Origin IGS: tctaacagcatataagaggagctaggacttagtcctagcttttttgatgagtaaagatataaaaatggatattttttgatttaggaaccaccctaattgatgagagggagatttatcatcttttcctaaaaaattgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcaattttttaggaaaagatgataaatctccctctcatcaattagggtggttcctaaatcaaaaaatatccatttttatatctttactcatcaaaaaagctaggactaagtcctagctcctcttatatgctgttaga Mask Tandem Repeat Region ================================================ tctaacagcatataagaggagctaggacttagtcctagcttttttgatgagtaaagatataaaaatggatattttttgatttaggaaccaccctaattgatgagagggagatttatcatcttttcctaaaaaattgc Find is-nt database================================================ Query_seq: SSA_0886:SSA_0887|SSA_0886:SSA_0887:Enolase, putative:hypothetical protein:-><-:881118..881254 137 tctaacagcatataagaggagctaggacttagtcctagcttttttgatgagtaaagatataaaaatggatattttttgatttaggaaccaccctaattgatgagagggagatttatcatcttttcctaaaaaattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0886:SSA_0887|SSA_0886:SSA_0887:Enolase, putative:hypothetical protein:-><-:881118..881254 137 tctaacagcatataagaggagctaggacttagtcctagcttttttgatgagtaaagatataaaaatggatattttttgatttaggaaccaccctaattgatgagagggagatttatcatcttttcctaaaaaattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0886:SSA_0887|SSA_0886:SSA_0887:Enolase, putative:hypothetical protein:-><-:881118..881254 137 tctaacagcatataagaggagctaggacttagtcctagcttttttgatgagtaaagatataaaaatggatattttttgatttaggaaccaccctaattgatgagagggagatttatcatcttttcctaaaaaattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctaacagcatataagaggagctaggacttagtcctagcttttttgatgagtaaagatataaaaatggatattttttgatttaggaaccaccctaattgatgagagggagatttatcatcttttcctaaaaaattgc Predict ORF larger than 30AA ================================================ tctaacagcatataagaggagctaggacttagtcctagcttttttgatgagtaaagatataaaaatggatattttttgatttaggaaccaccctaattgatgagagggagatttatcatcttttcctaaaaaattgc 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================================================ tctaacagcatataagaggagctaggacttagtcctagcttttttgatgagtaaagatataaaaatggatattttttgatttaggaaccaccctaattgatgagagggagatttatcatcttttcctaaaaaattgc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 87 HP_score: -13.2 Tail_Score: -2.83964 Start: 21 End: 39 Full_Region: ttactcatcaaaaaa gctaggac taa gtcctagc tcctcttatatgctg ....................gctaggactaagtcctagc.................................................................................................. Find igs database================================================ Query_seq: SSA_0886:SSA_0887|SSA_0886:SSA_0887:Enolase, putative:hypothetical protein:-><-:881118..881254 137 tctaacagcatataagaggagctaggacttagtcctagcttttttgatgagtaaagatataaaaatggatattttttgatttaggaaccaccctaattgatgagagggagatttatcatcttttcctaaaaaattgc Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: NC_009009_SSA_0886_SSA_0887|Enolase, putative:hypothetical protein|POSITIVE:NEGATIVE|[881118,881254]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 tctaacagcatataagaggagctaggacttagtcctagcttttttgatgagtaaagatataaaaatggatattttttgatttaggaaccaccctaattgatgagagggagatttatcatcttttcctaaaaaattgc tctaacagcatataagaggagctaggacttagtcctagcttttttgatgagtaaagatataaaaatggatattttttgatttaggaaccaccctaattgatgagagggagatttatcatcttttcctaaaaaattgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAACAGCAUAUAAGAGGAGCUAGGACUUAGUCCUAGCUUUUUUGAUGAGUAAAGAUAUAAAAAUGGAUAUUUUUUGAUUUAGGAACCACCCUAAUUGAUGAGAGGGAGAUUUAUCAUCUUUUCCUAAAAAAUUGC ........(((...((((((((((((((...)))))))))))))).)))...((((((((........))))))))...((((((((...((((..........)))).(((.....)))..))))))))....... (-33.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAUUUUUUAGGAAAAGAUGAUAAAUCUCCCUCUCAUCAAUUAGGGUGGUUCCUAAAUCAAAAAAUAUCCAUUUUUAUAUCUUUACUCAUCAAAAAAGCUAGGACUAAGUCCUAGCUCCUCUUAUAUGCUGUUAGA (((......(((((...(((((..((((.((((..........)))).)))).........((((((....))))))