Origin IGS: tgcgggaccaatcaatttttaggctgtttgtcagtttgaaaggaagggtgaagaaattttcttcgctttttttcttgttgaaaaaatagttctcatggaaacttttttcttgactttcttttttcttgtgttaaaatagttctcacgaaaactatttttacaaaggatacaggt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acctgtatcctttgtaaaaatagttttcgtgagaactattttaacacaagaaaaaagaaagtcaagaaaaaagtttccatgagaactattttttcaacaagaaaaaaagcgaagaaaatttcttcacccttcctttcaaactgacaaacagcctaaaaattgattggtcccgca Mask Tandem Repeat Region ================================================ tgcgggaccaatcaatttttaggctgtttgtcagtttgaaaggaagggtgaagaaattttcttcgctttttttcttgttgaaaaaatagttctcatggaaacttttttcttgactttcttttttcttgtgttaaaatagttctcacgaaaactatttttacaaaggatacaggt Find is-nt database================================================ Query_seq: SSA_0459:SSA_0460|SSA_0459:SSA_0460:hypothetical protein:Multiple antibiotic resistance operon transcription repressor (MarR), putative:->->:462574..462747 174 tgcgggaccaatcaatttttaggctgtttgtcagtttgaaaggaagggtgaagaaattttcttcgctttttttcttgttgaaaaaatagttctcatggaaacttttttcttgactttcttttttcttgtgttaaaatagttctcacgaaaactatttttacaaaggatacaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0459:SSA_0460|SSA_0459:SSA_0460:hypothetical protein:Multiple antibiotic resistance operon transcription repressor (MarR), putative:->->:462574..462747 174 tgcgggaccaatcaatttttaggctgtttgtcagtttgaaaggaagggtgaagaaattttcttcgctttttttcttgttgaaaaaatagttctcatggaaacttttttcttgactttcttttttcttgtgttaaaatagttctcacgaaaactatttttacaaaggatacaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0459:SSA_0460|SSA_0459:SSA_0460:hypothetical protein:Multiple antibiotic resistance operon transcription repressor (MarR), putative:->->:462574..462747 174 tgcgggaccaatcaatttttaggctgtttgtcagtttgaaaggaagggtgaagaaattttcttcgctttttttcttgttgaaaaaatagttctcatggaaacttttttcttgactttcttttttcttgtgttaaaatagttctcacgaaaactatttttacaaaggatacaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcgggaccaatcaatttttaggctgtttgtcagtttgaaaggaagggtgaagaaattttcttcgctttttttcttgttgaaaaaatagttctcatggaaacttttttcttgactttcttttttcttgtgttaaaatagttctcacgaaaactatttttacaaaggatacaggt Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: - Start: 34 End: 168 ................................. N S L F P S S I K K A K K R T S F I T R M S V K K K V K K K R T N F Y N E R F S N K C L M ...... tgcgggaccaatcaatttttaggctgtttgtcagtttgaaaggaagggtgaagaaattttcttcgctttttttcttgttgaaaaaatagttctcatggaaacttttttcttgactttcttttttcttgtgttaaaatagttctcacgaaaactatttttacaaaggatacaggt 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================================================ tgcgggaccaatcaatttttaggctgtttgtcagtttgaaaggaagggtgaagaaattttcttcgctttttttcttgttgaaaaaatagttctcatggaaacttttttcttgactttcttttttcttgtgttaaaatagttctcacgaaaactatttttacaaaggatacaggt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -8.2 Tail_Score: -5.95946 Start: 48 End: 66 Full_Region: AGTTTGAAAGGAAGG GTGAAGAA ATT TTCTTCGC TTTTTTTCTTGTTGA ...............................................GTGAAGAAATTTTCTTCGC............................................................................................................ Find igs database================================================ Query_seq: SSA_0459:SSA_0460|SSA_0459:SSA_0460:hypothetical protein:Multiple antibiotic resistance operon transcription repressor (MarR), putative:->->:462574..462747 174 tgcgggaccaatcaatttttaggctgtttgtcagtttgaaaggaagggtgaagaaattttcttcgctttttttcttgttgaaaaaatagttctcatggaaacttttttcttgactttcttttttcttgtgttaaaatagttctcacgaaaactatttttacaaaggatacaggt Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: NC_009009_SSA_0459_SSA_0460|hypothetical protein:Multiple antibiotic resistance operon transcription repressor (MarR), putative|POSITIVE:POSITIVE|[462574,462747]|174 HSP 1 e-value: 3.0E-29 bit: 129.0 Len: 65 Query Start:1 Query End:65 Subject Strand: POSITIVE Subject Start: 1 Subject End: 65 tgcgggaccaatcaatttttaggctgtttgtcagtttgaaaggaagggtgaagaaattttcttcg............................................................................................................. tgcgggaccaatcaatttttaggctgtttgtcagtttgaaaggaagggtgaagaaattttcttcg............................................................................................................. HSP 2 e-value: 7.0E-18 bit: 91.7 Len: 46 Query Start:129 Query End:174 Subject Strand: POSITIVE Subject Start: 129 Subject End: 174 ................................................................................................................................tgttaaaatagttctcacgaaaactatttttacaaaggatacaggt ................................................................................................................................tgttaaaatagttctcacgaaaactatttttacaaaggatacaggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCGGGACCAAUCAAUUUUUAGGCUGUUUGUCAGUUUGAAAGGAAGGGUGAAGAAAUUUUCUUCGCUUUUUUUCUUGUUGAAAAAAUAGUUCUCAUGGAAACUUUUUUCUUGACUUUCUUUUUUCUUGUGUUAAAAUAGUUCUCACGAAAACUAUUUUUACAAAGGAUACAGGU ......(((.......((((((((((.....)))))))))).((((((((((((.....)))))))))))).((((.(((.((((((((((.((.((..((((......(((((...............)))))...))))..)).)).)))))))))).)))))))....))) (-41.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUGUAUCCUUUGUAAAAAUAGUUUUCGUGAGAACUAUUUUAACACAAGAAAAAAGAAAGUCAAGAAAAAAGUUUCCAUGAGAACUAUUUUUUCAACAAGAAAAAAAGCGAAGAAAAUUUCUUCACCCUUCCUUUCAAACUGACAAACAGCCUAAAAAUUGAUUGGUCCCGCA ..((((.....(((.((((((((((((((((..((((.((((...((.............))....)))).))))..)))))))))))))))).)))...((((..(((.(((((.....)))))...)))..))))..........))))....................... (-33.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 67 21 59 13 NC_009009:SSA_1593|5end_Dipeptidase,_putative_1598054..1598284_NEGATIVE 297 148 103 111 62 NC_009009:SSA_1219|5end_Sortase,_putative_1241337..1241567_NEGATIVE 296 79 41 88 51 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 289 70 21 209 155 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 283 123 90 103 71 NC_009009:SSA_1502|5end_Conserved_uncharacterized_protein_(contains_LysM,_Lysin_motif)_1506219..1506449_NEGATIVE 266 48 1 166 118 NC_009009:SSA_0729|5end_hypothetical_protein_714397..714627_POSITIVE 264 43 1 227 188 NC_009009:SSA_1872|5end_Cell_division_protein,_putative_1869186..1869416_NEGATIVE 262 50 2 201 152 NC_009009:SSA_0398|5end_hypothetical_protein_396452..396682_NEGATIVE 256 107 61 104 58 NC_009009:SSA_0935|5end_tRNA_pseudouridine_synthase_B,_putative_944015..944245_POSITIVE 254 80 37 87 35 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 254 80 37 222 170 NC_009009:SSA_1411|5end_Glucose-1-phosphate_thymidylytransferase,_putative_1423960..1424190_NEGATIVE 254 136 93 132 88 NC_009009:SSA_0903|5end_NAD(P)H_dehydrogenase_(quinone),_putative_893242..893472_POSITIVE 248 48 1 170 126 NC_009009:SSA_0621|5end_SOS_responce_UmuC_protein,_putative_613737..613967_NEGATIVE 247 140 93 135 88 NC_009009:SSA_2312|5end_hypothetical_protein_2315281..2315511_NEGATIVE 243 69 30 202 156 NC_009009:SSA_0816|5end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797445..797675_POSITIVE 242 128 91 228 170 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 241 70 24 193 142 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 240 50 3 197 159 NC_009009:SSA_1973|5end_Histidine_kinase,_putative_1969507..1969737_NEGATIVE 238 44 9 207 172 NC_009009:SSA_1491|5end_Methionine_aminopeptidase_A,_putative_1497637..1497867_NEGATIVE 237 67 21 105 51 NC_009009:SSA_0690|5end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_674432..674662_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 70 25 133 85 NC_009009:SSA_1302|3end_tRNA_(Guanine-N(1)-)-methyltransferase,_putative_1321762..1321912_NEGATIVE 297 148 103 96 47 NC_009009:SSA_1220|3end_DNA_gyrase_A_subunit,_putative_1241352..1241502_NEGATIVE 295 89 41 67 18 NC_009009:SSA_0459|3end_hypothetical_protein_462513..462663_POSITIVE 289 70 21 73 19 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 278 78 37 94 44 NC_009009:SSA_1172|3end_hypothetical_protein_1199288..1199438_NEGATIVE 266 70 24 108 53 NC_009009:SSA_0907|3end_Fibronectin-binding_protein_A,_putative_917568..917718_NEGATIVE 256 107 61 100 54 NC_009009:SSA_0934|3end_HydD,_putative_944091..944241_POSITIVE 254 80 37 87 35 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 254 136 93 56 12 NC_009009:SSA_0901|3end_Alpha-acetolactate_decarboxylase,_putative_893246..893396_POSITIVE 253 49 1 71 32 NC_009009:SSA_1625|3end_Lactoylglutathione_lyase,_putative_1626577..1626727_NEGATIVE 249 50 1 62 9 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 243 59 14 130 86 NC_009009:SSA_2156|3end_Conserved_uncharacterized_protein_2156216..2156366_NEGATIVE 243 69 30 88 42 NC_009009:SSA_0815|3end_hypothetical_protein_797411..797561_POSITIVE 241 70 24 88 37 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 232 37 10 92 63 NC_009009:SSA_1010|3end_UDP-glucose_4-epimerase,_putative_1013862..1014012_POSITIVE 229 132 93 137 95 NC_009009:SSA_0637|3end_Tryptophan_synthase_beta_chain,_putative_627022..627172_POSITIVE 229 49 21 72 44 NC_009009:SSA_0135|3end_Multiple_antibiotic_resistance_operon_transcriptional_repressor_(MarR),_putative_131097..131247_POSITIVE 228 131 96 100 66 NC_009009:SSA_1873|3end_S-adenosyl-methyltransferase_mraW,_putative_1869194..1869344_NEGATIVE 227 35 1 42 6 NC_009009:SSA_2046|3end_Uridine_phosphorylase,_putative_2048957..2049107_NEGATIVE 227 40 2 147 120 NC_009009:SSA_0422|3end_Phosphoglycerate_mutase_family_protein,_putative_420839..420989_POSITIVE