Origin IGS: taaccggagttccacgacgtttccccgggaatggaaaaatcacctgtcgtgttgtcggcataaagaatgaatttgagaagtgcgttcattcattattcacatttaacagctatattttagggtgtgatgaaggatttgttgttctttattatgaatatggatactttaaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attttaaagtatccatattcataataaagaacaacaaatccttcatcacaccctaaaatatagctgttaaatgtgaataatgaatgaacgcacttctcaaattcattctttatgccgacaacacgacaggtgatttttccattcccggggaaacgtcgtggaactccggtta Mask Tandem Repeat Region ================================================ taaccggagttccacgacgtttccccgggaatggaaaaatcacctgtcgtgttgtcggcataaagaatgaatttgagaagtgcgttcattcattattcacatttaacagctatattttagggtgtgatgaaggatttgttgttctttattatgaatatggatactttaaaat Find is-nt database================================================ Query_seq: TF2799:TF2800|TF2799:TF2800:RNA polymerase ECF-type sigma factor:anti-sigma factor:->->:2985113..2985284 172 taaccggagttccacgacgtttccccgggaatggaaaaatcacctgtcgtgttgtcggcataaagaatgaatttgagaagtgcgttcattcattattcacatttaacagctatattttagggtgtgatgaaggatttgttgttctttattatgaatatggatactttaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2799:TF2800|TF2799:TF2800:RNA polymerase ECF-type sigma factor:anti-sigma factor:->->:2985113..2985284 172 taaccggagttccacgacgtttccccgggaatggaaaaatcacctgtcgtgttgtcggcataaagaatgaatttgagaagtgcgttcattcattattcacatttaacagctatattttagggtgtgatgaaggatttgttgttctttattatgaatatggatactttaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2799:TF2800|TF2799:TF2800:RNA polymerase ECF-type sigma factor:anti-sigma factor:->->:2985113..2985284 172 taaccggagttccacgacgtttccccgggaatggaaaaatcacctgtcgtgttgtcggcataaagaatgaatttgagaagtgcgttcattcattattcacatttaacagctatattttagggtgtgatgaaggatttgttgttctttattatgaatatggatactttaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaccggagttccacgacgtttccccgggaatggaaaaatcacctgtcgtgttgtcggcataaagaatgaatttgagaagtgcgttcattcattattcacatttaacagctatattttagggtgtgatgaaggatttgttgttctttattatgaatatggatactttaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 39 End: 170 ...................................... M T C R V V G I K N E F E K C V H S L F T F N S Y I L G C D E G F V V L Y Y E Y G Y F K .. taaccggagttccacgacgtttccccgggaatggaaaaatcacctgtcgtgttgtcggcataaagaatgaatttgagaagtgcgttcattcattattcacatttaacagctatattttagggtgtgatgaaggatttgttgttctttattatgaatatggatactttaaaat 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================================================ taaccggagttccacgacgtttccccgggaatggaaaaatcacctgtcgtgttgtcggcataaagaatgaatttgagaagtgcgttcattcattattcacatttaacagctatattttagggtgtgatgaaggatttgttgttctttattatgaatatggatactttaaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2799:TF2800|TF2799:TF2800:RNA polymerase ECF-type sigma factor:anti-sigma factor:->->:2985113..2985284 172 taaccggagttccacgacgtttccccgggaatggaaaaatcacctgtcgtgttgtcggcataaagaatgaatttgagaagtgcgttcattcattattcacatttaacagctatattttagggtgtgatgaaggatttgttgttctttattatgaatatggatactttaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 172 Len: 172 Subject: tfor_TF2799_TF2800|RNA polymerase ECF-type sigma factor:anti-sigma factor|POSITIVE:POSITIVE|[2985113,2985284]|172 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 taaccggagttccacgacgtttccccgggaatggaaaaatcacctgtcgtgttgtcggcataaagaatgaatttgagaagtgcgttcattcattattcacatttaacagctatattttagggtgtgatgaaggatttgttgttctttattatgaatatggatactttaaaat taaccggagttccacgacgtttccccgggaatggaaaaatcacctgtcgtgttgtcggcataaagaatgaatttgagaagtgcgttcattcattattcacatttaacagctatattttagggtgtgatgaaggatttgttgttctttattatgaatatggatactttaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACCGGAGUUCCACGACGUUUCCCCGGGAAUGGAAAAAUCACCUGUCGUGUUGUCGGCAUAAAGAAUGAAUUUGAGAAGUGCGUUCAUUCAUUAUUCACAUUUAACAGCUAUAUUUUAGGGUGUGAUGAAGGAUUUGUUGUUCUUUAUUAUGAAUAUGGAUACUUUAAAAU ...((((.....((((((((((((........))))).......)))))))...))))..(((((..(((((.((((.((((........)))).)))).)))))....((((((((......((((((((((((.....))))))))))))))))))))