Origin IGS: tgtggcgtgaactaagtaacaaatacaaatattttttaggtagttgagtatataagtttgccaaaaataatgacaaagattttatatgacaatgccaagatattatgctattatattagaaaagaactatgaaaaagcgttataatggaggtatatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatatacctccattataacgctttttcatagttcttttctaatataatagcataatatcttggcattgtcatataaaatctttgtcattatttttggcaaacttatatactcaactacctaaaaaatatttgtatttgttacttagttcacgccaca Mask Tandem Repeat Region ================================================ tgtggcgtgaactaagtaacaaatacaaatattttttaggtagttgagtatataagtttgccaaaaataatgacaaagattttatatgacaatgccaagatattatgctattatattagaaaagaactatgaaaaagcgttataatggaggtatatta Find is-nt database================================================ Query_seq: SSA_0948:SSA_0949|SSA_0948:SSA_0949:hypothetical protein:hypothetical protein:->->:955689..955846 158 tgtggcgtgaactaagtaacaaatacaaatattttttaggtagttgagtatataagtttgccaaaaataatgacaaagattttatatgacaatgccaagatattatgctattatattagaaaagaactatgaaaaagcgttataatggaggtatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0948:SSA_0949|SSA_0948:SSA_0949:hypothetical protein:hypothetical protein:->->:955689..955846 158 tgtggcgtgaactaagtaacaaatacaaatattttttaggtagttgagtatataagtttgccaaaaataatgacaaagattttatatgacaatgccaagatattatgctattatattagaaaagaactatgaaaaagcgttataatggaggtatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0948:SSA_0949|SSA_0948:SSA_0949:hypothetical protein:hypothetical protein:->->:955689..955846 158 tgtggcgtgaactaagtaacaaatacaaatattttttaggtagttgagtatataagtttgccaaaaataatgacaaagattttatatgacaatgccaagatattatgctattatattagaaaagaactatgaaaaagcgttataatggaggtatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtggcgtgaactaagtaacaaatacaaatattttttaggtagttgagtatataagtttgccaaaaataatgacaaagattttatatgacaatgccaagatattatgctattatattagaaaagaactatgaaaaagcgttataatggaggtatatta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 2 End: 106 . H R S S L L L Y L Y K K P L Q T Y L N A L F L S L S K I H C H W S I M .................................................... tgtggcgtgaactaagtaacaaatacaaatattttttaggtagttgagtatataagtttgccaaaaataatgacaaagattttatatgacaatgccaagatattatgctattatattagaaaagaactatgaaaaagcgttataatggaggtatatta 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: 83 Start: 64 End: 93 ...............................................................ATTGTCATATAAAATCTTTGTCATTATTTT................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 85 End: 114 ....................................................................................TATGACAATGCCAAGATATTATGCTATTAT............................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgtggcgtgaactaagtaacaaatacaaatattttttaggtagttgagtatataagtttgccaaaaataatgacaaagattttatatgacaatgccaagatattatgctattatattagaaaagaactatgaaaaagcgttataatggaggtatatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0948:SSA_0949|SSA_0948:SSA_0949:hypothetical protein:hypothetical protein:->->:955689..955846 158 tgtggcgtgaactaagtaacaaatacaaatattttttaggtagttgagtatataagtttgccaaaaataatgacaaagattttatatgacaatgccaagatattatgctattatattagaaaagaactatgaaaaagcgttataatggaggtatatta Intra-Species Hit: Count: 2 Min: 1 Max: 158 Len: 158 Subject: NC_009009_SSA_0948_SSA_0949|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[955689,955846]|158 HSP 1 e-value: 9.0E-85 bit: 313.0 Len: 158 Query Start:1 Query End:158 Subject Strand: POSITIVE Subject Start: 1 Subject End: 158 tgtggcgtgaactaagtaacaaatacaaatattttttaggtagttgagtatataagtttgccaaaaataatgacaaagattttatatgacaatgccaagatattatgctattatattagaaaagaactatgaaaaagcgttataatggaggtatatta tgtggcgtgaactaagtaacaaatacaaatattttttaggtagttgagtatataagtttgccaaaaataatgacaaagattttatatgacaatgccaagatattatgctattatattagaaaagaactatgaaaaagcgttataatggaggtatatta Subject: NC_009009_SSA_0947_SSA_0948|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[954937,955094]|158 HSP 1 e-value: 2.0E-49 bit: 196.0 Len: 158 Query Start:1 Query End:158 Subject Strand: POSITIVE Subject Start: 1 Subject End: 158 tgtggcgtgaactaagtaacaaatacaaatatttt-ttaggtagttgagtatataagtttgccaaaaataatgacaaagattttatatgacaatgccaagatattatgctattatattagaaaagaactatgaaaaagcgttataatggaggtatatta tgtggcgtgaactaagcgacaaatacaactattttcttaggtagttgaggatagaagtttgctaaaaataatga-aaagattttatatgacaatactaaggtattatgctattctattagaaaagaactatgaaaacgcgttataatggaggtatatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUGGCGUGAACUAAGUAACAAAUACAAAUAUUUUUUAGGUAGUUGAGUAUAUAAGUUUGCCAAAAAUAAUGACAAAGAUUUUAUAUGACAAUGCCAAGAUAUUAUGCUAUUAUAUUAGAAAAGAACUAUGAAAAAGCGUUAUAAUGGAGGUAUAUUA ..((((((.(((((..(((.(((((....))))).)))..)))))...((((((((((((.((.......)).))))...))))))))...)))))).(((((....((((((((.........................))))))))