Origin IGS: ctggttctccttttgagtttttctttaacgtgaaaagtcggtagattgtatgcaaaaacagcgtatcgctcaatacccgagaaattcattagccgcagaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatttctgcggctaatgaatttctcgggtattgagcgatacgctgtttttgcatacaatctaccgacttttcacgttaaagaaaaactcaaaaggagaaccag Mask Tandem Repeat Region ================================================ ctggttctccttttgagtttttctttaacgtgaaaagtcggtagattgtatgcaaaaacagcgtatcgctcaatacccgagaaattcattagccgcagaaatta Find is-nt database================================================ Query_seq: AA00860:AA00861|AA00860:AA00861:phosphoheptose isomerase:transcription repair coupling factor:->->:592588..592691 104 ctggttctccttttgagtttttctttaacgtgaaaagtcggtagattgtatgcaaaaacagcgtatcgctcaatacccgagaaattcattagccgcagaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00860:AA00861|AA00860:AA00861:phosphoheptose isomerase:transcription repair coupling factor:->->:592588..592691 104 ctggttctccttttgagtttttctttaacgtgaaaagtcggtagattgtatgcaaaaacagcgtatcgctcaatacccgagaaattcattagccgcagaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00860:AA00861|AA00860:AA00861:phosphoheptose isomerase:transcription repair coupling factor:->->:592588..592691 104 ctggttctccttttgagtttttctttaacgtgaaaagtcggtagattgtatgcaaaaacagcgtatcgctcaatacccgagaaattcattagccgcagaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctggttctccttttgagtttttctttaacgtgaaaagtcggtagattgtatgcaaaaacagcgtatcgctcaatacccgagaaattcattagccgcagaaatta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 3 End: 98 .. T R R K L K E K V H F T P L N Y A F V A Y R E I G S F N M L R M ...... ctggttctccttttgagtttttctttaacgtgaaaagtcggtagattgtatgcaaaaacagcgtatcgctcaatacccgagaaattcattagccgcagaaatta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 45 End: 74 ............................................ATTGAGCGATACGCTGTTTTTGCATACAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctggttctccttttgagtttttctttaacgtgaaaagtcggtagattgtatgcaaaaacagcgtatcgctcaatacccgagaaattcattagccgcagaaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA00860:AA00861|AA00860:AA00861:phosphoheptose isomerase:transcription repair coupling factor:->->:592588..592691 104 ctggttctccttttgagtttttctttaacgtgaaaagtcggtagattgtatgcaaaaacagcgtatcgctcaatacccgagaaattcattagccgcagaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: aact_AA00860_AA00861|phosphoheptose isomerase:transcription repair coupling factor|POSITIVE:POSITIVE|[592588,592691]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 ctggttctccttttgagtttttctttaacgtgaaaagtcggtagattgtatgcaaaaacagcgtatcgctcaatacccgagaaattcattagccgcagaaatta ctggttctccttttgagtttttctttaacgtgaaaagtcggtagattgtatgcaaaaacagcgtatcgctcaatacccgagaaattcattagccgcagaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGGUUCUCCUUUUGAGUUUUUCUUUAACGUGAAAAGUCGGUAGAUUGUAUGCAAAAACAGCGUAUCGCUCAAUACCCGAGAAAUUCAUUAGCCGCAGAAAUUA ....((((.((..((((((((((....((.......)).((((((.(((((((.......))))).)).))..)))).))))))))))..))....)))).... (-18.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUCUGCGGCUAAUGAAUUUCUCGGGUAUUGAGCGAUACGCUGUUUUUGCAUACAAUCUACCGACUUUUCACGUUAAAGAAAAACUCAAAAGGAGAACCAG ...(((((..(((...((((....((((..((((.((((..........))))...))))...))))...)))).)))..)))))..(((.....)))...... (-17.