Origin IGS: gcaatcgtagtttaaaattgatacggatattctgttttttcggtcgtaatcgtctcaacaatcagcgacgaaacgaggcaaaggtaagaaaatgtatcgggaatgcaatatcctctttatttccaatcaacgcctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaggcgttgattggaaataaagaggatattgcattcccgatacattttcttacctttgcctcgtttcgtcgctgattgttgagacgattacgaccgaaaaaacagaatatccgtatcaattttaaactacgattgc Mask Tandem Repeat Region ================================================ gcaatcgtagtttaaaattgatacggatattctgttttttcggtcgtaatcgtctcaacaatcagcgacgaaacgaggcaaaggtaagaaaatgtatcgggaatgcaatatcctctttatttccaatcaacgcctta Find is-nt database================================================ Query_seq: TF3024:TF3025|TF3024:TF3025:periplasmic protease:hypothetical protein:->->:3248775..3248911 137 gcaatcgtagtttaaaattgatacggatattctgttttttcggtcgtaatcgtctcaacaatcagcgacgaaacgaggcaaaggtaagaaaatgtatcgggaatgcaatatcctctttatttccaatcaacgcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3024:TF3025|TF3024:TF3025:periplasmic protease:hypothetical protein:->->:3248775..3248911 137 gcaatcgtagtttaaaattgatacggatattctgttttttcggtcgtaatcgtctcaacaatcagcgacgaaacgaggcaaaggtaagaaaatgtatcgggaatgcaatatcctctttatttccaatcaacgcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3024:TF3025|TF3024:TF3025:periplasmic protease:hypothetical protein:->->:3248775..3248911 137 gcaatcgtagtttaaaattgatacggatattctgttttttcggtcgtaatcgtctcaacaatcagcgacgaaacgaggcaaaggtaagaaaatgtatcgggaatgcaatatcctctttatttccaatcaacgcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaatcgtagtttaaaattgatacggatattctgttttttcggtcgtaatcgtctcaacaatcagcgacgaaacgaggcaaaggtaagaaaatgtatcgggaatgcaatatcctctttatttccaatcaacgcctta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 18 End: 137 ................. M I R I F C F F G R N R L N N Q R R N E A K V R K C I G N A I S S L F P I N A L Protein_Len: 30 Strand: - Start: 15 End: 104 .............. F Q Y P Y E T K E T T I T E V I L S S V L C L Y S F T D P M ................................. gcaatcgtagtttaaaattgatacggatattctgttttttcggtcgtaatcgtctcaacaatcagcgacgaaacgaggcaaaggtaagaaaatgtatcgggaatgcaatatcctctttatttccaatcaacgcctta 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================================================ gcaatcgtagtttaaaattgatacggatattctgttttttcggtcgtaatcgtctcaacaatcagcgacgaaacgaggcaaaggtaagaaaatgtatcgggaatgcaatatcctctttatttccaatcaacgcctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3024:TF3025|TF3024:TF3025:periplasmic protease:hypothetical protein:->->:3248775..3248911 137 gcaatcgtagtttaaaattgatacggatattctgttttttcggtcgtaatcgtctcaacaatcagcgacgaaacgaggcaaaggtaagaaaatgtatcgggaatgcaatatcctctttatttccaatcaacgcctta Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: tfor_TF3024_TF3025|periplasmic protease:hypothetical protein|POSITIVE:POSITIVE|[3248775,3248911]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 gcaatcgtagtttaaaattgatacggatattctgttttttcggtcgtaatcgtctcaacaatcagcgacgaaacgaggcaaaggtaagaaaatgtatcgggaatgcaatatcctctttatttccaatcaacgcctta gcaatcgtagtttaaaattgatacggatattctgttttttcggtcgtaatcgtctcaacaatcagcgacgaaacgaggcaaaggtaagaaaatgtatcgggaatgcaatatcctctttatttccaatcaacgcctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAUCGUAGUUUAAAAUUGAUACGGAUAUUCUGUUUUUUCGGUCGUAAUCGUCUCAACAAUCAGCGACGAAACGAGGCAAAGGUAAGAAAAUGUAUCGGGAAUGCAAUAUCCUCUUUAUUUCCAAUCAACGCCUUA ....((((.(((.....((((.((((.(((.(((......)))..))).)))).)))).....))).))))...(((((...((((........))))(((((((............))))))).......))))). (-25.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGCGUUGAUUGGAAAUAAAGAGGAUAUUGCAUUCCCGAUACAUUUUCUUACCUUUGCCUCGUUUCGUCGCUGAUUGUUGAGACGAUUACGACCGAAAAAACAGAAUAUCCGUAUCAAUUUUAAACUACGAUUGC ......((((((((((....((((((((((((......)))))..)))))))...((((.....((((((((.(((((((....)))))))))).)))))...))))...)))).))))))................ (-26.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 367 69 25 37 1 tfor:TF2435|5end_DNA_repair_protein_radC_2614352..2614582_POSITIVE 356 78 31 53 2 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 342 80 31 212 160 tfor:TF2196|5end_hypothetical_protein_2371678..2371908_POSITIVE 332 60 17 188 145 tfor:TF2151|5end_uridine_kinase_2323033..2323263_POSITIVE 327 84 41 226 190 tfor:TF1409|5end_outer_membrane_protein_TolC_1485479..1485709_POSITIVE 325 68 21 69 13 tfor:TF1210|5end_conserved_hypothetical_protein_1295695..1295925_POSITIVE 324 79 33 157 112 tfor:TF1398|5end_conserved_hypothetical_protein_1471474..1471704_POSITIVE 322 70 25 141 97 tfor:TF2500|5end_ABC_transporter,_ATP-binding_protein_2674449..2674679_POSITIVE 320 100 51 226 181 tfor:TF2177|5end_hypothetical_protein_2349281..2349511_POSITIVE 312 88 41 43 2 tfor:TF1739|5end_possible_sulfatase_1866983..1867213_POSITIVE 312 79 33 216 165 tfor:TF1733|5end_conserved_hypothetical_protein_1856015..1856245_POSITIVE 310 78 33 68 11 tfor:TF0464|5end_precorrin_methylase_480211..480441_POSITIVE 310 107 65 199 148 tfor:TF0144|5end_hypothetical_protein_151209..151439_POSITIVE 309 86 42 162 122 tfor:TF2530|5end_conserved_hypothetical_protein_2711416..2711646_POSITIVE 306 106 61 112 72 tfor:TF2108|5end_hypothetical_protein_2277385..2277615_POSITIVE 306 106 61 45 5 tfor:TF2106|5end_hypothetical_protein_2277318..2277548_POSITIVE 306 67 24 204 160 tfor:TF0765|5end_conserved_hypothetical_protein_811302..811532_POSITIVE 302 47 1 94 43 tfor:TF1575|5end_DNA-binding_response_regulator_1685177..1685407_POSITIVE 300 79 31 176 125 tfor:TF1768|5end_conserved_hypothetical_protein;_possible_transposase_1906526..1906756_POSITIVE 300 100 51 208 163 tfor:TF0344|5end_hypothetical_protein_366722..366952_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 100 51 126 68 tfor:TF1732|3end_conserved_hypothetical_protein_1855979..1856129_POSITIVE 345 100 57 54 2 tfor:TF1730|3end_diaminopimelate_decarboxylase_1855907..1856057_POSITIVE 324 79 33 137 92 tfor:TF1397|3end_glucosyltransferase_1471534..1471684_POSITIVE 322 70 25 89 45 tfor:TF2499|3end_possible_thioesterase_family_protein_2674477..2674627_POSITIVE 320 100 51 50 5 tfor:TF2176|3end_hypothetical_protein_2349185..2349335_POSITIVE 310 78 33 68 11 tfor:TF0463|3end_precorrin-6Y_C5,15-methyltransferase_480291..480441_POSITIVE 309 68 22 60 9 tfor:TF2615|3end_conserved_hypothetical_protein_2791209..2791359_POSITIVE 306 106 61 83 43 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 300 100 51 49 4 tfor:TF0342|3end_hypothetical_protein_366643..366793_POSITIVE 296 78 40 82 37 tfor:TF0431|3end_hypothetical_protein_452470..452620_POSITIVE 296 78 40 115 70 tfor:TF0430|3end_hypothetical_protein_452503..452653_POSITIVE 286 100 51 50 5 tfor:TF2170|3end_hypothetical_protein_2345070..2345220_POSITIVE 285 110 64 104 54 tfor:TF2594|3end_hypothetical_protein_2765125..2765275_POSITIVE 282 70 24 141 99 tfor:TF2548|3end_30S_ribosomal_protein_S12_2731704..2731854_POSITIVE 282 55 16 91 55 tfor:TF1326|3end_hypothetical_protein_1404100..1404250_POSITIVE 281 79 31 145 99 tfor:TF0595|3end_hypothetical_protein_628073..628223_POSITIVE 281 100 51 51 6 tfor:TF0348|3end_hypothetical_protein_370447..370597_POSITIVE 278 80 39 139 100 tfor:TF0934|3end_hypothetical_protein_975207..975357_POSITIVE 275 104 62 63 33 tfor:TF2018|3end_hypothetical_protein_2175315..2175465_POSITIVE 275 106 64 79 32 tfor:TF0451|3end_rhomboid_family_membrane_protein_471046..471196_POSITIVE