Origin IGS: taaagcctatggagaaaaacatctgaagtaaccggaaaagaccggacgatgctgtcccatcgttcgggtcatgaaattcatttactaacttttaatgtgaaaacaaattcataacaaaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattttgttatgaatttgttttcacattaaaagttagtaaatgaatttcatgacccgaacgatgggacagcatcgtccggtcttttccggttacttcagatgtttttctccataggcttta Mask Tandem Repeat Region ================================================ taaagcctatggagaaaaacatctgaagtaaccggaaaagaccggacgatgctgtcccatcgttcgggtcatgaaattcatttactaacttttaatgtgaaaacaaattcataacaaaatt Find is-nt database================================================ Query_seq: TF3010:TF3011|TF3010:TF3011:possible anti-sigma factor:outer membrane protein, TonB dependent receptor:->->:3230949..3231069 121 taaagcctatggagaaaaacatctgaagtaaccggaaaagaccggacgatgctgtcccatcgttcgggtcatgaaattcatttactaacttttaatgtgaaaacaaattcataacaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3010:TF3011|TF3010:TF3011:possible anti-sigma factor:outer membrane protein, TonB dependent receptor:->->:3230949..3231069 121 taaagcctatggagaaaaacatctgaagtaaccggaaaagaccggacgatgctgtcccatcgttcgggtcatgaaattcatttactaacttttaatgtgaaaacaaattcataacaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3010:TF3011|TF3010:TF3011:possible anti-sigma factor:outer membrane protein, TonB dependent receptor:->->:3230949..3231069 121 taaagcctatggagaaaaacatctgaagtaaccggaaaagaccggacgatgctgtcccatcgttcgggtcatgaaattcatttactaacttttaatgtgaaaacaaattcataacaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaagcctatggagaaaaacatctgaagtaaccggaaaagaccggacgatgctgtcccatcgttcgggtcatgaaattcatttactaacttttaatgtgaaaacaaattcataacaaaatt Predict ORF larger than 30AA ================================================ taaagcctatggagaaaaacatctgaagtaaccggaaaagaccggacgatgctgtcccatcgttcgggtcatgaaattcatttactaacttttaatgtgaaaacaaattcataacaaaatt 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================================================ taaagcctatggagaaaaacatctgaagtaaccggaaaagaccggacgatgctgtcccatcgttcgggtcatgaaattcatttactaacttttaatgtgaaaacaaattcataacaaaatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -6.2 Tail_Score: -4.21768 Start: 40 End: 70 Full_Region: gtaaatgaatttcat gacccgaacgatg ggacag catcgtccggtc ttttccggttacttc .......................................gacccgaacgatgggacagcatcgtccggtc................................................... TransTerm Strand: - Conf: 76 HP_score: -9.0 Tail_Score: -3.70019 Start: 42 End: 67 Full_Region: aatgaatttcatgac ccgaacgatg ggacag catcgtccgg tcttttccggttact .........................................ccgaacgatgggacagcatcgtccgg...................................................... Find igs database================================================ Query_seq: TF3010:TF3011|TF3010:TF3011:possible anti-sigma factor:outer membrane protein, TonB dependent receptor:->->:3230949..3231069 121 taaagcctatggagaaaaacatctgaagtaaccggaaaagaccggacgatgctgtcccatcgttcgggtcatgaaattcatttactaacttttaatgtgaaaacaaattcataacaaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 121 Len: 121 Subject: tfor_TF3010_TF3011|possible anti-sigma factor:outer membrane protein, TonB dependent receptor|POSITIVE:POSITIVE|[3230949,3231069]|121 HSP 1 e-value: 8.0E-63 bit: 240.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 taaagcctatggagaaaaacatctgaagtaaccggaaaagaccggacgatgctgtcccatcgttcgggtcatgaaattcatttactaacttttaatgtgaaaacaaattcataacaaaatt taaagcctatggagaaaaacatctgaagtaaccggaaaagaccggacgatgctgtcccatcgttcgggtcatgaaattcatttactaacttttaatgtgaaaacaaattcataacaaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGCCUAUGGAGAAAAACAUCUGAAGUAACCGGAAAAGACCGGACGAUGCUGUCCCAUCGUUCGGGUCAUGAAAUUCAUUUACUAACUUUUAAUGUGAAAACAAAUUCAUAACAAAAUU .......((((((.....((((..(((((............((((((((((......))))))))))...(((.....)))......)))))..)))).........))))))........ (-25.34) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUGUUAUGAAUUUGUUUUCACAUUAAAAGUUAGUAAAUGAAUUUCAUGACCCGAACGAUGGGACAGCAUCGUCCGGUCUUUUCCGGUUACUUCAGAUGUUUUUCUCCAUAGGCUUUA ......