Origin IGS: aatggcggaacgagatgaaatgataaatatttcgttcctttcgctttttcatctcggcttgtatctacaagcaatcatctgctattgagtaagtgactgggatgtcaggaagtttttgctataaaaaggtgaggctgaaacatgattttctaagcctcttttagaaaaggagcagcaggttggactcaacttttttaaatcatatc .........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 gatatgatttaaaaaagttgagtccaacctgctgctccttttctaaaagaggcttagaaaatcatgtttcagcctcacctttttatagcaaaaacttcctgacatcccagtcacttactcaatagcagatgattgcttgtagatacaagccgagatgaaaaagcgaaaggaacgaaatatttatcatttcatctcgttccgccatt Mask Tandem Repeat Region ================================================ aatggcggaacgagatgaaatgataaatatttcgttcctttcgctttttcatctcggcttgtatctacaagcaatcatctgctattgagtaagtgactgggatgtcaggaagtttttgctataaaaaggtgaggctgaaacatgattttctaagcctcttttagaaaaggagcagcaggttggactcaacttttttaaatcatatc Find is-nt database================================================ Query_seq: SSA_0150:SSA_0151|SSA_0150:SSA_0151:hypothetical protein:hypothetical protein:->->:145288..145493 206 aatggcggaacgagatgaaatgataaatatttcgttcctttcgctttttcatctcggcttgtatctacaagcaatcatctgctattgagtaagtgactgggatgtcaggaagtttttgctataaaaaggtgaggctgaaacatgattttctaagcctcttttagaaaaggagcagcaggttggactcaacttttttaaatcatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0150:SSA_0151|SSA_0150:SSA_0151:hypothetical protein:hypothetical protein:->->:145288..145493 206 aatggcggaacgagatgaaatgataaatatttcgttcctttcgctttttcatctcggcttgtatctacaagcaatcatctgctattgagtaagtgactgggatgtcaggaagtttttgctataaaaaggtgaggctgaaacatgattttctaagcctcttttagaaaaggagcagcaggttggactcaacttttttaaatcatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0150:SSA_0151|SSA_0150:SSA_0151:hypothetical protein:hypothetical protein:->->:145288..145493 206 aatggcggaacgagatgaaatgataaatatttcgttcctttcgctttttcatctcggcttgtatctacaagcaatcatctgctattgagtaagtgactgggatgtcaggaagtttttgctataaaaaggtgaggctgaaacatgattttctaagcctcttttagaaaaggagcagcaggttggactcaacttttttaaatcatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatggcggaacgagatgaaatgataaatatttcgttcctttcgctttttcatctcggcttgtatctacaagcaatcatctgctattgagtaagtgactgggatgtcaggaagtttttgctataaaaaggtgaggctgaaacatgattttctaagcctcttttagaaaaggagcagcaggttggactcaacttttttaaatcatatc Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 85 End: 189 .................................................................................... Q T L S Q S T L F N K S Y F P S A S V H N E L G R K S F S C C T P S M ................. aatggcggaacgagatgaaatgataaatatttcgttcctttcgctttttcatctcggcttgtatctacaagcaatcatctgctattgagtaagtgactgggatgtcaggaagtttttgctataaaaaggtgaggctgaaacatgattttctaagcctcttttagaaaaggagcagcaggttggactcaacttttttaaatcatatc 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================================================ aatggcggaacgagatgaaatgataaatatttcgttcctttcgctttttcatctcggcttgtatctacaagcaatcatctgctattgagtaagtgactgggatgtcaggaagtttttgctataaaaaggtgaggctgaaacatgattttctaagcctcttttagaaaaggagcagcaggttggactcaacttttttaaatcatatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -3.6 Tail_Score: -2.84801 Start: 146 End: 168 Full_Region: ccaacctgctgctcc ttttctaa aagaggc ttagaaaa tcatgtttcagcctc .................................................................................................................................................ttttctaaaagaggcttagaaaa...................................... TransTerm Strand: + Conf: 75 HP_score: -4.4 Tail_Score: -5.11613 Start: 179 End: 190 Full_Region: GAAAAGGAGCAGCAG GTTG GACT CAAC TTTTTTAAATCATAT ..................................................................................................................................................................................GTTGGACTCAAC................ Find igs database================================================ Query_seq: SSA_0150:SSA_0151|SSA_0150:SSA_0151:hypothetical protein:hypothetical protein:->->:145288..145493 206 aatggcggaacgagatgaaatgataaatatttcgttcctttcgctttttcatctcggcttgtatctacaagcaatcatctgctattgagtaagtgactgggatgtcaggaagtttttgctataaaaaggtgaggctgaaacatgattttctaagcctcttttagaaaaggagcagcaggttggactcaacttttttaaatcatatc Intra-Species Hit: Count: 1 Min: 1 Max: 206 Len: 206 Subject: NC_009009_SSA_0150_SSA_0151|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[145288,145493]|206 HSP 1 e-value: 1.0E-113 bit: 408.0 Len: 206 Query Start:1 Query End:206 Subject Strand: POSITIVE Subject Start: 1 Subject End: 206 aatggcggaacgagatgaaatgataaatatttcgttcctttcgctttttcatctcggcttgtatctacaagcaatcatctgctattgagtaagtgactgggatgtcaggaagtttttgctataaaaaggtgaggctgaaacatgattttctaagcctcttttagaaaaggagcagcaggttggactcaacttttttaaatcatatc aatggcggaacgagatgaaatgataaatatttcgttcctttcgctttttcatctcggcttgtatctacaagcaatcatctgctattgagtaagtgactgggatgtcaggaagtttttgctataaaaaggtgaggctgaaacatgattttctaagcctcttttagaaaaggagcagcaggttggactcaacttttttaaatcatatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGGCGGAACGAGAUGAAAUGAUAAAUAUUUCGUUCCUUUCGCUUUUUCAUCUCGGCUUGUAUCUACAAGCAAUCAUCUGCUAUUGAGUAAGUGACUGGGAUGUCAGGAAGUUUUUGCUAUAAAAAGGUGAGGCUGAAACAUGAUUUUCUAAGCCUCUUUUAGAAAAGGAGCAGCAGGUUGGACUCAACUUUUUUAAAUCAUAUC .((((((((((((((((..........)))))))))))....(((((((((((((.((((((....))))))..(((..((((....))))..)))..))))))..)))))))....)))))........((((((((((......))))..)))))).((((((((((((((((....)))..)))..))))))))))....... (-56.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAUGAUUUAAAAAAGUUGAGUCCAACCUGCUGCUCCUUUUCUAAAAGAGGCUUAGAAAAUCAUGUUUCAGCCUCACCUUUUUAUAGCAAAAACUUCCUGACAUCCCAGUCACUUACUCAAUAGCAGAUGAUUGCUUGUAGAUACAAGCCGAGAUGAAAAAGCGAAAGGAACGAAAUAUUUAUCAUUUCAUCUCGUUCCGCCAUU .....(((((((.....)))))))....((((((..............((((((..((((......)))))))))).......................((((......)))).........))))))......((((((....))))))((((((((((...(....)....((........)).)))))))))).......... (-43.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 118 73 136 93 NC_009009:SSA_0967|5end_hypothetical_protein_975872..976102_POSITIVE 310 193 154 130 95 NC_009009:SSA_0393|5end_Bacteriocin_ABC-type_exporter,_ATP_binding/permease_protein,_putative_388766..388996_POSITIVE 308 120 71 209 151 NC_009009:SSA_0397|5end_hypothetical_protein_394657..394887_NEGATIVE 305 160 111 103 53 NC_009009:SSA_0142|5end_hypothetical_protein_137230..137460_POSITIVE 299 83 41 60 19 NC_009009:SSA_0923|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933010..933240_POSITIVE 298 119 71 201 138 NC_009009:SSA_0370|5end_Acetyltransferase,_GNAT_family,_putative_360382..360612_NEGATIVE 296 137 98 190 147 NC_009009:SSA_1269|5end_hypothetical_protein_1293352..1293582_NEGATIVE 292 118 72 180 140 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 290 77 31 201 149 NC_009009:SSA_1390|5end_hypothetical_protein_1406118..1406348_NEGATIVE 288 77 31 157 122 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 286 177 133 178 132 NC_009009:SSA_1558|5end_Hydrolase,_HAD_superfamily_1560862..1561092_NEGATIVE 286 193 153 59 14 NC_009009:SSA_1188|5end_Ribonuclease_HII,_putative_1216819..1217049_NEGATIVE 285 120 77 198 149 NC_009009:SSA_0021|5end_hypothetical_protein_26842..27072_POSITIVE 284 160 114 54 3 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 281 187 142 155 112 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 279 194 155 141 101 NC_009009:SSA_2006|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme,_putative_2007215..2007445_NEGATIVE 277 177 131 107 63 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 274 86 42 163 123 NC_009009:SSA_2227|5end_Acetyl_transferase,_putative_2228261..2228491_NEGATIVE 274 83 50 68 37 NC_009009:SSA_1699|5end_hypothetical_protein_1691096..1691326_NEGATIVE 274 137 93 51 2 NC_009009:SSA_1084|5end_Conserved_uncharacterized_protein_1101675..1101905_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 160 111 91 43 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 308 82 41 132 96 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 296 137 98 66 23 NC_009009:SSA_1270|3end_Flavodoxin_1293476..1293626_NEGATIVE 292 160 113 74 28 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 288 68 26 145 104 NC_009009:SSA_1391|3end_hypothetical_protein_1406158..1406308_NEGATIVE 286 193 153 72 27 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 285 83 41 139 111 NC_009009:SSA_0994|3end_Peptidase_E,_putative_995390..995540_POSITIVE 285 98 56 60 10 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 281 187 142 140 97 NC_009009:SSA_1011|3end_hypothetical_protein_1014804..1014954_POSITIVE 279 137 97 48 1 NC_009009:SSA_1083|3end_Conserved_uncharacterized_protein_1101752..1101902_POSITIVE 273 180 133 52 1 NC_009009:SSA_1780|3end_Tyrosine_recombinase_xerD,_putative_1766416..1766566_NEGATIVE 272 158 116 137 83 NC_009009:SSA_0725|3end_hypothetical_protein_710812..710962_POSITIVE 271 197 154 47 8 NC_009009:SSA_2017|3end_Hypothetical_protein_(possibly_membrane-associated)_2016435..2016585_NEGATIVE 269 195 159 90 49 NC_009009:SSA_0015|3end_Membrane_ATPase_FtsH,_degrades_sigma32_(integral_membrane_cell-division_Zn_metallo-peptidase),_putative_15097..15247_POSITIVE 264 70 22 99 49 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 264 100 51 71 15 NC_009009:SSA_1941|3end_hypothetical_protein_1927129..1927279_NEGATIVE 262 79 31 108 56 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 261 159 115 75 36 NC_009009:SSA_0691|3end_D-ala,D-ala_ligase,_putative_676374..676524_POSITIVE 258 110 64 51 1 NC_009009:SSA_1034|3end_Conserved_uncharacterized_protein_1050252..1050402_POSITIVE 257 60 11 140 81 NC_009009:SSA_1118|3end_Peptide_methionine_sulfoxide_reductase,_putative_1144511..1144661_POSITIVE