Origin IGS: tgttcataacaaaagccgagactttactttaagcctcggctttattattttaccagtcgactaagcttaatcagataaaattttgactatctatgcttaattccggaatttaactcttttccactggaaaaacatttgatataatagtacacggagaaaaagaaaaagtagtttgctatgatggctattagcttgaagagcagactgaggcttagcctcaaagggagatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatctccctttgaggctaagcctcagtctgctcttcaagctaatagccatcatagcaaactactttttctttttctccgtgtactattatatcaaatgtttttccagtggaaaagagttaaattccggaattaagcatagatagtcaaaattttatctgattaagcttagtcgactggtaaaataataaagccgaggcttaaagtaaagtctcggcttttgttatgaaca Mask Tandem Repeat Region ================================================ tgttcataacaaaagccgagactttactttaagcctcggctttattattttaccagtcgactaagcttaatcagataaaattttgactatctatgcttaattccggaatttaactcttttccactggaaaaacatttgatataatagtacacggagaaaaagaaaaagtagtttgctatgatggctattagcttgaagagcagactgaggcttagcctcaaagggagatttt Find is-nt database================================================ Query_seq: SSA_2344:SSA_2345|SSA_2344:SSA_2345:hypothetical protein:hypothetical protein:->->:2346827..2347058 232 tgttcataacaaaagccgagactttactttaagcctcggctttattattttaccagtcgactaagcttaatcagataaaattttgactatctatgcttaattccggaatttaactcttttccactggaaaaacatttgatataatagtacacggagaaaaagaaaaagtagtttgctatgatggctattagcttgaagagcagactgaggcttagcctcaaagggagatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2344:SSA_2345|SSA_2344:SSA_2345:hypothetical protein:hypothetical protein:->->:2346827..2347058 232 tgttcataacaaaagccgagactttactttaagcctcggctttattattttaccagtcgactaagcttaatcagataaaattttgactatctatgcttaattccggaatttaactcttttccactggaaaaacatttgatataatagtacacggagaaaaagaaaaagtagtttgctatgatggctattagcttgaagagcagactgaggcttagcctcaaagggagatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2344:SSA_2345|SSA_2344:SSA_2345:hypothetical protein:hypothetical protein:->->:2346827..2347058 232 tgttcataacaaaagccgagactttactttaagcctcggctttattattttaccagtcgactaagcttaatcagataaaattttgactatctatgcttaattccggaatttaactcttttccactggaaaaacatttgatataatagtacacggagaaaaagaaaaagtagtttgctatgatggctattagcttgaagagcagactgaggcttagcctcaaagggagatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttcataacaaaagccgagactttactttaagcctcggctttattattttaccagtcgactaagcttaatcagataaaattttgactatctatgcttaattccggaatttaactcttttccactggaaaaacatttgatataatagtacacggagaaaaagaaaaagtagtttgctatgatggctattagcttgaagagcagactgaggcttagcctcaaagggagatttt Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: - Start: 90 End: 221 ......................................................................................... R H K I G S N L E K G S S F C K I Y Y Y V S F F F F Y N A I I A I L K F L L S L S L R M ........... tgttcataacaaaagccgagactttactttaagcctcggctttattattttaccagtcgactaagcttaatcagataaaattttgactatctatgcttaattccggaatttaactcttttccactggaaaaacatttgatataatagtacacggagaaaaagaaaaagtagtttgctatgatggctattagcttgaagagcagactgaggcttagcctcaaagggagatttt 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: 82 Start: 116 End: 145 ...................................................................................................................CTTTTCCACTGGAAAAACATTTGATATAAT....................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgttcataacaaaagccgagactttactttaagcctcggctttattattttaccagtcgactaagcttaatcagataaaattttgactatctatgcttaattccggaatttaactcttttccactggaaaaacatttgatataatagtacacggagaaaaagaaaaagtagtttgctatgatggctattagcttgaagagcagactgaggcttagcctcaaagggagatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2344:SSA_2345|SSA_2344:SSA_2345:hypothetical protein:hypothetical protein:->->:2346827..2347058 232 tgttcataacaaaagccgagactttactttaagcctcggctttattattttaccagtcgactaagcttaatcagataaaattttgactatctatgcttaattccggaatttaactcttttccactggaaaaacatttgatataatagtacacggagaaaaagaaaaagtagtttgctatgatggctattagcttgaagagcagactgaggcttagcctcaaagggagatttt Intra-Species Hit: Count: 1 Min: 1 Max: 232 Len: 232 Subject: NC_009009_SSA_2344_SSA_2345|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2346827,2347058]|232 HSP 1 e-value: 1.0E-128 bit: 460.0 Len: 232 Query Start:1 Query End:232 Subject Strand: POSITIVE Subject Start: 1 Subject End: 232 tgttcataacaaaagccgagactttactttaagcctcggctttattattttaccagtcgactaagcttaatcagataaaattttgactatctatgcttaattccggaatttaactcttttccactggaaaaacatttgatataatagtacacggagaaaaagaaaaagtagtttgctatgatggctattagcttgaagagcagactgaggcttagcctcaaagggagatttt tgttcataacaaaagccgagactttactttaagcctcggctttattattttaccagtcgactaagcttaatcagataaaattttgactatctatgcttaattccggaatttaactcttttccactggaaaaacatttgatataatagtacacggagaaaaagaaaaagtagtttgctatgatggctattagcttgaagagcagactgaggcttagcctcaaagggagatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUCAUAACAAAAGCCGAGACUUUACUUUAAGCCUCGGCUUUAUUAUUUUACCAGUCGACUAAGCUUAAUCAGAUAAAAUUUUGACUAUCUAUGCUUAAUUCCGGAAUUUAACUCUUUUCCACUGGAAAAACAUUUGAUAUAAUAGUACACGGAGAAAAAGAAAAAGUAGUUUGCUAUGAUGGCUAUUAGCUUGAAGAGCAGACUGAGGCUUAGCCUCAAAGGGAGAUUUU ..(((......(((((((((.(((......))).)))))))))....((((.((((.....(((((.((.(((((......))))).)).....))))).....((((..........)))).))))))))........................)))...........((((((((.....(((.....))).....))))))))(((((...)))))............. (-52.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCUCCCUUUGAGGCUAAGCCUCAGUCUGCUCUUCAAGCUAAUAGCCAUCAUAGCAAACUACUUUUUCUUUUUCUCCGUGUACUAUUAUAUCAAAUGUUUUUCCAGUGGAAAAGAGUUAAAUUCCGGAAUUAAGCAUAGAUAGUCAAAAUUUUAUCUGAUUAAGCUUAGUCGACUGGUAAAAUAAUAAAGCCGAGGCUUAAAGUAAAGUCUCGGCUUUUGUUAUGAACA ...........(((((((...)))))))...(((.....))).........(((((((((......................................((((((.(((((.((...(((((.((((....)))).....(((((((........)))))))....)))))..)).))))).))))))...((((((((((((......)))))))))))))))))))))... (-58.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 68 29 45 6 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 357 219 174 190 140 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 353 228 184 130 87 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 340 220 180 202 161 NC_009009:SSA_0780|5end_Acid_phosphatase_(PAP2_family),_putative_764748..764978_POSITIVE 328 227 188 71 33 NC_009009:SSA_1149|5end_Glycosyl_hydrolase,_family_1,_putative_1178399..1178629_POSITIVE 327 220 175 77 31 NC_009009:SSA_1106|5end_IgA-specific_metalloendopeptidase_1125974..1126204_POSITIVE 327 218 176 65 17 NC_009009:SSA_0735|5end_Integral_membrane_protein,_putative_717103..717333_POSITIVE 323 226 183 55 10 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 315 220 174 144 86 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 312 228 191 54 17 NC_009009:SSA_2050|5end_Arabinose_efflux_permease,_putative_2053255..2053485_POSITIVE 307 218 171 55 5 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 304 45 5 63 24 NC_009009:SSA_1575|5end_Glycosyl_transferase,_putative_1579110..1579340_NEGATIVE 301 216 182 59 20 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 301 224 181 170 118 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 301 229 181 213 155 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 300 59 14 133 86 NC_009009:SSA_0131|5end_30S_ribosomal_protein_S11,_putative_120717..120947_POSITIVE 292 219 172 158 104 NC_009009:SSA_0279|5end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_272319..272549_POSITIVE 290 230 184 44 1 NC_009009:SSA_1369|5end_FmtA-like_protein,_putative_1385929..1386159_NEGATIVE 289 219 171 165 106 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 289 226 190 73 35 NC_009009:SSA_2099|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2104313..2104543_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 228 183 84 41 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 353 228 184 130 87 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 340 220 180 59 18 NC_009009:SSA_0779|3end_Glycogen_phosphorylase,_putative_764685..764835_POSITIVE 328 227 188 65 27 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 327 218 176 78 30 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 323 226 183 77 32 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 315 220 174 144 86 NC_009009:SSA_1727|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1712467..1712617_NEGATIVE 307 218 171 54 4 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 306 43 1 74 35 NC_009009:SSA_2265|3end_Maltodextrin_phosphorylase,_putative_2261936..2262086_NEGATIVE 301 216 182 62 23 NC_009009:SSA_1973|3end_Histidine_kinase,_putative_1968407..1968557_NEGATIVE 300 59 14 113 66 NC_009009:SSA_0130|3end_30S_ribosomal_protein_S13,_putative_120777..120927_POSITIVE 296 218 173 85 43 NC_009009:SSA_0664|3end_Conserved_uncharacterized_protein_648784..648934_NEGATIVE 292 219 172 141 87 NC_009009:SSA_0278|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_272382..272532_POSITIVE 291 218 173 97 36 NC_009009:SSA_0966|3end_Uridine_kinase,_putative_975790..975940_POSITIVE 282 226 182 33 2 NC_009009:SSA_1002|3end_Alpha-galactosidase,_putative_1003942..1004092_POSITIVE 281 220 175 79 35 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 277 227 183 80 39 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 276 220 174 139 94 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 276 228 181 84 45 NC_009009:SSA_1552|3end_hypothetical_protein_1555130..1555280_POSITIVE 275 207 167 57 20 NC_009009:SSA_1280|3end_hypothetical_protein_1301108..1301258_NEGATIVE