Origin IGS: acgaaattccttggatgttagaaaaccaaggaattttttctatgaaacaaggaatatagtcgcactattatgaaagagaacagacaagcaaagaaaaagaggaaagtaaaactgcagctacctttgacaaatgagctgaatcaagattagattttgtatttcaaaaatttattggaacttttgtctttatgcgtttgtcgtgtcatcataaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttatgatgacacgacaaacgcataaagacaaaagttccaataaatttttgaaatacaaaatctaatcttgattcagctcatttgtcaaaggtagctgcagttttactttcctctttttctttgcttgtctgttctctttcataatagtgcgactatattccttgtttcatagaaaaaattccttggttttctaacatccaaggaatttcgt Mask Tandem Repeat Region ================================================ acgaaattccttggatgttagaaaaccaaggaattttttctatgaaacaaggaatatagtcgcactattatgaaagagaacagacaagcaaagaaaaagaggaaagtaaaactgcagctacctttgacaaatgagctgaatcaagattagattttgtatttcaaaaatttattggaacttttgtctttatgcgtttgtcgtgtcatcataaa Find is-nt database================================================ Query_seq: SSA_2247:SSA_2248|SSA_2247:SSA_2248:hypothetical protein:hypothetical protein:-><-:2243196..2243407 212 acgaaattccttggatgttagaaaaccaaggaattttttctatgaaacaaggaatatagtcgcactattatgaaagagaacagacaagcaaagaaaaagaggaaagtaaaactgcagctacctttgacaaatgagctgaatcaagattagattttgtatttcaaaaatttattggaacttttgtctttatgcgtttgtcgtgtcatcataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2247:SSA_2248|SSA_2247:SSA_2248:hypothetical protein:hypothetical protein:-><-:2243196..2243407 212 acgaaattccttggatgttagaaaaccaaggaattttttctatgaaacaaggaatatagtcgcactattatgaaagagaacagacaagcaaagaaaaagaggaaagtaaaactgcagctacctttgacaaatgagctgaatcaagattagattttgtatttcaaaaatttattggaacttttgtctttatgcgtttgtcgtgtcatcataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2247:SSA_2248|SSA_2247:SSA_2248:hypothetical protein:hypothetical protein:-><-:2243196..2243407 212 acgaaattccttggatgttagaaaaccaaggaattttttctatgaaacaaggaatatagtcgcactattatgaaagagaacagacaagcaaagaaaaagaggaaagtaaaactgcagctacctttgacaaatgagctgaatcaagattagattttgtatttcaaaaatttattggaacttttgtctttatgcgtttgtcgtgtcatcataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgaaattccttggatgttagaaaaccaaggaattttttctatgaaacaaggaatatagtcgcactattatgaaagagaacagacaagcaaagaaaaagaggaaagtaaaactgcagctacctttgacaaatgagctgaatcaagattagattttgtatttcaaaaatttattggaacttttgtctttatgcgtttgtcgtgtcatcataaa Predict ORF larger than 30AA ================================================ acgaaattccttggatgttagaaaaccaaggaattttttctatgaaacaaggaatatagtcgcactattatgaaagagaacagacaagcaaagaaaaagaggaaagtaaaactgcagctacctttgacaaatgagctgaatcaagattagattttgtatttcaaaaatttattggaacttttgtctttatgcgtttgtcgtgtcatcataaa 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: 81 Start: 123 End: 152 ..........................................................................................................................TTTGACAAATGAGCTGAATCAAGATTAGAT............................................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 180 End: 209 ...................................................................................................................................................................................TTTGTCTTTATGCGTTTGTCGTGTCATCAT... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acgaaattccttggatgttagaaaaccaaggaattttttctatgaaacaaggaatatagtcgcactattatgaaagagaacagacaagcaaagaaaaagaggaaagtaaaactgcagctacctttgacaaatgagctgaatcaagattagattttgtatttcaaaaatttattggaacttttgtctttatgcgtttgtcgtgtcatcataaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2247:SSA_2248|SSA_2247:SSA_2248:hypothetical protein:hypothetical protein:-><-:2243196..2243407 212 acgaaattccttggatgttagaaaaccaaggaattttttctatgaaacaaggaatatagtcgcactattatgaaagagaacagacaagcaaagaaaaagaggaaagtaaaactgcagctacctttgacaaatgagctgaatcaagattagattttgtatttcaaaaatttattggaacttttgtctttatgcgtttgtcgtgtcatcataaa Intra-Species Hit: Count: 1 Min: 1 Max: 212 Len: 212 Subject: NC_009009_SSA_2247_SSA_2248|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[2243196,2243407]|212 HSP 1 e-value: 1.0E-117 bit: 420.0 Len: 212 Query Start:1 Query End:212 Subject Strand: POSITIVE Subject Start: 1 Subject End: 212 acgaaattccttggatgttagaaaaccaaggaattttttctatgaaacaaggaatatagtcgcactattatgaaagagaacagacaagcaaagaaaaagaggaaagtaaaactgcagctacctttgacaaatgagctgaatcaagattagattttgtatttcaaaaatttattggaacttttgtctttatgcgtttgtcgtgtcatcataaa acgaaattccttggatgttagaaaaccaaggaattttttctatgaaacaaggaatatagtcgcactattatgaaagagaacagacaagcaaagaaaaagaggaaagtaaaactgcagctacctttgacaaatgagctgaatcaagattagattttgtatttcaaaaatttattggaacttttgtctttatgcgtttgtcgtgtcatcataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGAAAUUCCUUGGAUGUUAGAAAACCAAGGAAUUUUUUCUAUGAAACAAGGAAUAUAGUCGCACUAUUAUGAAAGAGAACAGACAAGCAAAGAAAAAGAGGAAAGUAAAACUGCAGCUACCUUUGACAAAUGAGCUGAAUCAAGAUUAGAUUUUGUAUUUCAAAAAUUUAUUGGAACUUUUGUCUUUAUGCGUUUGUCGUGUCAUCAUAAA .(((.((((((((.....(((((((..........))))))).....))))))))....))).....((((((..((.(...(((((((......(((((.((((((.......(((((....((....))..)))))..((((...((((((((........)))))))))))).)))))).)))))....))))))).).)).)))))). (-47.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUGAUGACACGACAAACGCAUAAAGACAAAAGUUCCAAUAAAUUUUUGAAAUACAAAAUCUAAUCUUGAUUCAGCUCAUUUGUCAAAGGUAGCUGCAGUUUUACUUUCCUCUUUUUCUUUGCUUGUCUGUUCUCUUUCAUAAUAGUGCGACUAUAUUCCUUGUUUCAUAGAAAAAAUUCCUUGGUUUUCUAACAUCCAAGGAAUUUCGU (((((((.((((.(((((..(((.(((((..(((((..........(((((.....))))).........(((((((((.((((.....))))))))).))))..)))))..))))).....))))))))..............((((.....))))......)))))))))))..(((((((((((...........)))))))))))... (-41.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 127 86 159 120 NC_009009:SSA_1800|5end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1782371..1782601_NEGATIVE 298 160 114 197 141 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 281 139 98 187 134 NC_009009:SSA_2366|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368869..2369099_NEGATIVE 265 153 111 208 156 NC_009009:SSA_2199|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit,_putative_2201108..2201338_NEGATIVE 261 89 48 192 150 NC_009009:SSA_1561|5end_Ribonuclease_III,_putative_1565883..1566113_NEGATIVE 255 125 82 106 57 NC_009009:SSA_1665|5end_hypothetical_protein_1665353..1665583_NEGATIVE 254 137 95 52 10 NC_009009:SSA_1390|5end_hypothetical_protein_1406118..1406348_NEGATIVE 251 210 172 38 3 NC_009009:SSA_1676|5end_Transcriptional_regulator,_LytTr_family,_putative_1671313..1671543_NEGATIVE 248 169 121 80 29 NC_009009:SSA_1981|5end_hypothetical_protein_1975421..1975651_NEGATIVE 246 78 35 197 148 NC_009009:SSA_1370|5end_CAAX_amino_terminal_protease_family,_putative_1386968..1387198_NEGATIVE 246 86 42 90 45 NC_009009:SSA_0274|5end_hypothetical_protein_269557..269787_NEGATIVE 237 210 172 92 47 NC_009009:SSA_0326|5end_Conserved_uncharacterized_BCR,_YbaB_family_319823..320053_NEGATIVE 235 190 141 152 103 NC_009009:SSA_0610|5end_LemA-like_protein,_putative_598968..599198_POSITIVE 234 87 56 39 3 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 233 119 71 179 135 NC_009009:SSA_0214|5end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210215..210445_POSITIVE 232 159 112 209 158 NC_009009:SSA_2058|5end_30S_ribosomal_protein_S15,_putative_2060354..2060584_NEGATIVE 231 120 75 52 3 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 227 138 115 27 1 NC_009009:SSA_1137|5end_Dihydrolipoamide_dehydrogenase,_putative_1164375..1164605_POSITIVE 224 207 161 167 127 NC_009009:SSA_1680|5end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1675200..1675430_NEGATIVE 224 207 161 168 128 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 160 114 79 23 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 261 89 48 70 28 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 258 209 167 137 100 NC_009009:SSA_0660|3end_Cell_division_protein_DivIVA,_putative_644672..644822_POSITIVE 255 125 82 84 35 NC_009009:SSA_1666|3end_Collagen-binding_surface_protein,_putative_1665375..1665525_NEGATIVE 252 41 3 74 39 NC_009009:SSA_0860|3end_N-acetylmuramidase/lysin,_putative_851738..851888_POSITIVE 248 169 121 74 23 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 246 78 35 114 65 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 234 87 56 37 1 NC_009009:SSA_2167|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165644..2165794_NEGATIVE 232 159 112 69 18 NC_009009:SSA_2059|3end_16S_rRNA_uridine-516_pseudouridylate_synthase,_putative_2060494..2060644_NEGATIVE 225 138 97 59 20 NC_009009:SSA_2094|3end_Conserved_uncharacterized_protein_2097990..2098140_NEGATIVE 222 119 76 79 25 NC_009009:SSA_1852|3end_Metal_dependent_phosphohydrolase_(HD_motif),_putative_1846869..1847019_NEGATIVE 220 127 81 60 15 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 218 162 129 30 1 NC_009009:SSA_1686|3end_hypothetical_protein_1680470..1680620_POSITIVE 217 125 85 64 31 NC_009009:SSA_1661|3end_hypothetical_protein_1657759..1657909_NEGATIVE 217 160 114 87 36 NC_009009:SSA_0477|3end_Cobalamin_biosynthesis_protein_CbiM_(ABC-type_cobalt_transporter),_putative_480085..480235_POSITIVE 214 63 28 118 77 NC_009009:SSA_0782|3end_Proton-translocating_ATPase,_F0_sector,_subunit_c,_putative_766859..767009_POSITIVE 213 156 112 88 41 NC_009009:SSA_1553|3end_Permease,_putative_1556032..1556182_POSITIVE 211 208 166 101 56 NC_009009:SSA_1278|3end_Rhodanese-like_domain_protein,_putative_1299563..1299713_NEGATIVE 211 190 144 83 41 NC_009009:SSA_0909|3end_Transcriptional_regulator,_AbrB_family_(stationary/sporulation_gene_expression),_putative_921158..921308_POSITIVE 211 143 103 89 44 NC_009009:SSA_0066|3end_hypothetical_protein_68095..68245_POSITIVE