Origin IGS: gctcttctccttaaataaaccaaattccttttttctagcaattattttttcaaaacaaagaataccgtctgcctactttttcaaaatctgacaaatactatccattcaattaaaatgaaccttggtcgcgcaatagagaatagcttcagttttccccaataataaatactcataagcgtctccgattattgcctaccgatacttttcgctctcaaggtatctaaca .........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 tgttagataccttgagagcgaaaagtatcggtaggcaataatcggagacgcttatgagtatttattattggggaaaactgaagctattctctattgcgcgaccaaggttcattttaattgaatggatagtatttgtcagattttgaaaaagtaggcagacggtattctttgttttgaaaaaataattgctagaaaaaaggaatttggtttatttaaggagaagagc Mask Tandem Repeat Region ================================================ gctcttctccttaaataaaccaaattccttttttctagcaattattttttcaaaacaaagaataccgtctgcctactttttcaaaatctgacaaatactatccattcaattaaaatgaaccttggtcgcgcaatagagaatagcttcagttttccccaataataaatactcataagcgtctccgattattgcctaccgatacttttcgctctcaaggtatctaaca Find is-nt database================================================ Query_seq: SSA_2175:SSA_2176|SSA_2175:SSA_2176:hypothetical protein:hypothetical protein:<-<-:2174133..2174358 226 gctcttctccttaaataaaccaaattccttttttctagcaattattttttcaaaacaaagaataccgtctgcctactttttcaaaatctgacaaatactatccattcaattaaaatgaaccttggtcgcgcaatagagaatagcttcagttttccccaataataaatactcataagcgtctccgattattgcctaccgatacttttcgctctcaaggtatctaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2175:SSA_2176|SSA_2175:SSA_2176:hypothetical protein:hypothetical protein:<-<-:2174133..2174358 226 gctcttctccttaaataaaccaaattccttttttctagcaattattttttcaaaacaaagaataccgtctgcctactttttcaaaatctgacaaatactatccattcaattaaaatgaaccttggtcgcgcaatagagaatagcttcagttttccccaataataaatactcataagcgtctccgattattgcctaccgatacttttcgctctcaaggtatctaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2175:SSA_2176|SSA_2175:SSA_2176:hypothetical protein:hypothetical protein:<-<-:2174133..2174358 226 gctcttctccttaaataaaccaaattccttttttctagcaattattttttcaaaacaaagaataccgtctgcctactttttcaaaatctgacaaatactatccattcaattaaaatgaaccttggtcgcgcaatagagaatagcttcagttttccccaataataaatactcataagcgtctccgattattgcctaccgatacttttcgctctcaaggtatctaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctcttctccttaaataaaccaaattccttttttctagcaattattttttcaaaacaaagaataccgtctgcctactttttcaaaatctgacaaatactatccattcaattaaaatgaaccttggtcgcgcaatagagaatagcttcagttttccccaataataaatactcataagcgtctccgattattgcctaccgatacttttcgctctcaaggtatctaaca Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 84 End: 173 ................................................................................... F R V F V I W E I L I F R P R A I S F L K L K G W Y Y I S M ..................................................... gctcttctccttaaataaaccaaattccttttttctagcaattattttttcaaaacaaagaataccgtctgcctactttttcaaaatctgacaaatactatccattcaattaaaatgaaccttggtcgcgcaatagagaatagcttcagttttccccaataataaatactcataagcgtctccgattattgcctaccgatacttttcgctctcaaggtatctaaca 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: 84 Start: 87 End: 116 ......................................................................................TCTGACAAATACTATCCATTCAATTAAAAT.............................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gctcttctccttaaataaaccaaattccttttttctagcaattattttttcaaaacaaagaataccgtctgcctactttttcaaaatctgacaaatactatccattcaattaaaatgaaccttggtcgcgcaatagagaatagcttcagttttccccaataataaatactcataagcgtctccgattattgcctaccgatacttttcgctctcaaggtatctaaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2175:SSA_2176|SSA_2175:SSA_2176:hypothetical protein:hypothetical protein:<-<-:2174133..2174358 226 gctcttctccttaaataaaccaaattccttttttctagcaattattttttcaaaacaaagaataccgtctgcctactttttcaaaatctgacaaatactatccattcaattaaaatgaaccttggtcgcgcaatagagaatagcttcagttttccccaataataaatactcataagcgtctccgattattgcctaccgatacttttcgctctcaaggtatctaaca Intra-Species Hit: Count: 1 Min: 1 Max: 226 Len: 226 Subject: NC_009009_SSA_2175_SSA_2176|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2174133,2174358]|226 HSP 1 e-value: 1.0E-125 bit: 448.0 Len: 226 Query Start:1 Query End:226 Subject Strand: POSITIVE Subject Start: 1 Subject End: 226 gctcttctccttaaataaaccaaattccttttttctagcaattattttttcaaaacaaagaataccgtctgcctactttttcaaaatctgacaaatactatccattcaattaaaatgaaccttggtcgcgcaatagagaatagcttcagttttccccaataataaatactcataagcgtctccgattattgcctaccgatacttttcgctctcaaggtatctaaca gctcttctccttaaataaaccaaattccttttttctagcaattattttttcaaaacaaagaataccgtctgcctactttttcaaaatctgacaaatactatccattcaattaaaatgaaccttggtcgcgcaatagagaatagcttcagttttccccaataataaatactcataagcgtctccgattattgcctaccgatacttttcgctctcaaggtatctaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUCUUCUCCUUAAAUAAACCAAAUUCCUUUUUUCUAGCAAUUAUUUUUUCAAAACAAAGAAUACCGUCUGCCUACUUUUUCAAAAUCUGACAAAUACUAUCCAUUCAAUUAAAAUGAACCUUGGUCGCGCAAUAGAGAAUAGCUUCAGUUUUCCCCAAUAAUAAAUACUCAUAAGCGUCUCCGAUUAUUGCCUACCGAUACUUUUCGCUCUCAAGGUAUCUAACA (((.(((((.........(((((.(((.((((..........((((((((......))))))))..(((....................)))...................)))).)))..))))).........))))).)))............(((((((....((.(....).)).....)))))))......((((((((........))))))))..... (-27.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUAGAUACCUUGAGAGCGAAAAGUAUCGGUAGGCAAUAAUCGGAGACGCUUAUGAGUAUUUAUUAUUGGGGAAAACUGAAGCUAUUCUCUAUUGCGCGACCAAGGUUCAUUUUAAUUGAAUGGAUAGUAUUUGUCAGAUUUUGAAAAAGUAGGCAGACGGUAUUCUUUGUUUUGAAAAAAUAAUUGCUAGAAAAAAGGAAUUUGGUUUAUUUAAGGAGAAGAGC ..((((...(((..(....((.((((((..((((((.......(....)))))))..)))))).)).)..)))....)))).(((.((((((.......(((((((.(((.((((........(((((.(.((((((....(((....)))..)))))).).))))).((((((.....))))))........)))).))).))))))).......)))))).))) (-41.65) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 811 140 91 231 182 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 326 218 171 79 20 NC_009009:SSA_0715|5end_DNA_uptake_protein,_putative_700726..700956_POSITIVE 321 159 116 46 3 NC_009009:SSA_1055|5end_Conserved_uncharacterized_protein_1070899..1071129_POSITIVE 308 220 176 145 96 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 297 219 174 190 140 NC_009009:SSA_1259|5end_Purine_nucleoside_phosphorylase,_putative_1285722..1285952_NEGATIVE 294 219 171 81 41 NC_009009:SSA_1607|5end_Formamidopyrimidine-DNA_glycosylase,_putative_1613255..1613485_NEGATIVE 294 147 120 176 148 NC_009009:SSA_1203|5end_hypothetical_protein_1226985..1227215_POSITIVE 287 219 172 192 138 NC_009009:SSA_0492|5end_NADH-dependent_flavin_oxidoreductase,_putative_491588..491818_POSITIVE 271 215 176 51 4 NC_009009:SSA_0199|5end_GTP_cyclohydrolase_I,_putative_198276..198506_POSITIVE 270 158 124 181 147 NC_009009:SSA_0759|5end_Acetylglutamate_kinase,_putative_741841..742071_POSITIVE 269 217 172 121 77 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 267 218 181 210 158 NC_009009:SSA_1704|5end_Conserved_uncharacterized_protein_1696401..1696631_NEGATIVE 267 219 175 67 30 NC_009009:SSA_0405|5end_Transcriptional_regulator,_XRE_family,_putative_401418..401648_POSITIVE 265 219 176 101 51 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 264 220 176 83 24 NC_009009:SSA_0553|5end_hypothetical_protein_548911..549141_POSITIVE 262 218 174 118 71 NC_009009:SSA_0916|5end_2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate_hydrolase,_putative_928085..928315_POSITIVE 261 103 63 138 99 NC_009009:SSA_0777|5end_Glycogen_biosynthesis_protein_GlgD,_putative_759430..759660_POSITIVE 257 198 168 160 125 NC_009009:SSA_0647|5end_hypothetical_protein_630998..631228_POSITIVE 255 170 121 210 149 NC_009009:SSA_2219|5end_UDP-glucose_4-epimerase,_putative_2220827..2221057_NEGATIVE 255 219 177 118 61 NC_009009:SSA_2214|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2,_putative_2215835..2216065_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 159 125 40 3 NC_009009:SSA_1054|3end_CBS_domain_protein,_putative_1070973..1071123_POSITIVE 308 220 176 145 96 NC_009009:SSA_0139|3end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134706..134856_POSITIVE 294 219 171 53 13 NC_009009:SSA_1608|3end_hypothetical_protein_1613283..1613433_NEGATIVE 291 218 174 146 110 NC_009009:SSA_1260|3end_Phosphopentomutase,_putative_1285752..1285902_NEGATIVE 289 155 117 56 19 NC_009009:SSA_0364|3end_Serine/threonine:Na+_symporter,_putative_355311..355461_NEGATIVE 287 219 172 137 83 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 274 198 155 149 108 NC_009009:SSA_1274|3end_hypothetical_protein_1295517..1295667_NEGATIVE 271 215 176 70 23 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 269 217 172 119 75 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 261 103 63 148 109 NC_009009:SSA_0776|3end_Glucose-1-phosphate_adenylyltransferase,_putative_759520..759670_POSITIVE 258 156 114 149 106 NC_009009:SSA_1047|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_1062845..1062995_POSITIVE 255 219 177 121 64 NC_009009:SSA_2215|3end_Oligosaccharide_repeat_unit_polymerase_Wzy,_putative_2215832..2215982_NEGATIVE 254 185 144 108 64 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 249 210 170 99 59 NC_009009:SSA_1186|3end_Acetyltransferase,_CysE/LacA/Lpx_A/NodL_family,_putative_1214656..1214806_NEGATIVE 247 208 175 151 113 NC_009009:SSA_1895|3end_Ribosome-binding_factor_A,_putative_1890815..1890965_NEGATIVE 247 215 171 119 67 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE 244 183 142 141 101 NC_009009:SSA_1245|3end_Transcriptional_regulator,_LysR_family,_putative_1269710..1269860_POSITIVE 242 195 153 68 20 NC_009009:SSA_1313|3end_hypothetical_protein_1329715..1329865_NEGATIVE 239 159 120 118 64 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 239 190 144 111 58 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE