Origin IGS: gagtgtgtcaaaattccgtttagagtaaaggatactatcatttgtataatttgtatagagaaaccgctaccaaaaggacaaaatcatcctacttgatagcggttttcccgatatgattaaggtggcatttgtgtctttttgttggaaaatccattttcggattttgacacagccccatatagaacgctgttttgaatgcctcagccctgaatatagcccaccccttcgaacgcttcttactagatctgacttagtgttgcatttataactggaatctgtacacggcaactacattatatatagaaaacggctatctttgcgaggttaagtccatcataagacaaaaacag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctgtttttgtcttatgatggacttaacctcgcaaagatagccgttttctatatataatgtagttgccgtgtacagattccagttataaatgcaacactaagtcagatctagtaagaagcgttcgaaggggtgggctatattcagggctgaggcattcaaaacagcgttctatatggggctgtgtcaaaatccgaaaatggattttccaacaaaaagacacaaatgccaccttaatcatatcgggaaaaccgctatcaagtaggatgattttgtccttttggtagcggtttctctatacaaattatacaaatgatagtatcctttactctaaacggaattttgacacactc Mask Tandem Repeat Region ================================================ gagtgtgtcaaaattccgtttagagtaaaggatactatcatttgtataatttgtatagagaaaccgctaccaaaaggacaaaatcatcctacttgatagcggttttcccgatatgattaaggtggcatttgtgtctttttgttggaaaatccattttcggattttgacacagccccatatagaacgctgttttgaatgcctcagccctgaatatagcccaccccttcgaacgcttcttactagatctgacttagtgttgcatttataactggaatctgtacacggcaactacattatatatagaaaacggctatctttgcgaggttaagtccatcataagacaaaaacag Find is-nt database================================================ Query_seq: PG1214:PG1215|PG1214:PG1215:hypothetical protein:lipoprotein protein, putative:->->:1294411..1294760 350 gagtgtgtcaaaattccgtttagagtaaaggatactatcatttgtataatttgtatagagaaaccgctaccaaaaggacaaaatcatcctacttgatagcggttttcccgatatgattaaggtggcatttgtgtctttttgttggaaaatccattttcggattttgacacagccccatatagaacgctgttttgaatgcctcagccctgaatatagcccaccccttcgaacgcttcttactagatctgacttagtgttgcatttataactggaatctgtacacggcaactacattatatatagaaaacggctatctttgcgaggttaagtccatcataagacaaaaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1214:PG1215|PG1214:PG1215:hypothetical protein:lipoprotein protein, putative:->->:1294411..1294760 350 gagtgtgtcaaaattccgtttagagtaaaggatactatcatttgtataatttgtatagagaaaccgctaccaaaaggacaaaatcatcctacttgatagcggttttcccgatatgattaaggtggcatttgtgtctttttgttggaaaatccattttcggattttgacacagccccatatagaacgctgttttgaatgcctcagccctgaatatagcccaccccttcgaacgcttcttactagatctgacttagtgttgcatttataactggaatctgtacacggcaactacattatatatagaaaacggctatctttgcgaggttaagtccatcataagacaaaaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1214:PG1215|PG1214:PG1215:hypothetical protein:lipoprotein protein, putative:->->:1294411..1294760 350 gagtgtgtcaaaattccgtttagagtaaaggatactatcatttgtataatttgtatagagaaaccgctaccaaaaggacaaaatcatcctacttgatagcggttttcccgatatgattaaggtggcatttgtgtctttttgttggaaaatccattttcggattttgacacagccccatatagaacgctgttttgaatgcctcagccctgaatatagcccaccccttcgaacgcttcttactagatctgacttagtgttgcatttataactggaatctgtacacggcaactacattatatatagaaaacggctatctttgcgaggttaagtccatcataagacaaaaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagtgtgtcaaaattccgtttagagtaaaggatactatcatttgtataatttgtatagagaaaccgctaccaaaaggacaaaatcatcctacttgatagcggttttcccgatatgattaaggtggcatttgtgtctttttgttggaaaatccattttcggattttgacacagccccatatagaacgctgttttgaatgcctcagccctgaatatagcccaccccttcgaacgcttcttactagatctgacttagtgttgcatttataactggaatctgtacacggcaactacattatatatagaaaacggctatctttgcgaggttaagtccatcataagacaaaaacag Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 83 End: 265 .................................................................................. M I L L D S G F P D M I K V A F V S F C W K I H F R I L T Q P H I E R C F