Origin IGS: taacgcaaggccagcctccagttctccgacagacaaatacggcaaaatcaacctgtgccttcaaaaacaaatcagaaatagagaaaaatttctttaattgaatcgtctattccgaaaaatcatcgtacttttgtaacctgaataaggaaaaggttatcattcctgacaaaaacaaagcaaagaaacaaagagcattacatattttaatcaattaattcttaaacgcaaa .........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 tttgcgtttaagaattaattgattaaaatatgtaatgctctttgtttctttgctttgtttttgtcaggaatgataaccttttccttattcaggttacaaaagtacgatgatttttcggaatagacgattcaattaaagaaatttttctctatttctgatttgtttttgaaggcacaggttgattttgccgtatttgtctgtcggagaactggaggctggccttgcgtta Mask Tandem Repeat Region ================================================ taacgcaaggccagcctccagttctccgacagacaaatacggcaaaatcaacctgtgccttcaaaaacaaatcagaaatagagaaaaatttctttaattgaatcgtctattccgaaaaatcatcgtacttttgtaacctgaataaggaaaaggttatcattcctgacaaaaacaaagcaaagaaacaaagagcattacatattttaatcaattaattcttaaacgcaaa Find is-nt database================================================ Query_seq: TF1942:TF1943|TF1942:TF1943:conserved hypothetical protein:phosphoenolpyruvate carboxykinase:->->:2090707..2090935 229 taacgcaaggccagcctccagttctccgacagacaaatacggcaaaatcaacctgtgccttcaaaaacaaatcagaaatagagaaaaatttctttaattgaatcgtctattccgaaaaatcatcgtacttttgtaacctgaataaggaaaaggttatcattcctgacaaaaacaaagcaaagaaacaaagagcattacatattttaatcaattaattcttaaacgcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1942:TF1943|TF1942:TF1943:conserved hypothetical protein:phosphoenolpyruvate carboxykinase:->->:2090707..2090935 229 taacgcaaggccagcctccagttctccgacagacaaatacggcaaaatcaacctgtgccttcaaaaacaaatcagaaatagagaaaaatttctttaattgaatcgtctattccgaaaaatcatcgtacttttgtaacctgaataaggaaaaggttatcattcctgacaaaaacaaagcaaagaaacaaagagcattacatattttaatcaattaattcttaaacgcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1942:TF1943|TF1942:TF1943:conserved hypothetical protein:phosphoenolpyruvate carboxykinase:->->:2090707..2090935 229 taacgcaaggccagcctccagttctccgacagacaaatacggcaaaatcaacctgtgccttcaaaaacaaatcagaaatagagaaaaatttctttaattgaatcgtctattccgaaaaatcatcgtacttttgtaacctgaataaggaaaaggttatcattcctgacaaaaacaaagcaaagaaacaaagagcattacatattttaatcaattaattcttaaacgcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacgcaaggccagcctccagttctccgacagacaaatacggcaaaatcaacctgtgccttcaaaaacaaatcagaaatagagaaaaatttctttaattgaatcgtctattccgaaaaatcatcgtacttttgtaacctgaataaggaaaaggttatcattcctgacaaaaacaaagcaaagaaacaaagagcattacatattttaatcaattaattcttaaacgcaaa Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 102 End: 212 ..................................................................................................... M V Y S E K S S Y F C N L N K E K V I I P D K N K A K K Q R A L H I L I N ................. Protein_Len: 34 Strand: - Start: 110 End: 211 ............................................................................................................. E S F D D Y K Q L R F L S F T I M G S L F L A F F C L A N C I K I M .................. Protein_Len: 34 Strand: - Start: 2 End: 103 . V C P W G G T R R C V F V A F D V Q A K L F L D S I S F F K K L Q M .............................................................................................................................. taacgcaaggccagcctccagttctccgacagacaaatacggcaaaatcaacctgtgccttcaaaaacaaatcagaaatagagaaaaatttctttaattgaatcgtctattccgaaaaatcatcgtacttttgtaacctgaataaggaaaaggttatcattcctgacaaaaacaaagcaaagaaacaaagagcattacatattttaatcaattaattcttaaacgcaaa 