Origin IGS: tagcaatgacggtacgagaaactcattgagagttcttttgtatgtgtaccaaaggcagtcgatatgggagcagaatcctttacagagtatgaataataaagaaacccatcggaagaattaaatacgcactaaattaattccgccaacgggtttatcattatatccctcggtttcaaatcgtttaaggcaggattactgcaaatcgttccactcatgtttgccatgttg .........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 caacatggcaaacatgagtggaacgatttgcagtaatcctgccttaaacgatttgaaaccgagggatataatgataaacccgttggcggaattaatttagtgcgtatttaattcttccgatgggtttctttattattcatactctgtaaaggattctgctcccatatcgactgcctttggtacacatacaaaagaactctcaatgagtttctcgtaccgtcattgcta Mask Tandem Repeat Region ================================================ tagcaatgacggtacgagaaactcattgagagttcttttgtatgtgtaccaaaggcagtcgatatgggagcagaatcctttacagagtatgaataataaagaaacccatcggaagaattaaatacgcactaaattaattccgccaacgggtttatcattatatccctcggtttcaaatcgtttaaggcaggattactgcaaatcgttccactcatgtttgccatgttg Find is-nt database================================================ Query_seq: PI0238:PI0239|PI0238:PI0239:two-component system response regulator:conserved hypothetical protein:->->:237887..238114 228 tagcaatgacggtacgagaaactcattgagagttcttttgtatgtgtaccaaaggcagtcgatatgggagcagaatcctttacagagtatgaataataaagaaacccatcggaagaattaaatacgcactaaattaattccgccaacgggtttatcattatatccctcggtttcaaatcgtttaaggcaggattactgcaaatcgttccactcatgtttgccatgttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0238:PI0239|PI0238:PI0239:two-component system response regulator:conserved hypothetical protein:->->:237887..238114 228 tagcaatgacggtacgagaaactcattgagagttcttttgtatgtgtaccaaaggcagtcgatatgggagcagaatcctttacagagtatgaataataaagaaacccatcggaagaattaaatacgcactaaattaattccgccaacgggtttatcattatatccctcggtttcaaatcgtttaaggcaggattactgcaaatcgttccactcatgtttgccatgttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0238:PI0239|PI0238:PI0239:two-component system response regulator:conserved hypothetical protein:->->:237887..238114 228 tagcaatgacggtacgagaaactcattgagagttcttttgtatgtgtaccaaaggcagtcgatatgggagcagaatcctttacagagtatgaataataaagaaacccatcggaagaattaaatacgcactaaattaattccgccaacgggtttatcattatatccctcggtttcaaatcgtttaaggcaggattactgcaaatcgttccactcatgtttgccatgttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagcaatgacggtacgagaaactcattgagagttcttttgtatgtgtaccaaaggcagtcgatatgggagcagaatcctttacagagtatgaataataaagaaacccatcggaagaattaaatacgcactaaattaattccgccaacgggtttatcattatatccctcggtttcaaatcgtttaaggcaggattactgcaaatcgttccactcatgtttgccatgttg Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 26 End: 118 ......................... M R V L L Y V Y Q R Q S I W E Q N P L Q S M N N K E T H R K N .............................................................................................................. Protein_Len: 35 Strand: + Start: 122 End: 226 ......................................................................................................................... M R T K L I P P T G L S L Y P S V S N R L R Q D Y C K S F H S C L P C .. Protein_Len: 32 Strand: + Start: 133 End: 228 .................................................................................................................................... M N S A N G F I I I S L G F K S F K A G L L Q I V P L M F A M L Protein_Len: 31 Strand: - Start: 132 End: 224 ................................................................................................................................... I L E A L P N I M I D R P K L D N L A P N S C I T G S M N A M .... Protein_Len: 30 Strand: - Start: 1 End: 90 L L S P V L F E N L T R K Y T Y W L C D I H S C F G K C L M .......................................................................................................................................... tagcaatgacggtacgagaaactcattgagagttcttttgtatgtgtaccaaaggcagtcgatatgggagcagaatcctttacagagtatgaataataaagaaacccatcggaagaattaaatacgcactaaattaattccgccaacgggtttatcattatatccctcggtttcaaatcgtttaaggcaggattactgcaaatcgttccactcatgtttgccatgttg 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: 81 Start: 93 End: 122 ............................................................................................TTTAATTCTTCCGATGGGTTTCTTTATTAT.......................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 157 End: 186 ............................................................................................................................................................CTTAAACGATTTGAAACCGAGGGATATAAT.......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagcaatgacggtacgagaaactcattgagagttcttttgtatgtgtaccaaaggcagtcgatatgggagcagaatcctttacagagtatgaataataaagaaacccatcggaagaattaaatacgcactaaattaattccgccaacgggtttatcattatatccctcggtttcaaatcgtttaaggcaggattactgcaaatcgttccactcatgtttgccatgttg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 68 HP_score: -4.1 Tail_Score: -4.78597 Start: 105 End: 150 Full_Region: ggatataatgataaa cccgttggcggaattaatt tagtgcgt atttaattcttccgatggg tttctttattattca ........................................................................................................cccgttggcggaattaatttagtgcgtatttaattcttccgatggg.............................................................................. Find igs database================================================ Query_seq: PI0238:PI0239|PI0238:PI0239:two-component system response regulator:conserved hypothetical protein:->->:237887..238114 228 tagcaatgacggtacgagaaactcattgagagttcttttgtatgtgtaccaaaggcagtcgatatgggagcagaatcctttacagagtatgaataataaagaaacccatcggaagaattaaatacgcactaaattaattccgccaacgggtttatcattatatccctcggtttcaaatcgtttaaggcaggattactgcaaatcgttccactcatgtttgccatgttg Intra-Species Hit: Count: 1 Min: 1 Max: 228 Len: 228 Subject: pint_PI0238_PI0239|two-component system response regulator:conserved hypothetical protein|POSITIVE:POSITIVE|[237887,238114]|228 HSP 1 e-value: 1.0E-126 bit: 452.0 Len: 228 Query Start:1 Query End:228 Subject Strand: POSITIVE Subject Start: 1 Subject End: 228 tagcaatgacggtacgagaaactcattgagagttcttttgtatgtgtaccaaaggcagtcgatatgggagcagaatcctttacagagtatgaataataaagaaacccatcggaagaattaaatacgcactaaattaattccgccaacgggtttatcattatatccctcggtttcaaatcgtttaaggcaggattactgcaaatcgttccactcatgtttgccatgttg tagcaatgacggtacgagaaactcattgagagttcttttgtatgtgtaccaaaggcagtcgatatgggagcagaatcctttacagagtatgaataataaagaaacccatcggaagaattaaatacgcactaaattaattccgccaacgggtttatcattatatccctcggtttcaaatcgtttaaggcaggattactgcaaatcgttccactcatgtttgccatgttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAAUGACGGUACGAGAAACUCAUUGAGAGUUCUUUUGUAUGUGUACCAAAGGCAGUCGAUAUGGGAGCAGAAUCCUUUACAGAGUAUGAAUAAUAAAGAAACCCAUCGGAAGAAUUAAAUACGCACUAAAUUAAUUCCGCCAACGGGUUUAUCAUUAUAUCCCUCGGUUUCAAAUCGUUUAAGGCAGGAUUACUGCAAAUCGUUCCACUCAUGUUUGCCAUGUUG (((((.....((((((((((.(((.....))))))))........)))))...((((...(((((((((((.(((.((......(((...(((((((....((((((...((..(((((((............)))))))..))...))))))...))))).)).))))).)))............((((.....)))).....)))))...)))))))))).))))) (-53.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAACAUGGCAAACAUGAGUGGAACGAUUUGCAGUAAUCCUGCCUUAAACGAUUUGAAACCGAGGGAUAUAAUGAUAAACCCGUUGGCGGAAUUAAUUUAGUGCGUAUUUAAUUCUUCCGAUGGGUUUCUUUAUUAUUCAUACUCUGUAAAGGAUUCUGCUCCCAUAUCGACUGCCUUUGGUACACAUACAAAAGAACUCUCAAUGAGUUUCUCGUACCGUCAUUGCUA .....(((((...((((.(((.((((...((((.((((((...((((.....)))).((.(((.((.(((((((.(((((((((((.((((((((............)))))))).)))))))))))..)))))))))...))).))..)))))))))).....((((((......))))))...........((((((.....)))))).)))).)))))))))))) (-63.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 344 190 141 63 20 pint:PI1884|5end_conserved_hypothetical_protein_1826883..1827113_POSITIVE 329 87 44 162 117 pint:PI0321|5end_conserved_hypothetical_protein_302598..302828_POSITIVE 294 220 173 219 170 pint:PI0645|5end_hypothetical_protein_586419..586649_POSITIVE 294 220 173 198 149 pint:PI0643|5end_hypothetical_protein_586398..586628_POSITIVE 289 218 177 70 23 pint:PI0380|5end_conserved_hypothetical_protein_350162..350392_POSITIVE 285 181 141 41 4 pint:PI0577|5end_conserved_hypothetical_protein_521811..522041_POSITIVE 275 220 182 170 137 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 272 170 121 57 14 pint:PI0139|5end_pyridoxine_biosynthesis_protein_131835..132065_POSITIVE 269 47 1 49 1 pint:PI1819|5end_hypothetical_protein_1756620..1756850_POSITIVE 269 92 52 56 5 pint:PI0155|5end_conserved_hypothetical_protein_148290..148520_POSITIVE 267 70 28 70 30 pint:PI0909|5end_possible_mutT/NUDIX_family_protein_837526..837756_POSITIVE 267 86 42 115 71 pint:PI0693|5end_periplasmic_iron_binding_protein,_ABC_transporter_628387..628617_POSITIVE 265 150 110 28 3 pint:PI0870|5end_branched-chain_amino_acid_aminotransferase_805933..806163_POSITIVE 262 180 134 207 154 pint:PI2005|5end_potassium_uptake_protein_1962950..1963180_POSITIVE 262 50 1 84 37 pint:PI0883|5end_para-aminobenzoate_synthase_component_I_816131..816361_POSITIVE 262 99 52 97 50 pint:PI0792|5end_conserved_hypothetical_protein_729068..729298_POSITIVE 261 189 141 210 163 pint:PI2095|5end_hypothetical_protein_2049195..2049425_POSITIVE 261 189 141 205 158 pint:PI2093|5end_hypothetical_protein_2049190..2049420_POSITIVE 261 189 141 195 148 pint:PI2092|5end_hypothetical_protein_2049180..2049410_POSITIVE 261 207 167 52 7 pint:PI1150|5end_30S_ribosomal_protein_S6_1075683..1075913_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 87 44 136 91 pint:PI0320|3end_probable_cobalamin_adenosyltransferase_302652..302802_POSITIVE 289 218 177 67 20 pint:PI0379|3end_conserved_hypothetical_protein_350239..350389_POSITIVE 287 151 134 105 88 pint:PI0233|3end_membrane_protein,_possible_exporter_233771..233921_POSITIVE 282 189 141 95 50 pint:PI0866|3end_hypothetical_protein_803993..804143_POSITIVE 279 85 43 122 63 pint:PI2092|3end_hypothetical_protein_2049406..2049556_POSITIVE 277 73 40 151 108 pint:PI0979|3end_transcriptional_regulator,_tetR_family_905678..905828_POSITIVE 267 70 28 76 36 pint:PI0908|3end_conserved_hypothetical_protein_837612..837762_POSITIVE 265 79 39 149 92 pint:PI2093|3end_hypothetical_protein_2049440..2049590_POSITIVE 262 50 1 76 29 pint:PI0882|3end_conserved_hypothetical_protein;_possible_para-aminobenzoate_synthase_component_I_816203..816353_POSITIVE 262 99 52 58 11 pint:PI0791|3end_conserved_hypothetical_protein_729109..729259_POSITIVE 261 207 167 46 1 pint:PI1149|3end_30S_ribosomal_protein_S18_1075757..1075907_POSITIVE 259 209 167 97 50 pint:PI0225|3end_conserved_hypothetical_protein_222759..222909_POSITIVE 253 68 37 134 94 pint:PI2025|3end_conserved_hypothetical_protein_1979452..1979602_POSITIVE 253 176 142 52 19 pint:PI1119|3end_glycosyl_transferases,_group_1_1044940..1045090_POSITIVE 252 216 178 137 100 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 251 210 169 61 21 pint:PI1048|3end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_967193..967343_POSITIVE 249 190 141 88 46 pint:PI0605|3end_chloromuconate_cycloisomerase_553026..553176_POSITIVE 249 170 124 86 34 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 248 93 53 56 5 pint:PI0903|3end_conserved_hypothetical_protein_833227..833377_POSITIVE 248 159 111 66 18 pint:PI0242|3end_hypothetical_protein_240227..240377_POSITIVE