Origin IGS: cttaaaaaattcctttattttttacattcgtaaaaacagagcaaaaatccatccctatataaaagcaaaaatctgagacttctgcctcagactttctgtatatttctgcagaatttgcccacatctggca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgccagatgtgggcaaattctgcagaaatatacagaaagtctgaggcagaagtctcagatttttgcttttatatagggatggatttttgctctgtttttacgaatgtaaaaaataaaggaattttttaag Mask Tandem Repeat Region ================================================ cttaaaaaattcctttattttttacattcgtaaaaacagagcaaaaatccatccctatataaaagcaaaaatctgagacttctgcctcagactttctgtatatttctgcagaatttgcccacatctggca Find is-nt database================================================ Query_seq: SSA_2233:SSA_2234|SSA_2233:SSA_2234:hypothetical protein:Phosphatidylserine/phosphatidylglycerophosphate/ cardiolipin synthase, phospholipase D family, putative:<-<-:2233201..2233330 130 cttaaaaaattcctttattttttacattcgtaaaaacagagcaaaaatccatccctatataaaagcaaaaatctgagacttctgcctcagactttctgtatatttctgcagaatttgcccacatctggca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2233:SSA_2234|SSA_2233:SSA_2234:hypothetical protein:Phosphatidylserine/phosphatidylglycerophosphate/ cardiolipin synthase, phospholipase D family, putative:<-<-:2233201..2233330 130 cttaaaaaattcctttattttttacattcgtaaaaacagagcaaaaatccatccctatataaaagcaaaaatctgagacttctgcctcagactttctgtatatttctgcagaatttgcccacatctggca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2233:SSA_2234|SSA_2233:SSA_2234:hypothetical protein:Phosphatidylserine/phosphatidylglycerophosphate/ cardiolipin synthase, phospholipase D family, putative:<-<-:2233201..2233330 130 cttaaaaaattcctttattttttacattcgtaaaaacagagcaaaaatccatccctatataaaagcaaaaatctgagacttctgcctcagactttctgtatatttctgcagaatttgcccacatctggca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttaaaaaattcctttattttttacattcgtaaaaacagagcaaaaatccatccctatataaaagcaaaaatctgagacttctgcctcagactttctgtatatttctgcagaatttgcccacatctggca Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 5 End: 124 .... * F I G K N K V N T F V S C F D M G I Y F C F D S V E A E S K R Y I E A S N A W M ...... cttaaaaaattcctttattttttacattcgtaaaaacagagcaaaaatccatccctatataaaagcaaaaatctgagacttctgcctcagactttctgtatatttctgcagaatttgcccacatctggca Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttaaaaaattcctttattttttacattcgtaaaaacagagcaaaaatccatccctatataaaagcaaaaatctgagacttctgcctcagactttctgtatatttctgcagaatttgcccacatctggca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 76 HP_score: -6.9 Tail_Score: -4.53303 Start: 65 End: 85 Full_Region: tacagaaagtctgag gcagaagtc tca gatttttgc ttttatatagggatg ................................................................gcagaagtctcagatttttgc............................................. Find igs database================================================ Query_seq: SSA_2233:SSA_2234|SSA_2233:SSA_2234:hypothetical protein:Phosphatidylserine/phosphatidylglycerophosphate/ cardiolipin synthase, phospholipase D family, putative:<-<-:2233201..2233330 130 cttaaaaaattcctttattttttacattcgtaaaaacagagcaaaaatccatccctatataaaagcaaaaatctgagacttctgcctcagactttctgtatatttctgcagaatttgcccacatctggca Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_009009_SSA_2233_SSA_2234|hypothetical protein:Phosphatidylserine/phosphatidylglycerophosphate/ cardiolipin synthase, phospholipase D family, putative|NEGATIVE:NEGATIVE|[2233201,2233330]|130 HSP 1 e-value: 4.0E-68 bit: 258.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 cttaaaaaattcctttattttttacattcgtaaaaacagagcaaaaatccatccctatataaaagcaaaaatctgagacttctgcctcagactttctgtatatttctgcagaatttgcccacatctggca cttaaaaaattcctttattttttacattcgtaaaaacagagcaaaaatccatccctatataaaagcaaaaatctgagacttctgcctcagactttctgtatatttctgcagaatttgcccacatctggca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAAAAAAUUCCUUUAUUUUUUACAUUCGUAAAAACAGAGCAAAAAUCCAUCCCUAUAUAAAAGCAAAAAUCUGAGACUUCUGCCUCAGACUUUCUGUAUAUUUCUGCAGAAUUUGCCCACAUCUGGCA ..((((((((......))))))))............(((((((((..........................((((((.(....).))))))..(((((((......)))))))))))).....))))... (-22.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCCAGAUGUGGGCAAAUUCUGCAGAAAUAUACAGAAAGUCUGAGGCAGAAGUCUCAGAUUUUUGCUUUUAUAUAGGGAUGGAUUUUUGCUCUGUUUUUACGAAUGUAAAAAAUAAAGGAAUUUUUUAAG .(((.......))).((((((((((((((.....(((((((((((((....))))))))))))).((((.....))))....))))))))....(((((((....))))))).....))))))....... (-32.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 935 130 81 221 172 NC_009009:SSA_2233|5end_hypothetical_protein_2233110..2233340_NEGATIVE 345 119 73 225 175 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 324 130 82 217 161 NC_009009:SSA_1404|5end_hypothetical_protein_1418723..1418953_NEGATIVE 316 129 85 191 143 NC_009009:SSA_0972|5end_hypothetical_protein_979973..980203_POSITIVE 314 130 81 63 12 NC_009009:SSA_0549|5end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_543556..543786_POSITIVE 313 90 48 184 138 NC_009009:SSA_0790|5end_hypothetical_protein_773047..773277_POSITIVE 296 118 73 179 122 NC_009009:SSA_1559|5end_Conserved_uncharacterized_protein_1561656..1561886_NEGATIVE 294 115 72 231 189 NC_009009:SSA_1899|5end_hypothetical_protein_1894739..1894969_NEGATIVE 292 95 64 224 192 NC_009009:SSA_0150|5end_hypothetical_protein_143936..144166_POSITIVE 291 129 81 140 91 NC_009009:SSA_0623|5end_hypothetical_protein_614512..614742_POSITIVE 291 130 83 50 5 NC_009009:SSA_0567|5end_Isochorismitase_family_protein,_putative_560805..561035_POSITIVE 290 109 80 176 145 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 287 118 76 137 96 NC_009009:SSA_0040|5end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_46308..46538_POSITIVE 284 130 81 62 12 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 279 130 84 68 10 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 274 119 73 40 7 NC_009009:SSA_0257|5end_N-acetylmuramidase/lysin,_putative_248878..249108_POSITIVE 269 127 81 200 139 NC_009009:SSA_0770|5end_Ribonucleoside-diphosphate_reductase,_putative_751411..751641_NEGATIVE 269 130 84 209 159 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 268 123 83 137 98 NC_009009:SSA_0631|5end_Tryptophan_synthase_beta_chain,_putative_619872..620102_POSITIVE 267 120 77 43 2 NC_009009:SSA_1174|5end_Dihydrolipoamide_dehydrogenase,_putative_1202854..1203084_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 95 64 41 9 NC_009009:SSA_0149|3end_hypothetical_protein_143833..143983_POSITIVE 291 130 83 50 5 NC_009009:SSA_0566|3end_GTP-sensing_transcriptional_pleiotropic_repressor,_putative_560885..561035_POSITIVE 289 129 81 143 95 NC_009009:SSA_1179|3end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1206640..1206790_NEGATIVE 287 118 76 150 109 NC_009009:SSA_0039|3end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_46401..46551_POSITIVE 284 130 81 69 19 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 282 130 81 136 86 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 271 120 71 62 6 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 271 87 49 119 83 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 266 130 87 137 95 NC_009009:SSA_0873|3end_ATP-dependent_DNA_helicase;_DNA_polymerase_III,_epsilon_subunit,_putative_867915..868065_POSITIVE 261 113 77 141 97 NC_009009:SSA_1300|3end_Maltose_ABC_transporter,_permease_protein,_putative_1318903..1319053_POSITIVE 261 118 72 147 101 NC_009009:SSA_0892|3end_ATP-binding_cassette_lipoprotein,_putative_884578..884728_POSITIVE 260 117 74 149 109 NC_009009:SSA_1029|3end_hypothetical_protein_1046167..1046317_NEGATIVE 259 130 82 53 14 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 255 129 81 66 7 NC_009009:SSA_0627|3end_hypothetical_protein_617975..618125_POSITIVE 254 128 81 61 6 NC_009009:SSA_0469|3end_Precorrin-6B_methylase_2,putative_472959..473109_POSITIVE 250 127 85 147 95 NC_009009:SSA_0917|3end_Cobalamin-independent_methionine_synthase_II,_putative_929087..929237_NEGATIVE 250 97 52 84 40 NC_009009:SSA_0688|3end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_672132..672282_POSITIVE 249 108 61 75 26 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 248 87 48 54 11 NC_009009:SSA_0766|3end_hypothetical_protein_746975..747125_POSITIVE 248 110 64 149 109 NC_009009:SSA_0330|3end_hypothetical_protein_325162..325312_POSITIVE