Origin IGS: tgacgctctcccaataaattccgtccgactaatcaaatatcataaaatacaccaaacatgtttacaaatcaacaagataaagaatcaacagaaaggtttcacacccttcaagaacaaaccgttaaaaaagcaaaaatcatatatttatatgattgacaaacggcccgaaatgatgtaatattgcagaagtatatcataatccccaaaaacg .........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 cgtttttggggattatgatatacttctgcaatattacatcatttcgggccgtttgtcaatcatataaatatatgatttttgcttttttaacggtttgttcttgaagggtgtgaaacctttctgttgattctttatcttgttgatttgtaaacatgtttggtgtattttatgatatttgattagtcggacggaatttattgggagagcgtca Mask Tandem Repeat Region ================================================ tgacgctctcccaataaattccgtccgactaatcaaatatcataaaatacaccaaacatgtttacaaatcaacaagataaagaatcaacagaaaggtttcacacccttcaagaacaaaccgttaaaaaagcaaaaatcatatatttatatgattgacaaacggcccgaaatgatgtaatattgcagaagtatatcataatccccaaaaacg Find is-nt database================================================ Query_seq: TF1574:TF1575|TF1574:TF1575:two-component system response regulator:DNA-binding response regulator:->->:1685106..1685316 211 tgacgctctcccaataaattccgtccgactaatcaaatatcataaaatacaccaaacatgtttacaaatcaacaagataaagaatcaacagaaaggtttcacacccttcaagaacaaaccgttaaaaaagcaaaaatcatatatttatatgattgacaaacggcccgaaatgatgtaatattgcagaagtatatcataatccccaaaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1574:TF1575|TF1574:TF1575:two-component system response regulator:DNA-binding response regulator:->->:1685106..1685316 211 tgacgctctcccaataaattccgtccgactaatcaaatatcataaaatacaccaaacatgtttacaaatcaacaagataaagaatcaacagaaaggtttcacacccttcaagaacaaaccgttaaaaaagcaaaaatcatatatttatatgattgacaaacggcccgaaatgatgtaatattgcagaagtatatcataatccccaaaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1574:TF1575|TF1574:TF1575:two-component system response regulator:DNA-binding response regulator:->->:1685106..1685316 211 tgacgctctcccaataaattccgtccgactaatcaaatatcataaaatacaccaaacatgtttacaaatcaacaagataaagaatcaacagaaaggtttcacacccttcaagaacaaaccgttaaaaaagcaaaaatcatatatttatatgattgacaaacggcccgaaatgatgtaatattgcagaagtatatcataatccccaaaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgacgctctcccaataaattccgtccgactaatcaaatatcataaaatacaccaaacatgtttacaaatcaacaagataaagaatcaacagaaaggtttcacacccttcaagaacaaaccgttaaaaaagcaaaaatcatatatttatatgattgacaaacggcccgaaatgatgtaatattgcagaagtatatcataatccccaaaaacg Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 58 End: 153 ......................................................... M F T N Q Q D K E S T E R F H T L Q E Q T V K K A K I I Y L Y D .......................................................... Protein_Len: 54 Strand: + Start: 14 End: 175 ............. M N S V R L I K Y H K I H Q T C L Q I N K I K N Q Q K G F T P F K N K P L K K Q K S Y I Y M I D K R P E M M .................................... Protein_Len: 32 Strand: - Start: 111 End: 206 .............................................................................................................. S C V T L F A F I M Y K Y S Q C V A R F S T I N C F Y I M I G M ..... tgacgctctcccaataaattccgtccgactaatcaaatatcataaaatacaccaaacatgtttacaaatcaacaagataaagaatcaacagaaaggtttcacacccttcaagaacaaaccgttaaaaaagcaaaaatcatatatttatatgattgacaaacggcccgaaatgatgtaatattgcagaagtatatcataatccccaaaaacg 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: 85 Start: 39 End: 68 ......................................TTTGTAAACATGTTTGGTGTATTTTATGAT............................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 152 End: 181 .......................................................................................................................................................ATTGACAAACGGCCCGAAATGATGTAATAT.............................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 44 End: 73 ...........................................GTTGATTTGTAAACATGTTTGGTGTATTTT.......................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgacgctctcccaataaattccgtccgactaatcaaatatcataaaatacaccaaacatgtttacaaatcaacaagataaagaatcaacagaaaggtttcacacccttcaagaacaaaccgttaaaaaagcaaaaatcatatatttatatgattgacaaacggcccgaaatgatgtaatattgcagaagtatatcataatccccaaaaacg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 58 HP_score: -5.3 Tail_Score: -3.39742 Start: 91 End: 109 Full_Region: taacggtttgttctt gaagggt gtgaa acctttc tgttgattctttatc ..........................................................................................gaagggtgtgaaacctttc...................................................................................................... TransTerm Strand: - Conf: 79 HP_score: -4.8 Tail_Score: -5.25735 Start: 137 End: 152 Full_Region: cgggccgtttgtcaa tcatat aaat atatga tttttgcttttttaa ........................................................................................................................................tcatataaatatatga........................................................... Find igs database================================================ Query_seq: TF1574:TF1575|TF1574:TF1575:two-component system response regulator:DNA-binding response regulator:->->:1685106..1685316 211 tgacgctctcccaataaattccgtccgactaatcaaatatcataaaatacaccaaacatgtttacaaatcaacaagataaagaatcaacagaaaggtttcacacccttcaagaacaaaccgttaaaaaagcaaaaatcatatatttatatgattgacaaacggcccgaaatgatgtaatattgcagaagtatatcataatccccaaaaacg Intra-Species Hit: Count: 1 Min: 1 Max: 211 Len: 211 Subject: tfor_TF1574_TF1575|two-component system response regulator:DNA-binding response regulator|POSITIVE:POSITIVE|[1685106,1685316]|211 HSP 1 e-value: 1.0E-63 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 tgacgctctcccaataaattccgtccgactaatcaaatatcataaaatacaccaaacatgtttacaaatcaacaagataaagaatcaacagaaaggtttcacacccttcaagaacaaaccgtt........................................................................................ tgacgctctcccaataaattccgtccgactaatcaaatatcataaaatacaccaaacatgtttacaaatcaacaagataaagaatcaacagaaaggtttcacacccttcaagaacaaaccgtt........................................................................................ HSP 2 e-value: 4.0E-35 bit: 149.0 Len: 75 Query Start:137 Query End:211 Subject Strand: POSITIVE Subject Start: 137 Subject End: 211 ........................................................................................................................................tcatatatttatatgattgacaaacggcccgaaatgatgtaatattgcagaagtatatcataatccccaaaaacg ........................................................................................................................................tcatatatttatatgattgacaaacggcccgaaatgatgtaatattgcagaagtatatcataatccccaaaaacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACGCUCUCCCAAUAAAUUCCGUCCGACUAAUCAAAUAUCAUAAAAUACACCAAACAUGUUUACAAAUCAACAAGAUAAAGAAUCAACAGAAAGGUUUCACACCCUUCAAGAACAAACCGUUAAAAAAGCAAAAAUCAUAUAUUUAUAUGAUUGACAAACGGCCCGAAAUGAUGUAAUAUUGCAGAAGUAUAUCAUAAUCCCCAAAAACG ..((..(((..(((((..........((....))..(((((((...............(((((............(((.....)))....(((.(((.....))).)))..)))))..(((((...........((((((((....))))))))....)))))......)))))))..))))).))).))..................... (-24.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUUUUGGGGAUUAUGAUAUACUUCUGCAAUAUUACAUCAUUUCGGGCCGUUUGUCAAUCAUAUAAAUAUAUGAUUUUUGCUUUUUUAACGGUUUGUUCUUGAAGGGUGUGAAACCUUUCUGUUGAUUCUUUAUCUUGUUGAUUUGUAAACAUGUUUGGUGUAUUUUAUGAUAUUUGAUUAGUCGGACGGAAUUUAUUGGGAGAGCGUCA (((((((....(((((((((((((...(((...((((((((...(((((((((.((.((((((((....))))))))...))......))))))))).....(((((((.....)))))))...................)))..)))))...)))..))))))))..))))).(((((....))))).............)))))))... (-41.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 42 2 152 98 tfor:TF1742|5end_TPR_repeat-containing_protein_1873129..1873359_POSITIVE 281 188 151 61 16 tfor:TF0429|5end_ABC_transporter,_ATP-binding_protein_450177..450407_POSITIVE 273 191 151 93 55 tfor:TF1198|5end_conserved_hypothetical_protein_1281464..1281694_POSITIVE 264 195 155 80 42 tfor:TF1331|5end_outer_membrane_protein_1409688..1409918_POSITIVE 264 189 153 82 42 tfor:TF1277|5end_electron_transfer_flavoprotein,_alpha_subunit_1363012..1363242_POSITIVE 253 190 144 220 175 tfor:TF1972|5end_conserved_hypothetical_protein_2118454..2118684_POSITIVE 248 127 88 220 180 tfor:TF2588|5end_coproporphryninogen_III_oxidase_2752117..2752347_POSITIVE 248 127 88 59 19 tfor:TF2587|5end_hypothetical_protein_2751956..2752186_POSITIVE 245 43 9 152 121 tfor:TF3018|5end_polyphosphate_kinase_3240122..3240352_POSITIVE 244 210 161 68 10 tfor:TF3026|5end_conserved_hypothetical_protein_3249137..3249367_POSITIVE 244 199 153 128 75 tfor:TF1743|5end_conserved_hypothetical_protein_1876708..1876938_POSITIVE 240 187 152 170 138 tfor:TF0636|5end_beta-galactosidase_670697..670927_POSITIVE 236 195 155 87 37 tfor:TF1574|5end_two-component_system_response_regulator_1681807..1682037_POSITIVE 235 184 151 35 1 tfor:TF1834|5end_3-isopropylmalate_dehydrogenase_1983161..1983391_POSITIVE 233 140 106 92 53 tfor:TF2081|5end_phosphopantetheine_adenylyltransferase_2248475..2248705_POSITIVE 232 175 142 203 172 tfor:TF1789|5end_conserved_hypothetical_protein_1930219..1930449_POSITIVE 230 194 155 177 119 tfor:TF2677|5end_aspartate_transaminase_2850809..2851039_POSITIVE 230 42 2 175 138 tfor:TF2100|5end_hypothetical_protein_2273424..2273654_POSITIVE 230 30 1 231 202 tfor:TF1587|5end_conserved_hypothetical_protein_1700245..1700475_POSITIVE 230 170 129 223 179 tfor:TF0469|5end_hypothetical_protein_486960..487190_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 162 129 91 58 tfor:TF1593|3end_hypothetical_protein_1709577..1709727_POSITIVE 264 195 155 73 35 tfor:TF1330|3end_hypothetical_protein_1409761..1409911_POSITIVE 264 189 153 70 30 tfor:TF1276|3end_acyl-CoA_dehydrogenase_(short_chain_coenzyme_A_dehydrogenase)_1363080..1363230_POSITIVE 248 127 88 87 47 tfor:TF2586|3end_conserved_hypothetical_protein_2752064..2752214_POSITIVE 240 187 152 151 119 tfor:TF0635|3end_glucosylceramidase_precursor_670758..670908_POSITIVE 237 204 161 49 4 tfor:TF0323|3end_NAD-dependent_epimerase/dehydratase_family_protein_351053..351203_POSITIVE 233 140 106 92 53 tfor:TF2080|3end_carboxyl-terminal_protease_2248555..2248705_POSITIVE 231 193 161 145 112 tfor:TF1152|3end_permease,_major_facilitator_superfamily_1234618..1234768_POSITIVE 230 194 155 119 61 tfor:TF2676|3end_conserved_hypothetical_protein_2850831..2850981_POSITIVE 230 42 2 90 53 tfor:TF2099|3end_D-tyrosyl-tRNA(Tyr)_deacylase_2273419..2273569_POSITIVE 228 28 5 129 106 tfor:TF1832|3end_3-isopropylmalate_dehydratase,_small_subunit_1981502..1981652_POSITIVE 227 40 2 56 20 tfor:TF0706|3end_possible_outer_membrane_transport_protein_750619..750769_POSITIVE 223 35 4 73 44 tfor:TF2366|3end_conserved_hypothetical_protein_2531892..2532042_POSITIVE 221 176 153 41 17 tfor:TF1199|3end_dephospho-CoA_kinase_1282797..1282947_POSITIVE 218 42 5 72 39 tfor:TF1816|3end_hypothetical_protein_1957974..1958124_POSITIVE 218 42 5 89 56 tfor:TF1817|3end_hypothetical_protein_1957991..1958141_POSITIVE 218 158 111 83 32 tfor:TF0506|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_helicase_532421..532571_POSITIVE 216 201 161 60 24 tfor:TF1941|3end_3-phosphoshikimate-1-carboxyvinyltransferase_2090183..2090333_POSITIVE 216 190 160 63 23 tfor:TF1791|3end_hypothetical_protein_1932527..1932677_POSITIVE 215 176 137 137 88 tfor:TF3149|3end_conserved_hypothetical_protein_3385592..3385742_POSITIVE