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================================================ taacgcaaggccagcctccagttctccgacagacaaatacggcaaaatcaacctgtgccttcaaaaacaaatcagaaatagagaaaaatttctttaattgaatcgtctattccgaaaaatcatcgtacttttgtaacctgaataaggaaaaggttatcattcctgacaaaaacaaagcaaagaaacaaagagcattacatattttaatcaattaattcttaaacgcaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1942:TF1943|TF1942:TF1943:conserved hypothetical protein:phosphoenolpyruvate carboxykinase:->->:2090707..2090935 229 taacgcaaggccagcctccagttctccgacagacaaatacggcaaaatcaacctgtgccttcaaaaacaaatcagaaatagagaaaaatttctttaattgaatcgtctattccgaaaaatcatcgtacttttgtaacctgaataaggaaaaggttatcattcctgacaaaaacaaagcaaagaaacaaagagcattacatattttaatcaattaattcttaaacgcaaa Intra-Species Hit: Count: 1 Min: 1 Max: 229 Len: 229 Subject: tfor_TF1942_TF1943|conserved hypothetical protein:phosphoenolpyruvate carboxykinase|POSITIVE:POSITIVE|[2090707,2090935]|229 HSP 1 e-value: 1.0E-127 bit: 454.0 Len: 229 Query Start:1 Query End:229 Subject Strand: POSITIVE Subject Start: 1 Subject End: 229 taacgcaaggccagcctccagttctccgacagacaaatacggcaaaatcaacctgtgccttcaaaaacaaatcagaaatagagaaaaatttctttaattgaatcgtctattccgaaaaatcatcgtacttttgtaacctgaataaggaaaaggttatcattcctgacaaaaacaaagcaaagaaacaaagagcattacatattttaatcaattaattcttaaacgcaaa taacgcaaggccagcctccagttctccgacagacaaatacggcaaaatcaacctgtgccttcaaaaacaaatcagaaatagagaaaaatttctttaattgaatcgtctattccgaaaaatcatcgtacttttgtaacctgaataaggaaaaggttatcattcctgacaaaaacaaagcaaagaaacaaagagcattacatattttaatcaattaattcttaaacgcaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGCAAGGCCAGCCUCCAGUUCUCCGACAGACAAAUACGGCAAAAUCAACCUGUGCCUUCAAAAACAAAUCAGAAAUAGAGAAAAAUUUCUUUAAUUGAAUCGUCUAUUCCGAAAAAUCAUCGUACUUUUGUAACCUGAAUAAGGAAAAGGUUAUCAUUCCUGACAAAAACAAAGCAAAGAAACAAAGAGCAUUACAUAUUUUAAUCAAUUAAUUCUUAAACGCAAA ....((.(((....)))...(((((.....((((......((((...........))))............((((...(((((((....))))))).))))...))))................((..((((((..(((.....)))...(((........)))............))))))..))..)))))...............................))... (-32.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGCGUUUAAGAAUUAAUUGAUUAAAAUAUGUAAUGCUCUUUGUUUCUUUGCUUUGUUUUUGUCAGGAAUGAUAACCUUUUCCUUAUUCAGGUUACAAAAGUACGAUGAUUUUUCGGAAUAGACGAUUCAAUUAAAGAAAUUUUUCUCUAUUUCUGAUUUGUUUUUGAAGGCACAGGUUGAUUUUGCCGUAUUUGUCUGUCGGAGAACUGGAGGCUGGCCUUGCGUUA .............................((((((.(((....(((((((((..(((...(((((.....((.((((((...........))))))))......(((.......))).....)))))..))).)))))))))...((((((((((((((...........((((.((.....)).))))..........))))))))..))))))..))).)))))).. (-43.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 49 3 76 18 tfor:TF1908|5end_possible_phosphoglycerate_mutase_2062695..2062925_POSITIVE 358 49 2 195 142 tfor:TF2906|5end_phosphatidylserine_decarboxylase_3102182..3102412_POSITIVE 332 64 21 51 3 tfor:TF1152|5end_permease,_major_facilitator_superfamily_1233267..1233497_POSITIVE 329 28 4 231 208 tfor:TF3006|5end_response_regulator,_transcriptional_regulator_RprY_3226360..3226590_POSITIVE 324 59 13 203 152 tfor:TF0955|5end_conserved_hypothetical_protein_999215..999445_POSITIVE 322 33 2 68 33 tfor:TF2322|5end_conserved_hypothetical_protein;_possible_lipoprotein_2482743..2482973_POSITIVE 317 58 13 83 29 tfor:TF0143|5end_aspartate--ammonia_ligase_151390..151620_POSITIVE 313 46 4 140 87 tfor:TF2776|5end_hypothetical_protein_2961470..2961700_POSITIVE 312 50 4 193 146 tfor:TF1440|5end_hypothetical_protein_1524599..1524829_POSITIVE 306 58 12 48 1 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 303 35 4 220 190 tfor:TF2391|5end_conserved_hypothetical_protein_2562128..2562358_POSITIVE 303 58 11 207 155 tfor:TF2348|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2511088..2511318_POSITIVE 302 49 4 84 43 tfor:TF0248|5end_hypothetical_protein_278249..278479_POSITIVE 301 29 7 230 206 tfor:TF0438|5end_polyferredoxin_461369..461599_POSITIVE 299 44 9 68 31 tfor:TF3116|5end_conserved_hypothetical_protein_3352136..3352366_POSITIVE 297 44 4 78 41 tfor:TF2021|5end_hypothetical_protein_2177702..2177932_POSITIVE 297 60 12 51 2 tfor:TF1148|5end_para-aminobenzoate_synthase_component_I_1228219..1228449_POSITIVE 296 140 96 58 12 tfor:TF2501|5end_DNA_mismatch_repair_protein_2676280..2676510_POSITIVE 296 44 10 156 118 tfor:TF2237|5end_two-component_system_response_regulator_involved_in_CTn_2412494..2412724_POSITIVE 293 60 17 106 61 tfor:TF2292|5end_hypothetical_protein_2447347..2447577_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 49 2 137 84 tfor:TF2904|3end_ATP-dependent__helicase,_possible_UvrD/REP_helicase_domain_protein_3102204..3102354_POSITIVE 317 58 13 96 42 tfor:TF0144|3end_hypothetical_protein_151483..151633_POSITIVE 305 45 8 49 15 tfor:TF0428|3end_methylmalonyl-CoA_mutase,_beta_subunit_450033..450183_POSITIVE 303 35 4 145 115 tfor:TF2390|3end_conserved_hypothetical_protein_2562133..2562283_POSITIVE 303 58 11 131 79 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 302 49 4 103 62 tfor:TF0247|3end_conserved_hypothetical_protein_278348..278498_POSITIVE 290 50 4 47 2 tfor:TF1542|3end_transcriptional_regulator_1649502..1649652_POSITIVE 285 60 11 103 51 tfor:TF1544|3end_possible_transcriptional_regulator_1651214..1651364_POSITIVE 284 44 4 63 10 tfor:TF2340|3end_hypothetical_protein_2500915..2501065_POSITIVE 282 44 5 84 38 tfor:TF0582|3end_hemolysin-related_protein,_with_CBS_domains;_possible_gliding-motility_related_protein_613263..613413_POSITIVE 275 58 12 148 108 tfor:TF2663|3end_hypothetical_protein_2841323..2841473_POSITIVE 272 44 4 149 116 tfor:TF3158|3end_inner_membrane_protein_3395206..3395356_POSITIVE 272 50 4 66 15 tfor:TF1255|3end_conserved_hypothetical_protein_1338151..1338301_POSITIVE 271 165 122 104 56 tfor:TF1624|3end_carboxyl-terminal_protease_1738972..1739122_POSITIVE 268 40 11 88 57 tfor:TF2683|3end_translation_initiation_factor_IF-2_2860756..2860906_POSITIVE 267 60 17 149 102 tfor:TF0029|3end_hypothetical_protein_25062..25212_POSITIVE 265 48 4 80 28 tfor:TF3109|3end_hypothetical_protein_3342803..3342953_POSITIVE 264 46 7 120 80 tfor:TF0064|3end_conserved_hypothetical_protein_70412..70562_POSITIVE 263 43 5 62 17 tfor:TF1002|3end_replicative_DNA_helicase_1058232..1058382_POSITIVE 263 32 4 139 109 tfor:TF0616|3end_conserved_hypothetical_protein_650658..650808_POSITIVE