Origin IGS: ccgaagattgtagtatagaatagaagtaattttttctcgatccggtagtatgcaacctgaaaaatttaggacactactgcaattttaccccctaataacaagcttttccccgaaaaacttctctgaaaaggctaatttccgcttgaaatcattgtgcagaaaaaaaaatcgttacttttggcttgttcatttcctatagctctgagagcgaatctcgttgctgtttgtgtcagagaagataaacttgcggggcggtgatatgatctaactaaattttttgtctaactaactaatcgtgaaaag .........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 cttttcacgattagttagttagacaaaaaatttagttagatcatatcaccgccccgcaagtttatcttctctgacacaaacagcaacgagattcgctctcagagctataggaaatgaacaagccaaaagtaacgatttttttttctgcacaatgatttcaagcggaaattagccttttcagagaagtttttcggggaaaagcttgttattagggggtaaaattgcagtagtgtcctaaatttttcaggttgcatactaccggatcgagaaaaaattacttctattctatactacaatcttcgg Mask Tandem Repeat Region ================================================ ccgaagattgtagtatagaatagaagtaattttttctcgatccggtagtatgcaacctgaaaaatttaggacactactgcaattttaccccctaataacaagcttttccccgaaaaacttctctgaaaaggctaatttccgcttgaaatcattgtgcagaaaaaaaaatcgttacttttggcttgttcatttcctatagctctgagagcgaatctcgttgctgtttgtgtcagagaagataaacttgcggggcggtgatatgatctaactaaattttttgtctaactaactaatcgtgaaaag Find is-nt database================================================ Query_seq: PG0120:PG0121|PG0120:PG0121:UDP-N-acetylglucosamine 2-epimerase:DNA-binding protein HU:->->:144305..144607 303 ccgaagattgtagtatagaatagaagtaattttttctcgatccggtagtatgcaacctgaaaaatttaggacactactgcaattttaccccctaataacaagcttttccccgaaaaacttctctgaaaaggctaatttccgcttgaaatcattgtgcagaaaaaaaaatcgttacttttggcttgttcatttcctatagctctgagagcgaatctcgttgctgtttgtgtcagagaagataaacttgcggggcggtgatatgatctaactaaattttttgtctaactaactaatcgtgaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0120:PG0121|PG0120:PG0121:UDP-N-acetylglucosamine 2-epimerase:DNA-binding protein HU:->->:144305..144607 303 ccgaagattgtagtatagaatagaagtaattttttctcgatccggtagtatgcaacctgaaaaatttaggacactactgcaattttaccccctaataacaagcttttccccgaaaaacttctctgaaaaggctaatttccgcttgaaatcattgtgcagaaaaaaaaatcgttacttttggcttgttcatttcctatagctctgagagcgaatctcgttgctgtttgtgtcagagaagataaacttgcggggcggtgatatgatctaactaaattttttgtctaactaactaatcgtgaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0120:PG0121|PG0120:PG0121:UDP-N-acetylglucosamine 2-epimerase:DNA-binding protein HU:->->:144305..144607 303 ccgaagattgtagtatagaatagaagtaattttttctcgatccggtagtatgcaacctgaaaaatttaggacactactgcaattttaccccctaataacaagcttttccccgaaaaacttctctgaaaaggctaatttccgcttgaaatcattgtgcagaaaaaaaaatcgttacttttggcttgttcatttcctatagctctgagagcgaatctcgttgctgtttgtgtcagagaagataaacttgcggggcggtgatatgatctaactaaattttttgtctaactaactaatcgtgaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccgaagattgtagtatagaatagaagtaattttttctcgatccggtagtatgcaacctgaaaaatttaggacactactgcaattttaccccctaataacaagcttttccccgaaaaacttctctgaaaaggctaatttccgcttgaaatcattgtgcagaaaaaaaaatcgttacttttggcttgttcatttcctatagctctgagagcgaatctcgttgctgtttgtgtcagagaagataaacttgcggggcggtgatatgatctaactaaattttttgtctaactaactaatcgtgaaaag Predict ORF larger than 30AA ================================================ Protein_Len: 59 Strand: + Start: 20 End: 196 ................... M E V I F S R S G S M Q P E K F R T L L Q F Y P L I T S F S P K N F S E K A N F R L K S L C R K K N R Y F W L V H F L ........................................................................................................... Protein_Len: 36 Strand: + Start: 148 End: 255 ................................................................................................................................................... M I V Q K K K S L L L A C S F P I A L R A N L V A V C V R E D K L A G R ................................................ Protein_Len: 33 Strand: - Start: 135 End: 233 ...................................................................................................................................... N G S S I M T C F F F D N S K A Q E N G I A R L A F R T A T Q T M ...................................................................... ccgaagattgtagtatagaatagaagtaattttttctcgatccggtagtatgcaacctgaaaaatttaggacactactgcaattttaccccctaataacaagcttttccccgaaaaacttctctgaaaaggctaatttccgcttgaaatcattgtgcagaaaaaaaaatcgttacttttggcttgttcatttcctatagctctgagagcgaatctcgttgctgtttgtgtcagagaagataaacttgcggggcggtgatatgatctaactaaattttttgtctaactaactaatcgtgaaaag 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================================================ ccgaagattgtagtatagaatagaagtaattttttctcgatccggtagtatgcaacctgaaaaatttaggacactactgcaattttaccccctaataacaagcttttccccgaaaaacttctctgaaaaggctaatttccgcttgaaatcattgtgcagaaaaaaaaatcgttacttttggcttgttcatttcctatagctctgagagcgaatctcgttgctgtttgtgtcagagaagataaacttgcggggcggtgatatgatctaactaaattttttgtctaactaactaatcgtgaaaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 46 HP_score: -2.1 Tail_Score: -3.52522 Start: 203 End: 217 Full_Region: CATTTCCTATAGCTC TGAGA GCGAA TCTCG TTGCTGTTTGTGTCA ..........................................................................................................................................................................................................TGAGAGCGAATCTCG...................................................................................... TransTerm Strand: + Conf: 43 HP_score: -3.4 Tail_Score: -2.7079 Start: 204 End: 216 Full_Region: ATTTCCTATAGCTCT GAGA GCGAA TCTC GTTGCTGTTTGTGTC ...........................................................................................................................................................................................................GAGAGCGAATCTC....................................................................................... Find igs database================================================ Query_seq: PG0120:PG0121|PG0120:PG0121:UDP-N-acetylglucosamine 2-epimerase:DNA-binding protein HU:->->:144305..144607 303 ccgaagattgtagtatagaatagaagtaattttttctcgatccggtagtatgcaacctgaaaaatttaggacactactgcaattttaccccctaataacaagcttttccccgaaaaacttctctgaaaaggctaatttccgcttgaaatcattgtgcagaaaaaaaaatcgttacttttggcttgttcatttcctatagctctgagagcgaatctcgttgctgtttgtgtcagagaagataaacttgcggggcggtgatatgatctaactaaattttttgtctaactaactaatcgtgaaaag Intra-Species Hit: Count: 1 Min: 1 Max: 303 Len: 303 Subject: NC_002950_PG0120_PG0121|UDP-N-acetylglucosamine 2-epimerase:DNA-binding protein HU|POSITIVE:POSITIVE|[144305,144607]|303 HSP 1 e-value: 1.0E-155 bit: 547.0 Len: 303 Query Start:1 Query End:303 Subject Strand: POSITIVE Subject Start: 1 Subject End: 303 ccgaagattgtagtatagaatagaagtaattttttctcgatccggtagtatgcaacctgaaaaatttaggacactactgcaattttaccccctaataacaagcttttccccgaaaaacttctctgaaaaggctaatttccgcttgaaatcattgtgcagnnnnnnnnntcgttacttttggcttgttcatttcctatagctctgagagcgaatctcgttgctgtttgtgtcagagaagataaacttgcggggcggtgatatgatctaactaaattttttgtctaactaactaatcgtgaaaag ccgaagattgtagtatagaatagaagtaattttttctcgatccggtagtatgcaacctgaaaaatttaggacactactgcaattttaccccctaataacaagcttttccccgaaaaacttctctgaaaaggctaatttccgcttgaaatcattgtgcagaaaaaaaaatcgttacttttggcttgttcatttcctatagctctgagagcgaatctcgttgctgtttgtgtcagagaagataaacttgcggggcggtgatatgatctaactaaattttttgtctaactaactaatcgtgaaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGAAGAUUGUAGUAUAGAAUAGAAGUAAUUUUUUCUCGAUCCGGUAGUAUGCAACCUGAAAAAUUUAGGACACUACUGCAAUUUUACCCCCUAAUAACAAGCUUUUCCCCGAAAAACUUCUCUGAAAAGGCUAAUUUCCGCUUGAAAUCAUUGUGCAGAAAAAAAAAUCGUUACUUUUGGCUUGUUCAUUUCCUAUAGCUCUGAGAGCGAAUCUCGUUGCUGUUUGUGUCAGAGAAGAUAAACUUGCGGGGCGGUGAUAUGAUCUAACUAAAUUUUUUGUCUAACUAACUAAUCGUGAAAAG .....(((((((((.((((...((((.(((((......((((..((((((((...(((((.....))))).)).))))))....(((((((((.....((((.(((((...))))).(((((((((..(((((((((((.((.((....))....)).))))...............)))))))...........(((((..(((((.....)))))..))))).....))))))))).....)))).)))).)))))...)))).....))))))))).))))))))..)))))........ (-67.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUCACGAUUAGUUAGUUAGACAAAAAAUUUAGUUAGAUCAUAUCACCGCCCCGCAAGUUUAUCUUCUCUGACACAAACAGCAACGAGAUUCGCUCUCAGAGCUAUAGGAAAUGAACAAGCCAAAAGUAACGAUUUUUUUUUCUGCACAAUGAUUUCAAGCGGAAAUUAGCCUUUUCAGAGAAGUUUUUCGGGGAAAAGCUUGUUAUUAGGGGGUAAAAUUGCAGUAGUGUCCUAAAUUUUUCAGGUUGCAUACUACCGGAUCGAGAAAAAAUUACUUCUAUUCUAUACUACAAUCUUCGG .(((((.(((((.(.((((..(((.((((((((((...(((...)))..(((..(((((.((((((((((...........(((...((((.....))))...)))..........(((((((......(..(((....((((((((.....(((((((.....))))))).......))))))))....)))..)....)))))))...)))))))))).)))).)..)))..))))))))))...)))....)))).).))))).)))))............................... (-63.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 259 215 137 88 NC_002950:PG0646|5end_iron_compound_ABC_transporter,_ATP-binding_protein_699071..699301_NEGATIVE 336 224 181 231 183 NC_002950:PG0273|5end_4'-phosphopantetheinyl_transferase_family_protein_305694..305924_POSITIVE 335 228 181 164 118 NC_002950:PG1709|5end_ISPg5,_transposase_Orf1_1794914..1795144_POSITIVE 334 258 219 80 41 NC_002950:PG0835|5end_hypothetical_protein_893580..893810_POSITIVE 333 230 181 175 125 NC_002950:PG0746|5end_sensor_histidine_kinase_793903..794133_NEGATIVE 331 240 191 112 63 NC_002950:PG1819|5end_hypothetical_protein_1914322..1914552_NEGATIVE 330 230 181 59 4 NC_002950:PG1603|5end_HAM1_protein_1682165..1682395_POSITIVE 323 234 200 155 123 NC_002950:PG0191|5end_outer_membrane_protein,_putative_226858..227088_POSITIVE 320 257 215 175 136 NC_002950:PG0933|5end_translation_elongation_factor_G,_putative_989997..990227_POSITIVE 312 233 199 220 180 NC_002950:PG0290|5end_hypothetical_protein_323904..324134_POSITIVE 311 266 225 180 126 NC_002950:PG0352|5end_sialidase,_putative_387187..387417_POSITIVE 306 214 171 181 129 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 306 250 201 231 171 NC_002950:PG1306|5end_metallo-beta-lactamase_family_protein_1387187..1387417_NEGATIVE 306 258 213 191 146 NC_002950:PG0063|5end_outer_membrane_efflux_protein_77056..77286_NEGATIVE 305 240 192 209 148 NC_002950:PG0397|5end_hypothetical_protein_434602..434832_NEGATIVE 303 239 192 146 91 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 303 217 179 164 118 NC_002950:PG1199|5end_hypothetical_protein_1276893..1277123_POSITIVE 301 259 212 215 145 NC_002950:PG0414|5end_hypothetical_protein_453652..453882_NEGATIVE 300 50 3 182 141 NC_002950:PG2049|5end_hypothetical_protein_2148904..2149134_NEGATIVE 299 258 214 147 87 NC_002950:PG0205|5end_peptide_chain_release_factor_3_242093..242323_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 259 215 129 80 NC_002950:PG0647|3end_iron_compound_ABC_transporter,_permease_protein_699079..699229_NEGATIVE 329 260 217 128 87 NC_002950:PG0085|3end_alpha-galactosidase_100556..100706_POSITIVE 326 160 118 118 86 NC_002950:PG1690|3end_Sua5/YciO/YrdC/YwlC_family_protein_1775171..1775321_NEGATIVE 323 234 200 137 105 NC_002950:PG0190|3end_undecaprenyl_diphosphate_synthase_226920..227070_POSITIVE 319 229 181 140 89 NC_002950:PG1761|3end_acetyltransferase,_GNAT_family_1847739..1847889_POSITIVE 318 231 197 150 112 NC_002950:PG0949|3end_hypothetical_protein_1009773..1009923_POSITIVE 311 235 199 85 42 NC_002950:PG1881|3end_hypothetical_protein_1978046..1978196_POSITIVE 306 238 200 66 21 NC_002950:PG0419|3end_hypothetical_protein_459702..459852_NEGATIVE 305 256 215 142 100 NC_002950:PG1594|3end_ComEC/Rec2-related_protein_1672052..1672202_NEGATIVE 300 250 207 70 20 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 297 255 212 146 83 NC_002950:PG0415|3end_peptidyl-prolyl_cis-trans_isomerase,_PPIC-type_453714..453864_NEGATIVE 295 239 193 77 34 NC_002950:PG0754|3end_DNA_topoisomerase_I_803389..803539_POSITIVE 294 219 179 83 47 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE 294 221 181 117 79 NC_002950:PG1270|3end_hypothetical_protein_1349278..1349428_NEGATIVE 292 190 142 114 58 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 291 232 194 136 91 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 291 239 198 133 95 NC_002950:PG0677|3end_saccharopine_dehydrogenase_728926..729076_POSITIVE 289 245 203 59 19 NC_002950:PG2132|3end_fimbrilin_2238943..2239093_POSITIVE 288 258 217 127 81 NC_002950:PG0684|3end_ABC_transporter,_permease_protein,_putative_740103..740253_POSITIVE 287 260 216 85 45 NC_002950:PG0951|3end_phosphoribosylaminoimidazole_carboxylase,_PurE_protein_1010828..1010978_POSITIVE