...))))).... (-37.61) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUAAAGUAUCCAUAUUCAUAAUAAAGAACAACAAAUCCUUCAUCACACCCUAAAAUAUAGCUGUUAAAUGUGAAUAAUGAAUGAACGCACUUCUCAAAUUCAUUCUUUAUGCCGACAACACGACAGGUGAUUUUUCCAUUCCCGGGGAAACGUCGUGGAACUCCGGUUA ...............((((((((.....(((..........)))...(((..(((.....))).)))....))))))))..(((((((.............))))))).....((((....((((((....(.(((..((......))..))))))))))......)))).. (-25.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 34 4 51 14 tfor:TF1798|5end_aldose_1-epimerase_1938815..1939045_POSITIVE 363 59 11 86 36 tfor:TF0994|5end_maltose_O-acetyltransferase_1049127..1049357_POSITIVE 358 59 15 196 144 tfor:TF0250|5end_glycosyltransferase_Family_2_protein_279176..279406_POSITIVE 349 48 4 124 62 tfor:TF2760|5end_MarR__family_transcriptional_regulator_2945019..2945249_POSITIVE 347 48 4 50 1 tfor:TF2322|5end_conserved_hypothetical_protein;_possible_lipoprotein_2482743..2482973_POSITIVE 342 50 3 70 5 tfor:TF2767|5end_2-oxoglutarate_synthase,_alpha_subunit_2952215..2952445_POSITIVE 342 59 15 190 156 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 339 163 121 93 45 tfor:TF1208|5end_anti-sigma_factor_1293596..1293826_POSITIVE 338 59 11 157 106 tfor:TF2711|5end_hemolysis_secretion_protein_2884543..2884773_POSITIVE 337 59 18 168 115 tfor:TF2941|5end_50S_ribosomal_protein_L1_3141828..3142058_POSITIVE 326 50 5 116 64 tfor:TF0309|5end_conserved_hypothetical_protein_334174..334404_POSITIVE 319 69 27 46 1 tfor:TF0749|5end_protease_II_795562..795792_POSITIVE 318 50 2 230 173 tfor:TF2398|5end_magnesium_chelatase,_D/I_family_2569549..2569779_POSITIVE 318 60 11 183 126 tfor:TF0063|5end_conserved_hypothetical_protein_66110..66340_POSITIVE 317 59 11 202 148 tfor:TF0971|5end_conserved_hypothetical_protein_1021355..1021585_POSITIVE 315 57 11 151 101 tfor:TF2848|5end_cobalamin_biosynthesis_protein_3036368..3036598_POSITIVE 314 60 18 102 50 tfor:TF0148|5end_conserved_hypothetical_protein_159448..159678_POSITIVE 312 89 47 81 33 tfor:TF2149|5end_deoxyribose-phosphate_aldolase_2322119..2322349_POSITIVE 312 57 15 82 31 tfor:TF0001|5end_hypothetical_protein_-116..114_POSITIVE 309 59 22 186 138 tfor:TF0436|5end_conserved_hyothetical_protein_459207..459437_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 59 15 101 67 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 338 59 11 149 98 tfor:TF2710|3end_ABC_transporter,_ATP-binding_protein/permease_component_2884615..2884765_POSITIVE 337 59 18 150 97 tfor:TF2940|3end_50S_ribosomal_protein_L11_3141890..3142040_POSITIVE 319 50 4 108 59 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 315 59 13 50 2 tfor:TF0699|3end_pyridoxal_phosphate_biosynthetic_protein_742745..742895_POSITIVE 312 89 47 71 23 tfor:TF2148|3end_conserved_hypothetical_protein_2322189..2322339_POSITIVE 305 50 3 64 16 tfor:TF2881|3end_conserved_hypothetical_protein_3072380..3072530_POSITIVE 304 59 15 150 102 tfor:TF2573|3end_50S_ribosomal_protein_L15_2743857..2744007_POSITIVE 301 60 13 57 2 tfor:TF2646|3end_conserved_hypothetical_protein_2816697..2816847_POSITIVE 301 59 15 144 101 tfor:TF0970|3end_2-keto-3-deoxygluconate_kinase_1021540..1021690_POSITIVE 301 59 12 63 18 tfor:TF0372|3end_transcriptional_regulator_391118..391268_POSITIVE 299 49 7 138 93 tfor:TF0141|3end_exodeoxyribonuclease_VII,_large_subunit_149830..149980_POSITIVE 292 50 2 137 95 tfor:TF2841|3end_conserved_hypothetical_protein_3032156..3032306_POSITIVE 291 57 16 46 11 tfor:TF1828|3end_hypothetical_protein_1977425..1977575_POSITIVE 291 85 41 79 23 tfor:TF1822|3end_outer_membrane_lipoprotein_silC_precursor_1969193..1969343_POSITIVE 289 50 4 125 82 tfor:TF2734|3end_conserved_hypothetical_protein_2916738..2916888_POSITIVE 289 35 3 73 41 tfor:TF1665|3end_conserved_hypothetical_protein_1779578..1779728_POSITIVE 287 59 11 106 59 tfor:TF2694|3end_hypothetical_protein_2870863..2871013_POSITIVE 286 50 4 124 71 tfor:TF3086|3end_conserved_hypothetical_protein_3319949..3320099_POSITIVE 286 70 26 147 97 tfor:TF1683|3end_conserved_hypothetical_protein_1796511..1796661_POSITIVE