Origin IGS: aaaagacgatgtcgcagaagcaatttttttattttctagtcccgagaggacgattaggagtttttagagccccagagagcaagaaaaacccgtcaatcgcctcaccaaaagaaattctttctataataaagcaagctgagacacgattgtcccagcctcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggaggctgggacaatcgtgtctcagcttgctttattatagaaagaatttcttttggtgaggcgattgacgggtttttcttgctctctggggctctaaaaactcctaatcgtcctctcgggactagaaaataaaaaaattgcttctgcgacatcgtctttt Mask Tandem Repeat Region ================================================ aaaagacgatgtcgcagaagcaatttttttattttctagtcccgagaggacgattaggagtttttagagccccagagagcaagaaaaacccgtcaatcgcctcaccaaaagaaattctttctataataaagcaagctgagacacgattgtcccagcctcc Find is-nt database================================================ Query_seq: SSA_2300:SSA_2301|SSA_2300:SSA_2301:hypothetical protein:S-layer protein/ peptidoglycan endo-beta-N-acetylglucosaminidase, putative:<-<-:2302599..2302758 160 aaaagacgatgtcgcagaagcaatttttttattttctagtcccgagaggacgattaggagtttttagagccccagagagcaagaaaaacccgtcaatcgcctcaccaaaagaaattctttctataataaagcaagctgagacacgattgtcccagcctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2300:SSA_2301|SSA_2300:SSA_2301:hypothetical protein:S-layer protein/ peptidoglycan endo-beta-N-acetylglucosaminidase, putative:<-<-:2302599..2302758 160 aaaagacgatgtcgcagaagcaatttttttattttctagtcccgagaggacgattaggagtttttagagccccagagagcaagaaaaacccgtcaatcgcctcaccaaaagaaattctttctataataaagcaagctgagacacgattgtcccagcctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2300:SSA_2301|SSA_2300:SSA_2301:hypothetical protein:S-layer protein/ peptidoglycan endo-beta-N-acetylglucosaminidase, putative:<-<-:2302599..2302758 160 aaaagacgatgtcgcagaagcaatttttttattttctagtcccgagaggacgattaggagtttttagagccccagagagcaagaaaaacccgtcaatcgcctcaccaaaagaaattctttctataataaagcaagctgagacacgattgtcccagcctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaagacgatgtcgcagaagcaatttttttattttctagtcccgagaggacgattaggagtttttagagccccagagagcaagaaaaacccgtcaatcgcctcaccaaaagaaattctttctataataaagcaagctgagacacgattgtcccagcctcc Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 9 End: 158 ........ M S Q K Q F F Y F L V P R G R L G V F R A P E S K K N P S I A S P K E I L S I I K Q A E T R L S Q P .. Protein_Len: 32 Strand: - Start: 32 End: 127 ............................... K R T G L P R N P T K L A G S L L F F G D I A E G F S I R E I M ................................. aaaagacgatgtcgcagaagcaatttttttattttctagtcccgagaggacgattaggagtttttagagccccagagagcaagaaaaacccgtcaatcgcctcaccaaaagaaattctttctataataaagcaagctgagacacgattgtcccagcctcc 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================================================ aaaagacgatgtcgcagaagcaatttttttattttctagtcccgagaggacgattaggagtttttagagccccagagagcaagaaaaacccgtcaatcgcctcaccaaaagaaattctttctataataaagcaagctgagacacgattgtcccagcctcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2300:SSA_2301|SSA_2300:SSA_2301:hypothetical protein:S-layer protein/ peptidoglycan endo-beta-N-acetylglucosaminidase, putative:<-<-:2302599..2302758 160 aaaagacgatgtcgcagaagcaatttttttattttctagtcccgagaggacgattaggagtttttagagccccagagagcaagaaaaacccgtcaatcgcctcaccaaaagaaattctttctataataaagcaagctgagacacgattgtcccagcctcc Intra-Species Hit: Count: 1 Min: 1 Max: 160 Len: 160 Subject: NC_009009_SSA_2300_SSA_2301|hypothetical protein:S-layer protein/ peptidoglycan endo-beta-N-acetylglucosaminidase, putative|NEGATIVE:NEGATIVE|[2302599,2302758]|160 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 aaaagacgatgtcgcagaagcaannnnnnnattttctagtcccgagaggacgattaggagtttttagagccccagagagcaagaaaaacccgtcaatcgcctcaccaaaagaaattctttctataataaagcaagctgagacacgattgtcccagcctcc aaaagacgatgtcgcagaagcaatttttttattttctagtcccgagaggacgattaggagtttttagagccccagagagcaagaaaaacccgtcaatcgcctcaccaaaagaaattctttctataataaagcaagctgagacacgattgtcccagcctcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGACGAUGUCGCAGAAGCAAUUUUUUUAUUUUCUAGUCCCGAGAGGACGAUUAGGAGUUUUUAGAGCCCCAGAGAGCAAGAAAAACCCGUCAAUCGCCUCACCAAAAGAAAUUCUUUCUAUAAUAAAGCAAGCUGAGACACGAUUGUCCCAGCCUCC ....(((...)))..(((((.(((((((((....((.......))((((.(((((.((.((((((...((........))...))))))))...)))))))))....))))))))).)))))............((((.((((....)))).)))).... (-35.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAGGCUGGGACAAUCGUGUCUCAGCUUGCUUUAUUAUAGAAAGAAUUUCUUUUGGUGAGGCGAUUGACGGGUUUUUCUUGCUCUCUGGGGCUCUAAAAACUCCUAAUCGUCCUCUCGGGACUAGAAAAUAAAAAAAUUGCUUCUGCGACAUCGUCUUUU (.(((((((((((....))))))))))).).........((((((.((((((((.(.((((((((((..((((((((...((((....))))...)))))))).)))))).)))).).)))..))))).........((((....)))).....)))))) (-52.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 979 90 41 181 132 NC_009009:SSA_2300|5end_hypothetical_protein_2302508..2302738_NEGATIVE 339 158 114 175 136 NC_009009:SSA_0325|5end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_317603..317833_POSITIVE 336 80 39 227 181 NC_009009:SSA_1015|5end_4-hydroxybenzoate_octaprenyltransferase,_putative_1018703..1018933_POSITIVE 316 90 47 66 9 NC_009009:SSA_0794|5end_Zn-dependent_protease,_putative_775896..776126_POSITIVE 314 79 36 48 10 NC_009009:SSA_0695|5end_hypothetical_protein_678449..678679_POSITIVE 311 158 114 131 90 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 310 107 70 188 151 NC_009009:SSA_1370|5end_CAAX_amino_terminal_protease_family,_putative_1386968..1387198_NEGATIVE 308 118 72 186 145 NC_009009:SSA_1999|5end_hypothetical_protein_1996974..1997204_NEGATIVE 306 106 64 203 169 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 300 104 69 213 175 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 298 78 32 51 3 NC_009009:SSA_1574|5end_Glycosyl_transferase,_family_1,_putative_1577930..1578160_NEGATIVE 297 160 114 64 27 NC_009009:SSA_0026|5end_Fatty_acid/phospholipid_synthesis_protein_plsX,_putative_30473..30703_POSITIVE 296 105 72 74 46 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 294 159 117 137 100 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 288 54 11 221 184 NC_009009:SSA_1731|5end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716808..1717038_NEGATIVE 285 108 66 210 156 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 282 155 117 42 9 NC_009009:SSA_1701|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1692054..1692284_NEGATIVE 281 50 6 215 158 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 281 156 113 146 97 NC_009009:SSA_1260|5end_Phosphopentomutase,_putative_1286963..1287193_NEGATIVE 280 80 32 63 15 NC_009009:SSA_0374|5end_Peptide_methionine_sulfoxide_reductase_msrA/msrB,_putative_363163..363393_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 90 43 150 101 NC_009009:SSA_1065|3end_Beta-hexosamidase_A,_putative_1084130..1084280_POSITIVE 339 158 114 85 46 NC_009009:SSA_0324|3end_Conserved_uncharacterized_protein_317593..317743_POSITIVE 337 160 116 88 39 NC_009009:SSA_1617|3end_hypothetical_protein_1620436..1620586_NEGATIVE 333 159 115 72 28 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 328 157 133 76 51 NC_009009:SSA_0304|3end_Bacterial_cell_wall_degradation_(CHAP/LysM_domains),_putative_301888..302038_POSITIVE 322 159 135 83 59 NC_009009:SSA_1554|3end_hypothetical_protein_1556847..1556997_POSITIVE 311 158 114 83 42 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 310 107 70 105 68 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 298 78 32 49 1 NC_009009:SSA_1575|3end_Glycosyl_transferase,_putative_1577932..1578082_NEGATIVE 298 50 1 111 53 NC_009009:SSA_0052|3end_Transcriptional_regulator,_GntR_family,_putative_55942..56092_NEGATIVE 297 160 114 58 21 NC_009009:SSA_0025|3end_DNA_repair_protein_recO,_putative_30547..30697_POSITIVE 296 105 72 59 31 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 294 159 117 84 47 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 288 54 11 113 76 NC_009009:SSA_1732|3end_Uracil_phosphoribosyltransferase,_putative_1716916..1717066_NEGATIVE 284 159 128 83 50 NC_009009:SSA_1729|3end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1714539..1714689_NEGATIVE 283 157 134 147 125 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 281 54 15 87 45 NC_009009:SSA_2068|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_2070931..2071081_NEGATIVE 281 159 128 41 14 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 281 156 113 132 83 NC_009009:SSA_1261|3end_Ribose-5-phosphate_isomerase_A,_putative_1286977..1287127_NEGATIVE 275 78 31 62 8 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE