Origin IGS: cgttttatgtttgcataaaagctaatagagtagtcccaactgcatcctctacgcgatttccagctccacgcgctctctaaaagatttcctgcaggtgatatgtctctagaaaacattatagcacgattggaaaaatttgcaagag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctcttgcaaatttttccaatcgtgctataatgttttctagagacatatcacctgcaggaaatcttttagagagcgcgtggagctggaaatcgcgtagaggatgcagttgggactactctattagcttttatgcaaacataaaacg Mask Tandem Repeat Region ================================================ cgttttatgtttgcataaaagctaatagagtagtcccaactgcatcctctacgcgatttccagctccacgcgctctctaaaagatttcctgcaggtgatatgtctctagaaaacattatagcacgattggaaaaatttgcaagag Find is-nt database================================================ Query_seq: SSA_1572:SSA_1573|SSA_1572:SSA_1573:hypothetical protein:hypothetical protein:<-<-:1575999..1576143 145 cgttttatgtttgcataaaagctaatagagtagtcccaactgcatcctctacgcgatttccagctccacgcgctctctaaaagatttcctgcaggtgatatgtctctagaaaacattatagcacgattggaaaaatttgcaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1572:SSA_1573|SSA_1572:SSA_1573:hypothetical protein:hypothetical protein:<-<-:1575999..1576143 145 cgttttatgtttgcataaaagctaatagagtagtcccaactgcatcctctacgcgatttccagctccacgcgctctctaaaagatttcctgcaggtgatatgtctctagaaaacattatagcacgattggaaaaatttgcaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1572:SSA_1573|SSA_1572:SSA_1573:hypothetical protein:hypothetical protein:<-<-:1575999..1576143 145 cgttttatgtttgcataaaagctaatagagtagtcccaactgcatcctctacgcgatttccagctccacgcgctctctaaaagatttcctgcaggtgatatgtctctagaaaacattatagcacgattggaaaaatttgcaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgttttatgtttgcataaaagctaatagagtagtcccaactgcatcctctacgcgatttccagctccacgcgctctctaaaagatttcctgcaggtgatatgtctctagaaaacattatagcacgattggaaaaatttgcaagag Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 40 End: 144 ....................................... M H P L R D F Q L H A L S K R F P A G D M S L E N I I A R L E K F A R . Protein_Len: 39 Strand: - Start: 3 End: 119 .. K I N A Y F S I S Y D W S C G R R S K W S W A S E L L N G A P S I D R S F M M .......................... cgttttatgtttgcataaaagctaatagagtagtcccaactgcatcctctacgcgatttccagctccacgcgctctctaaaagatttcctgcaggtgatatgtctctagaaaacattatagcacgattggaaaaatttgcaagag 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: 81 Start: 115 End: 144 ..................................................................................................................TCTTGCAAATTTTTCCAATCGTGCTATAAT. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgttttatgtttgcataaaagctaatagagtagtcccaactgcatcctctacgcgatttccagctccacgcgctctctaaaagatttcctgcaggtgatatgtctctagaaaacattatagcacgattggaaaaatttgcaagag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1572:SSA_1573|SSA_1572:SSA_1573:hypothetical protein:hypothetical protein:<-<-:1575999..1576143 145 cgttttatgtttgcataaaagctaatagagtagtcccaactgcatcctctacgcgatttccagctccacgcgctctctaaaagatttcctgcaggtgatatgtctctagaaaacattatagcacgattggaaaaatttgcaagag Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_009009_SSA_1572_SSA_1573|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1575999,1576143]|145 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 cgttttatgtttgcataaaagctaatagagtagtcccaactgcatcctctacgcgatttccagctccacgcgctctctaaaagatttcctgcaggtgatatgtctctagaaaacattatagcacgattggaaaaatttgcaagag cgttttatgtttgcataaaagctaatagagtagtcccaactgcatcctctacgcgatttccagctccacgcgctctctaaaagatttcctgcaggtgatatgtctctagaaaacattatagcacgattggaaaaatttgcaagag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUUUAUGUUUGCAUAAAAGCUAAUAGAGUAGUCCCAACUGCAUCCUCUACGCGAUUUCCAGCUCCACGCGCUCUCUAAAAGAUUUCCUGCAGGUGAUAUGUCUCUAGAAAACAUUAUAGCACGAUUGGAAAAAUUUGCAAGAG ..(((((((....))))))).........(((((....)))))...((((..(((((((((((.....((.(((.((((..((((..((....))......)))).)))).........))).)).)))))))...)))).)))) (-25.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUUGCAAAUUUUUCCAAUCGUGCUAUAAUGUUUUCUAGAGACAUAUCACCUGCAGGAAAUCUUUUAGAGAGCGCGUGGAGCUGGAAAUCGCGUAGAGGAUGCAGUUGGGACUACUCUAUUAGCUUUUAUGCAAACAUAAAACG (((((((.....((((((..((((((...(((((((...))))))).....(((.(((....))).)))..))))))......))))))..))).))))..((((...(((.(((......))))))...))))........... (-31.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1052 80 31 171 122 NC_009009:SSA_1572|5end_hypothetical_protein_1575908..1576138_NEGATIVE 363 109 61 58 10 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 352 79 33 58 20 NC_009009:SSA_1911|5end_Conserved_uncharacterized_protein_1903105..1903335_NEGATIVE 347 80 33 76 17 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 337 76 34 68 27 NC_009009:SSA_1432|5end_HflX_GTPase,_putative_1439901..1440131_NEGATIVE 332 109 62 49 9 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 332 78 32 45 1 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 326 65 21 225 171 NC_009009:SSA_1401|5end_Transcriptional_regulator_GntR_family_1413062..1413292_POSITIVE 326 66 24 40 4 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 320 79 31 218 170 NC_009009:SSA_1508|5end_ABC-type_lipopolysaccharide_transport_system,_permease_component,_putative_1513250..1513480_NEGATIVE 320 74 35 188 150 NC_009009:SSA_0533|5end_Glycerol_dehydratase_large_subunit_pduC,_putative_528970..529200_POSITIVE 320 79 32 198 148 NC_009009:SSA_0249|5end_hypothetical_protein_241751..241981_POSITIVE 314 75 33 214 166 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 311 75 33 49 6 NC_009009:SSA_0199|5end_GTP_cyclohydrolase_I,_putative_198276..198506_POSITIVE 310 110 61 162 93 NC_009009:SSA_0895|5end_ATP-binding_cassette_transporter-like_protein,_putative_886466..886696_POSITIVE 303 90 42 69 28 NC_009009:SSA_1410|5end_DTDP-4-keto-6-deoxyglucose-3,5-epimerase,_putative_1423086..1423316_NEGATIVE 303 107 63 205 161 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 298 96 52 197 148 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 297 78 31 67 13 NC_009009:SSA_0483|5end_Siroheme_synthase,_putative_484045..484275_POSITIVE 296 107 63 54 1 NC_009009:SSA_1165|5end_Transcriptional_regulator,_GntR_family,_putative_1191087..1191317_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 97 54 139 99 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 379 97 59 136 95 NC_009009:SSA_0046|3end_Adenylosuccinate_lyase,_putative_52269..52419_POSITIVE 369 76 31 150 99 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 352 79 33 50 12 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 347 80 33 83 24 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 326 66 24 53 17 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 321 76 40 36 2 NC_009009:SSA_1433|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase,_putative_1439933..1440083_NEGATIVE 311 75 33 68 25 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 310 110 61 149 80 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 303 90 42 64 23 NC_009009:SSA_1411|3end_Glucose-1-phosphate_thymidylytransferase,_putative_1423091..1423241_NEGATIVE 297 78 31 55 1 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 292 80 33 68 3 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 291 76 31 125 71 NC_009009:SSA_0582|3end_Methylase,_putative_574583..574733_POSITIVE 288 78 36 151 111 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 287 97 52 133 83 NC_009009:SSA_1423|3end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1431561..1431711_NEGATIVE 284 79 33 151 110 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 280 109 61 134 80 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 279 92 53 82 41 NC_009009:SSA_0379|3end_PTS_system,_beta-glucoside-specific_EII_component,_putative_370833..370983_POSITIVE 278 70 21 71 10 NC_009009:SSA_0733|3end_hypothetical_protein_716937..717087_POSITIVE 278 68 21 101 53 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE