Origin IGS: agaaataaaaacgcggctgggacagataatgtctcagcttttaaatagtcgatagctcttgatgcgctagctgatagagctttttctttgtgcgagaaaagtcctgagcagaaagagtttttttgagacgaaatatgttaaaatgaagagagggaggatttcctggaaggagacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagtctccttccaggaaatcctccctctcttcattttaacatatttcgtctcaaaaaaactctttctgctcaggacttttctcgcacaaagaaaaagctctatcagctagcgcatcaagagctatcgactatttaaaagctgagacattatctgtcccagccgcgtttttatttct Mask Tandem Repeat Region ================================================ agaaataaaaacgcggctgggacagataatgtctcagcttttaaatagtcgatagctcttgatgcgctagctgatagagctttttctttgtgcgagaaaagtcctgagcagaaagagtttttttgagacgaaatatgttaaaatgaagagagggaggatttcctggaaggagacta Find is-nt database================================================ Query_seq: SSA_0304:SSA_0305|SSA_0304:SSA_0305:Bacterial cell wall degradation (CHAP/LysM domains), putative:hypothetical protein:->->:301949..302124 176 agaaataaaaacgcggctgggacagataatgtctcagcttttaaatagtcgatagctcttgatgcgctagctgatagagctttttctttgtgcgagaaaagtcctgagcagaaagagtttttttgagacgaaatatgttaaaatgaagagagggaggatttcctggaaggagacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0304:SSA_0305|SSA_0304:SSA_0305:Bacterial cell wall degradation (CHAP/LysM domains), putative:hypothetical protein:->->:301949..302124 176 agaaataaaaacgcggctgggacagataatgtctcagcttttaaatagtcgatagctcttgatgcgctagctgatagagctttttctttgtgcgagaaaagtcctgagcagaaagagtttttttgagacgaaatatgttaaaatgaagagagggaggatttcctggaaggagacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0304:SSA_0305|SSA_0304:SSA_0305:Bacterial cell wall degradation (CHAP/LysM domains), putative:hypothetical protein:->->:301949..302124 176 agaaataaaaacgcggctgggacagataatgtctcagcttttaaatagtcgatagctcttgatgcgctagctgatagagctttttctttgtgcgagaaaagtcctgagcagaaagagtttttttgagacgaaatatgttaaaatgaagagagggaggatttcctggaaggagacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaataaaaacgcggctgggacagataatgtctcagcttttaaatagtcgatagctcttgatgcgctagctgatagagctttttctttgtgcgagaaaagtcctgagcagaaagagtttttttgagacgaaatatgttaaaatgaagagagggaggatttcctggaaggagacta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 71 End: 175 ...................................................................... M I E L F L C A R K V L S R K S F F E T K Y V K M K R G R I S W K E T . Protein_Len: 30 Strand: - Start: 70 End: 159 ..................................................................... S I S S K R Q A L F T R L L F L K K S V F Y T L I F L P L M ................. Protein_Len: 31 Strand: - Start: 44 End: 136 ........................................... I T S L E Q H A L Q Y L K K K T R S F D Q A S L T K K L R F M ........................................ Protein_Len: 44 Strand: - Start: 3 End: 134 .. F L F A A P V S L T E A K L Y D I A R S A S A S L A K E K H S F L G S C F S N K Q S S M .......................................... agaaataaaaacgcggctgggacagataatgtctcagcttttaaatagtcgatagctcttgatgcgctagctgatagagctttttctttgtgcgagaaaagtcctgagcagaaagagtttttttgagacgaaatatgttaaaatgaagagagggaggatttcctggaaggagacta 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================================================ agaaataaaaacgcggctgggacagataatgtctcagcttttaaatagtcgatagctcttgatgcgctagctgatagagctttttctttgtgcgagaaaagtcctgagcagaaagagtttttttgagacgaaatatgttaaaatgaagagagggaggatttcctggaaggagacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0304:SSA_0305|SSA_0304:SSA_0305:Bacterial cell wall degradation (CHAP/LysM domains), putative:hypothetical protein:->->:301949..302124 176 agaaataaaaacgcggctgggacagataatgtctcagcttttaaatagtcgatagctcttgatgcgctagctgatagagctttttctttgtgcgagaaaagtcctgagcagaaagagtttttttgagacgaaatatgttaaaatgaagagagggaggatttcctggaaggagacta Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: NC_009009_SSA_0304_SSA_0305|Bacterial cell wall degradation (CHAP/LysM domains), putative:hypothetical protein|POSITIVE:POSITIVE|[301949,302124]|176 HSP 1 e-value: 7.0E-83 bit: 307.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 agaaataaaaacgcggctgggacagataatgtctcagcttttaaatagtcgatagctcttgatgcgctagctgatagagctttttctttgtgcgagaaaagtcctgagcagaaagagnnnnnnngagacgaaatatgttaaaatgaagagagggaggatttcctggaaggagacta agaaataaaaacgcggctgggacagataatgtctcagcttttaaatagtcgatagctcttgatgcgctagctgatagagctttttctttgtgcgagaaaagtcctgagcagaaagagtttttttgagacgaaatatgttaaaatgaagagagggaggatttcctggaaggagacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAUAAAAACGCGGCUGGGACAGAUAAUGUCUCAGCUUUUAAAUAGUCGAUAGCUCUUGAUGCGCUAGCUGAUAGAGCUUUUUCUUUGUGCGAGAAAAGUCCUGAGCAGAAAGAGUUUUUUUGAGACGAAAUAUGUUAAAAUGAAGAGAGGGAGGAUUUCCUGGAAGGAGACUA .........(((..((((((((((.....))))))))))........(((...((((((....((....))....))))))..((((((.(((.((.......))..))).)))))).........))).......)))...........(((((....)))))...((....)). (-44.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUCUCCUUCCAGGAAAUCCUCCCUCUCUUCAUUUUAACAUAUUUCGUCUCAAAAAAACUCUUUCUGCUCAGGACUUUUCUCGCACAAAGAAAAAGCUCUAUCAGCUAGCGCAUCAAGAGCUAUCGACUAUUUAAAAGCUGAGACAUUAUCUGUCCCAGCCGCGUUUUUAUUUCU (((((.......(((....)))......................................(((((.(((..((((...)))).))).)))))...((((((....((....))....))))))...))))).......((((.((((.....)))).))))............... (-31.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 80 31 158 105 NC_009009:SSA_1324|5end_Ceramide_glucosyltransferase,_putative_1341618..1341848_NEGATIVE 323 97 52 70 17 NC_009009:SSA_2322|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327044..2327274_POSITIVE 322 97 51 158 92 NC_009009:SSA_1743|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1730170..1730400_POSITIVE 320 80 34 166 118 NC_009009:SSA_1379|5end_hypothetical_protein_1398528..1398758_NEGATIVE 319 61 30 43 8 NC_009009:SSA_1746|5end_hypothetical_protein_1732945..1733175_NEGATIVE 316 79 31 48 4 NC_009009:SSA_1383|5end_Aspartate_aminotransferase,_putative_1401718..1401948_NEGATIVE 311 99 52 171 120 NC_009009:SSA_1006|5end_Dextransucrase,_putative_1007076..1007306_POSITIVE 310 57 12 214 158 NC_009009:SSA_0638|5end_Tryptophan_synthase_alpha_chain,_putative_626935..627165_POSITIVE 306 90 49 231 176 NC_009009:SSA_1198|5end_ATPase_(PilT_family),_putative_1223314..1223544_NEGATIVE 305 60 11 226 166 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 302 39 5 212 178 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 300 97 51 166 116 NC_009009:SSA_1969|5end_Acetolactate_synthase_small_subunit,_putative_1965222..1965452_NEGATIVE 300 79 31 178 128 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 297 94 56 181 147 NC_009009:SSA_1203|5end_hypothetical_protein_1226985..1227215_POSITIVE 293 95 53 193 137 NC_009009:SSA_1105|5end_50S_ribosomal_protein_L7/_L12,_putative_1125317..1125547_POSITIVE 292 97 56 146 106 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 291 59 12 56 6 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 288 60 13 202 160 NC_009009:SSA_1303|5end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322992..1323222_NEGATIVE 287 88 47 219 177 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 284 103 66 46 8 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 425 59 15 57 17 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 334 60 12 49 4 NC_009009:SSA_1747|3end_hypothetical_protein_1732938..1733088_NEGATIVE 324 58 15 107 61 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 317 103 66 86 42 NC_009009:SSA_0402|3end_Histidine_kinase,_putative_400099..400249_POSITIVE 316 79 31 51 7 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 308 60 11 74 28 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 306 40 4 88 55 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 302 97 51 151 96 NC_009009:SSA_1831|3end_hypothetical_protein_1821994..1822144_POSITIVE 293 95 53 119 63 NC_009009:SSA_1104|3end_50S_ribosomal_protein_L10,_putative_1125323..1125473_POSITIVE 290 46 6 47 12 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 288 60 13 107 65 NC_009009:SSA_1304|3end_hypothetical_protein_1323087..1323237_NEGATIVE 281 60 16 143 90 NC_009009:SSA_0278|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_272382..272532_POSITIVE 281 76 31 151 105 NC_009009:SSA_0056|3end_Phosphotransferase_system_sugar-specific_EIID_component,_putative_60830..60980_POSITIVE 279 92 52 123 85 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 278 96 55 59 16 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 276 91 54 73 33 NC_009009:SSA_1907|3end_hypothetical_protein_1900813..1900963_POSITIVE 275 80 32 121 65 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 272 79 31 61 26 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE 272 80 32 69 17 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE 272 97 52 129 93 NC_009009:SSA_0418|3end_AraC-type_DNA-binding_domain-containing_protein,_putative_416184..416334_POSITIVE