Origin IGS: gtagagggcccgacaaatttcagaaaaacagaaaatctatatattaacctattgaaaacttcctctttctatggtatgatgaaagaggtctcaagaatcgttgggaggataagac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtcttatcctcccaacgattcttgagacctctttcatcataccatagaaagaggaagttttcaataggttaatatatagattttctgtttttctgaaatttgtcgggccctctac Mask Tandem Repeat Region ================================================ gtagagggcccgacaaatttcagaaaaacagaaaatctatatattaacctattgaaaacttcctctttctatggtatgatgaaagaggtctcaagaatcgttgggaggataagac Find is-nt database================================================ Query_seq: SSA_0069:SSA_0070|SSA_0069:SSA_0070:Hypothetical protein, possibly membrane-associated:Acetylxylan esterase, putative:->->:73858..73972 115 gtagagggcccgacaaatttcagaaaaacagaaaatctatatattaacctattgaaaacttcctctttctatggtatgatgaaagaggtctcaagaatcgttgggaggataagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0069:SSA_0070|SSA_0069:SSA_0070:Hypothetical protein, possibly membrane-associated:Acetylxylan esterase, putative:->->:73858..73972 115 gtagagggcccgacaaatttcagaaaaacagaaaatctatatattaacctattgaaaacttcctctttctatggtatgatgaaagaggtctcaagaatcgttgggaggataagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0069:SSA_0070|SSA_0069:SSA_0070:Hypothetical protein, possibly membrane-associated:Acetylxylan esterase, putative:->->:73858..73972 115 gtagagggcccgacaaatttcagaaaaacagaaaatctatatattaacctattgaaaacttcctctttctatggtatgatgaaagaggtctcaagaatcgttgggaggataagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtagagggcccgacaaatttcagaaaaacagaaaatctatatattaacctattgaaaacttcctctttctatggtatgatgaaagaggtctcaagaatcgttgggaggataagac Predict ORF larger than 30AA ================================================ gtagagggcccgacaaatttcagaaaaacagaaaatctatatattaacctattgaaaacttcctctttctatggtatgatgaaagaggtctcaagaatcgttgggaggataagac 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: 89 Start: 51 End: 80 ..................................................ATTGAAAACTTCCTCTTTCTATGGTATGAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtagagggcccgacaaatttcagaaaaacagaaaatctatatattaacctattgaaaacttcctctttctatggtatgatgaaagaggtctcaagaatcgttgggaggataagac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0069:SSA_0070|SSA_0069:SSA_0070:Hypothetical protein, possibly membrane-associated:Acetylxylan esterase, putative:->->:73858..73972 115 gtagagggcccgacaaatttcagaaaaacagaaaatctatatattaacctattgaaaacttcctctttctatggtatgatgaaagaggtctcaagaatcgttgggaggataagac Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_009009_SSA_0069_SSA_0070|Hypothetical protein, possibly membrane-associated:Acetylxylan esterase, putative|POSITIVE:POSITIVE|[73858,73972]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 gtagagggcccgacaaatttcagaaaaacagaaaatctatatattaacctattgaaaacttcctctttctatggtatgatgaaagaggtctcaagaatcgttgggaggataagac gtagagggcccgacaaatttcagaaaaacagaaaatctatatattaacctattgaaaacttcctctttctatggtatgatgaaagaggtctcaagaatcgttgggaggataagac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAGAGGGCCCGACAAAUUUCAGAAAAACAGAAAAUCUAUAUAUUAACCUAUUGAAAACUUCCUCUUUCUAUGGUAUGAUGAAAGAGGUCUCAAGAAUCGUUGGGAGGAUAAGAC ........((((((...((((.........)))).................((((......((((((((...........))))))))..)))).....)))))).......... (-21.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUUAUCCUCCCAACGAUUCUUGAGACCUCUUUCAUCAUACCAUAGAAAGAGGAAGUUUUCAAUAGGUUAAUAUAUAGAUUUUCUGUUUUUCUGAAAUUUGUCGGGCCCUCUAC ..........(((.((((...((.(((((((((((...........))))))))........((((((..(((......))).))))))..))).))..)))).)))........ (-20.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 107 62 148 97 NC_009009:SSA_0366|5end_hypothetical_protein_357506..357736_POSITIVE 296 109 64 126 69 NC_009009:SSA_2162|5end_hypothetical_protein_2160592..2160822_POSITIVE 290 106 64 53 4 NC_009009:SSA_1611|5end_Era-like_GTP-binding_protein,_putative_1616032..1616262_NEGATIVE 274 104 61 224 185 NC_009009:SSA_0214|5end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210215..210445_POSITIVE 272 97 51 224 172 NC_009009:SSA_0365|5end_Small-conductance_mechanosensitive_efflux_channel,_putative_356621..356851_POSITIVE 260 93 59 133 95 NC_009009:SSA_1276|5end_Conserved_uncharacterized_protein_1298446..1298676_NEGATIVE 260 108 72 65 25 NC_009009:SSA_0155|5end_hypothetical_protein_150961..151191_POSITIVE 256 92 53 134 91 NC_009009:SSA_1096|5end_Methyltransferase,_putative_1113072..1113302_POSITIVE 253 108 62 230 178 NC_009009:SSA_0538|5end_PduH_protein,_putative_533794..534024_POSITIVE 250 107 66 38 7 NC_009009:SSA_0861|5end_hypothetical_protein_852977..853207_NEGATIVE 250 99 64 209 168 NC_009009:SSA_0215|5end_Periplasmic_sugar-binding_protein_(ribose_porter),_putative_210891..211121_POSITIVE 242 106 61 66 15 NC_009009:SSA_2051|5end_Oligoendopeptidase,_putative_2054731..2054961_POSITIVE 238 109 81 27 2 NC_009009:SSA_0137|5end_ABC_transporter_(permease),_Zn_porter,_putative_131717..131947_POSITIVE 237 100 57 53 5 NC_009009:SSA_2108|5end_Glyceraldehyde_3-phosphate_dehydrogenase,_putative_2112464..2112694_NEGATIVE 237 100 59 149 96 NC_009009:SSA_1695|5end_Transcriptional_antiterminator,_BglG/SacY_family_(induction_of_sugar_metabolism),_putative_1688010..1688240_NEGATIVE 237 109 61 45 5 NC_009009:SSA_0302|5end_Phosphoglycerate_kinase,_putative_294890..295120_POSITIVE 232 96 56 62 22 NC_009009:SSA_1422|5end_hypothetical_protein_1431555..1431785_NEGATIVE 232 110 61 153 92 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 230 105 63 95 41 NC_009009:SSA_1614|5end_Acetyltransferase,_GNAT_family,_putative_1618045..1618275_NEGATIVE 230 107 61 140 95 NC_009009:SSA_1252|5end_hypothetical_protein_1277505..1277735_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 107 62 126 75 NC_009009:SSA_0365|3end_Small-conductance_mechanosensitive_efflux_channel,_putative_357564..357714_POSITIVE 260 93 59 103 65 NC_009009:SSA_1277|3end_D-alanyl-D-alanine_carboxypeptidase_1298476..1298626_NEGATIVE 256 92 53 70 27 NC_009009:SSA_1095|3end_Peptidoglycan_hydrolase,_putative_1113088..1113238_POSITIVE 249 109 84 34 7 NC_009009:SSA_0136|3end_ABC_transporter,_Zn_porter,_putative_131804..131954_POSITIVE 242 38 2 62 33 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE 232 96 56 56 16 NC_009009:SSA_1423|3end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1431561..1431711_NEGATIVE 230 107 61 149 95 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 229 100 56 52 9 NC_009009:SSA_1194|3end_Aspartate-semialdehyde_dehydrogenase,_putative_1220113..1220263_NEGATIVE 222 88 55 79 49 NC_009009:SSA_0768|3end_Ribonucleoside-diphosphate_reductase_2,_beta_subunit,_putative_748136..748286_NEGATIVE 216 108 82 87 63 NC_009009:SSA_1723|3end_hypothetical_protein_1709893..1710043_POSITIVE 216 110 61 137 81 NC_009009:SSA_1535|3end_hypothetical_protein_1542457..1542607_NEGATIVE 213 93 59 107 79 NC_009009:SSA_1897|3end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894154..1894304_NEGATIVE 213 97 60 63 16 NC_009009:SSA_0305|3end_hypothetical_protein_302589..302739_POSITIVE 209 108 63 142 100 NC_009009:SSA_1086|3end_TRNA_nucleotidyltransferase,_putative_1104607..1104757_POSITIVE 208 105 65 104 57 NC_009009:SSA_1144|3end_Beta-N-acetylhexosaminidase,_putative_1173649..1173799_NEGATIVE 207 104 61 136 98 NC_009009:SSA_2013|3end_hypothetical_protein_2013470..2013620_NEGATIVE 207 103 61 127 82 NC_009009:SSA_0519|3end_Ethanolamine_ammonia-lyase_large_subunit,_putative_519525..519675_POSITIVE 206 110 77 43 2 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 205 103 63 58 7 NC_009009:SSA_1667|3end_hypothetical_protein_1667519..1667669_NEGATIVE 205 99 61 139 101 NC_009009:SSA_1050|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1065741..1065891_POSITIVE