Origin IGS: atttccctccgattcatttaataatttttaactcccttataaaacaaatgtcattataactttttgattttgaattgtaaatccttaaaataaatatatgagttatttctaaataggaaatactaataaatcccccagcagcctcctgctgggggatcgtcattagttcaaagcttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caagctttgaactaatgacgatcccccagcaggaggctgctgggggatttattagtatttcctatttagaaataactcatatatttattttaaggatttacaattcaaaatcaaaaagttataatgacatttgttttataagggagttaaaaattattaaatgaatcggagggaaat Mask Tandem Repeat Region ================================================ atttccctccgattcatttaataatttttaactcccttataaaacaaatgtcattataactttttgattttgaattgtaaatccttaaaataaatatatgagttatttctaaataggaaatactaataaatcccccagcagcctcctgctgggggatcgtcattagttcaaagcttg Find is-nt database================================================ Query_seq: SSA_1702:SSA_1703|SSA_1702:SSA_1703:hypothetical protein:Methionyl-tRNA synthetase, putative:<-<-:1693553..1693729 177 atttccctccgattcatttaataatttttaactcccttataaaacaaatgtcattataactttttgattttgaattgtaaatccttaaaataaatatatgagttatttctaaataggaaatactaataaatcccccagcagcctcctgctgggggatcgtcattagttcaaagcttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1702:SSA_1703|SSA_1702:SSA_1703:hypothetical protein:Methionyl-tRNA synthetase, putative:<-<-:1693553..1693729 177 atttccctccgattcatttaataatttttaactcccttataaaacaaatgtcattataactttttgattttgaattgtaaatccttaaaataaatatatgagttatttctaaataggaaatactaataaatcccccagcagcctcctgctgggggatcgtcattagttcaaagcttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1702:SSA_1703|SSA_1702:SSA_1703:hypothetical protein:Methionyl-tRNA synthetase, putative:<-<-:1693553..1693729 177 atttccctccgattcatttaataatttttaactcccttataaaacaaatgtcattataactttttgattttgaattgtaaatccttaaaataaatatatgagttatttctaaataggaaatactaataaatcccccagcagcctcctgctgggggatcgtcattagttcaaagcttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttccctccgattcatttaataatttttaactcccttataaaacaaatgtcattataactttttgattttgaattgtaaatccttaaaataaatatatgagttatttctaaataggaaatactaataaatcccccagcagcctcctgctgggggatcgtcattagttcaaagcttg Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: - Start: 17 End: 163 ................ K I I K L E R I F C I D N Y S K S K S N Y I R L I F I H T I E L Y S I S I F G G A A E Q Q P I T M .............. atttccctccgattcatttaataatttttaactcccttataaaacaaatgtcattataactttttgattttgaattgtaaatccttaaaataaatatatgagttatttctaaataggaaatactaataaatcccccagcagcctcctgctgggggatcgtcattagttcaaagcttg 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: 88 Start: 53 End: 82 ....................................................ATTTACAATTCAAAATCAAAAAGTTATAAT............................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttccctccgattcatttaataatttttaactcccttataaaacaaatgtcattataactttttgattttgaattgtaaatccttaaaataaatatatgagttatttctaaataggaaatactaataaatcccccagcagcctcctgctgggggatcgtcattagttcaaagcttg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -13.0 Tail_Score: -2.84098 Start: 128 End: 159 Full_Region: ATAGGAAATACTAAT AAATCCCCCAGCAG CCTC CTGCTGGGGGATCG TCATTAGTTCAAAGC ...............................................................................................................................AAATCCCCCAGCAGCCTCCTGCTGGGGGATCG.................. Find igs database================================================ Query_seq: SSA_1702:SSA_1703|SSA_1702:SSA_1703:hypothetical protein:Methionyl-tRNA synthetase, putative:<-<-:1693553..1693729 177 atttccctccgattcatttaataatttttaactcccttataaaacaaatgtcattataactttttgattttgaattgtaaatccttaaaataaatatatgagttatttctaaataggaaatactaataaatcccccagcagcctcctgctgggggatcgtcattagttcaaagcttg Intra-Species Hit: Count: 1 Min: 1 Max: 177 Len: 177 Subject: NC_009009_SSA_1702_SSA_1703|hypothetical protein:Methionyl-tRNA synthetase, putative|NEGATIVE:NEGATIVE|[1693553,1693729]|177 HSP 1 e-value: 5.0E-96 bit: 351.0 Len: 177 Query Start:1 Query End:177 Subject Strand: POSITIVE Subject Start: 1 Subject End: 177 atttccctccgattcatttaataatttttaactcccttataaaacaaatgtcattataactttttgattttgaattgtaaatccttaaaataaatatatgagttatttctaaataggaaatactaataaatcccccagcagcctcctgctgggggatcgtcattagttcaaagcttg atttccctccgattcatttaataatttttaactcccttataaaacaaatgtcattataactttttgattttgaattgtaaatccttaaaataaatatatgagttatttctaaataggaaatactaataaatcccccagcagcctcctgctgggggatcgtcattagttcaaagcttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCCCUCCGAUUCAUUUAAUAAUUUUUAACUCCCUUAUAAAACAAAUGUCAUUAUAACUUUUUGAUUUUGAAUUGUAAAUCCUUAAAAUAAAUAUAUGAGUUAUUUCUAAAUAGGAAAUACUAAUAAAUCCCCCAGCAGCCUCCUGCUGGGGGAUCGUCAUUAGUUCAAAGCUUG ..........(((((((........((((((.....((((((..((((.((((..(.....)..))))))))..))))))....)))))).......))))))).........((((....((((((..((((((((((((....))))))))))))....))))))......)))) (-39.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGCUUUGAACUAAUGACGAUCCCCCAGCAGGAGGCUGCUGGGGGAUUUAUUAGUAUUUCCUAUUUAGAAAUAACUCAUAUAUUUAUUUUAAGGAUUUACAAUUCAAAAUCAAAAAGUUAUAAUGACAUUUGUUUUAUAAGGGAGUUAAAAAUUAUUAAAUGAAUCGGAGGGAAAU ....((((((((((((((..((((((((((((....))))))))))))))))))))(((((((...(((((.....((((.(((..(((((...(((((........)))))..))))).)))))))......)))))..)))))))..................))))))...... (-46.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 730 140 91 231 182 NC_009009:SSA_1702|5end_hypothetical_protein_1693462..1693692_NEGATIVE 362 169 133 57 12 NC_009009:SSA_0761|5end_Transcriptional_regulator,_XRE_family,_putative_743877..744107_POSITIVE 352 169 131 221 174 NC_009009:SSA_0492|5end_NADH-dependent_flavin_oxidoreductase,_putative_491588..491818_POSITIVE 322 169 133 210 166 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 316 170 135 141 107 NC_009009:SSA_0675|5end_Exodeoxyribonuclease_VII_small_subunit,_putative_658389..658619_POSITIVE 309 169 134 87 55 NC_009009:SSA_1469|5end_Shikimate_dehydrogenase,_putative_1476317..1476547_NEGATIVE 309 169 133 51 7 NC_009009:SSA_0901|5end_Alpha-acetolactate_decarboxylase,_putative_892447..892677_POSITIVE 303 157 131 168 128 NC_009009:SSA_0765|5end_hypothetical_protein_745519..745749_POSITIVE 299 162 132 131 98 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 294 168 131 72 18 NC_009009:SSA_0587|5end_Metal-dependent_amidase/aminoacylase/carboxypeptidase,_putative_578539..578769_POSITIVE 293 170 121 72 16 NC_009009:SSA_0847|5end_6-phosphofructokinase,_putative_833372..833602_POSITIVE 292 170 137 184 145 NC_009009:SSA_0434|5end_Glutamate_formiminotransferase,_putative_436568..436798_NEGATIVE 291 166 132 202 147 NC_009009:SSA_0893|5end_ATP-binding_cassette_transporter-like_protein,_putative_884527..884757_POSITIVE 290 149 128 74 49 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 286 167 122 205 164 NC_009009:SSA_0579|5end_Hydrolase,_HAD_superfamily,_putative_572220..572450_POSITIVE 283 157 132 158 117 NC_009009:SSA_2002|5end_tRNA_pseudouridine_synthase_A,_putative_1998959..1999189_NEGATIVE 281 170 129 62 10 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 278 170 134 66 25 NC_009009:SSA_1938|5end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1925738..1925968_NEGATIVE 278 167 138 230 195 NC_009009:SSA_0450|5end_Elongation_factor_P,_putative_450587..450817_POSITIVE 274 156 115 222 186 NC_009009:SSA_1739|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1725540..1725770_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 398 160 115 54 1 NC_009009:SSA_0604|3end_hypothetical_protein_592992..593142_POSITIVE 357 163 123 128 75 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 323 162 130 139 103 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 309 169 134 97 65 NC_009009:SSA_1470|3end_3-dehydroquinate_dehydratase,_putative_1476307..1476457_NEGATIVE 299 162 132 134 101 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 299 169 131 45 7 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 292 170 137 63 24 NC_009009:SSA_0435|3end_Urocanate_hydratase,_putative_436689..436839_NEGATIVE 291 159 133 137 111 NC_009009:SSA_2121|3end_Cell_wall_surface_anchor_family_protein,_putative_2122222..2122372_NEGATIVE 281 168 130 146 103 NC_009009:SSA_2226|3end_Organic_radical_activating_chaperone,_putative_2227151..2227301_NEGATIVE 277 166 126 147 93 NC_009009:SSA_0406|3end_hypothetical_protein_402196..402346_NEGATIVE 272 159 114 53 9 NC_009009:SSA_0068|3end_Alcohol-acetaldehyde_dehydrogenase,_putative_72848..72998_POSITIVE 270 170 133 97 55 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 269 162 135 145 114 NC_009009:SSA_2174|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_2171991..2172141_NEGATIVE 269 168 139 136 99 NC_009009:SSA_0989|3end_Conserved_protein,_possible_transcriptional_regulator_(sigma-70,_region_4),_putative_991816..991966_POSITIVE 267 155 113 58 25 NC_009009:SSA_1387|3end_hypothetical_protein_1403497..1403647_NEGATIVE 266 152 129 151 117 NC_009009:SSA_0716|3end_Competence_protein,_putative_703710..703860_POSITIVE 261 170 134 67 18 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE 259 157 139 69 47 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE 259 163 138 132 98 NC_009009:SSA_0299|3end_hypothetical_protein_293342..293492_POSITIVE 257 157 130 54 18 NC_009009:SSA_1155|3end_Serine_hydroxymethyltransferase,_putative_1184640..1184790_POSITIVE