E C L S P E Y S P P L R T L L T R S D L V L H ..................................................................................... Protein_Len: 30 Strand: + Start: 261 End: 350 .................................................................................................................................................................................................................................................................... M Y N W N L Y T A T T L Y I E N G Y L C E V K S I I R Q K Q Protein_Len: 41 Strand: - Start: 92 End: 214 ........................................................................................... K I A T K G I H N L H C K H R K T P F D M K P N Q C L G M Y F A T K F A E A R F M ........................................................................................................................................ Protein_Len: 60 Strand: - Start: 70 End: 288 ..................................................................... S I I L T A N T D K Q Q F I W K R I K V C G W I S R Q K S H R L G S Y L G G R R V S R V L D S K T N C K Y S S D T C P M .............................................................. gagtgtgtcaaaattccgtttagagtaaaggatactatcatttgtataatttgtatagagaaaccgctaccaaaaggacaaaatcatcctacttgatagcggttttcccgatatgattaaggtggcatttgtgtctttttgttggaaaatccattttcggattttgacacagccccatatagaacgctgttttgaatgcctcagccctgaatatagcccaccccttcgaacgcttcttactagatctgacttagtgttgcatttataactggaatctgtacacggcaactacattatatatagaaaacggctatctttgcgaggttaagtccatcataagacaaaaacag Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gagtgtgtcaaaattccgtttagagtaaaggatactatcatttgtataatttgtatagagaaaccgctaccaaaaggacaaaatcatcctacttgatagcggttttcccgatatgattaaggtggcatttgtgtctttttgttggaaaatccattttcggattttgacacagccccatatagaacgctgttttgaatgcctcagccctgaatatagcccaccccttcgaacgcttcttactagatctgacttagtgttgcatttataactggaatctgtacacggcaactacattatatatagaaaacggctatctttgcgaggttaagtccatcataagacaaaaacag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 55 HP_score: -2.5 Tail_Score: -4.13282 Start: 64 End: 102 Full_Region: ATTTGTATAGAGAAA CCGCTACCAAAAGGA CAAAATCA TCCTACTTGATAGCGG TTTTCCCGATATGAT ...............................................................CCGCTACCAAAAGGACAAAATCATCCTACTTGATAGCGG........................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 79 HP_score: -8.3 Tail_Score: -4.128 Start: 64 End: 102 Full_Region: atcatatcgggaaaa ccgctatcaagtaggatg attt tgtccttttggtagcgg tttctctatacaaat ...............................................................ccgctatcaagtaggatgattttgtccttttggtagcgg........................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: PG1214:PG1215|PG1214:PG1215:hypothetical protein:lipoprotein protein, putative:->->:1294411..1294760 350 gagtgtgtcaaaattccgtttagagtaaaggatactatcatttgtataatttgtatagagaaaccgctaccaaaaggacaaaatcatcctacttgatagcggttttcccgatatgattaaggtggcatttgtgtctttttgttggaaaatccattttcggattttgacacagccccatatagaacgctgttttgaatgcctcagccctgaatatagcccaccccttcgaacgcttcttactagatctgacttagtgttgcatttataactggaatctgtacacggcaactacattatatatagaaaacggctatctttgcgaggttaagtccatcataagacaaaaacag Intra-Species Hit: Count: 2 Min: 1 Max: 350 Len: 350 Subject: NC_002950_PG1214_PG1215|hypothetical protein:lipoprotein protein, putative|POSITIVE:POSITIVE|[1294411,1294760]|350 HSP 1 e-value: 0.0 bit: 694.0 Len: 350 Query Start:1 Query End:350 Subject Strand: POSITIVE Subject Start: 1 Subject End: 350 gagtgtgtcaaaattccgtttagagtaaaggatactatcatttgtataatttgtatagagaaaccgctaccaaaaggacaaaatcatcctacttgatagcggttttcccgatatgattaaggtggcatttgtgtctttttgttggaaaatccattttcggattttgacacagccccatatagaacgctgttttgaatgcctcagccctgaatatagcccaccccttcgaacgcttcttactagatctgacttagtgttgcatttataactggaatctgtacacggcaactacattatatatagaaaacggctatctttgcgaggttaagtccatcataagacaaaaacag gagtgtgtcaaaattccgtttagagtaaaggatactatcatttgtataatttgtatagagaaaccgctaccaaaaggacaaaatcatcctacttgatagcggttttcccgatatgattaaggtggcatttgtgtctttttgttggaaaatccattttcggattttgacacagccccatatagaacgctgttttgaatgcctcagccctgaatatagcccaccccttcgaacgcttcttactagatctgacttagtgttgcatttataactggaatctgtacacggcaactacattatatatagaaaacggctatctttgcgaggttaagtccatcataagacaaaaacag Subject: NC_002950_PG2029_PG2030|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2129263,2129886]|624 HSP 1 e-value: 1.0E-42 bit: 174.0 Len: 172 Query Start:5 Query End:176 Subject Strand: NEGATIVE Subject Start: 36 Subject End: 203 ....gtgtcaaaattccgtttagagtaaaggatactatcatttgtataatttgtatagagaaaccgctaccaaaaggacaaaatcatcctacttgatagcggttttcccgatatgattaaggtggcatttgtgtcttttt----gttggaaaatcc-attttcggattttgacacagcccc.............................................................................................................................................................................. ....gtgtcaaaattcagtttagagtaaaggatactatcat---------ttgtataggaaaaccgctaccaaatggacaaaatcatcctacttgatagcggtttttcctttatgattaaggtggcatttgtgtctttttgatagttggaaaatccttttttcggattttgacacagcccc.............................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUGUGUCAAAAUUCCGUUUAGAGUAAAGGAUACUAUCAUUUGUAUAAUUUGUAUAGAGAAACCGCUACCAAAAGGACAAAAUCAUCCUACUUGAUAGCGGUUUUCCCGAUAUGAUUAAGGUGGCAUUUGUGUCUUUUUGUUGGAAAAUCCAUUUUCGGAUUUUGACACAGCCCCAUAUAGAACGCUGUUUUGAAUGCCUCAGCCCUGAAUAUAGCCCACCCCUUCGAACGCUUCUUACUAGAUCUGACUUAGUGUUGCAUUUAUAACUGGAAUCUGUACACGGCAACUACAUUAUAUAUAGAAAACGGCUAUCUUUGCGAGGUUAAGUCCAUCAUAAGACAAAAACAG ..((.((((.......((((..(((....((.........((((((....(..(((.(..(((((((((.(((.((((........))))..))).)))))))))..)..)))..)....((.(((...((((((.....(((.(((((....))))).)))...))))))))))).))))))..(((((.((.(..((....))..).)).)))))...)).)))..))))..........(((..(((((((..(((((...(((.(((...((((((.(..(........)..).))))))...))).)))...)))))..))))))).)))....))))...)).. (-82.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUUUUGUCUUAUGAUGGACUUAACCUCGCAAAGAUAGCCGUUUUCUAUAUAUAAUGUAGUUGCCGUGUACAGAUUCCAGUUAUAAAUGCAACACUAAGUCAGAUCUAGUAAGAAGCGUUCGAAGGGGUGGGCUAUAUUCAGGGCUGAGGCAUUCAAAACAGCGUUCUAUAUGGGGCUGUGUCAAAAUCCGAAAAUGGAUUUUCCAACAAAAAGACACAAAUGCCACCUUAAUCAUAUCGGGAAAACCGCUAUCAAGUAGGAUGAUUUUGUCCUUUUGGUAGCGGUUUCUCUAUACAAAUUAUACAAAUGAUAGUAUCCUUUACUCUAAACGGAAUUUUGACACACUC ((((((((((.....((.((......))))))))))))))..((...((((((...))))))..)).((((..(((((((.(((...(((((..(((((.(......)))))..)..))))).((((((((((.((((((..((.((((............)))).))..))))))...(((((((((((((......)))))))..........))))))....)))))...(((((...((((((.(((((((((((.(((((......)))))))))))))))))))))).(((.....)))....))))).....)))))......))))))))))..)))).... (-89.