Origin IGS: taatagatgaggctagggaatccctagccttttatctttaaaaatactgctaaatctcatgtagcaaaagtctaaatcatttgtaacatgacaaaaacataactctaaaaaaactgacatgtaaatattgtatgatttttttatcatcaaattatacggagaaacacattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatgtgtttctccgtataatttgatgataaaaaaatcatacaatatttacatgtcagtttttttagagttatgtttttgtcatgttacaaatgatttagacttttgctacatgagatttagcagtatttttaaagataaaaggctagggattccctagcctcatctatta Mask Tandem Repeat Region ================================================ taatagatgaggctagggaatccctagccttttatctttaaaaatactgctaaatctcatgtagcaaaagtctaaatcatttgtaacatgacaaaaacataactctaaaaaaactgacatgtaaatattgtatgatttttttatcatcaaattatacggagaaacacattt Find is-nt database================================================ Query_seq: SSA_0303:SSA_0304|SSA_0303:SSA_0304:surface protein C:Bacterial cell wall degradation (CHAP/LysM domains), putative:->->:301112..301282 171 taatagatgaggctagggaatccctagccttttatctttaaaaatactgctaaatctcatgtagcaaaagtctaaatcatttgtaacatgacaaaaacataactctaaaaaaactgacatgtaaatattgtatgatttttttatcatcaaattatacggagaaacacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0303:SSA_0304|SSA_0303:SSA_0304:surface protein C:Bacterial cell wall degradation (CHAP/LysM domains), putative:->->:301112..301282 171 taatagatgaggctagggaatccctagccttttatctttaaaaatactgctaaatctcatgtagcaaaagtctaaatcatttgtaacatgacaaaaacataactctaaaaaaactgacatgtaaatattgtatgatttttttatcatcaaattatacggagaaacacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0303:SSA_0304|SSA_0303:SSA_0304:surface protein C:Bacterial cell wall degradation (CHAP/LysM domains), putative:->->:301112..301282 171 taatagatgaggctagggaatccctagccttttatctttaaaaatactgctaaatctcatgtagcaaaagtctaaatcatttgtaacatgacaaaaacataactctaaaaaaactgacatgtaaatattgtatgatttttttatcatcaaattatacggagaaacacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatagatgaggctagggaatccctagccttttatctttaaaaatactgctaaatctcatgtagcaaaagtctaaatcatttgtaacatgacaaaaacataactctaaaaaaactgacatgtaaatattgtatgatttttttatcatcaaattatacggagaaacacattt Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: - Start: 16 End: 150 ............... P I G L R K D K F I S S F R M Y C F D L D N T V H C F C L E L F V S M Y I N Y S K K I M M ..................... taatagatgaggctagggaatccctagccttttatctttaaaaatactgctaaatctcatgtagcaaaagtctaaatcatttgtaacatgacaaaaacataactctaaaaaaactgacatgtaaatattgtatgatttttttatcatcaaattatacggagaaacacattt 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================================================ taatagatgaggctagggaatccctagccttttatctttaaaaatactgctaaatctcatgtagcaaaagtctaaatcatttgtaacatgacaaaaacataactctaaaaaaactgacatgtaaatattgtatgatttttttatcatcaaattatacggagaaacacattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0303:SSA_0304|SSA_0303:SSA_0304:surface protein C:Bacterial cell wall degradation (CHAP/LysM domains), putative:->->:301112..301282 171 taatagatgaggctagggaatccctagccttttatctttaaaaatactgctaaatctcatgtagcaaaagtctaaatcatttgtaacatgacaaaaacataactctaaaaaaactgacatgtaaatattgtatgatttttttatcatcaaattatacggagaaacacattt Intra-Species Hit: Count: 1 Min: 1 Max: 171 Len: 171 Subject: NC_009009_SSA_0303_SSA_0304|surface protein C:Bacterial cell wall degradation (CHAP/LysM domains), putative|POSITIVE:POSITIVE|[301112,301282]|171 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 171 Query Start:1 Query End:171 Subject Strand: POSITIVE Subject Start: 1 Subject End: 171 taatagatgaggctagggaatccctagccttttatctttaaaaatactgctaaatctcatgtagcaaaagtctaaatcatttgtaacatgacaaaaacataactctnnnnnnnctgacatgtaaatattgtatgannnnnnnatcatcaaattatacggagaaacacattt taatagatgaggctagggaatccctagccttttatctttaaaaatactgctaaatctcatgtagcaaaagtctaaatcatttgtaacatgacaaaaacataactctaaaaaaactgacatgtaaatattgtatgatttttttatcatcaaattatacggagaaacacattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAGAUGAGGCUAGGGAAUCCCUAGCCUUUUAUCUUUAAAAAUACUGCUAAAUCUCAUGUAGCAAAAGUCUAAAUCAUUUGUAACAUGACAAAAACAUAACUCUAAAAAAACUGACAUGUAAAUAUUGUAUGAUUUUUUUAUCAUCAAAUUAUACGGAGAAACACAUUU ....((((((((((((((...))))))))))..))))...................((((((.(((((.(.......).))))).))))))...........((((......((......)).....(((.(((((......)))))))).......)))).......... (-35.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUGUGUUUCUCCGUAUAAUUUGAUGAUAAAAAAAUCAUACAAUAUUUACAUGUCAGUUUUUUUAGAGUUAUGUUUUUGUCAUGUUACAAAUGAUUUAGACUUUUGCUACAUGAGAUUUAGCAGUAUUUUUAAAGAUAAAAGGCUAGGGAUUCCCUAGCCUCAUCUAUUA ...(((...((((.(((....((((((((......))))).)))....)))................(((...((((..(((((.......)))))..))))....)))....))))....)))..........((((...(((((((((...))))))))).)))).... (-38.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 39 9 223 186 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 276 57 11 66 31 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 276 39 6 188 151 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 272 92 52 226 184 NC_009009:SSA_1409|5end_DTDP-glucose-4,6-dehydratase,_putative_1422255..1422485_NEGATIVE 269 88 44 78 39 NC_009009:SSA_0012|5end_Beta-lactamase_class_A,_putative_9916..10146_POSITIVE 268 50 7 53 14 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 265 58 11 202 156 NC_009009:SSA_1771|5end_Conserved_DNA_methyltransferase_protein,_putative_1758799..1759029_NEGATIVE 253 31 5 133 108 NC_009009:SSA_2330|5end_Acetyltransferase,_putative_2333655..2333885_NEGATIVE 251 39 7 54 23 NC_009009:SSA_0638|5end_Tryptophan_synthase_alpha_chain,_putative_626935..627165_POSITIVE 247 30 3 53 32 NC_009009:SSA_0493|5end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_492868..493098_POSITIVE 243 36 11 206 178 NC_009009:SSA_2279|5end_hypothetical_protein_2281910..2282140_NEGATIVE 243 29 3 48 12 NC_009009:SSA_0396|5end_hypothetical_protein_393595..393825_NEGATIVE 234 50 6 134 82 NC_009009:SSA_2089|5end_L-xylulose-5-phosphate_3-epimerase,_putative_2094339..2094569_NEGATIVE 234 36 7 216 190 NC_009009:SSA_1571|5end_Threonyl-tRNA_synthetase,_putative_1575154..1575384_NEGATIVE 233 34 7 72 41 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 232 60 12 54 12 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 232 50 6 70 16 NC_009009:SSA_0647|5end_hypothetical_protein_630998..631228_POSITIVE 230 50 9 70 22 NC_009009:SSA_1562|5end_hypothetical_protein_1566364..1566594_NEGATIVE 229 65 23 213 163 NC_009009:SSA_0092|5end_V-type_sodium_ATPase,_subunit_B,_putative_92895..93125_POSITIVE 227 70 21 163 112 NC_009009:SSA_1284|5end_hypothetical_protein_1304979..1305209_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 409 37 5 86 54 NC_009009:SSA_0303|3end_surface_protein_C_301051..301201_POSITIVE 311 37 5 86 49 NC_009009:SSA_0020|3end_Ribose-phosphate_pyrophosphokinase_1,_putative_26609..26759_POSITIVE 276 57 11 79 44 NC_009009:SSA_1551|3end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1552652..1552802_NEGATIVE 269 88 44 85 46 NC_009009:SSA_0011|3end_hypothetical_protein_10003..10153_POSITIVE 265 58 11 106 60 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 257 50 5 98 40 NC_009009:SSA_1161|3end_hypothetical_protein_1188443..1188593_POSITIVE 253 31 5 92 67 NC_009009:SSA_2331|3end_D-alanine_transfer_protein,_putative_2333696..2333846_NEGATIVE 253 34 5 44 11 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 251 39 7 61 30 NC_009009:SSA_0637|3end_Tryptophan_synthase_beta_chain,_putative_627022..627172_POSITIVE 245 56 11 118 66 NC_009009:SSA_1604|3end_Protein-export_membrane_protein_secG,_putative_1610198..1610348_NEGATIVE 235 39 1 99 54 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 235 31 5 62 31 NC_009009:SSA_1162|3end_Possible_fimbrial_assembly_protein_fimC,_putative_1188489..1188639_NEGATIVE 234 50 6 130 78 NC_009009:SSA_2090|3end_Hexulose-6-phosphate_synthase,_putative_2094343..2094493_NEGATIVE 233 34 7 72 41 NC_009009:SSA_1841|3end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1834422..1834572_NEGATIVE 232 50 6 68 14 NC_009009:SSA_0646|3end_hypothetical_protein_631076..631226_POSITIVE 231 40 8 86 53 NC_009009:SSA_2271|3end_hypothetical_protein_2272238..2272388_NEGATIVE 227 70 21 149 98 NC_009009:SSA_1285|3end_hypothetical_protein_1304993..1305143_NEGATIVE 223 49 5 51 9 NC_009009:SSA_1085|3end_Dihydrodipicolinate_reductase,_putative_1103411..1103561_POSITIVE 222 56 12 135 89 NC_009009:SSA_0214|3end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210690..210840_POSITIVE 221 38 5 99 67 NC_009009:SSA_1850|3end_DNA-directed_RNA_polymerase,_subunit_K/omega,_putative_1845710..1845860_NEGATIVE