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 69 30 53 14 aact:AA01197|5end_conserved_hypothetical_protein_820863..821093_POSITIVE 344 42 3 58 15 aact:AA00631|5end_hypothetical_protein_433678..433908_POSITIVE 343 100 58 197 156 aact:AA02195|5end_oxaloacetate_decarboxylase_alpha_chain_1494501..1494731_POSITIVE 312 100 60 217 171 aact:AA00290|5end_conserved_hypothetical_protein_201272..201502_POSITIVE 287 69 23 159 102 aact:AA02328|5end_anti-sigma_factor_B_antagonist_1589300..1589530_POSITIVE 286 57 16 140 92 aact:AA00929|5end_DNA_gyrase_subunit_B_637797..638027_POSITIVE 285 80 37 63 18 aact:AA01258|5end_TRK_system_potassium_uptake_protein_852891..853121_POSITIVE 280 100 62 210 184 aact:AA01746|5end_thiol:disulfide_interchange_protein_1180636..1180866_POSITIVE 279 95 51 168 128 aact:AA01276|5end_heptosyltransferase_III_864730..864960_POSITIVE 275 96 59 229 197 aact:AA02724|5end_seryl-tRNA_ligase_1906357..1906587_POSITIVE 275 96 59 135 103 aact:AA02723|5end_hypothetical_protein_1906263..1906493_POSITIVE 273 100 51 83 21 aact:AA01996|5end_prephenate_dehydrogenase_1355314..1355544_POSITIVE 270 79 38 140 107 aact:AA01813|5end_electron_transport_complex_protein_1220949..1221179_POSITIVE 266 79 31 157 111 aact:AA00163|5end_type_IV_prepilin_peptidase;_type_II_secretion_pathway_related_protein_116006..116236_POSITIVE 265 79 37 69 25 aact:AA02006|5end_PEP--fructosephosphotransferase_system_repressor,_DeoR_family_1363930..1364160_POSITIVE 265 70 29 47 1 aact:AA00759|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_I_520603..520833_POSITIVE 262 99 59 178 139 aact:AA01948|5end_ABC_transporter_permease,_membrane_spanning_protein_1317250..1317480_POSITIVE 261 100 51 137 80 aact:AA01330|5end_LOS_biosynthesis_enzyme_(beta-1,4-galactosyltransferase)_897653..897883_POSITIVE 260 80 34 58 18 aact:AA00579|5end_probable_DNA_recombination_protein_395265..395495_POSITIVE 251 79 37 60 15 aact:AA02964|5end_opacity_associated_protein_A_2072738..2072968_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 69 30 65 26 aact:AA01196|3end_1-acyl-sn-glycerol-3-phosphate_acetyltransferase_820955..821105_POSITIVE 280 100 62 126 100 aact:AA01745|3end_conserved_hypothetical_protein_(possible_peptide_chain_release_factor_2)_1180632..1180782_POSITIVE 276 67 23 147 95 aact:AA02327|3end_possible_ABC-type_transport_system_1589373..1589523_POSITIVE 275 96 59 144 112 aact:AA02722|3end_cytidine_deaminase_1906352..1906502_POSITIVE 273 100 51 83 21 aact:AA01995|3end_conserved_hypothetical_protein_(possible_chorismate_mutase)_1355394..1355544_POSITIVE 270 79 38 144 111 aact:AA01811|3end_electron_transport_complex_protein_1221033..1221183_POSITIVE 265 79 37 79 35 aact:AA02005|3end_vancomycin_sensitivity;_SanA_protein_1364020..1364170_POSITIVE 265 70 29 60 14 aact:AA00758|3end_hypothetical_protein_520696..520846_POSITIVE 262 79 31 86 36 aact:AA00475|3end_conserved_hypothetical_protein_(possible_N6-adenine-specific_methylase)_332282..332432_POSITIVE 261 100 51 133 76 aact:AA01329|3end_LOS_biosynthesis_enzyme_(D-glycero-D-manno-heptosyl_transferase)_897729..897879_POSITIVE 255 80 31 104 48 aact:AA02545|3end_conserved_hypothetical_protein_1774221..1774371_POSITIVE 251 98 51 69 34 aact:AA01194|3end_acyl_carrier_protein_819923..820073_POSITIVE 250 100 60 66 16 aact:AA02652|3end_conserved_hypothetical_protein_1848591..1848741_POSITIVE 250 100 61 122 75 aact:AA02543|3end_conserved_hypothetical_protein_1773434..1773584_POSITIVE 250 69 30 71 33 aact:AA01083|3end_preprotein_translocase_SecA_subunit_750970..751120_POSITIVE 246 65 24 142 102 aact:AA00825|3end_P-protein_(chorismate_mutase/prephenate_dehydratase)_568257..568407_POSITIVE 246 100 52 81 31 aact:AA00044|3end_formate_dependent_nitrite_reductase,_Fe-S_protein/_anaerobic_DMSO_reductase_B_36094..36244_POSITIVE 245 64 23 119 86 aact:AA01089|3end_hypothetical_protein_753597..753747_POSITIVE 244 69 28 47 2 aact:AA00362|3end_30S_ribosomal_protein_S3_245631..245781_POSITIVE 241 95 58 142 109 aact:AA01287|3end_transposase_872169..872319_POSITIVE