Origin IGS: tctactacctccgtattgctttaagttagttgggttcattaaaattcgctgcaaaagtatggattattctcataaatatgcgactaaagagcagtacaaaatcaatgaagacgaaaagaaagacaaagacctctccacaggattctgacgaataaatgccattccctctttgaaggggtttaagccgaaccagcataagaaaagagaacgatcaagtgcgaaatcatttgatttcaagcagatacctatatgtggggattgtcgattaggcggaataactatacttttgtttgaaacaaaacaatattttttcgt .........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 acgaaaaaatattgttttgtttcaaacaaaagtatagttattccgcctaatcgacaatccccacatataggtatctgcttgaaatcaaatgatttcgcacttgatcgttctcttttcttatgctggttcggcttaaaccccttcaaagagggaatggcatttattcgtcagaatcctgtggagaggtctttgtctttcttttcgtcttcattgattttgtactgctctttagtcgcatatttatgagaataatccatacttttgcagcgaattttaatgaacccaactaacttaaagcaatacggaggtagtaga Mask Tandem Repeat Region ================================================ tctactacctccgtattgctttaagttagttgggttcattaaaattcgctgcaaaagtatggattattctcataaatatgcgactaaagagcagtacaaaatcaatgaagacgaaaagaaagacaaagacctctccacaggattctgacgaataaatgccattccctctttgaaggggtttaagccgaaccagcataagaaaagagaacgatcaagtgcgaaatcatttgatttcaagcagatacctatatgtggggattgtcgattaggcggaataactatacttttgtttgaaacaaaacaatattttttcgt Find is-nt database================================================ Query_seq: PG1235:PG1236|PG1235:PG1236:epimerase/reductase, putative:hypothetical protein:<-->:1311347..1311661 315 tctactacctccgtattgctttaagttagttgggttcattaaaattcgctgcaaaagtatggattattctcataaatatgcgactaaagagcagtacaaaatcaatgaagacgaaaagaaagacaaagacctctccacaggattctgacgaataaatgccattccctctttgaaggggtttaagccgaaccagcataagaaaagagaacgatcaagtgcgaaatcatttgatttcaagcagatacctatatgtggggattgtcgattaggcggaataactatacttttgtttgaaacaaaacaatattttttcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1235:PG1236|PG1235:PG1236:epimerase/reductase, putative:hypothetical protein:<-->:1311347..1311661 315 tctactacctccgtattgctttaagttagttgggttcattaaaattcgctgcaaaagtatggattattctcataaatatgcgactaaagagcagtacaaaatcaatgaagacgaaaagaaagacaaagacctctccacaggattctgacgaataaatgccattccctctttgaaggggtttaagccgaaccagcataagaaaagagaacgatcaagtgcgaaatcatttgatttcaagcagatacctatatgtggggattgtcgattaggcggaataactatacttttgtttgaaacaaaacaatattttttcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1235:PG1236|PG1235:PG1236:epimerase/reductase, putative:hypothetical protein:<-->:1311347..1311661 315 tctactacctccgtattgctttaagttagttgggttcattaaaattcgctgcaaaagtatggattattctcataaatatgcgactaaagagcagtacaaaatcaatgaagacgaaaagaaagacaaagacctctccacaggattctgacgaataaatgccattccctctttgaaggggtttaagccgaaccagcataagaaaagagaacgatcaagtgcgaaatcatttgatttcaagcagatacctatatgtggggattgtcgattaggcggaataactatacttttgtttgaaacaaaacaatattttttcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctactacctccgtattgctttaagttagttgggttcattaaaattcgctgcaaaagtatggattattctcataaatatgcgactaaagagcagtacaaaatcaatgaagacgaaaagaaagacaaagacctctccacaggattctgacgaataaatgccattccctctttgaaggggtttaagccgaaccagcataagaaaagagaacgatcaagtgcgaaatcatttgatttcaagcagatacctatatgtggggattgtcgattaggcggaataactatacttttgtttgaaacaaaacaatattttttcgt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 38 End: 145 ..................................... M K I R C K S M D Y S H K Y A T K E Q Y K I N E D E K K D K D L S T G F .......................................................................................................................................................................... Protein_Len: 41 Strand: + Start: 30 End: 152 ............................. M G S L K F A A K V W I I L I N M R L K S S T K S M K T K R K T K T S P Q D S D E ................................................................................................................................................................... Protein_Len: 54 Strand: + Start: 152 End: 313 ....................................................................................................................................................... M N A I P S L K G F K P N Q H K K R E R S S A K S F D F K Q I P I C G D C R L G G I T I L L F E T K Q Y F F .. Protein_Len: 60 Strand: - Start: 73 End: 282 ........................................................................ L S S S F F S L S R E V P N Q R I F A M G E K F P N L G F W C L F L S R D L A F D N S K L C I G I H P S Q R N P P I V M ................................. Protein_Len: 56 Strand: - Start: 29 End: 196 ............................ N P E N F N A A F T H I I R M F I R S F L L V F D I F V F L F V F V E G C S E S S Y I G N G R Q L P K L R V L M ....................................................................................................................... tctactacctccgtattgctttaagttagttgggttcattaaaattcgctgcaaaagtatggattattctcataaatatgcgactaaagagcagtacaaaatcaatgaagacgaaaagaaagacaaagacctctccacaggattctgacgaataaatgccattccctctttgaaggggtttaagccgaaccagcataagaaaagagaacgatcaagtgcgaaatcatttgatttcaagcagatacctatatgtggggattgtcgattaggcggaataactatacttttgtttgaaacaaaacaatattttttcgt 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================================================ tctactacctccgtattgctttaagttagttgggttcattaaaattcgctgcaaaagtatggattattctcataaatatgcgactaaagagcagtacaaaatcaatgaagacgaaaagaaagacaaagacctctccacaggattctgacgaataaatgccattccctctttgaaggggtttaagccgaaccagcataagaaaagagaacgatcaagtgcgaaatcatttgatttcaagcagatacctatatgtggggattgtcgattaggcggaataactatacttttgtttgaaacaaaacaatattttttcgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -2.9 Tail_Score: -3.53811 Start: 212 End: 231 Full_Region: AAGAAAAGAGAACGA TCAAGTG CGAAAT CATTTGA TTTCAAGCAGATACC ...................................................................................................................................................................................................................TCAAGTGCGAAATCATTTGA.................................................................................... Find igs database================================================ Query_seq: PG1235:PG1236|PG1235:PG1236:epimerase/reductase, putative:hypothetical protein:<-->:1311347..1311661 315 tctactacctccgtattgctttaagttagttgggttcattaaaattcgctgcaaaagtatggattattctcataaatatgcgactaaagagcagtacaaaatcaatgaagacgaaaagaaagacaaagacctctccacaggattctgacgaataaatgccattccctctttgaaggggtttaagccgaaccagcataagaaaagagaacgatcaagtgcgaaatcatttgatttcaagcagatacctatatgtggggattgtcgattaggcggaataactatacttttgtttgaaacaaaacaatattttttcgt Intra-Species Hit: Count: 1 Min: 1 Max: 315 Len: 315 Subject: NC_002950_PG1235_PG1236|epimerase/reductase, putative:hypothetical protein|NEGATIVE:POSITIVE|[1311347,1311661]|315 HSP 1 e-value: 1.0E-178 bit: 624.0 Len: 315 Query Start:1 Query End:315 Subject Strand: POSITIVE Subject Start: 1 Subject End: 315 tctactacctccgtattgctttaagttagttgggttcattaaaattcgctgcaaaagtatggattattctcataaatatgcgactaaagagcagtacaaaatcaatgaagacgaaaagaaagacaaagacctctccacaggattctgacgaataaatgccattccctctttgaaggggtttaagccgaaccagcataagaaaagagaacgatcaagtgcgaaatcatttgatttcaagcagatacctatatgtggggattgtcgattaggcggaataactatacttttgtttgaaacaaaacaatattttttcgt tctactacctccgtattgctttaagttagttgggttcattaaaattcgctgcaaaagtatggattattctcataaatatgcgactaaagagcagtacaaaatcaatgaagacgaaaagaaagacaaagacctctccacaggattctgacgaataaatgccattccctctttgaaggggtttaagccgaaccagcataagaaaagagaacgatcaagtgcgaaatcatttgatttcaagcagatacctatatgtggggattgtcgattaggcggaataactatacttttgtttgaaacaaaacaatattttttcgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUACUACCUCCGUAUUGCUUUAAGUUAGUUGGGUUCAUUAAAAUUCGCUGCAAAAGUAUGGAUUAUUCUCAUAAAUAUGCGACUAAAGAGCAGUACAAAAUCAAUGAAGACGAAAAGAAAGACAAAGACCUCUCCACAGGAUUCUGACGAAUAAAUGCCAUUCCCUCUUUGAAGGGGUUUAAGCCGAACCAGCAUAAGAAAAGAGAACGAUCAAGUGCGAAAUCAUUUGAUUUCAAGCAGAUACCUAUAUGUGGGGAUUGUCGAUUAGGCGGAAUAACUAUACUUUUGUUUGAAACAAAACAAUAUUUUUUCGU ............((((((((((...(((((.(((((......)))))...(((....((((((....)).))))....))).))))))))))))))).............(((((((((..(((((.....((((((((((..((((.(................((((((.....(((((.....))))).........))))))...(((((((((......)))))))))....)))))..))....)))))))))))))..((((((((((.........))))))))))............))))))))) (-70.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGAAAAAAUAUUGUUUUGUUUCAAACAAAAGUAUAGUUAUUCCGCCUAAUCGACAAUCCCCACAUAUAGGUAUCUGCUUGAAAUCAAAUGAUUUCGCACUUGAUCGUUCUCUUUUCUUAUGCUGGUUCGGCUUAAACCCCUUCAAAGAGGGAAUGGCAUUUAUUCGUCAGAAUCCUGUGGAGAGGUCUUUGUCUUUCUUUUCGUCUUCAUUGAUUUUGUACUGCUCUUUAGUCGCAUAUUUAUGAGAAUAAUCCAUACUUUUGCAGCGAAUUUUAAUGAACCCAACUAACUUAAAGCAAUACGGAGGUAGUAGA .........((((((((((.......(((((((((.(((((((.........(((((.((.(...((((((..(((((..((((((....)))))).....((.((((((((((((....((..((...((......))))..)))))))))))))))).......).))))..))))))..).))...))))).............((((.(((..(((((((.....)))).))).))).)))))))))))..))))))))).............((....)).......))))))))))............. (-61.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 858 140 91 231 182 NC_002950:PG1235|5end_epimerase/reductase,_putative_1311256..1311486_NEGATIVE 356 293 251 213 161 NC_002950:PG1476|5end_conjugative_transposon_protein_TraM_1553219..1553449_NEGATIVE 329 187 154 189 152 NC_002950:PG2201|5end_peptide_deformylase_2309412..2309642_NEGATIVE 326 189 142 183 130 NC_002950:PG0531|5end_NAD(+)_synthetase_581139..581369_NEGATIVE 316 300 251 112 52 NC_002950:PG2090|5end_cation_efflux_family_protein_2190230..2190460_POSITIVE 312 187 144 186 137 NC_002950:PG0017|5end_sensor_histidine_kinase_18307..18537_POSITIVE 303 200 156 142 109 NC_002950:PG1626|5end_hypothetical_protein_1708742..1708972_POSITIVE 300 50 6 141 84 NC_002950:PG2116|5end_hypothetical_protein_2224635..2224865_POSITIVE 297 290 241 85 20 NC_002950:PG1314|5end_chorismate_synthase_1395468..1395698_NEGATIVE 297 200 151 65 22 NC_002950:PG0272|5end_CBS_domain_protein_304399..304629_POSITIVE 294 194 161 228 189 NC_002950:PG1663|5end_ABC_transporter,_ATP-binding_protein_1745129..1745359_POSITIVE 292 280 242 231 186 NC_002950:PG1858|5end_flavodoxin_1957035..1957265_NEGATIVE 292 186 141 210 166 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 290 196 157 37 1 NC_002950:PG0132|5end_hypothetical_protein_152879..153109_POSITIVE 288 180 139 57 8 NC_002950:PG0546|5end_hypothetical_protein_600391..600621_NEGATIVE 286 189 143 216 163 NC_002950:PG1604|5end_immunoreactive_84_kDa_antigen_PG93_1682737..1682967_POSITIVE 286 180 133 199 146 NC_002950:PG0679|5end_outer_membrane_efflux_protein_729594..729824_POSITIVE 282 274 237 63 15 NC_002950:PG0365|5end_3'-5'_exonuclease_domain_protein_400178..400408_NEGATIVE 280 179 131 162 99 NC_002950:PG0767|5end_4-alpha-glucanotransferase_820533..820763_NEGATIVE 278 113 76 55 17 NC_002950:PG1020|5end_hypothetical_protein_1080568..1080798_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 187 154 84 47 NC_002950:PG2202|3end_Holliday_junction_resolvase-like_protein_2309517..2309667_NEGATIVE 326 189 142 73 20 NC_002950:PG0532|3end_hypothetical_protein_581249..581399_NEGATIVE 320 194 165 111 87 NC_002950:PG2095|3end_lipoprotein,_putative_2198290..2198440_NEGATIVE 317 274 232 143 102 NC_002950:PG1348|3end_conserved_hypothetical_protein_TIGR00147_1429569..1429719_POSITIVE 306 187 147 97 59 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 303 281 242 93 47 NC_002950:PG1859|3end_glycerate_kinase_family_protein_1957174..1957324_NEGATIVE 303 200 156 38 5 NC_002950:PG1625|3end_hypothetical_protein_1708718..1708868_POSITIVE 299 178 131 81 23 NC_002950:PG1732|3end_integrase/recombinase_XerD_1821177..1821327_POSITIVE 295 186 144 121 84 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 283 169 121 62 7 NC_002950:PG1630|3end_hypothetical_protein_1712142..1712292_POSITIVE 280 190 141 77 41 NC_002950:PG0954|3end_TPR_domain_protein_1015005..1015155_POSITIVE 278 210 166 54 7 NC_002950:PG1102|3end_hypothetical_protein_1170860..1171010_NEGATIVE 270 150 107 59 13 NC_002950:PG1835|3end_lipoprotein,_putative_1928520..1928670_POSITIVE 270 274 234 104 43 NC_002950:PG0095|3end_DNA_mismatch_repair_protein_112088..112238_NEGATIVE 268 219 172 114 50 NC_002950:PG1160|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_1238981..1239131_NEGATIVE 268 273 233 130 77 NC_002950:PG0398|3end_recF_protein_434616..434766_NEGATIVE 265 270 229 61 13 NC_002950:PG1429|3end_hypothetical_protein_1515003..1515153_NEGATIVE 265 160 111 62 14 NC_002950:PG0430|3end_ferrodoxin_oxidoreductase_beta_subunit_469073..469223_POSITIVE 263 210 164 51 6 NC_002950:PG0146|3end_hypothetical_protein_168408..168558_NEGATIVE 262 189 142 111 64 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE