Origin IGS: tccctcgactttctatagactattatagcataatatgcagtacaacatcttttaaatcctctgcgacattaaagacgacatcatataaatgaccaaataaaaaaaggcgcaaaagcgccagttcat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atgaactggcgcttttgcgcctttttttatttggtcatttatatgatgtcgtctttaatgtcgcagaggatttaaaagatgttgtactgcatattatgctataatagtctatagaaagtcgaggga Mask Tandem Repeat Region ================================================ tccctcgactttctatagactattatagcataatatgcagtacaacatcttttaaatcctctgcgacattaaagacgacatcatataaatgaccaaataaaaaaaggcgcaaaagcgccagttcat Find is-nt database================================================ Query_seq: SSA_2271:SSA_2272|SSA_2271:SSA_2272:hypothetical protein:hypothetical protein:<-<-:2272541..2272666 126 tccctcgactttctatagactattatagcataatatgcagtacaacatcttttaaatcctctgcgacattaaagacgacatcatataaatgaccaaataaaaaaaggcgcaaaagcgccagttcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2271:SSA_2272|SSA_2271:SSA_2272:hypothetical protein:hypothetical protein:<-<-:2272541..2272666 126 tccctcgactttctatagactattatagcataatatgcagtacaacatcttttaaatcctctgcgacattaaagacgacatcatataaatgaccaaataaaaaaaggcgcaaaagcgccagttcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2271:SSA_2272|SSA_2271:SSA_2272:hypothetical protein:hypothetical protein:<-<-:2272541..2272666 126 tccctcgactttctatagactattatagcataatatgcagtacaacatcttttaaatcctctgcgacattaaagacgacatcatataaatgaccaaataaaaaaaggcgcaaaagcgccagttcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccctcgactttctatagactattatagcataatatgcagtacaacatcttttaaatcctctgcgacattaaagacgacatcatataaatgaccaaataaaaaaaggcgcaaaagcgccagttcat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 26 End: 121 ......................... L M I H L V V D K L D E A V N F V V D Y L H G F L F L R L L A M ..... tccctcgactttctatagactattatagcataatatgcagtacaacatcttttaaatcctctgcgacattaaagacgacatcatataaatgaccaaataaaaaaaggcgcaaaagcgccagttcat 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================================================ tccctcgactttctatagactattatagcataatatgcagtacaacatcttttaaatcctctgcgacattaaagacgacatcatataaatgaccaaataaaaaaaggcgcaaaagcgccagttcat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2271:SSA_2272|SSA_2271:SSA_2272:hypothetical protein:hypothetical protein:<-<-:2272541..2272666 126 tccctcgactttctatagactattatagcataatatgcagtacaacatcttttaaatcctctgcgacattaaagacgacatcatataaatgaccaaataaaaaaaggcgcaaaagcgccagttcat Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_009009_SSA_2271_SSA_2272|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2272541,2272666]|126 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 tccctcgactttctatagactattatagcataatatgcagtacaacatcttttaaatcctctgcgacattaaagacgacatcatataaatgaccaaatnnnnnnnggcgcaaaagcgccagttcat tccctcgactttctatagactattatagcataatatgcagtacaacatcttttaaatcctctgcgacattaaagacgacatcatataaatgaccaaataaaaaaaggcgcaaaagcgccagttcat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCUCGACUUUCUAUAGACUAUUAUAGCAUAAUAUGCAGUACAACAUCUUUUAAAUCCUCUGCGACAUUAAAGACGACAUCAUAUAAAUGACCAAAUAAAAAAAGGCGCAAAAGCGCCAGUUCAU ....(((.((((((((((....)))))).......(((((....................))))).....)))).)))..((((....)))).............(((((....)))))....... (-19.05) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAACUGGCGCUUUUGCGCCUUUUUUUAUUUGGUCAUUUAUAUGAUGUCGUCUUUAAUGUCGCAGAGGAUUUAAAAGAUGUUGUACUGCAUAUUAUGCUAUAAUAGUCUAUAGAAAGUCGAGGGA .......(((((....)))))............(((((....))))).(((.(((((((((.(((((.(((.........))).).))))))))))..(((((......))))).))).))).... (-26.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 833 50 1 141 92 NC_009009:SSA_2271|5end_hypothetical_protein_2272450..2272680_NEGATIVE 258 34 2 134 99 NC_009009:SSA_2241|5end_Conserved_uncharacterized_protein_2237943..2238173_NEGATIVE 246 119 96 197 173 NC_009009:SSA_1561|5end_Ribonuclease_III,_putative_1565883..1566113_NEGATIVE 245 78 57 49 26 NC_009009:SSA_0565|5end_hypothetical_protein_557230..557460_POSITIVE 244 75 35 118 65 NC_009009:SSA_0202|5end_hypothetical_protein_200534..200764_POSITIVE 226 79 36 128 87 NC_009009:SSA_1312|5end_RADC-like_protein,_putative_1329663..1329893_NEGATIVE 221 79 36 115 63 NC_009009:SSA_2212|5end_Possible_polysaccharide_transport_protein,_putative_2213928..2214158_NEGATIVE 221 65 23 113 73 NC_009009:SSA_1027|5end_hypothetical_protein_1043527..1043757_POSITIVE 216 69 21 207 137 NC_009009:SSA_0766|5end_hypothetical_protein_746242..746472_POSITIVE 213 50 2 149 99 NC_009009:SSA_0668|5end_hypothetical_protein_650737..650967_POSITIVE 210 59 11 137 82 NC_009009:SSA_0063|5end_Holliday_junction_DNA_helicase_ruvB,_putative_65335..65565_POSITIVE 209 41 1 128 93 NC_009009:SSA_1928|5end_Acyl-CoA_dehydrogenase,_putative_1917010..1917240_NEGATIVE 202 33 3 130 98 NC_009009:SSA_1271|5end_Conserved_uncharacterized_protein_1293972..1294202_POSITIVE 202 95 56 71 24 NC_009009:SSA_0636|5end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625184..625414_POSITIVE 201 84 42 163 124 NC_009009:SSA_0777|5end_Glycogen_biosynthesis_protein_GlgD,_putative_759430..759660_POSITIVE 199 94 56 207 174 NC_009009:SSA_0124|5end_30S_ribosomal_protein_S5,_putative_116422..116652_POSITIVE 196 42 2 157 102 NC_009009:SSA_2022|5end_Transcriptional_regulator,_MerR_family_(multidrug-efflux_transporter_genes),_putative_2023572..2023802_POSITIVE 196 29 1 65 33 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 195 41 1 132 95 NC_009009:SSA_1655|5end_hypothetical_protein_1651816..1652046_NEGATIVE 195 40 3 136 97 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 246 119 96 75 51 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 244 75 35 116 63 NC_009009:SSA_0201|3end_ABC_multidrug_transporter_(3-component_subtilin_immunity_exporter),_putative_200612..200762_POSITIVE 241 120 72 89 38 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 240 110 61 149 98 NC_009009:SSA_1065|3end_Beta-hexosamidase_A,_putative_1084130..1084280_POSITIVE 226 50 1 88 41 NC_009009:SSA_2252|3end_hypothetical_protein_2248212..2248362_NEGATIVE 226 79 36 76 35 NC_009009:SSA_1313|3end_hypothetical_protein_1329715..1329865_NEGATIVE 221 65 23 123 83 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 217 100 57 43 5 NC_009009:SSA_2080|3end_hypothetical_protein_2084598..2084748_NEGATIVE 217 41 2 48 7 NC_009009:SSA_1532|3end_Membrane-fusion_protein_/_periplasmic_component_of_efflux_system,_putative_1539460..1539610_NEGATIVE 213 50 2 89 39 NC_009009:SSA_0667|3end_Transcriptional_regulator,_putative_650757..650907_POSITIVE 209 41 1 109 74 NC_009009:SSA_1929|3end_Macrophage_infectivity_potentiator_protein,_putative_1917029..1917179_NEGATIVE 206 59 16 106 58 NC_009009:SSA_0698|3end_Peptide_chain_release_factor_3,_putative_682007..682157_POSITIVE 202 60 21 92 40 NC_009009:SSA_2209|3end_Penicillin-binding_protein_2A,_putative_2208144..2208294_NEGATIVE 195 41 1 68 31 NC_009009:SSA_1656|3end_Nisin_resistance_protein,_putative_1651880..1652030_NEGATIVE 193 38 1 115 82 NC_009009:SSA_1428|3end_hypothetical_protein_1435638..1435788_NEGATIVE 193 119 100 83 61 NC_009009:SSA_0774|3end_NADP-dependent_glyceraldehyde-3-phosphate_dehydrogenase,_putative_756075..756225_POSITIVE 192 120 76 40 1 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 190 118 106 118 105 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 189 88 46 49 6 NC_009009:SSA_1710|3end_Transcriptional_regulator,_XRE_family,_putative_1699011..1699161_POSITIVE 189 82 58 141 114 NC_009009:SSA_1646|3end_hypothetical_protein_1646322..1646472_NEGATIVE