....))))). (-22.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUACCUCCAUUAUAACGCUUUUUCAUAGUUCUUUUCUAAUAUAAUAGCAUAAUAUCUUGGCAUUGUCAUAUAAAAUCUUUGUCAUUAUUUUUGGCAAACUUAUAUACUCAACUACCUAAAAAAUAUUUGUAUUUGUUACUUAGUUCACGCCACA ....................(((......(((.......))).......))).........((((...((.((((((....(((((((.......))))))).))))))))..(((((..(((.(((((....))))).)))..)))))...)))).. (-19.92) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 110 69 188 151 NC_009009:SSA_0291|5end_Oxidoreductase,_putative_285362..285592_POSITIVE 234 140 91 71 15 NC_009009:SSA_1696|5end_Tagatose_1,6-diphosphate_aldolase_2,_putative_1689187..1689417_NEGATIVE 203 80 38 177 128 NC_009009:SSA_0057|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_60762..60992_POSITIVE 202 60 16 73 27 NC_009009:SSA_0995|5end_Antibiotic-resistance_protein,_alpha/beta_superfamily_hydrolase,_putative_995716..995946_POSITIVE 197 109 81 167 140 NC_009009:SSA_0822|5end_Large_conductance_mechano-sensitive_ion_channel,_putative_801972..802202_NEGATIVE 193 62 37 40 12 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 193 126 81 124 68 NC_009009:SSA_0353|5end_Conserved_uncharacterized_protein_345940..346170_POSITIVE 185 47 1 201 157 NC_009009:SSA_2079|5end_Acetyltransferase,_putative_2083971..2084201_POSITIVE 182 75 40 199 167 NC_009009:SSA_0904|5end_CshA-like_fibrillar_surface_protein_A_893906..894136_POSITIVE 181 110 71 160 122 NC_009009:SSA_2279|5end_hypothetical_protein_2281910..2282140_NEGATIVE 175 64 37 57 32 NC_009009:SSA_1727|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713420..1713650_NEGATIVE 175 91 55 90 54 NC_009009:SSA_1180|5end_hypothetical_protein_1208559..1208789_NEGATIVE 174 110 67 70 30 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 173 48 1 132 76 NC_009009:SSA_0417|5end_5,10-methylenetetrahydrofolate_reductase,_putative_414280..414510_POSITIVE 173 109 67 206 161 NC_009009:SSA_0013|5end_Cell_cycle_control_ATPase,_PP-loop_superfamily,_putative_11196..11426_POSITIVE 172 75 38 68 22 NC_009009:SSA_2360|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase,_putative_2363779..2364009_NEGATIVE 172 150 106 141 103 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 171 111 79 150 115 NC_009009:SSA_1377|5end_Asparaginyl-tRNA_synthetase,_putative_1397614..1397844_NEGATIVE 170 47 1 48 2 NC_009009:SSA_2187|5end_Conserved_hypothetical_membrane_associated_protein_2188026..2188256_POSITIVE 168 88 43 88 44 NC_009009:SSA_0012|5end_Beta-lactamase_class_A,_putative_9916..10146_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 234 140 91 67 11 NC_009009:SSA_1697|3end_Tagatose-6-phosphate_kinase,_putative_1689191..1689341_NEGATIVE 193 62 37 50 22 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 175 64 37 53 28 NC_009009:SSA_1728|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713424..1713574_NEGATIVE 175 91 55 57 21 NC_009009:SSA_1181|3end_Hydrolase,_alpha/beta_superfamily,_putative_1208592..1208742_NEGATIVE 174 110 67 68 28 NC_009009:SSA_2167|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165644..2165794_NEGATIVE 172 150 106 130 92 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 171 111 79 128 93 NC_009009:SSA_1378|3end_hypothetical_protein_1397636..1397786_NEGATIVE 170 139 94 89 50 NC_009009:SSA_0884|3end_hypothetical_protein_878725..878875_NEGATIVE 170 63 32 128 101 NC_009009:SSA_0631|3end_Tryptophan_synthase_beta_chain,_putative_621133..621283_POSITIVE 168 88 43 95 51 NC_009009:SSA_0011|3end_hypothetical_protein_10003..10153_POSITIVE 166 102 72 51 16 NC_009009:SSA_1048|3end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1064184..1064334_POSITIVE 165 93 55 79 49 NC_009009:SSA_2013|3end_hypothetical_protein_2013470..2013620_NEGATIVE 165 142 104 37 7 NC_009009:SSA_1392|3end_hypothetical_protein_1406792..1406942_NEGATIVE 164 75 37 63 28 NC_009009:SSA_0052|3end_Transcriptional_regulator,_GntR_family,_putative_55942..56092_NEGATIVE 162 110 87 119 102 NC_009009:SSA_0540|3end_Glycerol_uptake_facilitator_protein,_putative_535748..535898_POSITIVE 159 110 80 135 112 NC_009009:SSA_1064|3end_hypothetical_protein_1080325..1080475_NEGATIVE 158 100 51 103 41 NC_009009:SSA_0035|3end_Bifunctional_purine_biosynthesis_protein_purH,_putative_41957..42107_POSITIVE 157 62 38 141 104 NC_009009:SSA_2344|3end_hypothetical_protein_2346766..2346916_POSITIVE 157 49 2 115 58 NC_009009:SSA_1212|3end_Ribose-phosphate_pyrophosphokinase_2,_putative_1236437..1236587_POSITIVE 156 75 31 132 93 NC_009009:SSA_0276|3end_Glycosyltransferase,_family_2/glycosyltransferase_family_8,_putative_270667..270817_POSITIVE