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 264 223 173 131 NC_002950:PG2166|5end_hypothetical_protein_2271809..2272039_POSITIVE 360 160 113 183 135 NC_002950:PG1593|5end_shikimate_kinase_1671503..1671733_POSITIVE 342 210 180 155 125 NC_002950:PG1746|5end_ISPg2,_transposase_1832230..1832460_NEGATIVE 342 210 180 155 125 NC_002950:PG0865|5end_ISPg2,_transposase_928896..929126_NEGATIVE 341 230 184 163 114 NC_002950:PG1154|5end_hypothetical_protein_1235825..1236055_NEGATIVE 326 262 224 65 29 NC_002950:PG2186|5end_transcriptional_regulator,_putative_2293619..2293849_NEGATIVE 326 209 180 154 125 NC_002950:PG2176|5end_ISPg2,_transposase_2284345..2284575_NEGATIVE 326 209 180 154 125 NC_002950:PG1350|5end_ISPg2,_transposase_1430866..1431096_POSITIVE 326 209 180 154 125 NC_002950:PG0277|5end_ISPg2,_transposase_308856..309086_POSITIVE 325 250 201 60 10 NC_002950:PG1900|5end_ribosome-associated_GTPase_2000746..2000976_NEGATIVE 317 193 159 229 197 NC_002950:PG1392|5end_rod_shape-determining_protein_RodA,_putative_1474416..1474646_NEGATIVE 317 260 216 64 17 NC_002950:PG1190|5end_glycerate_dehydrogenase_1272112..1272342_POSITIVE 314 230 185 65 14 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 309 237 192 218 158 NC_002950:PG1163|5end_cobyrinic_acid_a,c-diamide_synthase_1243381..1243611_NEGATIVE 307 136 95 174 123 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 304 257 216 220 176 NC_002950:PG1807|5end_v-type_ATPase,_subunit_K_1902069..1902299_POSITIVE 304 143 101 85 33 NC_002950:PG0444|5end_oligopeptide_transporter,_OPT_family_483256..483486_POSITIVE 303 135 93 174 133 NC_002950:PG0447|5end_hypothetical_protein_487278..487508_POSITIVE 301 228 185 202 153 NC_002950:PG0538|5end_outer_membrane_efflux_protein_589142..589372_POSITIVE 301 135 91 67 26 NC_002950:PG0082|5end_hypothetical_protein_96044..96274_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 659 176 131 55 5 NC_002950:PG2029|3end_hypothetical_protein_2129202..2129352_POSITIVE 360 160 113 135 87 NC_002950:PG1592|3end_HDIG_domain_protein_1671535..1671685_POSITIVE 344 186 141 46 10 NC_002950:PG1950|3end_hypothetical_protein_2040840..2040990_POSITIVE 333 200 152 77 37 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 329 218 180 67 29 NC_002950:PG0428|3end_hypothetical_protein_465753..465903_NEGATIVE 314 236 193 88 33 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 311 260 216 110 55 NC_002950:PG1797|3end_DNA-binding_response_regulator/sensor_histidine_kinase_1892978..1893128_POSITIVE 305 228 187 88 36 NC_002950:PG0753|3end_protease_800288..800438_POSITIVE 305 238 191 66 22 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE 302 283 247 38 4 NC_002950:PG1314|3end_chorismate_synthase_1394362..1394512_NEGATIVE 297 279 231 108 51 NC_002950:PG1317|3end_hypothetical_protein_1396744..1396894_NEGATIVE 296 176 157 29 10 NC_002950:PG1715|3end_hypothetical_protein_1803393..1803543_NEGATIVE 295 240 193 66 20 NC_002950:PG1078|3end_electron_transfer_flavoprotein,_alpha_subunit_1146525..1146675_POSITIVE 294 199 151 81 29 NC_002950:PG2170|3end_sugar_transporter_2276685..2276835_NEGATIVE 294 202 161 45 10 NC_002950:PG1755|3end_fructose-bisphosphate_aldolase_1842397..1842547_NEGATIVE 293 200 159 41 6 NC_002950:PG1235|3end_epimerase/reductase,_putative_1310300..1310450_NEGATIVE 292 229 181 90 37 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 291 228 181 55 14 NC_002950:PG0503|3end_dipeptidyl_aminopeptidase_IV_544211..544361_POSITIVE 287 210 166 147 96 NC_002950:PG1134|3end_thioredoxin_reductase_1215371..1215521_POSITIVE 286 140 94 101 61 NC_002950:PG0212|3end_precorrin-6Y_C5,15-methyltransferase,_decarboxylating_247824..247974_NEGATIVE