Origin IGS: taaaaaccgatgatgcctatgagaaagtttaaatgacctttataaaaaaagagagccgggcagataccgcaaatatcgcccggccgaagtgaaattaattatcaggaatattaataattaaaatcgtacaaatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatttgtacgattttaattattaatattcctgataattaatttcacttcggccgggcgatatttgcggtatctgcccggctctctttttttataaaggtcatttaaactttctcataggcatcatcggttttta Mask Tandem Repeat Region ================================================ taaaaaccgatgatgcctatgagaaagtttaaatgacctttataaaaaaagagagccgggcagataccgcaaatatcgcccggccgaagtgaaattaattatcaggaatattaataattaaaatcgtacaaatat Find is-nt database================================================ Query_seq: TF1977:TF1978|TF1977:TF1978:anti-sigma factor:outer membrane protein, TonB dependent receptor:->->:2124488..2124622 135 taaaaaccgatgatgcctatgagaaagtttaaatgacctttataaaaaaagagagccgggcagataccgcaaatatcgcccggccgaagtgaaattaattatcaggaatattaataattaaaatcgtacaaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1977:TF1978|TF1977:TF1978:anti-sigma factor:outer membrane protein, TonB dependent receptor:->->:2124488..2124622 135 taaaaaccgatgatgcctatgagaaagtttaaatgacctttataaaaaaagagagccgggcagataccgcaaatatcgcccggccgaagtgaaattaattatcaggaatattaataattaaaatcgtacaaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1977:TF1978|TF1977:TF1978:anti-sigma factor:outer membrane protein, TonB dependent receptor:->->:2124488..2124622 135 taaaaaccgatgatgcctatgagaaagtttaaatgacctttataaaaaaagagagccgggcagataccgcaaatatcgcccggccgaagtgaaattaattatcaggaatattaataattaaaatcgtacaaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaccgatgatgcctatgagaaagtttaaatgacctttataaaaaaagagagccgggcagataccgcaaatatcgcccggccgaagtgaaattaattatcaggaatattaataattaaaatcgtacaaatat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 3 End: 95 .. F G I I G I L F N L H G K Y F F L A P C I G C I D G P R L S M ........................................ taaaaaccgatgatgcctatgagaaagtttaaatgacctttataaaaaaagagagccgggcagataccgcaaatatcgcccggccgaagtgaaattaattatcaggaatattaataattaaaatcgtacaaatat 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================================================ taaaaaccgatgatgcctatgagaaagtttaaatgacctttataaaaaaagagagccgggcagataccgcaaatatcgcccggccgaagtgaaattaattatcaggaatattaataattaaaatcgtacaaatat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 80 HP_score: -7.8 Tail_Score: -4.45201 Start: 53 End: 85 Full_Region: aattaatttcacttc ggccgggcgatatt tgc ggtatctgcccggctc tctttttttataaag ....................................................ggccgggcgatatttgcggtatctgcccggctc.................................................. TransTerm Strand: - Conf: 86 HP_score: -11.5 Tail_Score: -3.81806 Start: 55 End: 84 Full_Region: attaatttcacttcg gccgggcgatatt tgc ggtatctgcccggc tctctttttttataa ......................................................gccgggcgatatttgcggtatctgcccggc................................................... Find igs database================================================ Query_seq: TF1977:TF1978|TF1977:TF1978:anti-sigma factor:outer membrane protein, TonB dependent receptor:->->:2124488..2124622 135 taaaaaccgatgatgcctatgagaaagtttaaatgacctttataaaaaaagagagccgggcagataccgcaaatatcgcccggccgaagtgaaattaattatcaggaatattaataattaaaatcgtacaaatat Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: tfor_TF1977_TF1978|anti-sigma factor:outer membrane protein, TonB dependent receptor|POSITIVE:POSITIVE|[2124488,2124622]|135 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 taaaaaccgatgatgcctatgagaaagtttaaatgacctttatnnnnnnngagagccgggcagataccgcaaatatcgcccggccgaagtgaaattaattatcaggaatattaataattaaaatcgtacaaatat taaaaaccgatgatgcctatgagaaagtttaaatgacctttataaaaaaagagagccgggcagataccgcaaatatcgcccggccgaagtgaaattaattatcaggaatattaataattaaaatcgtacaaatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAACCGAUGAUGCCUAUGAGAAAGUUUAAAUGACCUUUAUAAAAAAAGAGAGCCGGGCAGAUACCGCAAAUAUCGCCCGGCCGAAGUGAAAUUAAUUAUCAGGAAUAUUAAUAAUUAAAAUCGUACAAAUAU ......((((((((...((((((...(((.....))).))))))........(.(((((((.((((.......))))))))))))............)))))).))............................. (-25.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUUGUACGAUUUUAAUUAUUAAUAUUCCUGAUAAUUAAUUUCACUUCGGCCGGGCGAUAUUUGCGGUAUCUGCCCGGCUCUCUUUUUUUAUAAAGGUCAUUUAAACUUUCUCAUAGGCAUCAUCGGUUUUUA ...((((((.((..((((((((((.......))))))))))..)).....(((((((((((((.....))))).)))))))).........)))))).(((.................))).............. (-30.63) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 390 85 51 229 194 tfor:TF2855|5end_ATPase,_AAA_family_3040657..3040887_POSITIVE 375 99 55 73 15 tfor:TF0248|5end_hypothetical_protein_278249..278479_POSITIVE 361 91 55 51 16 tfor:TF3145|5end_conserved_hypothetical_protein;_possible_GTP_cyclohydrolase_I_family_3381254..3381484_POSITIVE 355 86 44 181 119 tfor:TF3140|5end_Na+-translocating_NADH-quinone_reductase,_subunit_B_3373309..3373539_POSITIVE 354 87 55 30 3 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 354 86 53 34 6 tfor:TF2043|5end_fructokinase_2202267..2202497_POSITIVE 350 87 51 48 20 tfor:TF0681|5end_sugar_kinase,_PfkB_family_723155..723385_POSITIVE 349 91 55 195 160 tfor:TF1831|5end_conserved_hypothetical_protein_1980365..1980595_POSITIVE 343 90 55 81 37 tfor:TF1464|5end_conserved_hypothetical_protein_1553467..1553697_POSITIVE 343 96 53 231 186 tfor:TF0252|5end_hypothetical_protein_283530..283760_POSITIVE 341 86 55 193 150 tfor:TF1599|5end_ribonuclease_P_protein_component_1713564..1713794_POSITIVE 339 94 53 202 153 tfor:TF2368|5end_uridine_phosphorylase_2533666..2533896_POSITIVE 338 85 46 190 146 tfor:TF0594|5end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_626971..627201_POSITIVE 336 91 52 41 8 tfor:TF2337|5end_conserved_hypothetical_protein_2497997..2498227_POSITIVE 334 91 51 195 149 tfor:TF0713|5end_polypeptide_deformylase;_formylmethionine_deformylase;_763440..763670_POSITIVE 333 91 54 204 165 tfor:TF0765|5end_conserved_hypothetical_protein_811302..811532_POSITIVE 332 91 55 64 17 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 330 97 53 90 40 tfor:TF1955|5end_amino_acid_exporter,_possible_threonine_efflux_protein_2106952..2107182_POSITIVE 328 85 52 161 127 tfor:TF0023|5end_possible_response_element_in_two_component_regulation_19446..19676_POSITIVE 325 86 53 200 162 tfor:TF2397|5end_magnesium_and_cobalt_transport_protein_2568545..2568775_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 390 100 54 79 21 tfor:TF0073|3end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_82051..82201_POSITIVE 375 99 55 92 34 tfor:TF0247|3end_conserved_hypothetical_protein_278348..278498_POSITIVE 354 86 53 43 15 tfor:TF2042|3end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2202356..2202506_POSITIVE 349 91 55 151 116 tfor:TF1830|3end_3-isopropylmalate_dehydratase,_large_subunit_1980401..1980551_POSITIVE 346 84 55 36 7 tfor:TF1977|3end_anti-sigma_factor_2124427..2124577_POSITIVE 343 96 53 150 105 tfor:TF0251|3end_conserved_hypothetical_protein;_possible_exporter_283529..283679_POSITIVE 339 90 55 42 3 tfor:TF1462|3end_erythronate-4-phosphate_dehydrogenase_1553508..1553658_POSITIVE 336 91 52 123 90 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 333 91 56 29 3 tfor:TF2246|3end_hypothetical_protein_2421550..2421700_POSITIVE 325 90 50 59 15 tfor:TF1744|3end_phenylacetate-CoA_ligase_1879218..1879368_POSITIVE 325 89 56 61 32 tfor:TF0696|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_740741..740891_POSITIVE 317 91 55 49 11 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 316 86 50 59 13 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 314 92 52 47 12 tfor:TF2275|3end_conserved_hypothetical_protein_2438300..2438450_POSITIVE 310 86 55 68 32 tfor:TF0235|3end_hypothetical_protein_261849..261999_POSITIVE 303 86 51 109 58 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 303 107 67 61 15 tfor:TF0062|3end_conserved_hypothetical_protein_66180..66330_POSITIVE 300 91 53 65 17 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 298 93 54 138 108 tfor:TF2886|3end_RNA_methylase_SpoU_family_3076270..3076420_POSITIVE 297 91 54 131 90 tfor:TF2882|3end_conserved_hypothetical_protein_3074401..3074551_POSITIVE