((((((((((..(((..((.......))....)))..)).)))))))).....(.((((((.((((((..((((......))))........))))))..)).)))).)...... (-23.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 66 27 227 182 tfor:TF0971|5end_conserved_hypothetical_protein_1021355..1021585_POSITIVE 391 70 21 194 131 tfor:TF2390|5end_conserved_hypothetical_protein_2560509..2560739_POSITIVE 377 80 31 106 49 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 369 74 32 107 64 tfor:TF0036|5end_beta-hexosaminidase_precursor_35821..36051_POSITIVE 358 70 23 189 136 tfor:TF0013|5end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_6414..6644_POSITIVE 351 73 32 203 162 tfor:TF3082|5end_conserved_hypothetical_protein_3316431..3316661_POSITIVE 351 73 32 82 41 tfor:TF2202|5end_hypothetical_protein_2378682..2378912_POSITIVE 346 80 32 213 162 tfor:TF2381|5end_muramidase/hemagglutinin_2545757..2545987_POSITIVE 339 73 32 223 180 tfor:TF2048|5end_conserved_hypothetical_protein_2210643..2210873_POSITIVE 338 68 22 111 54 tfor:TF0750|5end_conserved_hypothetical_protein_797776..798006_POSITIVE 335 67 24 175 113 tfor:TF1268|5end_conserved_hypothetical_protein_1354085..1354315_POSITIVE 333 70 28 218 173 tfor:TF1467|5end_conserved_hypothetical_protein_1557011..1557241_POSITIVE 332 70 21 115 50 tfor:TF2517|5end_hypothetical_protein_2695089..2695319_POSITIVE 332 73 33 64 25 tfor:TF2290|5end_ABC_transporter,_ATP-binding/permease_component_2443942..2444172_POSITIVE 332 68 32 226 184 tfor:TF2016|5end_hypothetical_protein_2172948..2173178_POSITIVE 332 84 41 152 105 tfor:TF1623|5end_5-formyltetrahydrofolate_cyclo-ligase_1736698..1736928_POSITIVE 331 69 28 147 100 tfor:TF1161|5end_large_conductance_mechanosensitive_channel_protein_1240931..1241161_POSITIVE 328 69 23 207 155 tfor:TF1990|5end_outer_membrane_protein_2141320..2141550_POSITIVE 326 69 23 92 49 tfor:TF2332|5end_signal_peptidase_I_2491694..2491924_POSITIVE 326 69 23 180 130 tfor:TF1063|5end_possible_amidase_enhancer_precursor;_sporulation-related_protein_1132671..1132901_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 369 74 32 107 64 tfor:TF0035|3end_sialidase_35901..36051_POSITIVE 339 67 21 150 90 tfor:TF2389|3end_conserved_hypothetical_protein_2560548..2560698_POSITIVE 338 68 22 86 29 tfor:TF0749|3end_protease_II_797831..797981_POSITIVE 336 73 33 53 2 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 332 73 33 46 7 tfor:TF2289|3end_secretion_protein,_possible_HlyD_family_2444004..2444154_POSITIVE 332 84 41 137 90 tfor:TF1622|3end_conserved_hypothetical_protein_1736763..1736913_POSITIVE 331 69 28 144 97 tfor:TF1160|3end_MutT/nudix_family_protein_1241008..1241158_POSITIVE 326 69 23 85 42 tfor:TF2331|3end_conserved_hypothetical_protein_2491767..2491917_POSITIVE 325 69 27 59 4 tfor:TF1422|3end_GLCNAC_transferase_(UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)-pyr_ophosphoryl-undecaprenol_N-acetylglucosamine_transferase)_1505823..1505973_POSITIVE 324 73 31 147 96 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 321 56 19 137 107 tfor:TF0141|3end_exodeoxyribonuclease_VII,_large_subunit_149830..149980_POSITIVE 318 80 34 109 64 tfor:TF1719|3end_ribonuclease_R_1843668..1843818_POSITIVE 318 76 33 77 39 tfor:TF1683|3end_conserved_hypothetical_protein_1796511..1796661_POSITIVE 317 80 31 62 13 tfor:TF0776|3end_ABC_transporter,_permease_component_826173..826323_POSITIVE 315 80 31 72 24 tfor:TF2251|3end_conjugative_transposon_protein,_TraE_2424687..2424837_POSITIVE 315 70 33 61 25 tfor:TF0616|3end_conserved_hypothetical_protein_650658..650808_POSITIVE 314 67 23 144 99 tfor:TF2255|3end_transfer_region-related_protein,_TraH_2427961..2428111_POSITIVE 309 64 40 126 99 tfor:TF0462|3end_possible_cobalamin_biosynthesis_precorrin-3_methylase_479095..479245_POSITIVE 308 74 33 150 108 tfor:TF3026|3end_conserved_hypothetical_protein_3250254..3250404_POSITIVE 306 75 32 150 117 tfor:TF3087|3end_conserved_hypothetical_protein_3322582..3322732_POSITIVE