Origin IGS: tgagcttgttcttaggtaaagaaaaaacgcctaattaggcgttttttagattttccttcacagtgtcattgctagactggctggctggtgtcgagctaatatttaggtatgtagtattatgttatgacttatgaatagtactagcgaaagaaaaatttaggtagataaagtaatttttacaattaaaggagattgt .........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 acaatctcctttaattgtaaaaattactttatctacctaaatttttctttcgctagtactattcataagtcataacataatactacatacctaaatattagctcgacaccagccagccagtctagcaatgacactgtgaaggaaaatctaaaaaacgcctaattaggcgttttttctttacctaagaacaagctca Mask Tandem Repeat Region ================================================ tgagcttgttcttaggtaaagaaaaaacgcctaattaggcgttttttagattttccttcacagtgtcattgctagactggctggctggtgtcgagctaatatttaggtatgtagtattatgttatgacttatgaatagtactagcgaaagaaaaatttaggtagataaagtaatttttacaattaaaggagattgt Find is-nt database================================================ Query_seq: AA01894:AA01895|AA01894:AA01895:conserved hypothetical protein (possible transthyretin-like periplasmic protein):hypothetical protein:->->:1279518..1279713 196 tgagcttgttcttaggtaaagaaaaaacgcctaattaggcgttttttagattttccttcacagtgtcattgctagactggctggctggtgtcgagctaatatttaggtatgtagtattatgttatgacttatgaatagtactagcgaaagaaaaatttaggtagataaagtaatttttacaattaaaggagattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01894:AA01895|AA01894:AA01895:conserved hypothetical protein (possible transthyretin-like periplasmic protein):hypothetical protein:->->:1279518..1279713 196 tgagcttgttcttaggtaaagaaaaaacgcctaattaggcgttttttagattttccttcacagtgtcattgctagactggctggctggtgtcgagctaatatttaggtatgtagtattatgttatgacttatgaatagtactagcgaaagaaaaatttaggtagataaagtaatttttacaattaaaggagattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01894:AA01895|AA01894:AA01895:conserved hypothetical protein (possible transthyretin-like periplasmic protein):hypothetical protein:->->:1279518..1279713 196 tgagcttgttcttaggtaaagaaaaaacgcctaattaggcgttttttagattttccttcacagtgtcattgctagactggctggctggtgtcgagctaatatttaggtatgtagtattatgttatgacttatgaatagtactagcgaaagaaaaatttaggtagataaagtaatttttacaattaaaggagattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagcttgttcttaggtaaagaaaaaacgcctaattaggcgttttttagattttccttcacagtgtcattgctagactggctggctggtgtcgagctaatatttaggtatgtagtattatgttatgacttatgaatagtactagcgaaagaaaaatttaggtagataaagtaatttttacaattaaaggagattgt Predict ORF larger than 30AA ================================================ tgagcttgttcttaggtaaagaaaaaacgcctaattaggcgttttttagattttccttcacagtgtcattgctagactggctggctggtgtcgagctaatatttaggtatgtagtattatgttatgacttatgaatagtactagcgaaagaaaaatttaggtagataaagtaatttttacaattaaaggagattgt 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================================================ tgagcttgttcttaggtaaagaaaaaacgcctaattaggcgttttttagattttccttcacagtgtcattgctagactggctggctggtgtcgagctaatatttaggtatgtagtattatgttatgacttatgaatagtactagcgaaagaaaaatttaggtagataaagtaatttttacaattaaaggagattgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 82 HP_score: -10.0 Tail_Score: -3.64703 Start: 21 End: 48 Full_Region: ctgtgaaggaaaatc taaaaaacgcct aatt aggcgttttttc tttacctaagaacaa ....................taaaaaacgcctaattaggcgttttttc.................................................................................................................................................... TransTerm Strand: - Conf: 93 HP_score: -8.1 Tail_Score: -5.65927 Start: 28 End: 41 Full_Region: ggaaaatctaaaaaa cgcct aatt aggcg ttttttctttaccta ...........................cgcctaattaggcg........................................................................................................................................................... Find igs database================================================ Query_seq: AA01894:AA01895|AA01894:AA01895:conserved hypothetical protein (possible transthyretin-like periplasmic protein):hypothetical protein:->->:1279518..1279713 196 tgagcttgttcttaggtaaagaaaaaacgcctaattaggcgttttttagattttccttcacagtgtcattgctagactggctggctggtgtcgagctaatatttaggtatgtagtattatgttatgacttatgaatagtactagcgaaagaaaaatttaggtagataaagtaatttttacaattaaaggagattgt Intra-Species Hit: Count: 1 Min: 1 Max: 196 Len: 196 Subject: aact_AA01894_AA01895|conserved hypothetical protein (possible transthyretin-like periplasmic protein):hypothetical protein|POSITIVE:POSITIVE|[1279518,1279713]|196 HSP 1 e-value: 1.0E-107 bit: 389.0 Len: 196 Query Start:1 Query End:196 Subject Strand: POSITIVE Subject Start: 1 Subject End: 196 tgagcttgttcttaggtaaagaaaaaacgcctaattaggcgttttttagattttccttcacagtgtcattgctagactggctggctggtgtcgagctaatatttaggtatgtagtattatgttatgacttatgaatagtactagcgaaagaaaaatttaggtagataaagtaatttttacaattaaaggagattgt tgagcttgttcttaggtaaagaaaaaacgcctaattaggcgttttttagattttccttcacagtgtcattgctagactggctggctggtgtcgagctaatatttaggtatgtagtattatgttatgacttatgaatagtactagcgaaagaaaaatttaggtagataaagtaatttttacaattaaaggagattgt HSP 2 e-value: 7.0E-6 bit: 52.0 Len: 26 Query Start:22 Query End:47 Subject Strand: NEGATIVE Subject Start: 22 Subject End: 47 .....................aaaaaacgcctaattaggcgtttttt..................................................................................................................................................... .....................aaaaaacgcctaattaggcgtttttt..................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGCUUGUUCUUAGGUAAAGAAAAAACGCCUAAUUAGGCGUUUUUUAGAUUUUCCUUCACAGUGUCAUUGCUAGACUGGCUGGCUGGUGUCGAGCUAAUAUUUAGGUAUGUAGUAUUAUGUUAUGACUUAUGAAUAGUACUAGCGAAAGAAAAAUUUAGGUAGAUAAAGUAAUUUUUACAAUUAAAGGAGAUUGU ...(((((....)))))....(((((((((((....)))))))))))....(((((((....(((..((((((....((((((((....))).))))).(((((((((...(((((((((.(((((...)))))))))))))).(....)....))))))))).....))))))...))).....))))))).... (-45.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAUCUCCUUUAAUUGUAAAAAUUACUUUAUCUACCUAAAUUUUUCUUUCGCUAGUACUAUUCAUAAGUCAUAACAUAAUACUACAUACCUAAAUAUUAGCUCGACACCAGCCAGCCAGUCUAGCAAUGACACUGUGAAGGAAAAUCUAAAAAACGCCUAAUUAGGCGUUUUUUCUUUACCUAAGAACAAGCUCA (((((........))))).............(((........(((((((((((.(((...........(((((....(((((.............)))))(((.(((............))).))).)))))))))))))))))))...(((((((((((....))))))))))).........)))......... (-33.72) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 96 59 81 46 aact:AA01876|5end_PTS_system,_IIBC_components_1263365..1263595_POSITIVE 338 90 41 111 55 aact:AA01108|5end_hypothetical_protein_763646..763876_POSITIVE 322 93 59 46 10 aact:AA00062|5end_bicyclomycin_resistance_protein_(Sulfonamide_resistance_protein)_46889..47119_POSITIVE 321 99 53 63 26 aact:AA02296|5end_conserved_hypothetical_protein_(possible_cell_wall-associated_hydrolase)_1566070..1566300_POSITIVE 321 99 53 63 26 aact:AA00620|5end_hydrolase_425182..425412_POSITIVE 321 99 53 63 26 aact:AA00411|5end_hydrolase_275798..276028_POSITIVE 317 108 63 91 38 aact:AA00370|5end_30S_ribosomal_protein_S10_248620..248850_POSITIVE 316 93 52 176 144 aact:AA00528|5end_conserved_hypothetical_protein_361396..361626_POSITIVE 312 109 61 143 95 aact:AA01276|5end_heptosyltransferase_III_864730..864960_POSITIVE 312 108 61 85 44 aact:AA00794|5end_phosphohydrolase_543653..543883_POSITIVE 310 100 63 117 82 aact:AA02205|5end_short_chain_dehydrogenase/reductase_1501170..1501400_POSITIVE 310 96 62 64 33 aact:AA00048|5end_conserved_hypothetical_protein_38853..39083_POSITIVE 301 128 83 56 7 aact:AA02132|5end_dihydroorotate_dehydrogenase_1455089..1455319_POSITIVE 300 97 55 224 173 aact:AA01247|5end_hypothetical_protein_849664..849894_POSITIVE 299 96 61 67 27 aact:AA00575|5end_shikimate_5-dehydrogenase_393216..393446_POSITIVE 297 90 50 134 95 aact:AA01127|5end_energy_transducer_protein_772685..772915_POSITIVE 292 120 74 51 7 aact:AA01102|5end_pyrimidine_operon_regulatory_protein_760480..760710_POSITIVE 292 97 63 133 96 aact:AA00734|5end_citrate_lyase,_gamma_chain_(acyl_carrier_protein)_502528..502758_POSITIVE 292 97 61 35 4 aact:AA00202|5end_conserved_hypothetical_protein_(possible_membrane_protein)_140546..140776_POSITIVE 291 97 68 37 4 aact:AA00282|5end_peptidyl-prolyl_cis-trans_isomerase;_macrophage_infectivity_potentiator_198834..199064_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 96 59 142 107 aact:AA01875|3end_PTS_system,_glucose-specific_enzyme_II,_A_component_1263506..1263656_POSITIVE 355 57 14 77 34 aact:AA01894|3end_conserved_hypothetical_protein_(possible_transthyretin-like_periplasmic_protein)_1279457..1279607_POSITIVE 338 90 41 139 83 aact:AA01107|3end_adenylosuccinate_lyase_763754..763904_POSITIVE 317 108 63 71 18 aact:AA00369|3end_50S_ribosomal_protein_L3_248680..248830_POSITIVE 310 100 63 129 94 aact:AA02204|3end_hypothetical_protein_1501262..1501412_POSITIVE 309 97 57 133 87 aact:AA00391|3end_arsenate_reductase_265248..265398_POSITIVE 299 96 61 66 26 aact:AA00573|3end_chloramphenicol-sensitive_protein_RarD_393295..393445_POSITIVE 297 90 50 121 82 aact:AA01124.1|3end_biopolymer_transport_protein_D_772752..772902_POSITIVE 297 90 50 120 81 aact:AA01125|3end_hypothetical_protein_772751..772901_POSITIVE 292 97 63 38 1 aact:AA00733|3end_hypothetical_protein_502513..502663_POSITIVE 290 97 55 148 99 aact:AA00340|3end_NADP(H)_oxidoreductase_(NAD(P)H_dehydrogenase_(quinone))_229425..229575_POSITIVE 289 86 42 132 75 aact:AA01996|3end_prephenate_dehydrogenase_1356167..1356317_POSITIVE 285 94 59 37 2 aact:AA01407|3end_outer_membrane_antigenic_lipoprotein_b_precursor_950251..950401_POSITIVE 282 105 62 75 37 aact:AA02801|3end_myo-inositol_catabolism_protein_1969073..1969223_POSITIVE 277 118 75 110 66 aact:AA02970|3end_tyrosine_phenol-lyase_2077391..2077541_POSITIVE 275 126 82 139 101 aact:AA00580|3end_conserved_hypothetical_protein_(possible_membrane_protein)_397628..397778_POSITIVE 274 94 60 148 116 aact:AA01274|3end_hypothetical_protein_864832..864982_POSITIVE 274 108 67 149 103 aact:AA00799|3end_iron(III)_dicitrate_transport_ATP-binding_protein_548502..548652_POSITIVE 271 97 57 108 48 aact:AA01291|3end_excinuclease_ABC_subunit_A_876001..876151_POSITIVE 269 96 54 76 29 aact:AA00408|3end_SUN_protein_(FMU_protein)_273688..273838_POSITIVE