Origin IGS: atagtttcctttcttctattgaaaatatcgttttcactttcctacattcaccattttatcacttcttgtaaacactttcaagtattttgataagtttttgaaaagtcttgctttttttgacattttttgccaaaatagaggcatagaaagaaggttgtgacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggtcacaaccttctttctatgcctctattttggcaaaaaatgtcaaaaaaagcaagacttttcaaaaacttatcaaaatacttgaaagtgtttacaagaagtgataaaatggtgaatgtaggaaagtgaaaacgatattttcaatagaagaaaggaaactat Mask Tandem Repeat Region ================================================ atagtttcctttcttctattgaaaatatcgttttcactttcctacattcaccattttatcacttcttgtaaacactttcaagtattttgataagtttttgaaaagtcttgctttttttgacattttttgccaaaatagaggcatagaaagaaggttgtgacc Find is-nt database================================================ Query_seq: SSA_1576:SSA_1577|SSA_1576:SSA_1577:Catabolite control protein A, putative:Proline dipeptidase, putative:<-->:1580272..1580433 162 atagtttcctttcttctattgaaaatatcgttttcactttcctacattcaccattttatcacttcttgtaaacactttcaagtattttgataagtttttgaaaagtcttgctttttttgacattttttgccaaaatagaggcatagaaagaaggttgtgacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1576:SSA_1577|SSA_1576:SSA_1577:Catabolite control protein A, putative:Proline dipeptidase, putative:<-->:1580272..1580433 162 atagtttcctttcttctattgaaaatatcgttttcactttcctacattcaccattttatcacttcttgtaaacactttcaagtattttgataagtttttgaaaagtcttgctttttttgacattttttgccaaaatagaggcatagaaagaaggttgtgacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1576:SSA_1577|SSA_1576:SSA_1577:Catabolite control protein A, putative:Proline dipeptidase, putative:<-->:1580272..1580433 162 atagtttcctttcttctattgaaaatatcgttttcactttcctacattcaccattttatcacttcttgtaaacactttcaagtattttgataagtttttgaaaagtcttgctttttttgacattttttgccaaaatagaggcatagaaagaaggttgtgacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atagtttcctttcttctattgaaaatatcgttttcactttcctacattcaccattttatcacttcttgtaaacactttcaagtattttgataagtttttgaaaagtcttgctttttttgacattttttgccaaaatagaggcatagaaagaaggttgtgacc Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 53 End: 157 .................................................... M L S L L V N T F K Y F D K F L K S L A F F D I F C Q N R G I E R R L * ..... Protein_Len: 36 Strand: - Start: 37 End: 144 .................................... K G V N V M K D S R T F V K L Y K S L N K F L R A K K S M K Q W F L P M .................. atagtttcctttcttctattgaaaatatcgttttcactttcctacattcaccattttatcacttcttgtaaacactttcaagtattttgataagtttttgaaaagtcttgctttttttgacattttttgccaaaatagaggcatagaaagaaggttgtgacc 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: 53 End: 82 ....................................................CTTGAAAGTGTTTACAAGAAGTGATAAAAT................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 107 End: 136 ..........................................................................................................CTTGCTTTTTTTGACATTTTTTGCCAAAAT.......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atagtttcctttcttctattgaaaatatcgttttcactttcctacattcaccattttatcacttcttgtaaacactttcaagtattttgataagtttttgaaaagtcttgctttttttgacattttttgccaaaatagaggcatagaaagaaggttgtgacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1576:SSA_1577|SSA_1576:SSA_1577:Catabolite control protein A, putative:Proline dipeptidase, putative:<-->:1580272..1580433 162 atagtttcctttcttctattgaaaatatcgttttcactttcctacattcaccattttatcacttcttgtaaacactttcaagtattttgataagtttttgaaaagtcttgctttttttgacattttttgccaaaatagaggcatagaaagaaggttgtgacc Intra-Species Hit: Count: 1 Min: 1 Max: 162 Len: 162 Subject: NC_009009_SSA_1576_SSA_1577|Catabolite control protein A, putative:Proline dipeptidase, putative|NEGATIVE:POSITIVE|[1580272,1580433]|162 HSP 1 e-value: 1.0E-40 bit: 167.0 Len: 84 Query Start:1 Query End:84 Subject Strand: POSITIVE Subject Start: 1 Subject End: 84 atagtttcctttcttctattgaaaatatcgttttcactttcctacattcaccattttatcacttcttgtaaacactttcaagta.............................................................................. atagtttcctttcttctattgaaaatatcgttttcactttcctacattcaccattttatcacttcttgtaaacactttcaagta.............................................................................. HSP 2 e-value: 4.0E-10 bit: 65.9 Len: 33 Query Start:130 Query End:162 Subject Strand: POSITIVE Subject Start: 130 Subject End: 162 .................................................................................................................................ccaaaatagaggcatagaaagaaggttgtgacc .................................................................................................................................ccaaaatagaggcatagaaagaaggttgtgacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGUUUCCUUUCUUCUAUUGAAAAUAUCGUUUUCACUUUCCUACAUUCACCAUUUUAUCACUUCUUGUAAACACUUUCAAGUAUUUUGAUAAGUUUUUGAAAAGUCUUGCUUUUUUUGACAUUUUUUGCCAAAAUAGAGGCAUAGAAAGAAGGUUGUGACC ...(((.((((..(((((.(((((((...)))))))..........((((....(((((((...((((..........)))).....)))))))....))))..(((((.....(((((.((.....)).)))))..))))).)))))..))))....))). (-28.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUCACAACCUUCUUUCUAUGCCUCUAUUUUGGCAAAAAAUGUCAAAAAAAGCAAGACUUUUCAAAAACUUAUCAAAAUACUUGAAAGUGUUUACAAGAAGUGAUAAAAUGGUGAAUGUAGGAAAGUGAAAACGAUAUUUUCAAUAGAAGAAAGGAAACUAU ........((((..(((((((((........)))..((((((((.............((.((((.....(((((((((((((....)))))))........)))))).....))))...))....((....))))))))))..))))))..))))....... (-29.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 750 80 31 171 122 NC_009009:SSA_1576|5end_Catabolite_control_protein_A,_putative_1580181..1580411_NEGATIVE 268 130 86 222 185 NC_009009:SSA_1261|5end_Ribose-5-phosphate_isomerase_A,_putative_1287654..1287884_NEGATIVE 267 50 1 159 115 NC_009009:SSA_1961|5end_Amino_acid_ABC_transporter,_amino_acid-binding_protein/permease_protein,_putative_1958548..1958778_POSITIVE 264 140 97 141 91 NC_009009:SSA_0478|5end_Cobalt_transport_protein_cbiN,_putative_480002..480232_POSITIVE 260 144 106 199 161 NC_009009:SSA_1320|5end_hypothetical_protein_1337194..1337424_NEGATIVE 256 158 114 173 134 NC_009009:SSA_0544|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase,_putative_539819..540049_POSITIVE 254 108 62 221 157 NC_009009:SSA_2176|5end_hypothetical_protein_2175159..2175389_NEGATIVE 247 146 103 189 147 NC_009009:SSA_1544|5end_Conserved_uncharacterized_protein_1548796..1549026_NEGATIVE 246 142 104 131 86 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 241 149 107 223 167 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 239 147 104 207 157 NC_009009:SSA_0089|5end_V-type_sodium_ATPase,_subunit_F,_putative_89930..90160_POSITIVE 238 149 104 57 5 NC_009009:SSA_1262|5end_tRNA_modification_GTPase,_possibly_iron-binding,_putative_1287782..1288012_POSITIVE 236 160 111 195 148 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 234 54 14 144 99 NC_009009:SSA_1563|5end_Metal-dependent_hydrolase,_beta-lactamase_superfamily_I,_putative_1567256..1567486_NEGATIVE 234 66 22 123 75 NC_009009:SSA_0830|5end_Glycosyltransferase,_putative_812430..812660_POSITIVE 233 76 37 181 149 NC_009009:SSA_1806|5end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1790749..1790979_NEGATIVE 231 66 35 151 102 NC_009009:SSA_0094|5end_Cell_wall_metabolism,_LysM_type_protein,_putative_95345..95575_POSITIVE 229 160 117 167 122 NC_009009:SSA_0270|5end_Phosphotransferase_system_(PTS)_cellobiose-specific,_IIC_component,_putative_262873..263103_POSITIVE 227 148 104 215 162 NC_009009:SSA_2099|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2104313..2104543_NEGATIVE 226 150 106 153 97 NC_009009:SSA_1787|5end_Diaminopimelate_decarboxylase,_putative_1771551..1771781_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 140 97 144 94 NC_009009:SSA_0477|3end_Cobalamin_biosynthesis_protein_CbiM_(ABC-type_cobalt_transporter),_putative_480085..480235_POSITIVE 262 84 45 99 47 NC_009009:SSA_0195|3end_hypothetical_protein_195831..195981_POSITIVE 260 144 106 147 109 NC_009009:SSA_1321|3end_Ferrochelatase,_putative_1337246..1337396_NEGATIVE 257 158 111 76 12 NC_009009:SSA_2005|3end_Chaperone_protein_dnaJ,_putative_2005251..2005401_NEGATIVE 254 108 62 148 84 NC_009009:SSA_2177|3end_hypothetical_protein_2175232..2175382_NEGATIVE 246 142 104 138 93 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 240 157 114 151 113 NC_009009:SSA_0543|3end_SecA,_putative_539878..540028_POSITIVE 239 156 114 61 20 NC_009009:SSA_2108|3end_Glyceraldehyde_3-phosphate_dehydrogenase,_putative_2111457..2111607_NEGATIVE 234 54 14 134 89 NC_009009:SSA_1564|3end_Histidine_kinase,_putative_1567266..1567416_NEGATIVE 226 139 93 90 45 NC_009009:SSA_0157|3end_hypothetical_protein_153877..154027_POSITIVE 224 70 30 118 73 NC_009009:SSA_2299|3end_hypothetical_protein_2300655..2300805_NEGATIVE 224 117 73 92 45 NC_009009:SSA_1229|3end_hypothetical_protein_1252314..1252464_NEGATIVE 224 157 112 145 95 NC_009009:SSA_1023|3end_Von_Willebrand_factor-binding_protein_precursor,_putative_1041166..1041316_POSITIVE 223 46 1 118 81 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 220 50 1 106 42 NC_009009:SSA_1863|3end_NH(3)-dependent_NAD(+)_synthetase,_putative_1858589..1858739_NEGATIVE 219 146 101 122 66 NC_009009:SSA_1190|3end_Conserved_uncharacterized_protein_1217799..1217949_NEGATIVE 217 53 12 98 59 NC_009009:SSA_1380|3end_hypothetical_protein_1398538..1398688_NEGATIVE 215 146 105 57 1 NC_009009:SSA_0074|3end_ABC_transporter_substrate-binding_protein-sugar_transport,_putative_78975..79125_POSITIVE 213 160 111 63 5 NC_009009:SSA_1092|3end_Dihydrofolate_reductase,_putative_1110191..1110341_POSITIVE 209 140 94 133 82 NC_009009:SSA_1234|3end_5'-nucleotidase,_putative_1257636..1257786_NEGATIVE