Origin IGS: tgttcctccttttgcttctgtctcggaaataaatttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaatgtccgtatatatgcctaaaattaattatatattgctaatctacagaaatttatttcttactccaatccatgcatccaaattattgttattaaatagtttaatggagtttttaggtacaaacacggatattcattaaatttatttccgagacagaagcaaaaggaggaaca Mask Tandem Repeat Region ================================================ tgttcctccttttgcttctgtctcggaaataaatttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca Find is-nt database================================================ Query_seq: TF2175:TF2176|TF2175:TF2176:hypothetical protein:hypothetical protein:->->:2348876..2349050 175 tgttcctccttttgcttctgtctcggaaataaatttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2175:TF2176|TF2175:TF2176:hypothetical protein:hypothetical protein:->->:2348876..2349050 175 tgttcctccttttgcttctgtctcggaaataaatttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2175:TF2176|TF2175:TF2176:hypothetical protein:hypothetical protein:->->:2348876..2349050 175 tgttcctccttttgcttctgtctcggaaataaatttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttcctccttttgcttctgtctcggaaataaatttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: - Start: 38 End: 172 ..................................... H I D T N T G L F E M L S N L L L L K S A H I P T L F L N R Y I L L I Y N I K P M Y V S M ... tgttcctccttttgcttctgtctcggaaataaatttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca 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================================================ tgttcctccttttgcttctgtctcggaaataaatttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2175:TF2176|TF2175:TF2176:hypothetical protein:hypothetical protein:->->:2348876..2349050 175 tgttcctccttttgcttctgtctcggaaataaatttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca Intra-Species Hit: Count: 7 Min: 1 Max: 175 Len: 175 Subject: tfor_TF2175_TF2176|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2348876,2349050]|175 HSP 1 e-value: 8.0E-95 bit: 347.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 tgttcctccttttgcttctgtctcggaaataaatttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca tgttcctccttttgcttctgtctcggaaataaatttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca Subject: tfor_TF1369_TF1370|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1447647,1447991]|345 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 141 Query Start:35 Query End:175 Subject Strand: NEGATIVE Subject Start: 187 Subject End: 327 ..................................ttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca ..................................ttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca Subject: tfor_TF2966_TF2967|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3177733,3177904]|172 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:37 Query End:175 Subject Strand: POSITIVE Subject Start: 14 Subject End: 152 ....................................aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca ....................................aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca Subject: tfor_TF1890_TF1891|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2043154,2043528]|375 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:37 Query End:175 Subject Strand: POSITIVE Subject Start: 5 Subject End: 143 ....................................aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca ....................................aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca Subject: tfor_TF2478_TF2479|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2655674,2656131]|458 HSP 1 e-value: 3.0E-48 bit: 192.0 Len: 133 Query Start:41 Query End:173 Subject Strand: NEGATIVE Subject Start: 296 Subject End: 427 ........................................aatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacatt.. ........................................aatatccgtgtttgtacctaaaagctccattaaactatttaataacaataatttggatgtatggattgg-ggagggaataaatttctgtatatcagcaatatataattaattttaggcatatatacggacatt.. Subject: tfor_TF0899_TF0901|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[946220,946820]|601 HSP 1 e-value: 1.0E-41 bit: 170.0 Len: 142 Query Start:34 Query End:175 Subject Strand: POSITIVE Subject Start: 408 Subject End: 549 .................................tttaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca .................................tttaatgaatatccgtttttgcacctaaaaactctattaaactatttaacaacaataatttagatgtataggtcggagagagaaatagatttctgtatatcagcaatatataattaattttaggcatatatacggacattca Subject: tfor_TF2162_TF2163|thermolysin precursor:hypothetical protein|POSITIVE:POSITIVE|[2340774,2340941]|168 HSP 1 e-value: 4.0E-41 bit: 168.0 Len: 117 Query Start:59 Query End:175 Subject Strand: NEGATIVE Subject Start: 52 Subject End: 168 ..........................................................taaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca ..........................................................taaaagctccattaaactatttaataacaataatttggatgtatggattgaagcaagagataaatttctgtatatcagtaatatataattaattttaggcatatatacggacattca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUCCUCCUUUUGCUUCUGUCUCGGAAAUAAAUUUAAUGAAUAUCCGUGUUUGUACCUAAAAACUCCAUUAAACUAUUUAAUAACAAUAAUUUGGAUGCAUGGAUUGGAGUAAGAAAUAAAUUUCUGUAGAUUAGCAAUAUAUAAUUAAUUUUAGGCAUAUAUACGGACAUUCA ..........