Origin IGS: acatgctccttttcataaaacaattcgttccagcaactacaaggctactggaatcttatctaggggaggattttccataatctgtctgaaaaagaaaaatagctccctggaaacaggaagctctgacctctaaaagaggtgcccgaacagtatgatatcgcaaacctaaaaaaatgtcaaatgatttcattcggttt .........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 aaaccgaatgaaatcatttgacatttttttaggtttgcgatatcatactgttcgggcacctcttttagaggtcagagcttcctgtttccagggagctatttttctttttcagacagattatggaaaatcctcccctagataagattccagtagccttgtagttgctggaacgaattgttttatgaaaaggagcatgt Mask Tandem Repeat Region ================================================ acatgctccttttcataaaacaattcgttccagcaactacaaggctactggaatcttatctaggggaggattttccataatctgtctgaaaaagaaaaatagctccctggaaacaggaagctctgacctctaaaagaggtgcccgaacagtatgatatcgcaaacctaaaaaaatgtcaaatgatttcattcggttt Find is-nt database================================================ Query_seq: SSA_1994:SSA_1995|SSA_1994:SSA_1995:CTP synthase, putative:hypothetical protein:<-<-:1992565..1992761 197 acatgctccttttcataaaacaattcgttccagcaactacaaggctactggaatcttatctaggggaggattttccataatctgtctgaaaaagaaaaatagctccctggaaacaggaagctctgacctctaaaagaggtgcccgaacagtatgatatcgcaaacctaaaaaaatgtcaaatgatttcattcggttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1994:SSA_1995|SSA_1994:SSA_1995:CTP synthase, putative:hypothetical protein:<-<-:1992565..1992761 197 acatgctccttttcataaaacaattcgttccagcaactacaaggctactggaatcttatctaggggaggattttccataatctgtctgaaaaagaaaaatagctccctggaaacaggaagctctgacctctaaaagaggtgcccgaacagtatgatatcgcaaacctaaaaaaatgtcaaatgatttcattcggttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1994:SSA_1995|SSA_1994:SSA_1995:CTP synthase, putative:hypothetical protein:<-<-:1992565..1992761 197 acatgctccttttcataaaacaattcgttccagcaactacaaggctactggaatcttatctaggggaggattttccataatctgtctgaaaaagaaaaatagctccctggaaacaggaagctctgacctctaaaagaggtgcccgaacagtatgatatcgcaaacctaaaaaaatgtcaaatgatttcattcggttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acatgctccttttcataaaacaattcgttccagcaactacaaggctactggaatcttatctaggggaggattttccataatctgtctgaaaaagaaaaatagctccctggaaacaggaagctctgacctctaaaagaggtgcccgaacagtatgatatcgcaaacctaaaaaaatgtcaaatgatttcattcggttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 23 End: 130 ...................... M R S S N Y K A T G I L S R G G F S I I C L K K K N S S L E T G S S D L ................................................................... Protein_Len: 32 Strand: - Start: 63 End: 158 .............................................................. P L I K W L R D S F S F Y S G P F L F S Q G R F S T G S C Y S M ....................................... Protein_Len: 44 Strand: - Start: 59 End: 190 .......................................................... R P S S K G Y D T Q F L F I A G Q F C S A R V E L L P A R V T H Y R L G L F I D F S K M ....... acatgctccttttcataaaacaattcgttccagcaactacaaggctactggaatcttatctaggggaggattttccataatctgtctgaaaaagaaaaatagctccctggaaacaggaagctctgacctctaaaagaggtgcccgaacagtatgatatcgcaaacctaaaaaaatgtcaaatgatttcattcggttt 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: 92 Start: 152 End: 181 .......................................................................................................................................................TTTGACATTTTTTTAGGTTTGCGATATCAT................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acatgctccttttcataaaacaattcgttccagcaactacaaggctactggaatcttatctaggggaggattttccataatctgtctgaaaaagaaaaatagctccctggaaacaggaagctctgacctctaaaagaggtgcccgaacagtatgatatcgcaaacctaaaaaaatgtcaaatgatttcattcggttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -7.4 Tail_Score: -5.61881 Start: 100 End: 123 Full_Region: ctcttttagaggtca gagcttcctg tttc cagggagcta tttttctttttcaga ...................................................................................................gagcttcctgtttccagggagcta.......................................................................... TransTerm Strand: - Conf: 90 HP_score: -10.0 Tail_Score: -4.43511 Start: 102 End: 121 Full_Region: cttttagaggtcaga gcttcctg tttc cagggagc tatttttctttttca .....................................................................................................gcttcctgtttccagggagc............................................................................ Find igs database================================================ Query_seq: SSA_1994:SSA_1995|SSA_1994:SSA_1995:CTP synthase, putative:hypothetical protein:<-<-:1992565..1992761 197 acatgctccttttcataaaacaattcgttccagcaactacaaggctactggaatcttatctaggggaggattttccataatctgtctgaaaaagaaaaatagctccctggaaacaggaagctctgacctctaaaagaggtgcccgaacagtatgatatcgcaaacctaaaaaaatgtcaaatgatttcattcggttt Intra-Species Hit: Count: 1 Min: 1 Max: 197 Len: 197 Subject: NC_009009_SSA_1994_SSA_1995|CTP synthase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1992565,1992761]|197 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 197 Query Start:1 Query End:197 Subject Strand: POSITIVE Subject Start: 1 Subject End: 197 acatgctccttttcataaaacaattcgttccagcaactacaaggctactggaatcttatctaggggaggattttccataatctgtctgaaaaagaaaaatagctccctggaaacaggaagctctgacctctaaaagaggtgcccgaacagtatgatatcgcaaacctnnnnnnntgtcaaatgatttcattcggttt acatgctccttttcataaaacaattcgttccagcaactacaaggctactggaatcttatctaggggaggattttccataatctgtctgaaaaagaaaaatagctccctggaaacaggaagctctgacctctaaaagaggtgcccgaacagtatgatatcgcaaacctaaaaaaatgtcaaatgatttcattcggttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUGCUCCUUUUCAUAAAACAAUUCGUUCCAGCAACUACAAGGCUACUGGAAUCUUAUCUAGGGGAGGAUUUUCCAUAAUCUGUCUGAAAAAGAAAAAUAGCUCCCUGGAAACAGGAAGCUCUGACCUCUAAAAGAGGUGCCCGAACAGUAUGAUAUCGCAAACCUAAAAAAAUGUCAAAUGAUUUCAUUCGGUUU ..((.(((((((..((((........(((((((...((....))...))))))).))))..))))))).))....((((..((((.((............((((.((((....)))).))))...(((((.....)))))...)).)))))))).......(((((.........(((....))).......))))) (-43.69) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACCGAAUGAAAUCAUUUGACAUUUUUUUAGGUUUGCGAUAUCAUACUGUUCGGGCACCUCUUUUAGAGGUCAGAGCUUCCUGUUUCCAGGGAGCUAUUUUUCUUUUUCAGACAGAUUAUGGAAAAUCCUCCCCUAGAUAAGAUUCCAGUAGCCUUGUAGUUGCUGGAACGAAUUGUUUUAUGAAAAGGAGCAUGU ...((..(((((((.(((((...(((.((((((...(.(((.(((((((((..((..(((((.....)))))...(((((((((....)))))))))...........))..))))..)))))...))))...)))))).)))..(((((((((......))))))))).))))).))))))).....))....... (-55.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 949 70 21 161 112 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 322 141 102 225 187 NC_009009:SSA_1251|5end_Hydrolase,_HD_superfamily,_putative_1276790..1277020_NEGATIVE 316 146 106 225 181 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 311 145 101 65 23 NC_009009:SSA_0422|5end_Phosphoglycerate_mutase_family_protein,_putative_420157..420387_POSITIVE 308 66 21 153 102 NC_009009:SSA_1721|5end_DNA_polymerase_III,_delta'_subunit,_putative_1708028..1708258_NEGATIVE 308 68 21 53 11 NC_009009:SSA_0631|5end_Tryptophan_synthase_beta_chain,_putative_619872..620102_POSITIVE 306 155 115 79 37 NC_009009:SSA_1544|5end_Conserved_uncharacterized_protein_1548796..1549026_NEGATIVE 304 68 30 60 31 NC_009009:SSA_0189|5end_Competence_protein_ComGF,_putative_191015..191245_POSITIVE 299 150 104 60 9 NC_009009:SSA_0274|5end_hypothetical_protein_269557..269787_NEGATIVE 296 160 118 224 166 NC_009009:SSA_2235|5end_Conserved_uncharacterized_protein_2235450..2235680_NEGATIVE 291 167 121 101 53 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 289 141 102 59 21 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 287 69 23 65 3 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 287 143 102 202 150 NC_009009:SSA_1256|5end_NAD-dependent_deacetylase,_putative_1283094..1283324_NEGATIVE 287 69 26 170 125 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 286 147 102 211 171 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 281 144 102 142 96 NC_009009:SSA_1743|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1730170..1730400_POSITIVE 280 68 23 217 170 NC_009009:SSA_1487|5end_Conserved_uncharacterized_protein_1494190..1494420_NEGATIVE 280 150 101 225 171 NC_009009:SSA_0632|5end_Anthranilate_synthase_component_I,_putative_621458..621688_POSITIVE 279 149 105 75 18 NC_009009:SSA_0704|5end_Isocitrate_dehydrogenase_[NADP],_putative_689274..689504_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 145 101 68 26 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 306 155 115 63 21 NC_009009:SSA_1545|3end_Conserved_uncharacterized_protein_1548812..1548962_NEGATIVE 305 50 1 55 3 NC_009009:SSA_0631|3end_Tryptophan_synthase_beta_chain,_putative_621133..621283_POSITIVE 304 68 30 76 47 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 297 160 115 78 33 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 291 70 26 144 95 NC_009009:SSA_2293|3end_hypothetical_protein_2295955..2296105_POSITIVE 291 167 121 104 56 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 279 149 105 73 16 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 275 88 44 86 44 NC_009009:SSA_2022|3end_Transcriptional_regulator,_MerR_family_(multidrug-efflux_transporter_genes),_putative_2024488..2024638_POSITIVE 272 61 21 88 39 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 272 70 25 107 53 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 271 69 24 65 11 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 266 155 114 89 43 NC_009009:SSA_2367|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368845..2368995_NEGATIVE 264 69 22 142 101 NC_009009:SSA_1656|3end_Nisin_resistance_protein,_putative_1651880..1652030_NEGATIVE 262 146 101 42 9 NC_009009:SSA_1504|3end_hypothetical_protein_1506459..1506609_NEGATIVE 261 130 81 73 15 NC_009009:SSA_0210|3end_hypothetical_protein_208124..208274_POSITIVE 261 147 108 66 27 NC_009009:SSA_0209|3end_Glutamyl_aminopeptidase,_putative_206572..206722_NEGATIVE 260 156 115 51 7 NC_009009:SSA_1641|3end_MutT/nudix_family_protein,_putative_1642543..1642693_NEGATIVE 257 50 2 56 14 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 257 61 24 79 42 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE