Origin IGS: taattgaatgacagtaattcgtgagagatgtaaaagcaaagtgcaaacaggagtacataaatgtgcgaatttctgcatatgataagtaaatcaattcaatttttacttcttatttttgcaatcaatataaaacatggatcttcctgatatggatttgaagtgatgattatgtagaacttaaaaaaaagaatgtgcctatggggacggtatgacaaaaaagagattttattcggtgtataaccggagcaaagatgatgcgcctgacaaattttataaagtgtttttacacagtcgaatttgtcaaaactcagaaaacttatttgagtaaatcttagtgtttgtcgaattttcgacgaatgtatttagtaagtaattgatttaaaaaaaaagacaatttaaatttaagacgta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tacgtcttaaatttaaattgtctttttttttaaatcaattacttactaaatacattcgtcgaaaattcgacaaacactaagatttactcaaataagttttctgagttttgacaaattcgactgtgtaaaaacactttataaaatttgtcaggcgcatcatctttgctccggttatacaccgaataaaatctcttttttgtcataccgtccccataggcacattcttttttttaagttctacataatcatcacttcaaatccatatcaggaagatccatgttttatattgattgcaaaaataagaagtaaaaattgaattgatttacttatcatatgcagaaattcgcacatttatgtactcctgtttgcactttgcttttacatctctcacgaattactgtcattcaatta Mask Tandem Repeat Region ================================================ taattgaatgacagtaattcgtgagagatgtaaaagcaaagtgcaaacaggagtacataaatgtgcgaatttctgcatatgataagtaaatcaattcaatttttacttcttatttttgcaatcaatataaaacatggatcttcctgatatggatttgaagtgatgattatgtagaacttaaaaaaaagaatgtgcctatggggacggtatgacaaaaaagagattttattcggtgtataaccggagcaaagatgatgcgcctgacaaattttataaagtgtttttacacagtcgaatttgtcaaaactcagaaaacttatttgagtaaatcttagtgtttgtcgaattttcgacgaatgtatttagtaagtaattgatttaaaaaaaaagacaatttaaatttaagacgta Find is-nt database================================================ Query_seq: TF0127:TF0128|TF0127:TF0128:conserved hypothetical protein:hypothetical protein:->->:139921..140331 411 taattgaatgacagtaattcgtgagagatgtaaaagcaaagtgcaaacaggagtacataaatgtgcgaatttctgcatatgataagtaaatcaattcaatttttacttcttatttttgcaatcaatataaaacatggatcttcctgatatggatttgaagtgatgattatgtagaacttaaaaaaaagaatgtgcctatggggacggtatgacaaaaaagagattttattcggtgtataaccggagcaaagatgatgcgcctgacaaattttataaagtgtttttacacagtcgaatttgtcaaaactcagaaaacttatttgagtaaatcttagtgtttgtcgaattttcgacgaatgtatttagtaagtaattgatttaaaaaaaaagacaatttaaatttaagacgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0127:TF0128|TF0127:TF0128:conserved hypothetical protein:hypothetical protein:->->:139921..140331 411 taattgaatgacagtaattcgtgagagatgtaaaagcaaagtgcaaacaggagtacataaatgtgcgaatttctgcatatgataagtaaatcaattcaatttttacttcttatttttgcaatcaatataaaacatggatcttcctgatatggatttgaagtgatgattatgtagaacttaaaaaaaagaatgtgcctatggggacggtatgacaaaaaagagattttattcggtgtataaccggagcaaagatgatgcgcctgacaaattttataaagtgtttttacacagtcgaatttgtcaaaactcagaaaacttatttgagtaaatcttagtgtttgtcgaattttcgacgaatgtatttagtaagtaattgatttaaaaaaaaagacaatttaaatttaagacgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0127:TF0128|TF0127:TF0128:conserved hypothetical protein:hypothetical protein:->->:139921..140331 411 taattgaatgacagtaattcgtgagagatgtaaaagcaaagtgcaaacaggagtacataaatgtgcgaatttctgcatatgataagtaaatcaattcaatttttacttcttatttttgcaatcaatataaaacatggatcttcctgatatggatttgaagtgatgattatgtagaacttaaaaaaaagaatgtgcctatggggacggtatgacaaaaaagagattttattcggtgtataaccggagcaaagatgatgcgcctgacaaattttataaagtgtttttacacagtcgaatttgtcaaaactcagaaaacttatttgagtaaatcttagtgtttgtcgaattttcgacgaatgtatttagtaagtaattgatttaaaaaaaaagacaatttaaatttaagacgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattgaatgacagtaattcgtgagagatgtaaaagcaaagtgcaaacaggagtacataaatgtgcgaatttctgcatatgataagtaaatcaattcaatttttacttcttatttttgcaatcaatataaaacatggatcttcctgatatggatttgaagtgatgattatgtagaacttaaaaaaaagaatgtgcctatggggacggtatgacaaaaaagagattttattcggtgtataaccggagcaaagatgatgcgcctgacaaattttataaagtgtttttacacagtcgaatttgtcaaaactcagaaaacttatttgagtaaatcttagtgtttgtcgaattttcgacgaatgtatttagtaagtaattgatttaaaaaaaaagacaatttaaatttaagacgta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 209 End: 325 ................................................................................................................................................................................................................ M T K K R F Y S V Y N R S K D D A P D K F Y K V F L H S R I C Q N S E N L F E ...................................................................................... Protein_Len: 35 Strand: + Start: 228 End: 332 ................................................................................................................................................................................................................................... M R C I T G A K M M R L T N F I K C F Y T V E F V K T Q K T Y L S K S ............................................................................... Protein_Len: 35 Strand: - Start: 170 End: 274 ......................................................................................................................................................................... T S S L F F F T G I P V T H C F L S K I R H I V P A F I I R R V F K M ......................................................................................................................................... Protein_Len: 60 Strand: - Start: 99 End: 362 .................................................................................................. F L I H R H P R Y S L F S I K N P T Y G S C L H H A Q C I K Y L T K V C D F K D F S L F S I Q T F R L T Q R I K S S H M ................................................. Protein_Len: 31 Strand: - Start: 3 End: 95 .. N F S L L E H S I Y F C L A F L L V Y I H S N R C I I L L D M ............................................................................................................................................................................................................................................................................................................................ Protein_Len: 33 Strand: - Start: 2 End: 100 . I S H C Y N T L S T F A F H L C S Y M F T R I E A Y S L Y I L E M ....................................................................................................................................................................................................................................................................................................................... taattgaatgacagtaattcgtgagagatgtaaaagcaaagtgcaaacaggagtacataaatgtgcgaatttctgcatatgataagtaaatcaattcaatttttacttcttatttttgcaatcaatataaaacatggatcttcctgatatggatttgaagtgatgattatgtagaacttaaaaaaaagaatgtgcctatggggacggtatgacaaaaaagagattttattcggtgtataaccggagcaaagatgatgcgcctgacaaattttataaagtgtttttacacagtcgaatttgtcaaaactcagaaaacttatttgagtaaatcttagtgtttgtcgaattttcgacgaatgtatttagtaagtaattgatttaaaaaaaaagacaatttaaatttaagacgta 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================================================ taattgaatgacagtaattcgtgagagatgtaaaagcaaagtgcaaacaggagtacataaatgtgcgaatttctgcatatgataagtaaatcaattcaatttttacttcttatttttgcaatcaatataaaacatggatcttcctgatatggatttgaagtgatgattatgtagaacttaaaaaaaagaatgtgcctatggggacggtatgacaaaaaagagattttattcggtgtataaccggagcaaagatgatgcgcctgacaaattttataaagtgtttttacacagtcgaatttgtcaaaactcagaaaacttatttgagtaaatcttagtgtttgtcgaattttcgacgaatgtatttagtaagtaattgatttaaaaaaaaagacaatttaaatttaagacgta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0127:TF0128|TF0127:TF0128:conserved hypothetical protein:hypothetical protein:->->:139921..140331 