Origin IGS: gctcttgtctgaattatacttattctctgttattttttcaatttgcaatgatacgacaaaaatggcttaaaggcaaaatgccataatccggccctttctttacaactttgtctatcaaaaaaacacgacgaatgtctaaaagatccgatcgcgttgatacctatataaataagaacaaacggaaaggctactgtttaatcccggaatctatgccatagtattgcagaaagactatacccacaaaaagaaaagtgaagtgcgcccccaaagtcgttgcaaaccctcttcaaaactacttcgcacaaaaaaaagtgaaccctaaaag .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttttagggttcacttttttttgtgcgaagtagttttgaagagggtttgcaacgactttgggggcgcacttcacttttctttttgtgggtatagtctttctgcaatactatggcatagattccgggattaaacagtagcctttccgtttgttcttatttatataggtatcaacgcgatcggatcttttagacattcgtcgtgtttttttgatagacaaagttgtaaagaaagggccggattatggcattttgcctttaagccatttttgtcgtatcattgcaaattgaaaaaataacagagaataagtataattcagacaagagc Mask Tandem Repeat Region ================================================ gctcttgtctgaattatacttattctctgttattttttcaatttgcaatgatacgacaaaaatggcttaaaggcaaaatgccataatccggccctttctttacaactttgtctatcaaaaaaacacgacgaatgtctaaaagatccgatcgcgttgatacctatataaataagaacaaacggaaaggctactgtttaatcccggaatctatgccatagtattgcagaaagactatacccacaaaaagaaaagtgaagtgcgcccccaaagtcgttgcaaaccctcttcaaaactacttcgcacaaaaaaaagtgaaccctaaaag Find is-nt database================================================ Query_seq: PG0553:PG0554|PG0553:PG0554:extracellular protease, putative:hypothetical protein:<-->:611280..611604 325 gctcttgtctgaattatacttattctctgttattttttcaatttgcaatgatacgacaaaaatggcttaaaggcaaaatgccataatccggccctttctttacaactttgtctatcaaaaaaacacgacgaatgtctaaaagatccgatcgcgttgatacctatataaataagaacaaacggaaaggctactgtttaatcccggaatctatgccatagtattgcagaaagactatacccacaaaaagaaaagtgaagtgcgcccccaaagtcgttgcaaaccctcttcaaaactacttcgcacaaaaaaaagtgaaccctaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0553:PG0554|PG0553:PG0554:extracellular protease, putative:hypothetical protein:<-->:611280..611604 325 gctcttgtctgaattatacttattctctgttattttttcaatttgcaatgatacgacaaaaatggcttaaaggcaaaatgccataatccggccctttctttacaactttgtctatcaaaaaaacacgacgaatgtctaaaagatccgatcgcgttgatacctatataaataagaacaaacggaaaggctactgtttaatcccggaatctatgccatagtattgcagaaagactatacccacaaaaagaaaagtgaagtgcgcccccaaagtcgttgcaaaccctcttcaaaactacttcgcacaaaaaaaagtgaaccctaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0553:PG0554|PG0553:PG0554:extracellular protease, putative:hypothetical protein:<-->:611280..611604 325 gctcttgtctgaattatacttattctctgttattttttcaatttgcaatgatacgacaaaaatggcttaaaggcaaaatgccataatccggccctttctttacaactttgtctatcaaaaaaacacgacgaatgtctaaaagatccgatcgcgttgatacctatataaataagaacaaacggaaaggctactgtttaatcccggaatctatgccatagtattgcagaaagactatacccacaaaaagaaaagtgaagtgcgcccccaaagtcgttgcaaaccctcttcaaaactacttcgcacaaaaaaaagtgaaccctaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctcttgtctgaattatacttattctctgttattttttcaatttgcaatgatacgacaaaaatggcttaaaggcaaaatgccataatccggccctttctttacaactttgtctatcaaaaaaacacgacgaatgtctaaaagatccgatcgcgttgatacctatataaataagaacaaacggaaaggctactgtttaatcccggaatctatgccatagtattgcagaaagactatacccacaaaaagaaaagtgaagtgcgcccccaaagtcgttgcaaaccctcttcaaaactacttcgcacaaaaaaaagtgaaccctaaaag Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 108 End: 215 ........................................................................................................... M S I K K T R R M S K R S D R V D T Y I N K N K R K G Y C L I P E S M P .............................................................................................................. Protein_Len: 43 Strand: + Start: 191 End: 319 .............................................................................................................................................................................................. M F N P G I Y A I V L Q K D Y T H K K K S E V R P Q S R C K P S S K L L R T K K S E P ...... Protein_Len: 30 Strand: + Start: 234 End: 323 ......................................................................................................................................................................................................................................... M P T K R K V K C A P K V V A N P L Q N Y F A Q K K V N P K .. Protein_Len: 36 Strand: - Start: 198 End: 305 ..................................................................................................................................................................................................... D R F R H W L I A S L S Y G C F S F H L A G G F D N C V R K L V V E C M .................... Protein_Len: 31 Strand: - Start: 41 End: 133 ........................................ N A I I R C F H S L P L I G Y D P G K K V V K D I L F V R R M ................................................................................................................................................................................................ Protein_Len: 46 Strand: - Start: 33 End: 170 ................................ K K L K C H Y S L F P K F A F H W L G A R E K C S Q R D F F C S S H R F S G I A N I G I Y M ........................................................................................................................................................... gctcttgtctgaattatacttattctctgttattttttcaatttgcaatgatacgacaaaaatggcttaaaggcaaaatgccataatccggccctttctttacaactttgtctatcaaaaaaacacgacgaatgtctaaaagatccgatcgcgttgatacctatataaataagaacaaacggaaaggctactgtttaatcccggaatctatgccatagtattgcagaaagactatacccacaaaaagaaaagtgaagtgcgcccccaaagtcgttgcaaaccctcttcaaaactacttcgcacaaaaaaaagtgaaccctaaaag 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: 87 Start: 13 End: 42 ............ATTGAAAAAATAACAGAGAATAAGTATAAT........................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 48 End: 77 ...............................................TTTGCCTTTAAGCCATTTTTGTCGTATCAT........................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gctcttgtctgaattatacttattctctgttattttttcaatttgcaatgatacgacaaaaatggcttaaaggcaaaatgccataatccggccctttctttacaactttgtctatcaaaaaaacacgacgaatgtctaaaagatccgatcgcgttgatacctatataaataagaacaaacggaaaggctactgtttaatcccggaatctatgccatagtattgcagaaagactatacccacaaaaagaaaagtgaagtgcgcccccaaagtcgttgcaaaccctcttcaaaactacttcgcacaaaaaaaagtgaaccctaaaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0553:PG0554|PG0553:PG0554:extracellular protease, putative:hypothetical protein:<-->:611280..611604 325 gctcttgtctgaattatacttattctctgttattttttcaatttgcaatgatacgacaaaaatggcttaaaggcaaaatgccataatccggccctttctttacaactttgtctatcaaaaaaacacgacgaatgtctaaaagatccgatcgcgttgatacctatataaataagaacaaacggaaaggctactgtttaatcccggaatctatgccatagtattgcagaaagactatacccacaaaaagaaaagtgaagtgcgcccccaaagtcgttgcaaaccctcttcaaaactacttcgcacaaaaaaaagtgaaccctaaaag Intra-Species Hit: Count: 1 Min: 1 Max: 303 Len: 303 Subject: NC_002950_PG0553_PG0554|extracellular protease, putative:hypothetical protein|NEGATIVE:POSITIVE|[611280,611604]|325 HSP 1 e-value: 1.0E-158 bit: 559.0 Len: 303 Query Start:1 Query End:303 Subject Strand: POSITIVE Subject Start: 1 Subject End: 303 gctcttgtctgaattatacttattctctgttattttttcaatttgcaatgatacgacaaaaatggcttaaaggcaaaatgccataatccggccctttctttacaactttgtctatcnnnnnnncacgacgaatgtctaaaagatccgatcgcgttgatacctatataaataagaacaaacggaaaggctactgtttaatcccggaatctatgccatagtattgcagaaagactatacccacaaaaagaaaagtgaagtgcgcccccaaagtcgttgcaaaccctcttcaaaactacttcgcac...................... gctcttgtctgaattatacttattctctgttattttttcaatttgcaatgatacgacaaaaatggcttaaaggcaaaatgccataatccggccctttctttacaactttgtctatcaaaaaaacacgacgaatgtctaaaagatccgatcgcgttgatacctatataaataagaacaaacggaaaggctactgtttaatcccggaatctatgccatagtattgcagaaagactatacccacaaaaagaaaagtgaagtgcgcccccaaagtcgttgcaaaccctcttcaaaactacttcgcac...................