Origin IGS: ccgagtggcaggtttggcatggcctgcaaccaagaagaagttatttgtctttacgacatacttattctaccaagaaggtctacctttgtcaaatgattctgtttcaactcttttgtatgaggaattcaggctctttcat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atgaaagagcctgaattcctcatacaaaagagttgaaacagaatcatttgacaaaggtagaccttcttggtagaataagtatgtcgtaaagacaaataacttcttcttggttgcaggccatgccaaacctgccactcgg Mask Tandem Repeat Region ================================================ ccgagtggcaggtttggcatggcctgcaaccaagaagaagttatttgtctttacgacatacttattctaccaagaaggtctacctttgtcaaatgattctgtttcaactcttttgtatgaggaattcaggctctttcat Find is-nt database================================================ Query_seq: SSA_2058:SSA_2059|SSA_2058:SSA_2059:30S ribosomal protein S15, putative:16S rRNA uridine-516 pseudouridylate synthase, putative:<-<-:2060445..2060583 139 ccgagtggcaggtttggcatggcctgcaaccaagaagaagttatttgtctttacgacatacttattctaccaagaaggtctacctttgtcaaatgattctgtttcaactcttttgtatgaggaattcaggctctttcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2058:SSA_2059|SSA_2058:SSA_2059:30S ribosomal protein S15, putative:16S rRNA uridine-516 pseudouridylate synthase, putative:<-<-:2060445..2060583 139 ccgagtggcaggtttggcatggcctgcaaccaagaagaagttatttgtctttacgacatacttattctaccaagaaggtctacctttgtcaaatgattctgtttcaactcttttgtatgaggaattcaggctctttcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2058:SSA_2059|SSA_2058:SSA_2059:30S ribosomal protein S15, putative:16S rRNA uridine-516 pseudouridylate synthase, putative:<-<-:2060445..2060583 139 ccgagtggcaggtttggcatggcctgcaaccaagaagaagttatttgtctttacgacatacttattctaccaagaaggtctacctttgtcaaatgattctgtttcaactcttttgtatgaggaattcaggctctttcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccgagtggcaggtttggcatggcctgcaaccaagaagaagttatttgtctttacgacatacttattctaccaagaaggtctacctttgtcaaatgattctgtttcaactcttttgtatgaggaattcaggctctttcat Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 24 End: 137 ....................... M Q P R R S Y L S L R H T Y S T K K V Y L C Q M I L F Q L F C M R N S G S F .. Protein_Len: 45 Strand: + Start: 5 End: 139 .... M A G L A W P A T K K K L F V F T T Y L F Y Q E G L P L S N D S V S T L L Y E E F R L F H ccgagtggcaggtttggcatggcctgcaaccaagaagaagttatttgtctttacgacatacttattctaccaagaaggtctacctttgtcaaatgattctgtttcaactcttttgtatgaggaattcaggctctttcat 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: 90 Start: 64 End: 93 ...............................................................TTTGACAAAGGTAGACCTTCTTGGTAGAAT.............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ccgagtggcaggtttggcatggcctgcaaccaagaagaagttatttgtctttacgacatacttattctaccaagaaggtctacctttgtcaaatgattctgtttcaactcttttgtatgaggaattcaggctctttcat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2058:SSA_2059|SSA_2058:SSA_2059:30S ribosomal protein S15, putative:16S rRNA uridine-516 pseudouridylate synthase, putative:<-<-:2060445..2060583 139 ccgagtggcaggtttggcatggcctgcaaccaagaagaagttatttgtctttacgacatacttattctaccaagaaggtctacctttgtcaaatgattctgtttcaactcttttgtatgaggaattcaggctctttcat Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: NC_009009_SSA_2058_SSA_2059|30S ribosomal protein S15, putative:16S rRNA uridine-516 pseudouridylate synthase, putative|NEGATIVE:NEGATIVE|[2060445,2060583]|139 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 ccgagtggcaggtttggcatggcctgcaaccaagaagaagttatttgtctttacgacatacttattctaccaagaaggtctacctttgtcaaatgattctgtttcaactcttttgtatgaggaattcaggctctttcat ccgagtggcaggtttggcatggcctgcaaccaagaagaagttatttgtctttacgacatacttattctaccaagaaggtctacctttgtcaaatgattctgtttcaactcttttgtatgaggaattcaggctctttcat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGAGUGGCAGGUUUGGCAUGGCCUGCAACCAAGAAGAAGUUAUUUGUCUUUACGACAUACUUAUUCUACCAAGAAGGUCUACCUUUGUCAAAUGAUUCUGUUUCAACUCUUUUGUAUGAGGAAUUCAGGCUCUUUCAU ..(.((.(((((((......))))))).))).((((.((((....((((.....)))).)))).)))).....(((((....))))).......((..(((......(((........))).....)))..))...... (-31.