Origin IGS: taatcattaaacgatataatgatatattttgaaaggtattttctatggggcggtgaaagtgcgcaatgaataagtgttttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaattttatcgt .........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 acgataaaattttaatatgtcgggagcaaagataattatcctctccctcttgctctaatttatactccgcttttctaacgaacggtagcatttttcctaacgaacggtcgttttttcccgataaacggtatatttgctcttgaccagtgtttcataaatccacacaaacacacgctatctttatccggaaataccgagtgaccgattgaaaaaacacttattcattgcgcactttcaccgccccatagaaaatacctttcaaaatatatcattatatcgtttaatgatta Mask Tandem Repeat Region ================================================ taatcattaaacgatataatgatatattttgaaaggtattttctatggggcggtgaaagtgcgcaatgaataagtgttttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaattttatcgt Find is-nt database================================================ Query_seq: TF1096:TF1097|TF1096:TF1097:conserved hypothetical protein:hypothetical protein:->->:1165418..1165707 290 taatcattaaacgatataatgatatattttgaaaggtattttctatggggcggtgaaagtgcgcaatgaataagtgttttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaattttatcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1096:TF1097|TF1096:TF1097:conserved hypothetical protein:hypothetical protein:->->:1165418..1165707 290 taatcattaaacgatataatgatatattttgaaaggtattttctatggggcggtgaaagtgcgcaatgaataagtgttttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaattttatcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1096:TF1097|TF1096:TF1097:conserved hypothetical protein:hypothetical protein:->->:1165418..1165707 290 taatcattaaacgatataatgatatattttgaaaggtattttctatggggcggtgaaagtgcgcaatgaataagtgttttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaattttatcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatcattaaacgatataatgatatattttgaaaggtattttctatggggcggtgaaagtgcgcaatgaataagtgttttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaattttatcgt Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 70 End: 213 ..................................................................... M S V F S I G H S V F P D K D S V C L C G F M K H W S R A N I P F I G K K R P F V R K N A T V R ............................................................................. Protein_Len: 44 Strand: + Start: 158 End: 289 ............................................................................................................................................................. M Y R L S G K N D R S L G K M L P F V R K A E Y K L E Q E G E D N Y L C S R H I K I L S . Protein_Len: 44 Strand: - Start: 2 End: 133 . I M L R Y L S I N Q F T N E I P R H F H A I F L H K K L R D S P I E P Y L Y R T N T H M ............................................................................................................................................................. taatcattaaacgatataatgatatattttgaaaggtattttctatggggcggtgaaagtgcgcaatgaataagtgttttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaattttatcgt 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================================================ taatcattaaacgatataatgatatattttgaaaggtattttctatggggcggtgaaagtgcgcaatgaataagtgttttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaattttatcgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1096:TF1097|TF1096:TF1097:conserved hypothetical protein:hypothetical protein:->->:1165418..1165707 290 taatcattaaacgatataatgatatattttgaaaggtattttctatggggcggtgaaagtgcgcaatgaataagtgttttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaattttatcgt Intra-Species Hit: Count: 6 Min: 1 Max: 290 Len: 290 Subject: tfor_TF1096_TF1097|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1165418,1165707]|290 HSP 1 e-value: 1.0E-163 bit: 575.0 Len: 290 Query Start:1 Query End:290 Subject Strand: POSITIVE Subject Start: 1 Subject End: 290 taatcattaaacgatataatgatatattttgaaaggtattttctatggggcggtgaaagtgcgcaatgaataagtgttttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaattttatcgt taatcattaaacgatataatgatatattttgaaaggtattttctatggggcggtgaaagtgcgcaatgaataagtgttttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaattttatcgt Subject: tfor_TF1104_TF1105|hypothetical protein:arylsulfatase regulator; Fe-S oxidoreductase|POSITIVE:POSITIVE|[1172255,1172855]|601 HSP 1 e-value: 1.0E-120 bit: 432.0 Len: 278 Query Start:9 Query End:286 Subject Strand: POSITIVE Subject Start: 4 Subject End: 280 ........aaacgatataatgatatattttgaaaggtattttctatggggcggtgaaagtgcgcaatgaataagtgttttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaatttta.... ........aaacgatataatgatatattttgaaaggtattt-ctatggggcagtgaaagtgcgcaatgaataagtgtcttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacggcagttaagggcaaatataccgtttatcggaaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattggagcaagaaagggaggataattatctttgctcccgacatattaaaatttta.... Subject: tfor_TF1117_TF1118|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1189512,1191445]|1934 HSP 1 e-value: 1.0E-111 bit: 402.0 Len: 251 Query Start:36 Query End:286 Subject Strand: POSITIVE Subject Start: 1378 Subject End: 1628 ...................................gtattttctatggggcggtgaaagtgcgcaatgaataagtgttttttcaatcggtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaatttta.... ...................................gtattttctatggggcggtgaaagtgcgcaatgaataagtgtcttttcaattagtcactcggtatttccggataaagatagcgtgtgtttgtgtggatttatgaaacagcagtcaagggcaaatataccgtttatcggaaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattggagcaagaaagggaggataattatctttgctcccgacatattaaaatttta.... Subject: tfor_TF1092_TF1093|glycosyltransferase:hypothetical protein|POSITIVE:POSITIVE|[1161506,1162691]|1186 HSP 1 e-value: 4.0E-82 bit: 305.0 Len: 154 Query Start:98 Query End:251 Subject Strand: POSITIVE Subject Start: 1033 Subject End: 1186 .................................................................................................tatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagagg....................................... .................................................................................................tatttccggataaagatagcgtgtgtttgtgtggatttatgaaacactggtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagagg....................................... Subject: tfor_TF1071_TF1072|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1141748,1142530]|783 HSP 1 e-value: 9.0E-62 bit: 238.0 Len: 144 Query Start:147 Query End:290 Subject Strand: POSITIVE Subject Start: 105 Subject End: 248 ..................................................................................................................................................gtcaagagcaaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttgctcccgacatattaaaattttatcgt ..................................................................................................................................................gtcaagggcaaatataccgtttatcgaaaaaaaacgaccgttcgttaggaaaaatgctactgttcgttagaaaagcggagtataaattggagcaagagggagaggatgattatctttgctcccgacatattaaaattttatcgt Subject: tfor_TF1076_TF1077|possible glycerol kinase:conserved hypothetical protein|POSITIVE:POSITIVE|[1145742,1146521]|780 HSP 1 e-value: 1.0E-48 bit: 194.0 Len: 110 Query Start:155 Query End:264 Subject Strand: POSITIVE Subject Start: 27 Subject End: 136 ..........................................................................................................................................................caaatataccgtttatcgggaaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattagagcaagagggagaggataattatctttg.......................... ..........................................................................................................................................................caaatataccgtttatcggggaaaaacgaccgttcgttaggaaaaatgctaccgttcgttagaaaagcggagtataaattggagcaagagggagaggatgattatctttg.......................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCAUUAAACGAUAUAAUGAUAUAUUUUGAAAGGUAUUUUCUAUGGGGCGGUGAAAGUGCGCAAUGAAUAAGUGUUUUUUCAAUCGGUCACUCGGUAUUUCCGGAUAAAGAUAGCGUGUGUUUGUGUGGAUUUAUGAAACACUGGUCAAGAGCAAAUAUACCGUUUAUCGGGAAAAAACGACCGUUCGUUAGGAAAAAUGCUACCGUUCGUUAGAAAAGCGGAGUAUAAAUUAGAGCAAGAGGGAGAGGAUAAUUAUCUUUGCUCCCGACAUAUUAAAAUUUUAUCGU ..........((((((.(((..(((((((((.......(((((((..(((((((....(....)........(((((((((((...(((.....((((.(((((.((((((....(.((((((((((...((((..((...))..))))....))))))))))).)))))).))))).....)))).)))...))))))))))))))))))..))))))).))))))))).............(((((.((((....))))...)))))...........))).)))))) (-73.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGAUAAAAUUUUAAUAUGUCGGGAGCAAAGAUAAUUAUCCUCUCCCUCUUGCUCUAAUUUAUACUCCGCUUUUCUAACGAACGGUAGCAUUUUUCCUAACGAACGGUCGUUUUUUCCCGAUAAACGGUAUAUUUGCUCUUGACCAGUGUUUCAUAAAUCCACACAAACACACGCUAUCUUUAUCCGGAAAUACCGAGUGACCGAUUGAAAAAACACUUAUUCAUUGCGCACUUUCACCGCCCCAUAGAAAAUACCUUUCAAAAUAUAUCAUUAUAUCGUUUAAUGAUUA ((((((...........(((((((((........................((((..............(((.(((....))).)))))))........(((((....)))))..)))))))))...(((((((((((...(((..(((((((....((((..(((..........((....))..(((.....))).)))...))))....)))))))...)))..))...................((((.....)))).)))))))))....)))))).......... (-48.63) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 380 128 88 230 196 tfor:TF2534|5end_conserved_hypothetical_protein_2717044..2717274_POSITIVE 374 80 35 176 125 tfor:TF3115|5end_possible_sugar_kinase_3350428..3350658_POSITIVE 352 150 101 217 147 tfor:TF0621|5end_phosphate_starvation-inducible_protein,_PhoH_655679..655909_POSITIVE 350 249 205 125 61 tfor:TF2000|5end_conserved_hypothetical_protein_2153931..2154161_POSITIVE 336 230 181 93 28 tfor:TF2039|5end_possible_cell-cycle_regulation_histidine_triad_(HIT)_protein_2199318..2199548_POSITIVE 319 130 87 219 173 tfor:TF0784|5end_possible_biopolymer_transport_protein_837385..837615_POSITIVE 319 272 235 201 163 tfor:TF0554|5end_Bacteroides_aerotolerance_protein,_BatC_586303..586533_POSITIVE 317 230 185 184 131 tfor:TF0825|5end_hypothetical_protein_883597..883827_POSITIVE 315 269 221 123 72 tfor:TF1708|5end_transcriptional_regulator_1829185..1829415_POSITIVE 312 99 51 213 177 tfor:TF2926|5end_glycine_hydroxymethyltransferase_3128070..3128300_POSITIVE 312 130 83 173 129 tfor:TF1051|5end_glycoside_hydrolase_1111974..1112204_POSITIVE 310 228 181 137 98 tfor:TF0463|5end_precorrin-6Y_C5,15-methyltransferase_479015..479245_POSITIVE 306 208 162 219 182 tfor:TF3112|5end_Na+/H+_anitporter_3346775..3347005_POSITIVE 306 208 162 45 8 tfor:TF3111|5end_hypothetical_protein_3346601..3346831_POSITIVE 306 127 85 104 65 tfor:TF2668|5end_hypothetical_protein_2842471..2842701_POSITIVE 306 190 141 49 9 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 305 155 115 160 119 tfor:TF2617|5end_conserved_hypothetical_protein_2793812..2794042_POSITIVE 304 227 181 118 61 tfor:TF1945|5end_glycerate_dehydrogenase_2093229..2093459_POSITIVE 303 135 92 119 78 tfor:TF1230|5end_hypothetical_protein_1314905..1315135_POSITIVE 303 186 143 230 184 tfor:TF0272|5end_outer_membrane_protein_298547..298777_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 380 128 88 120 86 tfor:TF2533|3end_adenylosuccinate_synthetase_2717014..2717164_POSITIVE 337 123 82 144 104 tfor:TF0620|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_655735..655885_POSITIVE 314 229 181 104 51 tfor:TF3064|3end_oxidoreductase,_aldo/keto_reductase_family_3290984..3291134_POSITIVE 312 130 83 70 26 tfor:TF1050|3end_hypothetical_protein_1111951..1112101_POSITIVE 310 228 181 137 98 tfor:TF0462|3end_possible_cobalamin_biosynthesis_precorrin-3_methylase_479095..479245_POSITIVE 309 130 87 140 98 tfor:TF1768|3end_conserved_hypothetical_protein;_possible_transposase_1906881..1907031_POSITIVE 309 89 47 76 33 tfor:TF0815|3end_conserved_hypothetical_protein_873974..874124_POSITIVE 304 227 181 118 61 tfor:TF1944|3end_conserved_hypothetical_protein_2093309..2093459_POSITIVE 303 186 143 133 87 tfor:TF0271|3end_oxidase/dehydrogenase_298530..298680_POSITIVE 301 128 81 99 52 tfor:TF2357|3end_collagenase_2523900..2524050_POSITIVE 296 130 87 66 18 tfor:TF1605|3end_outer_membrane_protein,_TonB_dependent_receptor_1722414..1722564_POSITIVE 296 126 82 142 84 tfor:TF1262|3end_PDZ_domain_protein_1348831..1348981_POSITIVE 294 270 221 123 60 tfor:TF1292|3end_sensor_histidine_protein_kinase_1374554..1374704_POSITIVE 294 137 94 145 100 tfor:TF0867|3end_2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy_late_synthase;_2-oxoglutarate_decarboxylase_919381..919531_POSITIVE 293 249 201 131 75 tfor:TF2181|3end_conserved_hypothetical_protein_2354963..2355113_POSITIVE 292 270 221 76 19 tfor:TF0294|3end_possible_translation_factor_321902..322052_POSITIVE 291 128 85 141 93 tfor:TF0673|3end_conserved_hypothetical_protein_717355..717505_POSITIVE 291 89 41 70 32 tfor:TF0038|3end_conserved_hypothetical_protein_41213..41363_POSITIVE 290 249 201 97 45 tfor:TF1601|3end_conserved_hypothetical_protein_1715539..1715689_POSITIVE 289 149 102 71 24 tfor:TF2906|3end_phosphatidylserine_decarboxylase_3102933..3103083_POSITIVE