Origin IGS: tagagtttccaatcatagaaatcaaccaagtcgaaagacttggtttttttgtatccaaaaatcatttttatgttaaaacgctaacaaaaaataggattgtatgatataatttagacagattattgcgatttaggagatgttatgaataaaataaaagttatatgagattgttgattaggagatttttattagggggatccagatgaatgaatgcaatggcttactgttgctcattctctgatttaaaggatttgttattcttttttagaataatttgaaagggatttt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatccctttcaaattattctaaaaaagaataacaaatcctttaaatcagagaatgagcaacagtaagccattgcattcattcatctggatccccctaataaaaatctcctaatcaacaatctcatataacttttattttattcataacatctcctaaatcgcaataatctgtctaaattatatcatacaatcctattttttgttagcgttttaacataaaaatgatttttggatacaaaaaaaccaagtctttcgacttggttgatttctatgattggaaactcta Mask Tandem Repeat Region ================================================ tagagtttccaatcatagaaatcaaccaagtcgaaagacttggtttttttgtatccaaaaatcatttttatgttaaaacgctaacaaaaaataggattgtatgatataatttagacagattattgcgatttaggagatgttatgaataaaataaaagttatatgagattgttgattaggagatttttattagggggatccagatgaatgaatgcaatggcttactgttgctcattctctgatttaaaggatttgttattcttttttagaataatttgaaagggatttt Find is-nt database================================================ Query_seq: SSA_1105:SSA_1106|SSA_1105:SSA_1106:50S ribosomal protein L7/ L12, putative:IgA-specific metalloendopeptidase:->->:1125826..1126113 288 tagagtttccaatcatagaaatcaaccaagtcgaaagacttggtttttttgtatccaaaaatcatttttatgttaaaacgctaacaaaaaataggattgtatgatataatttagacagattattgcgatttaggagatgttatgaataaaataaaagttatatgagattgttgattaggagatttttattagggggatccagatgaatgaatgcaatggcttactgttgctcattctctgatttaaaggatttgttattcttttttagaataatttgaaagggatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1105:SSA_1106|SSA_1105:SSA_1106:50S ribosomal protein L7/ L12, putative:IgA-specific metalloendopeptidase:->->:1125826..1126113 288 tagagtttccaatcatagaaatcaaccaagtcgaaagacttggtttttttgtatccaaaaatcatttttatgttaaaacgctaacaaaaaataggattgtatgatataatttagacagattattgcgatttaggagatgttatgaataaaataaaagttatatgagattgttgattaggagatttttattagggggatccagatgaatgaatgcaatggcttactgttgctcattctctgatttaaaggatttgttattcttttttagaataatttgaaagggatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1105:SSA_1106|SSA_1105:SSA_1106:50S ribosomal protein L7/ L12, putative:IgA-specific metalloendopeptidase:->->:1125826..1126113 288 tagagtttccaatcatagaaatcaaccaagtcgaaagacttggtttttttgtatccaaaaatcatttttatgttaaaacgctaacaaaaaataggattgtatgatataatttagacagattattgcgatttaggagatgttatgaataaaataaaagttatatgagattgttgattaggagatttttattagggggatccagatgaatgaatgcaatggcttactgttgctcattctctgatttaaaggatttgttattcttttttagaataatttgaaagggatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagagtttccaatcatagaaatcaaccaagtcgaaagacttggtttttttgtatccaaaaatcatttttatgttaaaacgctaacaaaaaataggattgtatgatataatttagacagattattgcgatttaggagatgttatgaataaaataaaagttatatgagattgttgattaggagatttttattagggggatccagatgaatgaatgcaatggcttactgttgctcattctctgatttaaaggatttgttattcttttttagaataatttgaaagggatttt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 12 End: 101 ........... M I E I N Q V E R L G F F V S K N H F Y V K T L T K N R I V ........................................................................................................................................................................................... tagagtttccaatcatagaaatcaaccaagtcgaaagacttggtttttttgtatccaaaaatcatttttatgttaaaacgctaacaaaaaataggattgtatgatataatttagacagattattgcgatttaggagatgttatgaataaaataaaagttatatgagattgttgattaggagatttttattagggggatccagatgaatgaatgcaatggcttactgttgctcattctctgatttaaaggatttgttattcttttttagaataatttgaaagggatttt 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: 242 End: 271 .................................................................................................................................................................................................................................................TTTAAAGGATTTGTTATTCTTTTTTAGAAT................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagagtttccaatcatagaaatcaaccaagtcgaaagacttggtttttttgtatccaaaaatcatttttatgttaaaacgctaacaaaaaataggattgtatgatataatttagacagattattgcgatttaggagatgttatgaataaaataaaagttatatgagattgttgattaggagatttttattagggggatccagatgaatgaatgcaatggcttactgttgctcattctctgatttaaaggatttgttattcttttttagaataatttgaaagggatttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 86 HP_score: -9.9 Tail_Score: -3.66968 Start: 26 End: 43 Full_Region: ttggatacaaaaaaa ccaagtc tttc gacttgg ttgatttctatgatt .........................ccaagtctttcgacttgg..................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1105:SSA_1106|SSA_1105:SSA_1106:50S ribosomal protein L7/ L12, putative:IgA-specific metalloendopeptidase:->->:1125826..1126113 288 tagagtttccaatcatagaaatcaaccaagtcgaaagacttggtttttttgtatccaaaaatcatttttatgttaaaacgctaacaaaaaataggattgtatgatataatttagacagattattgcgatttaggagatgttatgaataaaataaaagttatatgagattgttgattaggagatttttattagggggatccagatgaatgaatgcaatggcttactgttgctcattctctgatttaaaggatttgttattcttttttagaataatttgaaagggatttt Intra-Species Hit: Count: 1 Min: 1 Max: 288 Len: 288 Subject: NC_009009_SSA_1105_SSA_1106|50S ribosomal protein L7/ L12, putative:IgA-specific metalloendopeptidase|POSITIVE:POSITIVE|[1125826, 1126113]|288 HSP 1 e-value: 1.0E-149 bit: 529.0 Len: 288 Query Start:1 Query End:288 Subject Strand: POSITIVE Subject Start: 1 Subject End: 288 tagagtttccaatcatagaaatcaaccaagtcgaaagacttggnnnnnnngtatccaaaaatcatttttatgttaaaacgctaacaaaaaataggattgtatgatataatttagacagattattgcgatttaggagatgttatgaataaaataaaagttatatgagattgttgattaggagatttttattagggggatccagatgaatgaatgcaatggcttactgttgctcattctctgatttaaaggatttgttattcttttttagaataatttgaaagggatttt tagagtttccaatcatagaaatcaaccaagtcgaaagacttggtttttttgtatccaaaaatcatttttatgttaaaacgctaacaaaaaataggattgtatgatataatttagacagattattgcgatttaggagatgttatgaataaaataaaagttatatgagattgttgattaggagatttttattagggggatccagatgaatgaatgcaatggcttactgttgctcattctctgatttaaaggatttgttattcttttttagaataatttgaaagggatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAGUUUCCAAUCAUAGAAAUCAACCAAGUCGAAAGACUUGGUUUUUUUGUAUCCAAAAAUCAUUUUUAUGUUAAAACGCUAACAAAAAAUAGGAUUGUAUGAUAUAAUUUAGACAGAUUAUUGCGAUUUAGGAGAUGUUAUGAAUAAAAUAAAAGUUAUAUGAGAUUGUUGAUUAGGAGAUUUUUAUUAGGGGGAUCCAGAUGAAUGAAUGCAAUGGCUUACUGUUGCUCAUUCUCUGAUUUAAAGGAUUUGUUAUUCUUUUUUAGAAUAAUUUGAAAGGGAUUUU .((((((((((((((....((((.((((((((....))))))))....(((((((....((((..((((.(((((......))))).))))...))))....)))))))....(((...(((((...(((((..........)))))..)))))..)))......))))..))))).))))))))).....((.(((((((((.((((((..(((((((....))))))))))))))))........)))))).))..(((((((((((....))))))))))).... (-69.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCCCUUUCAAAUUAUUCUAAAAAAGAAUAACAAAUCCUUUAAAUCAGAGAAUGAGCAACAGUAAGCCAUUGCAUUCAUUCAUCUGGAUCCCCCUAAUAAAAAUCUCCUAAUCAACAAUCUCAUAUAACUUUUAUUUUAUUCAUAACAUCUCCUAAAUCGCAAUAAUCUGUCUAAAUUAUAUCAUACAAUCCUAUUUUUUGUUAGCGUUUUAACAUAAAAAUGAUUUUUGGAUACAAAAAAACCAAGUCUUUCGACUUGGUUGAUUUCUAUGAUUGGAAACUCUA ...............(((((((.....))))))).............(((((((((((((((..(....)..))))..)))))).)))))....................(((((((......................................................((((((((....(((((.........((((.((((((....)))))).))))))))).))))))))......(((((((((....)))))))))........)))))))........ (-47.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 232 192 65 9 NC_009009:SSA_1180|5end_hypothetical_protein_1208559..1208789_NEGATIVE 276 232 191 63 16 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 275 233 191 66 27 NC_009009:SSA_0494|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_494407..494637_POSITIVE 273 240 191 153 97 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 269 259 213 179 136 NC_009009:SSA_2063|5end_Aminopeptidase_PepS,_putative_2064857..2065087_NEGATIVE 267 230 188 180 141 NC_009009:SSA_0307|5end_Glutamine_synthetase_type_1,_putative_302987..303217_POSITIVE 267 238 191 170 113 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 264 60 11 131 80 NC_009009:SSA_1957|5end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1954670..1954900_NEGATIVE 256 230 183 223 171 NC_009009:SSA_2072|5end_Phosphatidate_cytidylyltransferase,_putative_2075603..2075833_NEGATIVE 255 239 194 77 31 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 250 231 191 226 170 NC_009009:SSA_2011|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012856..2013086_NEGATIVE 250 206 169 224 183 NC_009009:SSA_0579|5end_Hydrolase,_HAD_superfamily,_putative_572220..572450_POSITIVE 248 254 213 215 173 NC_009009:SSA_1641|5end_MutT/nudix_family_protein,_putative_1643094..1643324_NEGATIVE 243 260 213 202 144 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 240 230 190 46 5 NC_009009:SSA_1078|5end_hypothetical_protein_1095742..1095972_POSITIVE 240 47 9 170 130 NC_009009:SSA_0841|5end_hypothetical_protein_826935..827165_POSITIVE 239 252 212 47 12 NC_009009:SSA_2252|5end_hypothetical_protein_2248649..2248879_NEGATIVE 239 240 191 205 155 NC_009009:SSA_1492|5end_hypothetical_protein_1498954..1499184_NEGATIVE 239 238 198 196 144 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 238 231 191 179 132 NC_009009:SSA_1825|5end_hypothetical_protein_1812951..1813181_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 244 201 150 106 NC_009009:SSA_0669|3end_ATP_dependent_protease,_putative_651450..651600_NEGATIVE 275 233 191 62 23 NC_009009:SSA_0493|3end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_494483..494633_POSITIVE 273 240 191 149 93 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 267 230 188 148 109 NC_009009:SSA_0306|3end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_303035..303185_POSITIVE 265 239 191 64 10 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 264 60 11 140 89 NC_009009:SSA_1958|3end_Adapter_protein_mecA,_putative_1954661..1954811_NEGATIVE 259 232 194 47 1 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 254 52 15 76 39 NC_009009:SSA_1105|3end_50S_ribosomal_protein_L7/_L12,_putative_1125765..1125915_POSITIVE 248 233 217 151 135 NC_009009:SSA_0917|3end_Cobalamin-independent_methionine_synthase_II,_putative_929087..929237_NEGATIVE 247 250 213 150 114 NC_009009:SSA_2064|3end_hypothetical_protein_2064879..2065029_NEGATIVE 243 57 16 142 92 NC_009009:SSA_1854|3end_Conserved_uncharacterized_protein_1849433..1849583_NEGATIVE 243 46 4 59 11 NC_009009:SSA_0383|3end_Beta-glucosidase,_putative_376053..376203_POSITIVE 242 230 183 150 88 NC_009009:SSA_0980|3end_3-isopropylmalate_dehydratase_large_subunit,_putative_985466..985616_POSITIVE 240 259 226 148 114 NC_009009:SSA_1136|3end_ATPases_with_chaperone_activity,_ATP-binding_subunit,_putative_1164247..1164397_POSITIVE 240 230 190 53 12 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 239 238 198 98 46 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 238 239 198 150 106 NC_009009:SSA_1308|3end_hypothetical_protein_1326267..1326417_NEGATIVE 238 53 17 59 17 NC_009009:SSA_1028|3end_Transcriptional_repressor,_XRE_family,_putative_1045290..1045440_NEGATIVE 238 230 181 69 15 NC_009009:SSA_0429|3end_Histidine_ammonia-lyase,_putative_429701..429851_NEGATIVE 233 247 208 44 1 NC_009009:SSA_1181|3end_Hydrolase,_alpha/beta_superfamily,_putative_1208592..1208742_NEGATIVE