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAAAGAGCCUGAAUUCCUCAUACAAAAGAGUUGAAACAGAAUCAUUUGACAAAGGUAGACCUUCUUGGUAGAAUAAGUAUGUCGUAAAGACAAAUAACUUCUUCUUGGUUGCAGGCCAUGCCAAACCUGCCACUCGG .(((..((..(((..((((((........)))..))).)))..))..........(((((......(((((.(((.((((.((((.....))))....)))).))).((((.....)))).)))))..)))))..))). (-25.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 987 50 1 141 92 NC_009009:SSA_2058|5end_30S_ribosomal_protein_S15,_putative_2060354..2060584_NEGATIVE 388 34 1 167 126 NC_009009:SSA_1280|5end_hypothetical_protein_1301596..1301826_NEGATIVE 365 48 2 189 136 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 354 48 3 64 14 NC_009009:SSA_1400|5end_Pyridoxal_kinase,_putative_1413072..1413302_NEGATIVE 351 58 12 224 169 NC_009009:SSA_0516|5end_AmiR_two-component_response_regulator_with_transcriptional_antiterminator_output_domain,_putative_514485..514715_POSITIVE 308 49 2 189 132 NC_009009:SSA_2036|5end_Conserved_hypothetical_cytosolic_protein_2040799..2041029_NEGATIVE 307 49 2 205 151 NC_009009:SSA_0522|5end_Ethanolamine_utilization_protein,_putative_521067..521297_POSITIVE 307 49 1 89 38 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 304 47 1 61 1 NC_009009:SSA_0756|5end_Alanyl-tRNA_synthetase,_putative_736736..736966_POSITIVE 298 40 3 52 3 NC_009009:SSA_2196|5end_Conserved_uncharacterized_protein_2197330..2197560_NEGATIVE 298 43 2 214 167 NC_009009:SSA_1595|5end_Tellurite_resistance,_putative_1601814..1602044_NEGATIVE 297 48 3 56 12 NC_009009:SSA_0609|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_598864..599094_NEGATIVE 291 48 1 173 113 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 291 37 1 62 20 NC_009009:SSA_0388|5end_Mismatch_repair_ATPase_(MutS_family),_putative_382474..382704_POSITIVE 287 50 2 223 173 NC_009009:SSA_1952|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1949624..1949854_NEGATIVE 282 50 1 224 170 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 282 40 1 201 163 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 281 41 1 162 118 NC_009009:SSA_0423|5end_hypothetical_protein_421347..421577_NEGATIVE 277 49 1 219 169 NC_009009:SSA_1579|5end_ABC-type_Fe3+-siderophore_transport_system,_ATPase_component,_putative_1582851..1583081_POSITIVE 275 90 45 154 108 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 27 1 142 114 NC_009009:SSA_1281|3end_Uracil-DNA_glycosylase,_putative_1301608..1301758_NEGATIVE 307 49 1 99 48 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 298 40 3 68 19 NC_009009:SSA_2197|3end_hypothetical_protein_2197314..2197464_NEGATIVE 291 48 1 98 38 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 275 49 3 84 36 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 273 46 7 96 59 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 272 90 44 54 2 NC_009009:SSA_0512|3end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_511625..511775_POSITIVE 270 49 5 62 20 NC_009009:SSA_1599|3end_hypothetical_protein_1605442..1605592_NEGATIVE 270 60 20 81 34 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 266 29 3 67 42 NC_009009:SSA_1780|3end_Tyrosine_recombinase_xerD,_putative_1766416..1766566_NEGATIVE 265 49 1 36 1 NC_009009:SSA_0776|3end_Glucose-1-phosphate_adenylyltransferase,_putative_759520..759670_POSITIVE 264 50 1 106 50 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 263 57 11 67 2 NC_009009:SSA_0039|3end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_46401..46551_POSITIVE 262 49 1 146 89 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 261 68 23 97 41 NC_009009:SSA_0947|3end_hypothetical_protein_954876..955026_POSITIVE 258 50 1 70 20 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 258 31 3 49 23 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 250 50 3 63 15 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 250 25 1 151 117 NC_009009:SSA_0458|3end_Formylmethionine_deformylase,_putative_462099..462249_POSITIVE 249 35 4 142 100 NC_009009:SSA_2107|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2109295..2109445_NEGATIVE