Origin IGS: ggctgcttccctaagacaagcaaaaactataacaagaatgataattcattctcggattatacaaaagaaacaggtcttctacctaactatggtatagaaaacctgtttctttttttcaattttttagttcattatctctgaatggtcgatagctcgcctccacaagattggagattaaaggaaaagaaataatgttttttcttgatatgccaatatatctgattcctctcaagctcctgacag .........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 ctgtcaggagcttgagaggaatcagatatattggcatatcaagaaaaaacattatttcttttcctttaatctccaatcttgtggaggcgagctatcgaccattcagagataatgaactaaaaaattgaaaaaaagaaacaggttttctataccatagttaggtagaagacctgtttcttttgtataatccgagaatgaattatcattcttgttatagtttttgcttgtcttagggaagcagcc Mask Tandem Repeat Region ================================================ ggctgcttccctaagacaagcaaaaactataacaagaatgataattcattctcggattatacaaaagaaacaggtcttctacctaactatggtatagaaaacctgtttctttttttcaattttttagttcattatctctgaatggtcgatagctcgcctccacaagattggagattaaaggaaaagaaataatgttttttcttgatatgccaatatatctgattcctctcaagctcctgacag Find is-nt database================================================ Query_seq: SSA_1971:SSA_1972|SSA_1971:SSA_1972:hypothetical protein:Two-component system transcriptional regulator (CheY domain and HTH-like DNA-binding domain), putative:-><-:1967658..1967900 243 ggctgcttccctaagacaagcaaaaactataacaagaatgataattcattctcggattatacaaaagaaacaggtcttctacctaactatggtatagaaaacctgtttctttttttcaattttttagttcattatctctgaatggtcgatagctcgcctccacaagattggagattaaaggaaaagaaataatgttttttcttgatatgccaatatatctgattcctctcaagctcctgacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1971:SSA_1972|SSA_1971:SSA_1972:hypothetical protein:Two-component system transcriptional regulator (CheY domain and HTH-like DNA-binding domain), putative:-><-:1967658..1967900 243 ggctgcttccctaagacaagcaaaaactataacaagaatgataattcattctcggattatacaaaagaaacaggtcttctacctaactatggtatagaaaacctgtttctttttttcaattttttagttcattatctctgaatggtcgatagctcgcctccacaagattggagattaaaggaaaagaaataatgttttttcttgatatgccaatatatctgattcctctcaagctcctgacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1971:SSA_1972|SSA_1971:SSA_1972:hypothetical protein:Two-component system transcriptional regulator (CheY domain and HTH-like DNA-binding domain), putative:-><-:1967658..1967900 243 ggctgcttccctaagacaagcaaaaactataacaagaatgataattcattctcggattatacaaaagaaacaggtcttctacctaactatggtatagaaaacctgtttctttttttcaattttttagttcattatctctgaatggtcgatagctcgcctccacaagattggagattaaaggaaaagaaataatgttttttcttgatatgccaatatatctgattcctctcaagctcctgacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggctgcttccctaagacaagcaaaaactataacaagaatgataattcattctcggattatacaaaagaaacaggtcttctacctaactatggtatagaaaacctgtttctttttttcaattttttagttcattatctctgaatggtcgatagctcgcctccacaagattggagattaaaggaaaagaaataatgttttttcttgatatgccaatatatctgattcctctcaagctcctgacag Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 119 End: 232 ...................................................................................................................... N K L E N D R F P R Y S A E V L N S I L P F S I I N K R S I G I Y R I G R M ........... ggctgcttccctaagacaagcaaaaactataacaagaatgataattcattctcggattatacaaaagaaacaggtcttctacctaactatggtatagaaaacctgtttctttttttcaattttttagttcattatctctgaatggtcgatagctcgcctccacaagattggagattaaaggaaaagaaataatgttttttcttgatatgccaatatatctgattcctctcaagctcctgacag 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================================================ ggctgcttccctaagacaagcaaaaactataacaagaatgataattcattctcggattatacaaaagaaacaggtcttctacctaactatggtatagaaaacctgtttctttttttcaattttttagttcattatctctgaatggtcgatagctcgcctccacaagattggagattaaaggaaaagaaataatgttttttcttgatatgccaatatatctgattcctctcaagctcctgacag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -8.1 Tail_Score: -3.78015 Start: 33 End: 54 Full_Region: ttcttttgtataatc cgagaatga atta tcattcttg ttatagtttttgctt ................................cgagaatgaattatcattcttg............................................................................................................................................................................................. TransTerm Strand: + Conf: 93 HP_score: -6.5 Tail_Score: -5.63857 Start: 67 End: 109 Full_Region: TCGGATTATACAAAA GAAACAGGTCTTCTACCTA ACTA TGGTATAGAAAACCTGTTTC TTTTTTTCAATTTTT ..................................................................GAAACAGGTCTTCTACCTAACTATGGTATAGAAAACCTGTTTC...................................................................................................................................... TransTerm Strand: - Conf: 89 HP_score: -8.7 Tail_Score: -4.57353 Start: 67 End: 109 Full_Region: aaaaattgaaaaaaa gaaacaggttttctatacca tagt taggtagaagacctgtttc ttttgtataatccga ..................................................................gaaacaggttttctataccatagttaggtagaagacctgtttc...................................................................................................................................... Find igs database================================================ Query_seq: SSA_1971:SSA_1972|SSA_1971:SSA_1972:hypothetical protein:Two-component system transcriptional regulator (CheY domain and HTH-like DNA-binding domain), putative:-><-:1967658..1967900 243 ggctgcttccctaagacaagcaaaaactataacaagaatgataattcattctcggattatacaaaagaaacaggtcttctacctaactatggtatagaaaacctgtttctttttttcaattttttagttcattatctctgaatggtcgatagctcgcctccacaagattggagattaaaggaaaagaaataatgttttttcttgatatgccaatatatctgattcctctcaagctcctgacag Intra-Species Hit: Count: 1 Min: 1 Max: 243 Len: 243 Subject: NC_009009_SSA_1971_SSA_1972|hypothetical protein:Two-component system transcriptional regulator (CheY domain and HTH-like DNA-binding domain), putative|POSITIVE:NEGATIVE|[1967658,1967900]|243 HSP 1 e-value: 1.0E-60 bit: 234.0 Len: 118 Query Start:126 Query End:243 Subject Strand: POSITIVE Subject Start: 126 Subject End: 243 .............................................................................................................................agttcattatctctgaatggtcgatagctcgcctccacaagattggagattaaaggaaaagaaataatgttttttcttgatatgccaatatatctgattcctctcaagctcctgacag .............................................................................................................................agttcattatctctgaatggtcgatagctcgcctccacaagattggagattaaaggaaaagaaataatgttttttcttgatatgccaatatatctgattcctctcaagctcctgacag HSP 2 e-value: 3.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 ggctgcttccctaagacaagcaaaaactataacaagaatgataattcattctcggattatacaaaagaaacaggtcttctacctaactatggtatagaaaacctgtttc...................................................................................................................................... ggctgcttccctaagacaagcaaaaactataacaagaatgataattcattctcggattatacaaaagaaacaggtcttctacctaactatggtatagaaaacctgtttc...................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCUGCUUCCCUAAGACAAGCAAAAACUAUAACAAGAAUGAUAAUUCAUUCUCGGAUUAUACAAAAGAAACAGGUCUUCUACCUAACUAUGGUAUAGAAAACCUGUUUCUUUUUUUCAAUUUUUUAGUUCAUUAUCUCUGAAUGGUCGAUAGCUCGCCUCCACAAGAUUGGAGAUUAAAGGAAAAGAAAUAAUGUUUUUUCUUGAUAUGCCAAUAUAUCUGAUUCCUCUCAAGCUCCUGACAG .(((.(((....)))...)))...(((((...(.(((((((....))))))).)........(((((((((((((.(((((((.......)))..)))).)))))))))))))...........)))))...............((((..((((...(((((......))))).....(((((((((((........))))))((((((....))))))...)))))....))))..)))).. (-58.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUCAGGAGCUUGAGAGGAAUCAGAUAUAUUGGCAUAUCAAGAAAAAACAUUAUUUCUUUUCCUUUAAUCUCCAAUCUUGUGGAGGCGAGCUAUCGACCAUUCAGAGAUAAUGAACUAAAAAAUUGAAAAAAAGAAACAGGUUUUCUAUACCAUAGUUAGGUAGAAGACCUGUUUCUUUUGUAUAAUCCGAGAAUGAAUUAUCAUUCUUGUUAUAGUUUUUGCUUGUCUUAGGGAAGCAGCC ((((..((((....(((((((...(((((......))))).(((((........))))).)))))))...))))..((((...(((((((((.........((((.......))))...((((((((...((((((((((((((((((..(((.......)))))))))))))))))))))........(((((((((....)))))))))...))))))))))))))))).)))).)))).. (-73.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 173 136 60 22 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 305 187 143 125 77 NC_009009:SSA_1554|5end_hypothetical_protein_1555949..1556179_POSITIVE 286 174 140 144 108 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 282 171 134 109 72 NC_009009:SSA_1378|5end_hypothetical_protein_1397998..1398228_NEGATIVE 282 162 136 36 5 NC_009009:SSA_0826|5end_hypothetical_protein_805098..805328_POSITIVE 279 239 199 208 167 NC_009009:SSA_0897|5end_Two_component_system_histidine_kinase,_putative_888358..888588_POSITIVE 278 169 136 113 80 NC_009009:SSA_2009|5end_Heat_shock_transcription_repressor_HrcA,_putative_2011132..2011362_NEGATIVE 278 167 124 47 3 NC_009009:SSA_1262|5end_tRNA_modification_GTPase,_possibly_iron-binding,_putative_1287782..1288012_POSITIVE 278 162 123 54 7 NC_009009:SSA_0865|5end_hypothetical_protein_856378..856608_POSITIVE 275 150 102 133 92 NC_009009:SSA_1041|5end_Sugar_ABC_transporter,_permease_protein,_putative_1056398..1056628_POSITIVE 275 167 121 107 55 NC_009009:SSA_0427|5end_DNA-binding_transcriptional_activator,_SARP_family,_putative_424497..424727_POSITIVE 271 148 104 113 59 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 271 173 136 73 22 NC_009009:SSA_0591|5end_Conserved_uncharacterized_protein_582769..582999_POSITIVE 270 158 126 51 9 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 268 239 191 148 96 NC_009009:SSA_2231|5end_Heme/copper-type_cytochrome/quinol_oxidases,_subunit_1,_putative_2232928..2233158_NEGATIVE 268 170 138 71 37 NC_009009:SSA_1953|5end_NifU_family_protein,_putative_1950079..1950309_NEGATIVE 267 183 142 63 9 NC_009009:SSA_1040|5end_Sugar_ABC_transporter,_permease_protein,_putative_1055302..1055532_POSITIVE 264 175 136 46 8 NC_009009:SSA_0698|5end_Peptide_chain_release_factor_3,_putative_680383..680613_POSITIVE 264 171 135 142 98 NC_009009:SSA_0482|5end_ATP:cobalamin_adenosyl_transferase,_putative_483458..483688_POSITIVE 263 172 135 199 150 NC_009009:SSA_1801|5end_hypothetical_protein_1783314..1783544_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 187 143 128 80 NC_009009:SSA_1553|3end_Permease,_putative_1556032..1556182_POSITIVE 286 174 140 79 43 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 275 150 102 131 90 NC_009009:SSA_1040|3end_Sugar_ABC_transporter,_permease_protein,_putative_1056476..1056626_POSITIVE 270 239 201 68 20 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 268 239 191 109 57 NC_009009:SSA_2233|3end_hypothetical_protein_2232967..2233117_NEGATIVE 268 170 138 84 50 NC_009009:SSA_1954|3end_Aminotransferase,_class-V,_putative_1950066..1950216_NEGATIVE 267 183 142 70 16 NC_009009:SSA_1039|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_1055389..1055539_POSITIVE 264 171 135 145 101 NC_009009:SSA_0481|3end_Cobyric_acid_synthase,_putative_483541..483691_POSITIVE 263 172 135 144 95 NC_009009:SSA_1802|3end_Snf2_family_protein,_putative_1783369..1783519_NEGATIVE 263 173 135 139 110 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 262 159 114 134 89 NC_009009:SSA_1719|3end_Conserved_uncharacterized_protein_1705924..1706074_NEGATIVE 258 37 1 89 54 NC_009009:SSA_2359|3end_Glucose_inhibited_division_protein_A,_putative_2360613..2360763_NEGATIVE 258 158 119 40 7 NC_009009:SSA_2282|3end_Phage_infection_protein,_putative_2282377..2282527_NEGATIVE 254 166 124 61 4 NC_009009:SSA_2130|3end_hypothetical_protein_2134020..2134170_POSITIVE 251 237 197 150 105 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 249 166 121 131 78 NC_009009:SSA_2222|3end_Tyrosine-protein_kinase_Wze,_putative_2223299..2223449_NEGATIVE 240 183 143 73 26 NC_009009:SSA_0896|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_888441..888591_POSITIVE 239 174 134 115 75 NC_009009:SSA_0838|3end_GtfB,_putative_826829..826979_POSITIVE 239 164 121 139 96 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 239 157 113 151 97 NC_009009:SSA_0332|3end_hypothetical_protein_326924..327074_POSITIVE