Origin IGS: atgtcctccagtttcgaatttctctaaactcgcccctgcatttcgtttttatcttaaatgaagtactagttctcacgaagctcgaactgcatcaatggtcctaaattcaactgagcctaataacttgtttctgcaaggaaattaaggaacgtagttctcgcatagctcgaactgcatcaatggccctaaattcaactacgcctaaaggcttgtttcattaagggccatagaaaaagcgggacacatagccccgctgcttc .........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 gaagcagcggggctatgtgtcccgctttttctatggcccttaatgaaacaagcctttaggcgtagttgaatttagggccattgatgcagttcgagctatgcgagaactacgttccttaatttccttgcagaaacaagttattaggctcagttgaatttaggaccattgatgcagttcgagcttcgtgagaactagtacttcatttaagataaaaacgaaatgcaggggcgagtttagagaaattcgaaactggaggacat Mask Tandem Repeat Region ================================================ atgtcctccagtttcgaatttctctaaactcgcccctgcatttcgtttttatcttaaatgaagtactagttctcacgaagctcgaactgcatcaatggtcctaaattcaactgagcctaataacttgtttctgcaaggaaattaaggaacgtagttctcgcatagctcgaactgcatcaatggccctaaattcaactacgcctaaaggcttgtttcattaagggccatagaaaaagcgggacacatagccccgctgcttc Find is-nt database================================================ Query_seq: SSA_1308:SSA_1309|SSA_1308:SSA_1309:hypothetical protein:RNA-binding protein (KH domain), putative:<-<-:1326909..1327168 260 atgtcctccagtttcgaatttctctaaactcgcccctgcatttcgtttttatcttaaatgaagtactagttctcacgaagctcgaactgcatcaatggtcctaaattcaactgagcctaataacttgtttctgcaaggaaattaaggaacgtagttctcgcatagctcgaactgcatcaatggccctaaattcaactacgcctaaaggcttgtttcattaagggccatagaaaaagcgggacacatagccccgctgcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1308:SSA_1309|SSA_1308:SSA_1309:hypothetical protein:RNA-binding protein (KH domain), putative:<-<-:1326909..1327168 260 atgtcctccagtttcgaatttctctaaactcgcccctgcatttcgtttttatcttaaatgaagtactagttctcacgaagctcgaactgcatcaatggtcctaaattcaactgagcctaataacttgtttctgcaaggaaattaaggaacgtagttctcgcatagctcgaactgcatcaatggccctaaattcaactacgcctaaaggcttgtttcattaagggccatagaaaaagcgggacacatagccccgctgcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1308:SSA_1309|SSA_1308:SSA_1309:hypothetical protein:RNA-binding protein (KH domain), putative:<-<-:1326909..1327168 260 atgtcctccagtttcgaatttctctaaactcgcccctgcatttcgtttttatcttaaatgaagtactagttctcacgaagctcgaactgcatcaatggtcctaaattcaactgagcctaataacttgtttctgcaaggaaattaaggaacgtagttctcgcatagctcgaactgcatcaatggccctaaattcaactacgcctaaaggcttgtttcattaagggccatagaaaaagcgggacacatagccccgctgcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgtcctccagtttcgaatttctctaaactcgcccctgcatttcgtttttatcttaaatgaagtactagttctcacgaagctcgaactgcatcaatggtcctaaattcaactgagcctaataacttgtttctgcaaggaaattaaggaacgtagttctcgcatagctcgaactgcatcaatggccctaaattcaactacgcctaaaggcttgtttcattaagggccatagaaaaagcgggacacatagccccgctgcttc Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 105 End: 218 ........................................................................................................ M Q L S L I T C F C K E I K E R S S R I A R T A S M A L N S T T P K G L F H .......................................... atgtcctccagtttcgaatttctctaaactcgcccctgcatttcgtttttatcttaaatgaagtactagttctcacgaagctcgaactgcatcaatggtcctaaattcaactgagcctaataacttgtttctgcaaggaaattaaggaacgtagttctcgcatagctcgaactgcatcaatggccctaaattcaactacgcctaaaggcttgtttcattaagggccatagaaaaagcgggacacatagccccgctgcttc 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================================================ atgtcctccagtttcgaatttctctaaactcgcccctgcatttcgtttttatcttaaatgaagtactagttctcacgaagctcgaactgcatcaatggtcctaaattcaactgagcctaataacttgtttctgcaaggaaattaaggaacgtagttctcgcatagctcgaactgcatcaatggccctaaattcaactacgcctaaaggcttgtttcattaagggccatagaaaaagcgggacacatagccccgctgcttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1308:SSA_1309|SSA_1308:SSA_1309:hypothetical protein:RNA-binding protein (KH domain), putative:<-<-:1326909..1327168 260 atgtcctccagtttcgaatttctctaaactcgcccctgcatttcgtttttatcttaaatgaagtactagttctcacgaagctcgaactgcatcaatggtcctaaattcaactgagcctaataacttgtttctgcaaggaaattaaggaacgtagttctcgcatagctcgaactgcatcaatggccctaaattcaactacgcctaaaggcttgtttcattaagggccatagaaaaagcgggacacatagccccgctgcttc Intra-Species Hit: Count: 1 Min: 1 Max: 260 Len: 260 Subject: NC_009009_SSA_1308_SSA_1309|hypothetical protein:RNA-binding protein (KH domain), putative|NEGATIVE:NEGATIVE|[1326909,1327168]|260 HSP 1 e-value: 1.0E-145 bit: 515.0 Len: 260 Query Start:1 Query End:260 Subject Strand: POSITIVE Subject Start: 1 Subject End: 260 atgtcctccagtttcgaatttctctaaactcgcccctgcatttcgtttttatcttaaatgaagtactagttctcacgaagctcgaactgcatcaatggtcctaaattcaactgagcctaataacttgtttctgcaaggaaattaaggaacgtagttctcgcatagctcgaactgcatcaatggccctaaattcaactacgcctaaaggcttgtttcattaagggccatagaaaaagcgggacacatagccccgctgcttc atgtcctccagtttcgaatttctctaaactcgcccctgcatttcgtttttatcttaaatgaagtactagttctcacgaagctcgaactgcatcaatggtcctaaattcaactgagcctaataacttgtttctgcaaggaaattaaggaacgtagttctcgcatagctcgaactgcatcaatggccctaaattcaactacgcctaaaggcttgtttcattaagggccatagaaaaagcgggacacatagccccgctgcttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUCCUCCAGUUUCGAAUUUCUCUAAACUCGCCCCUGCAUUUCGUUUUUAUCUUAAAUGAAGUACUAGUUCUCACGAAGCUCGAACUGCAUCAAUGGUCCUAAAUUCAACUGAGCCUAAUAACUUGUUUCUGCAAGGAAAUUAAGGAACGUAGUUCUCGCAUAGCUCGAACUGCAUCAAUGGCCCUAAAUUCAACUACGCCUAAAGGCUUGUUUCAUUAAGGGCCAUAGAAAAAGCGGGACACAUAGCCCCGCUGCUUC ...((((.(((((..((((((..(((.............(((((((((.......)))))))))..((((((...........))))))......)))....)))))))))))..........(((((....))))).......))))..(((((((..((...))..)))))))....((((((((.(((..(((...(((....)))..)))..))).)))))))).(((..((((((.(.....).))))))..))) (-66.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGCAGCGGGGCUAUGUGUCCCGCUUUUUCUAUGGCCCUUAAUGAAACAAGCCUUUAGGCGUAGUUGAAUUUAGGGCCAUUGAUGCAGUUCGAGCUAUGCGAGAACUACGUUCCUUAAUUUCCUUGCAGAAACAAGUUAUUAGGCUCAGUUGAAUUUAGGACCAUUGAUGCAGUUCGAGCUUCGUGAGAACUAGUACUUCAUUUAAGAUAAAAACGAAAUGCAGGGGCGAGUUUAGAGAAAUUCGAAACUGGAGGACAU ((((.((((((((.....)))))))).)))).((((((((.(((..(((..(((....)))...)))..))).))))))))..(((.(((((..((...))..))))).)))(((((.....(((((((........(((((.(((..((......))..).))...((((.(((...((.(((....)))))...))).))))...)))))........))))))).(((((((....)))))))......)))))... (-82.29) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 929 120 71 211 162 NC_009009:SSA_1308|5end_hypothetical_protein_1326818..1327048_NEGATIVE 362 210 165 189 142 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 322 257 213 158 109 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 314 249 201 58 6 NC_009009:SSA_1257|5end_hypothetical_protein_1283867..1284097_NEGATIVE 312 185 145 195 148 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 310 260 214 135 87 NC_009009:SSA_1643|5end_hypothetical_protein_1645269..1645499_NEGATIVE 299 130 87 54 6 NC_009009:SSA_2052|5end_Thioredoxin,_putative_2057507..2057737_NEGATIVE 299 228 181 161 85 NC_009009:SSA_1823|5end_hypothetical_protein_1812513..1812743_NEGATIVE 299 257 213 159 107 NC_009009:SSA_1647|5end_hypothetical_protein_1647169..1647399_NEGATIVE 298 43 2 223 175 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 297 249 201 62 13 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 293 201 163 38 5 NC_009009:SSA_1406|5end_Histone_acetyltransferase_HPA2,_putative_1420315..1420545_NEGATIVE 292 187 145 59 8 NC_009009:SSA_0272|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_266023..266253_POSITIVE 287 189 160 147 119 NC_009009:SSA_0075|5end_ABC_sugar_transporter,_permease_protein,_putative_78963..79193_POSITIVE 283 213 171 45 7 NC_009009:SSA_1356|5end_Helicase_subunit_of_the_DNA_excision_repair_complex,_subunit_B,_putative_1371915..1372145_NEGATIVE 282 215 171 209 140 NC_009009:SSA_1655|5end_hypothetical_protein_1651816..1652046_NEGATIVE 280 250 206 68 14 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 280 218 172 209 158 NC_009009:SSA_0488|5end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_488364..488594_POSITIVE 278 109 62 69 32 NC_009009:SSA_0438|5end_Single-strand_binding_protein,_putative_440615..440845_POSITIVE 277 197 153 59 15 NC_009009:SSA_1784|5end_Glutamate_racemase,_putative_1769897..1770127_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 239 200 40 1 NC_009009:SSA_2094|3end_Conserved_uncharacterized_protein_2097990..2098140_NEGATIVE 362 229 184 62 16 NC_009009:SSA_0042|3end_Amino_acid_recemase,_putative_48671..48821_POSITIVE 355 220 176 142 97 NC_009009:SSA_0040|3end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_47479..47629_POSITIVE 322 259 218 89 48 NC_009009:SSA_0917|3end_Cobalamin-independent_methionine_synthase_II,_putative_929087..929237_NEGATIVE 314 249 201 67 15 NC_009009:SSA_1258|3end_Purine_nucleoside_phosphorylase,_family_1,_putative_1283858..1284008_NEGATIVE 302 257 216 49 2 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 299 118 74 73 27 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 297 249 201 65 16 NC_009009:SSA_0977|3end_3-isopropylmalate_dehydrogenase,_putative_983819..983969_POSITIVE 290 48 3 143 94 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 287 189 160 79 51 NC_009009:SSA_0074|3end_ABC_transporter_substrate-binding_protein-sugar_transport,_putative_78975..79125_POSITIVE 285 230 183 56 2 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 283 117 72 53 1 NC_009009:SSA_1051|3end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1066808..1066958_POSITIVE 282 215 171 145 76 NC_009009:SSA_1656|3end_Nisin_resistance_protein,_putative_1651880..1652030_NEGATIVE 281 208 162 145 106 NC_009009:SSA_0768|3end_Ribonucleoside-diphosphate_reductase_2,_beta_subunit,_putative_748136..748286_NEGATIVE 281 257 216 78 27 NC_009009:SSA_0304|3end_Bacterial_cell_wall_degradation_(CHAP/LysM_domains),_putative_301888..302038_POSITIVE 278 109 62 57 20 NC_009009:SSA_0437|3end_30S_ribosomal_protein_S6,_putative_440683..440833_POSITIVE 276 259 229 108 78 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 276 230 183 82 38 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 273 198 152 127 71 NC_009009:SSA_0716|3end_Competence_protein,_putative_703710..703860_POSITIVE 272 48 2 129 89 NC_009009:SSA_1757|3end_hypothetical_protein_1745282..1745432_NEGATIVE