..........))))).....(((((((((...)))))))))..)))))..)))....... (-28.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 45 8 180 142 NC_009009:SSA_1861|5end_Aminopeptidase_C,_putative_1857902..1858132_NEGATIVE 298 43 1 130 80 NC_009009:SSA_1673|5end_hypothetical_protein_1670353..1670583_POSITIVE 295 43 8 212 177 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 285 41 14 202 175 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 283 45 7 179 128 NC_009009:SSA_0155|5end_hypothetical_protein_150961..151191_POSITIVE 277 44 7 210 170 NC_009009:SSA_1796|5end_Transcription_elongation_factor_GreA,_putative_1778307..1778537_NEGATIVE 268 50 7 103 53 NC_009009:SSA_1672|5end_hypothetical_protein_1670389..1670619_NEGATIVE 266 45 15 148 120 NC_009009:SSA_2202|5end_Elongation_factor_Ts,_putative_2203350..2203580_NEGATIVE 259 60 11 160 112 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 258 44 7 185 151 NC_009009:SSA_2105|5end_hypothetical_protein_2107802..2108032_NEGATIVE 254 48 7 211 164 NC_009009:SSA_0221|5end_PTS_system,_mannose-specific_IIC_component,_putative_216370..216600_POSITIVE 252 51 15 160 120 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 249 46 8 73 33 NC_009009:SSA_0267|5end_ROK_family_protein,_putative_262069..262299_NEGATIVE 246 47 8 74 24 NC_009009:SSA_0735|5end_Integral_membrane_protein,_putative_717103..717333_POSITIVE 245 50 7 195 156 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 243 109 66 135 95 NC_009009:SSA_0398|5end_hypothetical_protein_396452..396682_NEGATIVE 239 40 19 182 161 NC_009009:SSA_0434|5end_Glutamate_formiminotransferase,_putative_436568..436798_NEGATIVE 238 58 17 220 180 NC_009009:SSA_0450|5end_Elongation_factor_P,_putative_450587..450817_POSITIVE 237 59 12 174 113 NC_009009:SSA_1068|5end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1087355..1087585_POSITIVE 237 45 8 208 170 NC_009009:SSA_0023|5end_Aspartate_aminotransferase,_putative_28529..28759_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 58 15 91 46 NC_009009:SSA_0886|3end_Enolase,_putative_881057..881207_POSITIVE 349 42 1 71 30 NC_009009:SSA_1161|3end_hypothetical_protein_1188443..1188593_POSITIVE 301 45 8 101 63 NC_009009:SSA_1862|3end_hypothetical_protein_1857981..1858131_NEGATIVE 289 48 7 132 89 NC_009009:SSA_1479|3end_Transposase,_putative_1483889..1484039_POSITIVE 287 40 1 71 32 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 287 45 5 109 66 NC_009009:SSA_0710|3end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_694773..694923_NEGATIVE 287 60 14 76 26 NC_009009:SSA_0708|3end_hypothetical_protein_694757..694907_POSITIVE 284 42 10 62 26 NC_009009:SSA_1162|3end_Possible_fimbrial_assembly_protein_fimC,_putative_1188489..1188639_NEGATIVE 283 45 7 88 37 NC_009009:SSA_0154|3end_hypothetical_protein_150950..151100_POSITIVE 281 45 1 86 40 NC_009009:SSA_0718|3end_Conserved_uncharacterized_protein_704935..705085_POSITIVE 277 44 7 69 29 NC_009009:SSA_1797|3end_Aminodeoxychorismate_lyase,_putative_1778448..1778598_NEGATIVE 270 54 14 67 18 NC_009009:SSA_1964|3end_conserved_uncharacterized_protein_1960996..1961146_NEGATIVE 269 53 12 82 42 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 266 45 15 75 47 NC_009009:SSA_2203|3end_30S_ribosomal_protein_S2,_putative_2203423..2203573_NEGATIVE 264 48 7 69 26 NC_009009:SSA_0234|3end_hypothetical_protein_228423..228573_NEGATIVE 259 60 11 84 36 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 257 46 1 89 39 NC_009009:SSA_0987|3end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_990594..990744_POSITIVE 255 50 6 67 23 NC_009009:SSA_2354|3end_hypothetical_protein_2355605..2355755_NEGATIVE 255 56 11 140 92 NC_009009:SSA_0732|3end_Transposase,_putative_715711..715861_NEGATIVE 252 51 15 68 28 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE