Origin IGS: cggagcctccattatacaaatctaataggaaggggacaaaaagctgcaactttcctttttatctatactataccacatttttttcactttttgcctccttttacgaatgataagttaggaggatataaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttatatcctcctaacttatcattcgtaaaaggaggcaaaaagtgaaaaaaatgtggtatagtatagataaaaaggaaagttgcagctttttgtccccttcctattagatttgtataatggaggctccg Mask Tandem Repeat Region ================================================ cggagcctccattatacaaatctaataggaaggggacaaaaagctgcaactttcctttttatctatactataccacatttttttcactttttgcctccttttacgaatgataagttaggaggatataaa Find is-nt database================================================ Query_seq: SSA_0213:SSA_0214|SSA_0213:SSA_0214:hypothetical protein:Single-strand DNA-binding protein (conjugal DNA-protein transfer system), putative:<-->:210226..210354 129 cggagcctccattatacaaatctaataggaaggggacaaaaagctgcaactttcctttttatctatactataccacatttttttcactttttgcctccttttacgaatgataagttaggaggatataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0213:SSA_0214|SSA_0213:SSA_0214:hypothetical protein:Single-strand DNA-binding protein (conjugal DNA-protein transfer system), putative:<-->:210226..210354 129 cggagcctccattatacaaatctaataggaaggggacaaaaagctgcaactttcctttttatctatactataccacatttttttcactttttgcctccttttacgaatgataagttaggaggatataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0213:SSA_0214|SSA_0213:SSA_0214:hypothetical protein:Single-strand DNA-binding protein (conjugal DNA-protein transfer system), putative:<-->:210226..210354 129 cggagcctccattatacaaatctaataggaaggggacaaaaagctgcaactttcctttttatctatactataccacatttttttcactttttgcctccttttacgaatgataagttaggaggatataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cggagcctccattatacaaatctaataggaaggggacaaaaagctgcaactttcctttttatctatactataccacatttttttcactttttgcctccttttacgaatgataagttaggaggatataaa Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 25 End: 129 ........................ M G R G Q K A A T F L F I Y T I P H F F H F L P P F T N D K L G G Y K cggagcctccattatacaaatctaataggaaggggacaaaaagctgcaactttcctttttatctatactataccacatttttttcactttttgcctccttttacgaatgataagttaggaggatataaa 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: 85 Start: 11 End: 40 ..........TTTGTCCCCTTCCTATTAGATTTGTATAAT......................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cggagcctccattatacaaatctaataggaaggggacaaaaagctgcaactttcctttttatctatactataccacatttttttcactttttgcctccttttacgaatgataagttaggaggatataaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0213:SSA_0214|SSA_0213:SSA_0214:hypothetical protein:Single-strand DNA-binding protein (conjugal DNA-protein transfer system), putative:<-->:210226..210354 129 cggagcctccattatacaaatctaataggaaggggacaaaaagctgcaactttcctttttatctatactataccacatttttttcactttttgcctccttttacgaatgataagttaggaggatataaa Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_009009_SSA_0213_SSA_0214|hypothetical protein:Single-strand DNA-binding protein (conjugal DNA-protein transfer system), putative|NEGATIVE:POSITIVE|[210226,210354]|129 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 cggagcctccattatacaaatctaataggaaggggacaaaaagctgcaactttcctttttatctatactataccacannnnnnncactttttgcctccttttacgaatgataagttaggaggatataaa cggagcctccattatacaaatctaataggaaggggacaaaaagctgcaactttcctttttatctatactataccacatttttttcactttttgcctccttttacgaatgataagttaggaggatataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGAGCCUCCAUUAUACAAAUCUAAUAGGAAGGGGACAAAAAGCUGCAACUUUCCUUUUUAUCUAUACUAUACCACAUUUUUUUCACUUUUUGCCUCCUUUUACGAAUGAUAAGUUAGGAGGAUAUAAA .....(((((.....((..(((.....((((((((.(((((((.((......................................))))))))).))))))))......)))..))..)))))....... (-21.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUAUCCUCCUAACUUAUCAUUCGUAAAAGGAGGCAAAAAGUGAAAAAAAUGUGGUAUAGUAUAGAUAAAAAGGAAAGUUGCAGCUUUUUGUCCCCUUCCUAUUAGAUUUGUAUAAUGGAGGCUCCG .......(((((..((..(((........((((.((((((((((..((.........(((.......)))..........))...)))))))))).)))).......)))..)).....)))))..... (-23.07) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 917 50 1 141 92 NC_009009:SSA_0213|5end_hypothetical_protein_210135..210365_NEGATIVE 334 50 9 140 96 NC_009009:SSA_0864|5end_hypothetical_protein_856318..856548_NEGATIVE 288 48 1 173 126 NC_009009:SSA_1377|5end_Asparaginyl-tRNA_synthetase,_putative_1397614..1397844_NEGATIVE 273 99 52 140 84 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 269 80 32 60 7 NC_009009:SSA_2229|5end_hypothetical_protein_2228994..2229224_NEGATIVE 264 39 1 178 137 NC_009009:SSA_1772|5end_hypothetical_protein_1759545..1759775_NEGATIVE 261 99 53 116 63 NC_009009:SSA_0248|5end_hypothetical_protein_241360..241590_POSITIVE 258 55 17 165 125 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 250 120 73 123 78 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 250 119 75 198 152 NC_009009:SSA_0569|5end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563613..563843_POSITIVE 248 98 51 168 112 NC_009009:SSA_0510|5end_L-threonine-O-3-phosphate_decarboxylase,_putative_508523..508753_POSITIVE 248 33 5 230 202 NC_009009:SSA_0367|5end_hypothetical_protein_358309..358539_POSITIVE 247 118 84 129 88 NC_009009:SSA_1444|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1447267..1447497_NEGATIVE 244 36 3 146 115 NC_009009:SSA_0070|5end_Acetylxylan_esterase,_putative_73833..74063_POSITIVE 242 120 73 165 108 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 241 46 1 200 149 NC_009009:SSA_1279|5end_Oxidoreductase,_putative_1300832..1301062_NEGATIVE 239 118 78 131 78 NC_009009:SSA_1143|5end_Na+-driven_multidrug_efflux_pump,_putative_1173497..1173727_NEGATIVE 238 117 82 123 86 NC_009009:SSA_0969|5end_hypothetical_protein_977212..977442_POSITIVE 236 50 1 125 47 NC_009009:SSA_1914|5end_hypothetical_protein_1905195..1905425_NEGATIVE 236 69 22 119 66 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 48 1 151 104 NC_009009:SSA_1378|3end_hypothetical_protein_1397636..1397786_NEGATIVE 269 80 32 91 38 NC_009009:SSA_2230|3end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2228963..2229113_NEGATIVE 261 99 53 131 78 NC_009009:SSA_0247|3end_hypothetical_protein_241455..241605_POSITIVE 260 40 5 60 25 NC_009009:SSA_0366|3end_hypothetical_protein_358212..358362_POSITIVE 250 120 73 122 77 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 248 98 51 103 47 NC_009009:SSA_0509|3end_Propanediol_utilization_protein,_putative_508538..508688_POSITIVE 247 118 84 94 53 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 236 69 22 63 10 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 233 98 54 148 102 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 232 62 27 74 37 NC_009009:SSA_1752|3end_Phosphotransferase_system,_trehalose-specific_IIBC_component,_putative_1739812..1739962_NEGATIVE 229 64 23 90 40 NC_009009:SSA_1511|3end_Glycosyltransferase,_putative_1515450..1515600_NEGATIVE 227 70 25 120 55 NC_009009:SSA_0714|3end_hypothetical_protein_700649..700799_POSITIVE 223 90 43 55 12 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 221 112 71 136 81 NC_009009:SSA_1231|3end_hypothetical_protein_1253649..1253799_NEGATIVE 221 98 53 140 84 NC_009009:SSA_0624|3end_hypothetical_protein_615698..615848_POSITIVE 221 47 1 150 103 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 219 98 51 72 20 NC_009009:SSA_1244|3end_hypothetical_protein_1268465..1268615_NEGATIVE 218 61 23 62 26 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 216 79 31 138 78 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 215 88 42 79 29 NC_009009:SSA_1468|3end_3-dehydroquinate_synthase,_putative_1474385..1474535_NEGATIVE