Origin IGS: aaaatgtttcgatttttgtaagaatacaaactttttcgtaatttagtagccaatttgagtaactatataaacaatcatttttaactaattaaatttttaccatgtcagagaataatttaaacacactgtctgctcacattgagatgaagaaagtgtggcagctattaggaattgtgctgataacagccgtagtctggaaccttcccatctca .........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 tgagatgggaaggttccagactacggctgttatcagcacaattcctaatagctgccacactttcttcatctcaatgtgagcagacagtgtgtttaaattattctctgacatggtaaaaatttaattagttaaaaatgattgtttatatagttactcaaattggctactaaattacgaaaaagtttgtattcttacaaaaatcgaaacatttt Mask Tandem Repeat Region ================================================ aaaatgtttcgatttttgtaagaatacaaactttttcgtaatttagtagccaatttgagtaactatataaacaatcatttttaactaattaaatttttaccatgtcagagaataatttaaacacactgtctgctcacattgagatgaagaaagtgtggcagctattaggaattgtgctgataacagccgtagtctggaaccttcccatctca Find is-nt database================================================ Query_seq: PI0693:PI0694|PI0693:PI0694:periplasmic iron binding protein, ABC transporter:Na+/dicarboxylate or sulfate symporter:->->:629673..629884 212 aaaatgtttcgatttttgtaagaatacaaactttttcgtaatttagtagccaatttgagtaactatataaacaatcatttttaactaattaaatttttaccatgtcagagaataatttaaacacactgtctgctcacattgagatgaagaaagtgtggcagctattaggaattgtgctgataacagccgtagtctggaaccttcccatctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0693:PI0694|PI0693:PI0694:periplasmic iron binding protein, ABC transporter:Na+/dicarboxylate or sulfate symporter:->->:629673..629884 212 aaaatgtttcgatttttgtaagaatacaaactttttcgtaatttagtagccaatttgagtaactatataaacaatcatttttaactaattaaatttttaccatgtcagagaataatttaaacacactgtctgctcacattgagatgaagaaagtgtggcagctattaggaattgtgctgataacagccgtagtctggaaccttcccatctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0693:PI0694|PI0693:PI0694:periplasmic iron binding protein, ABC transporter:Na+/dicarboxylate or sulfate symporter:->->:629673..629884 212 aaaatgtttcgatttttgtaagaatacaaactttttcgtaatttagtagccaatttgagtaactatataaacaatcatttttaactaattaaatttttaccatgtcagagaataatttaaacacactgtctgctcacattgagatgaagaaagtgtggcagctattaggaattgtgctgataacagccgtagtctggaaccttcccatctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatgtttcgatttttgtaagaatacaaactttttcgtaatttagtagccaatttgagtaactatataaacaatcatttttaactaattaaatttttaccatgtcagagaataatttaaacacactgtctgctcacattgagatgaagaaagtgtggcagctattaggaattgtgctgataacagccgtagtctggaaccttcccatctca Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 93 End: 212 ............................................................................................ M F T M S E N N L N T L S A H I E M K K V W Q L L G I V L I T A V V W N L P I S aaaatgtttcgatttttgtaagaatacaaactttttcgtaatttagtagccaatttgagtaactatataaacaatcatttttaactaattaaatttttaccatgtcagagaataatttaaacacactgtctgctcacattgagatgaagaaagtgtggcagctattaggaattgtgctgataacagccgtagtctggaaccttcccatctca 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================================================ aaaatgtttcgatttttgtaagaatacaaactttttcgtaatttagtagccaatttgagtaactatataaacaatcatttttaactaattaaatttttaccatgtcagagaataatttaaacacactgtctgctcacattgagatgaagaaagtgtggcagctattaggaattgtgctgataacagccgtagtctggaaccttcccatctca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0693:PI0694|PI0693:PI0694:periplasmic iron binding protein, ABC transporter:Na+/dicarboxylate or sulfate symporter:->->:629673..629884 212 aaaatgtttcgatttttgtaagaatacaaactttttcgtaatttagtagccaatttgagtaactatataaacaatcatttttaactaattaaatttttaccatgtcagagaataatttaaacacactgtctgctcacattgagatgaagaaagtgtggcagctattaggaattgtgctgataacagccgtagtctggaaccttcccatctca Intra-Species Hit: Count: 1 Min: 1 Max: 212 Len: 212 Subject: pint_PI0693_PI0694|periplasmic iron binding protein, ABC transporter:Na+/dicarboxylate or sulfate symporter|POSITIVE:POSITIVE|[629673,629884]|212 HSP 1 e-value: 1.0E-117 bit: 420.0 Len: 212 Query Start:1 Query End:212 Subject Strand: POSITIVE Subject Start: 1 Subject End: 212 aaaatgtttcgatttttgtaagaatacaaactttttcgtaatttagtagccaatttgagtaactatataaacaatcatttttaactaattaaatttttaccatgtcagagaataatttaaacacactgtctgctcacattgagatgaagaaagtgtggcagctattaggaattgtgctgataacagccgtagtctggaaccttcccatctca aaaatgtttcgatttttgtaagaatacaaactttttcgtaatttagtagccaatttgagtaactatataaacaatcatttttaactaattaaatttttaccatgtcagagaataatttaaacacactgtctgctcacattgagatgaagaaagtgtggcagctattaggaattgtgctgataacagccgtagtctggaaccttcccatctca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUGUUUCGAUUUUUGUAAGAAUACAAACUUUUUCGUAAUUUAGUAGCCAAUUUGAGUAACUAUAUAAACAAUCAUUUUUAACUAAUUAAAUUUUUACCAUGUCAGAGAAUAAUUUAAACACACUGUCUGCUCACAUUGAGAUGAAGAAAGUGUGGCAGCUAUUAGGAAUUGUGCUGAUAACAGCCGUAGUCUGGAACCUUCCCAUCUCA ..........(((....((((((((....((......))....((((.(((.....).)).))))...........................))))))))...))).((((..........((((((.(((.(((.....)))....))).)))))).......(((((...((.((((....))))))...)))))..........)))). (-35.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGAUGGGAAGGUUCCAGACUACGGCUGUUAUCAGCACAAUUCCUAAUAGCUGCCACACUUUCUUCAUCUCAAUGUGAGCAGACAGUGUGUUUAAAUUAUUCUCUGACAUGGUAAAAAUUUAAUUAGUUAAAAAUGAUUGUUUAUAUAGUUACUCAAAUUGGCUACUAAAUUACGAAAAAGUUUGUAUUCUUACAAAAAUCGAAACAUUUU ((((((((((((((..(((.(((..((((....))))...........))))))....)))))).)))))))).(((((((((((...(((((.............)))))......((((((..(((((((...(((((((....)))))))......))))))).))))))........)))))....))))))................ (-39.24) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 196 158 161 111 pint:PI0773|5end_D-3-phosphoglycerate_dehydrogenase_708498..708728_POSITIVE 303 170 123 51 2 pint:PI1568|5end_OmpA_family_protein_1489584..1489814_POSITIVE 301 190 142 142 82 pint:PI1170|5end_possible_response_regulator_1090596..1090826_POSITIVE 296 200 153 61 16 pint:PI0813|5end_conserved_hypothetical_protein_751095..751325_POSITIVE 294 162 124 82 32 pint:PI0719|5end_conserved_hypothetical_protein_653043..653273_POSITIVE 293 162 121 57 21 pint:PI2158|5end_glycosyl_transferase,_group_2_family_protein_2104392..2104622_POSITIVE 293 190 146 84 47 pint:PI0431|5end_Xaa-Pro_aminopeptidase_403064..403294_POSITIVE 292 192 152 94 59 pint:PI0736|5end_transcriptional_regulator,_TetR_family_670580..670810_POSITIVE 288 170 130 214 169 pint:PI0993|5end_probable_TPR-repeat-containing_protein_917175..917405_POSITIVE 288 200 153 226 173 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 288 200 153 152 99 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 285 187 143 64 14 pint:PI1542|5end_mobilization_protein_1461728..1461958_POSITIVE 282 179 132 106 54 pint:PI0906|5end_hypothetical_protein_835653..835883_POSITIVE 278 197 153 50 3 pint:PI2042|5end_cation-transporting_ATPase_1994175..1994405_POSITIVE 276 191 152 71 33 pint:PI0708|5end_conserved_hypothetical_protein_644475..644705_POSITIVE 274 176 136 188 134 pint:PI1047|5end_conserved_hypothetical_protein_965614..965844_POSITIVE 274 207 179 188 160 pint:PI0506|5end_conserved_hypothetical_protein_465501..465731_POSITIVE 273 195 154 113 79 pint:PI2162|5end_conserved_hypothetical_protein_2108796..2109026_POSITIVE 272 158 125 55 24 pint:PI0851|5end_hypothetical_protein_784310..784540_POSITIVE 270 197 151 106 66 pint:PI0168|5end_methionyl-tRNA_synthetase_(methionine--tRNA_ligase)_161181..161411_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 196 158 64 14 pint:PI0772|3end_conserved_hypothetical_protein_708481..708631_POSITIVE 321 193 154 135 90 pint:PI0846|3end_transcription_regulator,_CRP_family_781009..781159_POSITIVE 303 187 141 140 85 pint:PI0979|3end_transcriptional_regulator,_tetR_family_905678..905828_POSITIVE 301 199 153 127 70 pint:PI1380|3end_conserved_hypothetical_protein_1303242..1303392_POSITIVE 301 190 142 149 89 pint:PI1169|3end_hypothetical_protein_1090683..1090833_POSITIVE 300 193 154 38 3 pint:PI2044|3end_hypothetical_protein_1997351..1997501_POSITIVE 300 170 123 129 72 pint:PI1541|3end_hypothetical_protein_1461884..1462034_POSITIVE 294 162 124 79 29 pint:PI0717|3end_conserved_hypothetical_protein_653120..653270_POSITIVE 294 163 126 52 3 pint:PI0508|3end_possible_cell_filamentation_protein_467436..467586_POSITIVE 293 162 121 42 6 pint:PI2157|3end_xanthosine_triphosphate_pyrophosphatase,_HAM1_family_2104457..2104607_POSITIVE 293 189 149 129 85 pint:PI1918|3end_uracil-DNA_glycosylase_1862224..1862374_POSITIVE 293 190 146 41 4 pint:PI0430|3end_periplasmic_protease;_MdsD_protein_403101..403251_POSITIVE 280 170 127 81 30 pint:PI1815|3end_polyphosphate-selective_porin_O_1754510..1754660_POSITIVE 276 187 149 75 30 pint:PI1367|3end_redox-sensitive_transcriptional_activator,__OxyR_1287863..1288013_POSITIVE 274 176 136 142 88 pint:PI1045|3end_cytidine/deoxycytidylate_deaminase_family_protein_965648..965798_POSITIVE 271 167 124 55 3 pint:PI0992|3end_RNA_polymerase_sigma-70_factor_917222..917372_POSITIVE 270 197 151 103 63 pint:PI0166|3end_hypothetical_protein_161258..161408_POSITIVE 269 161 125 150 110 pint:PI1136|3end_conserved_hypothetical_protein_1062541..1062691_POSITIVE 268 190 142 140 89 pint:PI0059|3end_peptide_chain_release_factor_RF-2_58171..58321_POSITIVE 266 199 151 60 6 pint:PI0428|3end_hypothetical_protein_396321..396471_POSITIVE