166 gacgattgaggggcaaatattatactgtggccgtaacctgtttagaagatctttatggacttgatagccatattcgatacatcaactgtccggcgtgagcaatgataggcaaagattagacaatgtgcaagacaaaacggaacgacgagagaagaatacgaatctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacgattgaggggcaaatattatactgtggccgtaacctgtttagaagatctttatggacttgatagccatattcgatacatcaactgtccggcgtgagcaatgataggcaaagattagacaatgtgcaagacaaaacggaacgacgagagaagaatacgaatctc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 6 End: 95 ..... M R G K Y Y T V A V T C L E D L Y G L D S H I R Y I N C P A ....................................................................... Protein_Len: 30 Strand: + Start: 77 End: 166 ............................................................................ M H Q L S G V S N D R Q R L D N V Q D K T E R R E K N T N L gacgattgaggggcaaatattatactgtggccgtaacctgtttagaagatctttatggacttgatagccatattcgatacatcaactgtccggcgtgagcaatgataggcaaagattagacaatgtgcaagacaaaacggaacgacgagagaagaatacgaatctc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 102 End: 131 .....................................................................................................CTTGCACATTGTCTAATCTTTGCCTATCAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacgattgaggggcaaatattatactgtggccgtaacctgtttagaagatctttatggacttgatagccatattcgatacatcaactgtccggcgtgagcaatgataggcaaagattagacaatgtgcaagacaaaacggaacgacgagagaagaatacgaatctc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0918:PG0919|PG0918:PG0919:hypothetical protein:dihydroorotase:<-<-:978909..979074 166 gacgattgaggggcaaatattatactgtggccgtaacctgtttagaagatctttatggacttgatagccatattcgatacatcaactgtccggcgtgagcaatgataggcaaagattagacaatgtgcaagacaaaacggaacgacgagagaagaatacgaatctc Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: NC_002950_PG0918_PG0919|hypothetical protein:dihydroorotase|NEGATIVE:NEGATIVE|[978909, 979074]|166 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 gacgattgaggggcaaatattatactgtggccgtaacctgtttagaagatctttatggacttgatagccatattcgatacatcaactgtccggcgtgagcaatgataggcaaagattagacaatgtgcaagacaaaacggaacgacgagagaagaatacgaatctc gacgattgaggggcaaatattatactgtggccgtaacctgtttagaagatctttatggacttgatagccatattcgatacatcaactgtccggcgtgagcaatgataggcaaagattagacaatgtgcaagacaaaacggaacgacgagagaagaatacgaatctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACGAUUGAGGGGCAAAUAUUAUACUGUGGCCGUAACCUGUUUAGAAGAUCUUUAUGGACUUGAUAGCCAUAUUCGAUACAUCAACUGUCCGGCGUGAGCAAUGAUAGGCAAAGAUUAGACAAUGUGCAAGACAAAACGGAACGACGAGAGAAGAAUACGAAUCUC .......((((..(............((..((((....(((((((...(((..(((((.((....)))))))...))).......(((((..((....))...))))).......))))))).(((.....)))..)))).))..(....)........)..)))) (-31.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAUUCGUAUUCUUCUCUCGUCGUUCCGUUUUGUCUUGCACAUUGUCUAAUCUUUGCCUAUCAUUGCUCACGCCGGACAGUUGAUGUAUCGAAUAUGGCUAUCAAGUCCAUAAAGAUCUUCUAAACAGGUUACGGCCACAGUAUAAUAUUUGCCCCUCAAUCGUC (((....(((((...((...(((((.((((((.((((((((((((((((.......((........)).......)))))).)).)))).....(((((((....)).))))).)))).....)))).))..)))))...))...)))))......)))....... (-26.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 957 110 61 201 152 NC_002950:PG0918|5end_hypothetical_protein_978818..979048_NEGATIVE 377 129 88 48 1 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 374 100 55 54 8 NC_002950:PG2126|5end_conserved_hypothetical_protein_TIGR00044_2233112..2233342_NEGATIVE 318 127 86 70 32 NC_002950:PG1611|5end_hypothetical_protein_1691487..1691717_NEGATIVE 314 70 25 90 47 NC_002950:PG2207|5end_hypothetical_protein_2320161..2320391_NEGATIVE 311 129 87 75 35 NC_002950:PG0415|5end_peptidyl-prolyl_cis-trans_isomerase,_PPIC-type_455096..455326_NEGATIVE 297 100 52 226 182 NC_002950:PG0191|5end_outer_membrane_protein,_putative_226858..227088_POSITIVE 293 110 61 51 5 NC_002950:PG1283|5end_hypothetical_protein_1360553..1360783_POSITIVE 290 156 124 58 24 NC_002950:PG2155|5end_lipoprotein,_putative_2261862..2262092_NEGATIVE 288 128 85 103 41 NC_002950:PG0723|5end_hypothetical_protein_774949..775179_POSITIVE 285 110 71 147 105 NC_002950:PG1852|5end_exonuclease_1951973..1952203_NEGATIVE 285 43 1 77 34 NC_002950:PG1069|5end_alcohol_dehydrogenase,_zinc-containing,_putative_1135499..1135729_POSITIVE 280 100 55 159 113 NC_002950:PG0653|5end_phosphoserine_phosphatase_705454..705684_NEGATIVE 275 94 51 188 143 NC_002950:PG0483|5end_kinase,_putative_523844..524074_NEGATIVE 274 60 11 106 52 NC_002950:PG1153|5end_hypothetical_protein_1235689..1235919_NEGATIVE 273 98 55 177 126 NC_002950:PG0648|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_701285..701515_NEGATIVE 273 50 1 210 145 NC_002950:PG0593|5end_htrA_protein_650362..650592_POSITIVE 273 40 8 42 8 NC_002950:PG0430|5end_ferrodoxin_oxidoreductase_beta_subunit_467986..468216_POSITIVE 272 140 91 51 2 NC_002950:PG0633|5end_hypothetical_protein_685301..685531_POSITIVE 272 69 29 48 14 NC_002950:PG0517|5end_hypothetical_protein_562097..562327_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 100 55 57 11 NC_002950:PG2127|3end_hypothetical_protein_2233109..2233259_NEGATIVE 351 101 67 88 55 NC_002950:PG2076|3end_hypothetical_protein_2177073..2177223_POSITIVE 318 127 86 45 7 NC_002950:PG1612|3end_methylmalonyl-CoA_decarboxylase,_alpha_subunit_1691512..1691662_NEGATIVE 316 139 92 56 1 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 285 110 71 134 92 NC_002950:PG1853|3end_DNA_polymerase_III,_beta_subunit_1951986..1952136_NEGATIVE 280 100 55 100 54 NC_002950:PG0654|3end_hypothetical_protein_705513..705663_NEGATIVE 279 70 25 151 102 NC_002950:PG2114|3end_hypothetical_protein_2223982..2224132_NEGATIVE 277 68 23 145 100 NC_002950:PG0084|3end_L-serine_dehydratase,_iron-sulfur-dependent,_single_chain_form_99111..99261_POSITIVE 274 60 11 98 44 NC_002950:PG1154|3end_hypothetical_protein_1235697..1235847_NEGATIVE 273 100 51 84 25 NC_002950:PG1732|3end_integrase/recombinase_XerD_1821177..1821327_POSITIVE 273 45 4 141 99 NC_002950:PG0479|3end_hypothetical_protein_520545..520695_POSITIVE 273 130 86 130 74 NC_002950:PG0031|3end_hypothetical_protein_36905..37055_NEGATIVE 270 94 61 35 5 NC_002950:PG1003|3end_hypothetical_protein_1060304..1060454_POSITIVE 269 122 84 88 49 NC_002950:PG1987|3end_CRISPR-associated_TM1811_family_protein_2075786..2075936_NEGATIVE 267 108 63 63 22 NC_002950:PG1946|3end_ABC_3_transporter_family_protein_2033019..2033169_POSITIVE 266 70 23 114 66 NC_002950:PG1225|3end_ABC_transporter,_ATP-binding_protein_1303336..1303486_POSITIVE 265 69 27 39 3 NC_002950:PG1988|3end_hypothetical_protein_2077425..2077575_NEGATIVE 265 43 8 35 1 NC_002950:PG1068|3end_hypothetical_protein_1135537..1135687_POSITIVE 262 109 74 69 34 NC_002950:PG1970|3end_hypothetical_protein_2059484..2059634_NEGATIVE 262 139 96 48 3 NC_002950:PG1004|3end_prolyl_oligopeptidase_family_protein_1060433..1060583_NEGATIVE