((((.(((((...))))).)))).....(((((.(((((((.(((.(((((((((((((......(((((((..........))))))).......)))))).(((((....)))))...(((((........)))))..))))))).))).))))))).))))) (-34.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUGUCCGUAUAUAUGCCUAAAAUUAAUUAUAUAUUGCUAAUCUACAGAAAUUUAUUUCUUACUCCAAUCCAUGCAUCCAAAUUAUUGUUAUUAAAUAGUUUAAUGGAGUUUUUAGGUACAAACACGGAUAUUCAUUAAAUUUAUUUCCGAGACAGAAGCAAAAGGAGGAACA (((((((((((.....(((((((((.......................(((((....)))))........(((((......((((((((.......)))))))).)))))..))))))))).....))))))))))).........(((((...............))))).... (-34.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 773 140 91 215 166 tfor:TF1370|5end_conserved_hypothetical_protein_1447852..1448082_POSITIVE 640 90 41 172 123 tfor:TF2479|5end_conserved_hypothetical_protein_2655992..2656222_POSITIVE 640 90 41 123 74 tfor:TF2163|5end_hypothetical_protein_2340802..2341032_POSITIVE 584 90 41 185 136 tfor:TF0845|5end_hypothetical_protein_896419..896649_POSITIVE 341 67 21 89 41 tfor:TF1377|5end_conserved_hypothetical_protein_1453767..1453997_POSITIVE 295 67 32 213 178 tfor:TF0671|5end_histidine_kinase_sensor_protein_715103..715333_POSITIVE 280 67 38 210 183 tfor:TF1265|5end_dihydroorotate_dehydrogenase_1352360..1352590_POSITIVE 271 50 10 197 152 tfor:TF0280|5end_hypothetical_protein_308807..309037_POSITIVE 269 58 15 158 111 tfor:TF0239|5end_conserved_hypothetical_protein_268894..269124_POSITIVE 268 29 1 65 35 tfor:TF2307|5end_two-component_system_sensor_histidine_kinase/response_2462618..2462848_POSITIVE 268 67 21 225 182 tfor:TF1868|5end_conserved_hypothetical_protein;_possible_transposase_2022598..2022828_POSITIVE 268 67 21 89 46 tfor:TF1867|5end_transposase_2022462..2022692_POSITIVE 261 59 14 80 24 tfor:TF2807|5end_possible_chloride_channel_protein_2996637..2996867_POSITIVE 254 58 16 226 173 tfor:TF2597|5end_outer_membrane_receptor_protein;_possible_TonB_dependent_receptor_2767916..2768146_POSITIVE 248 60 19 194 154 tfor:TF2304|5end_OmpA_family_protein_2459320..2459550_POSITIVE 247 49 6 91 48 tfor:TF3078|5end_ribonucleoside_diphosphate_reductase,_alpha_subunit_3306609..3306839_POSITIVE 247 60 11 60 5 tfor:TF2633|5end_ABC_transporter,_ATP-binding_protein/permease_component_2802013..2802243_POSITIVE 247 49 2 134 86 tfor:TF1598|5end_conserved_hypothetical_protein_1713358..1713588_POSITIVE 241 55 18 100 57 tfor:TF1149|5end_conserved_hypothetical_protein;_possible_branched-chain_amino_acid_aminotransferase_1229218..1229448_POSITIVE 240 59 12 54 4 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 411 170 138 34 2 tfor:TF2162|3end_thermolysin_precursor_2340713..2340863_POSITIVE 341 67 21 111 63 tfor:TF1376|3end_possible_transposase_1453869..1454019_POSITIVE 295 67 32 111 76 tfor:TF0670|3end_possible_transposase_715081..715231_POSITIVE 280 67 38 111 84 tfor:TF2479|3end_conserved_hypothetical_protein_2657043..2657193_POSITIVE 280 67 38 111 84 tfor:TF1264|3end_possible_transposase_1352341..1352491_POSITIVE 279 78 34 119 80 tfor:TF1096|3end_conserved_hypothetical_protein_1165357..1165507_POSITIVE 269 58 15 141 94 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 268 29 1 60 30 tfor:TF2305|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2462693..2462843_POSITIVE 268 67 21 111 68 tfor:TF1866|3end_conserved_hypothetical_protein;_possible_transposase_2022564..2022714_POSITIVE 262 48 1 47 3 tfor:TF0270|3end_transposase_element_298074..298224_POSITIVE 255 32 1 148 121 tfor:TF2118|3end_conserved_hypothetical_protein_2291693..2291843_POSITIVE 248 60 19 97 57 tfor:TF2303|3end_conserved_hypothetical_protein_2459303..2459453_POSITIVE 247 49 2 114 66 tfor:TF1597|3end_TatD_family_protein_1713418..1713568_POSITIVE 241 55 18 69 26 tfor:TF1148|3end_para-aminobenzoate_synthase_component_I_1229267..1229417_POSITIVE 237 50 2 97 32 tfor:TF1160|3end_MutT/nudix_family_protein_1241008..1241158_POSITIVE 234 26 1 143 113 tfor:TF3144|3end_phosphomannomutase/phosphoglucomutase_3381184..3381334_POSITIVE 231 58 15 108 56 tfor:TF2487|3end_transposase_2663956..2664106_POSITIVE 230 25 1 31 4 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 230 27 1 122 101 tfor:TF2158|3end_conserved_hypothetical_protein_2334584..2334734_POSITIVE 228 138 91 87 33 tfor:TF0750|3end_conserved_hypothetical_protein_798698..798848_POSITIVE