411 taattgaatgacagtaattcgtgagagatgtaaaagcaaagtgcaaacaggagtacataaatgtgcgaatttctgcatatgataagtaaatcaattcaatttttacttcttatttttgcaatcaatataaaacatggatcttcctgatatggatttgaagtgatgattatgtagaacttaaaaaaaagaatgtgcctatggggacggtatgacaaaaaagagattttattcggtgtataaccggagcaaagatgatgcgcctgacaaattttataaagtgtttttacacagtcgaatttgtcaaaactcagaaaacttatttgagtaaatcttagtgtttgtcgaattttcgacgaatgtatttagtaagtaattgatttaaaaaaaaagacaatttaaatttaagacgta Intra-Species Hit: Count: 1 Min: 1 Max: 411 Len: 411 Subject: tfor_TF0127_TF0128|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[139921,140331]|411 HSP 1 e-value: 0.0 bit: 714.0 Len: 411 Query Start:1 Query End:411 Subject Strand: POSITIVE Subject Start: 1 Subject End: 411 taattgaatgacagtaattcgtgagagatgtaaaagcaaagtgcaaacaggagtacataaatgtgcgaatttctgcatatgataagtaaatcaattcaatttttacttcttatttttgcaatcaatataaaacatggatcttcctgatatggatttgaagtgatgattatgtagaacttnnnnnnnngaatgtgcctatggggacggtatgacaaaaaagagattttattcggtgtataaccggagcaaagatgatgcgcctgacaaattttataaagtgtttttacacagtcgaatttgtcaaaactcagaaaacttatttgagtaaatcttagtgtttgtcgaattttcgacgaatgtatttagtaagtaattgatttnnnnnnnnngacaatttaaatttaagacgta taattgaatgacagtaattcgtgagagatgtaaaagcaaagtgcaaacaggagtacataaatgtgcgaatttctgcatatgataagtaaatcaattcaatttttacttcttatttttgcaatcaatataaaacatggatcttcctgatatggatttgaagtgatgattatgtagaacttaaaaaaaagaatgtgcctatggggacggtatgacaaaaaagagattttattcggtgtataaccggagcaaagatgatgcgcctgacaaattttataaagtgtttttacacagtcgaatttgtcaaaactcagaaaacttatttgagtaaatcttagtgtttgtcgaattttcgacgaatgtatttagtaagtaattgatttaaaaaaaaagacaatttaaatttaagacgta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUGAAUGACAGUAAUUCGUGAGAGAUGUAAAAGCAAAGUGCAAACAGGAGUACAUAAAUGUGCGAAUUUCUGCAUAUGAUAAGUAAAUCAAUUCAAUUUUUACUUCUUAUUUUUGCAAUCAAUAUAAAACAUGGAUCUUCCUGAUAUGGAUUUGAAGUGAUGAUUAUGUAGAACUUAAAAAAAAGAAUGUGCCUAUGGGGACGGUAUGACAAAAAAGAGAUUUUAUUCGGUGUAUAACCGGAGCAAAGAUGAUGCGCCUGACAAAUUUUAUAAAGUGUUUUUACACAGUCGAAUUUGUCAAAACUCAGAAAACUUAUUUGAGUAAAUCUUAGUGUUUGUCGAAUUUUCGACGAAUGUAUUUAGUAAGUAAUUGAUUUAAAAAAAAAGACAAUUUAAAUUUAAGACGUA .(((((.(((.(((.((((((((....(((((....(...((....))..)..))))).....)))))))).))))))........((((((((((.....((((((((((.((((((((.((.((((((..(((.(.((.(((......)))...))..).))).)))))).))...............(((.((....)).)))...)).)))))).)))).....((((((.....))))))...(((((........((((((((((.((...((((....)))).)).))))))))))..(((((((.......)))))))..))))).(..((((((((....))))))))..)....)))))).))))))))))..........)))))............... (-84.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACGUCUUAAAUUUAAAUUGUCUUUUUUUUUAAAUCAAUUACUUACUAAAUACAUUCGUCGAAAAUUCGACAAACACUAAGAUUUACUCAAAUAAGUUUUCUGAGUUUUGACAAAUUCGACUGUGUAAAAACACUUUAUAAAAUUUGUCAGGCGCAUCAUCUUUGCUCCGGUUAUACACCGAAUAAAAUCUCUUUUUUGUCAUACCGUCCCCAUAGGCACAUUCUUUUUUUUAAGUUCUACAUAAUCAUCACUUCAAAUCCAUAUCAGGAAGAUCCAUGUUUUAUAUUGAUUGCAAAAAUAAGAAGUAAAAAUUGAAUUGAUUUACUUAUCAUAUGCAGAAAUUCGCACAUUUAUGUACUCCUGUUUGCACUUUGCUUUUACAUCUCUCACGAAUUACUGUCAUUCAAUUA ....................((((.(((((..(((((((.....((...........(((((....))))).........................((((((((....(((((((((.....((((....)))).......)))))))))((.(((.......))).))((((((.....((.(((((......))))))).....((.((....)).)).....................)))))).................))))))))......)).....)))))))..))))).))))......((((((((((((......))))...((((.((((((.(((....))).....(((..((.....))....))).......)))))).)))).)))))))). (-60.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 236 193 203 153 tfor:TF2899|5end_conserved_hypothetical_protein_3087495..3087725_POSITIVE 332 233 191 161 108 tfor:TF1648|5end_hypothetical_protein_1759338..1759568_POSITIVE 298 259 217 157 119 tfor:TF3139|5end_Na+-translocating_NADH-quinone_reductase,_subunit_C_3372581..3372811_POSITIVE 292 248 203 57 10 tfor:TF1881|5end_hypothetical_protein_2033412..2033642_POSITIVE 290 268 224 188 142 tfor:TF0143|5end_aspartate--ammonia_ligase_151390..151620_POSITIVE 290 267 231 226 195 tfor:TF0038|5end_conserved_hypothetical_protein_39907..40137_POSITIVE 289 246 203 177 135 tfor:TF1003|5end_conserved_hypothetical_protein;_possible_secreted_glycosylhydrolase_1058177..1058407_POSITIVE 286 264 222 50 11 tfor:TF0881|5end_conserved_hypothetical_protein_934459..934689_POSITIVE 285 236 194 87 47 tfor:TF1599|5end_ribonuclease_P_protein_component_1713564..1713794_POSITIVE 284 263 231 150 119 tfor:TF2820|5end_argininosuccinate_synthetase_3009876..3010106_POSITIVE 284 176 132 111 54 tfor:TF1164|5end_two-component_system_sensor_histidine_kinase_1243682..1243912_POSITIVE 282 248 201 169 131 tfor:TF0890|5end_transfer_region-related_protein,_TraQ_940014..940244_POSITIVE 278 267 227 67 19 tfor:TF2528|5end_anti-sigma_factor_2708961..2709191_POSITIVE 276 262 226 229 185 tfor:TF1732|5end_conserved_hypothetical_protein_1854619..1854849_POSITIVE 273 248 205 177 122 tfor:TF3124|5end_dTDP-glucose_4,6-dehydratase_3358655..3358885_POSITIVE 272 264 221 183 136 tfor:TF1928|5end_conserved_hypothetical_protein_2075529..2075759_POSITIVE 271 264 230 83 35 tfor:TF0063|5end_conserved_hypothetical_protein_66110..66340_POSITIVE 269 79 37 79 28 tfor:TF2595|5end_conserved_hypothetical_protein_2765084..2765314_POSITIVE 268 261 231 177 136 tfor:TF2318|5end_conserved_hypothetical_protein_2475603..2475833_POSITIVE 268 73 39 69 29 tfor:TF1555|5end_hypothetical_protein_1661061..1661291_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 259 217 150 112 tfor:TF3138|3end_Na+-translocating_quinone_reductase,_subunit_D_3372654..3372804_POSITIVE 293 246 202 137 86 tfor:TF0109|3end_diacylglycerol_kinase_116536..116686_POSITIVE 285 236 194 102 62 tfor:TF1598|3end_conserved_hypothetical_protein_1713659..1713809_POSITIVE 284 263 231 150 119 tfor:TF2819|3end_N-acetyl-gamma-glutamylphosphate_reductase_3009956..3010106_POSITIVE 284 176 132 120 63 tfor:TF1163|3end_two-component_system_response_regulator_1243771..1243921_POSITIVE 271 264 230 73 25 tfor:TF0062|3end_conserved_hypothetical_protein_66180..66330_POSITIVE 266 55 20 145 94 tfor:TF1034|3end_conserved_hypothetical_protein_1095901..1096051_POSITIVE 264 255 220 128 93 tfor:TF2087|3end_conserved_hypothetical_protein_2257694..2257844_POSITIVE 263 272 231 87 36 tfor:TF2879|3end_tRNA_(guanine-N-1)-methyltransferase_3069008..3069158_POSITIVE 261 262 229 124 86 tfor:TF2999|3end_conserved_hypothetical_protein_3215891..3216041_POSITIVE 261 235 196 120 90 tfor:TF2190|3end_conserved_hypothetical_protein_2365646..2365796_POSITIVE 260 245 203 151 110 tfor:TF1002|3end_replicative_DNA_helicase_1058232..1058382_POSITIVE 259 263 228 54 17 tfor:TF1925|3end_hypothetical_protein_2075101..2075251_POSITIVE 258 212 193 133 111 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 257 262 221 133 90 tfor:TF0081|3end_pantothenate_kinase_88494..88644_POSITIVE 256 239 191 84 15 tfor:TF2391|3end_conserved_hypothetical_protein_2563464..2563614_POSITIVE 256 56 17 45 3 tfor:TF1733|3end_conserved_hypothetical_protein_1856562..1856712_POSITIVE 255 239 191 137 81 tfor:TF2074|3end_pyridoxal-phosphate-dependent_aminotransferase_2240950..2241100_POSITIVE 254 261 221 141 106 tfor:TF0607|3end_DnaK_suppressor_protein_637898..638048_POSITIVE 250 268 241 141 112 tfor:TF3157|3end_sodium/solute_symporter_3393787..3393937_POSITIVE