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUCUUGUCUGAAUUAUACUUAUUCUCUGUUAUUUUUUCAAUUUGCAAUGAUACGACAAAAAUGGCUUAAAGGCAAAAUGCCAUAAUCCGGCCCUUUCUUUACAACUUUGUCUAUCAAAAAAACACGACGAAUGUCUAAAAGAUCCGAUCGCGUUGAUACCUAUAUAAAUAAGAACAAACGGAAAGGCUACUGUUUAAUCCCGGAAUCUAUGCCAUAGUAUUGCAGAAAGACUAUACCCACAAAAAGAAAAGUGAAGUGCGCCCCCAAAGUCGUUGCAAACCCUCUUCAAAACUACUUCGCAC ..((((.((((....(((((.....((((((..(((((..(((((...(((((.((((((..((....(((((......(((.......)))))))).....))..)))))))))))....(((.(((((...(((.....))).)).))).)))..........))))))))))..))))))..(((....((((.......))))....)))..)))))..)))))))).......(((..........)))..(((((......((((.(((...............))).))))))))) (-49.86) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGCGAAGUAGUUUUGAAGAGGGUUUGCAACGACUUUGGGGGCGCACUUCACUUUUCUUUUUGUGGGUAUAGUCUUUCUGCAAUACUAUGGCAUAGAUUCCGGGAUUAAACAGUAGCCUUUCCGUUUGUUCUUAUUUAUAUAGGUAUCAACGCGAUCGGAUCUUUUAGACAUUCGUCGUGUUUUUUUGAUAGACAAAGUUGUAAAGAAAGGGCCGGAUUAUGGCAUUUUGCCUUUAAGCCAUUUUUGUCGUAUCAUUGCAAAUUGAAAAAAUAACAGAGAAUAAGUAUAAUUCAGACAAGAGC ((((..........(((((.(.((((.(((.....))).)))).).)))))......(((((((........((..(.((((((..(((((((.((((....((.((((((((..(((..((((...((((((.((((((...((((((((((((.(((((.........))))))))))).....))))..)).....))))))..))))))))))....)))...)))..))))).)))))).)))))))..)))))).)..)).......)))))))....))))............... (-63.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 878 100 51 191 142 NC_002950:PG0553|5end_extracellular_protease,_putative_611189..611419_NEGATIVE 352 228 184 217 174 NC_002950:PG2108|5end_thiazole_synthase_2217450..2217680_NEGATIVE 311 190 144 76 26 NC_002950:PG0076|5end_N-acetylmuramoyl-L-alanine_amidase,_family_4_91333..91563_NEGATIVE 294 230 184 63 3 NC_002950:PG0659|5end_hypothetical_protein_709148..709378_NEGATIVE 290 97 53 44 5 NC_002950:PG1297|5end_ribosomal_protein_S1_1375831..1376061_POSITIVE 284 265 221 231 183 NC_002950:PG1348|5end_conserved_hypothetical_protein_TIGR00147_1428608..1428838_POSITIVE 282 108 61 131 71 NC_002950:PG0337|5end_hypothetical_protein_371529..371759_NEGATIVE 278 299 251 88 41 NC_002950:PG1387|5end_hypothetical_protein_1470058..1470288_NEGATIVE 276 272 242 152 117 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 275 288 251 40 3 NC_002950:PG1831|5end_ATP-dependent_DNA_helicase_RecQ_1925422..1925652_NEGATIVE 275 165 125 230 194 NC_002950:PG0213|5end_precorrin-3_methylase/precorrin-8X_methylmutase_250464..250694_NEGATIVE 273 287 241 136 96 NC_002950:PG0563|5end_hypothetical_protein_621438..621668_NEGATIVE 271 300 252 216 153 NC_002950:PG1459|5end_hypothetical_protein_1539769..1539999_NEGATIVE 271 162 122 168 133 NC_002950:PG0401|5end_hypothetical_protein_439306..439536_NEGATIVE 270 290 247 229 190 NC_002950:PG1662|5end_hypothetical_protein_1744736..1744966_POSITIVE 269 148 105 50 9 NC_002950:PG0510|5end_hypothetical_protein_550060..550290_NEGATIVE 269 213 172 230 191 NC_002950:PG0162|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_185086..185316_NEGATIVE 268 288 257 38 5 NC_002950:PG0960|5end_tRNA_(guanine-N(7)-)-methyltransferase_1021895..1022125_NEGATIVE 266 158 122 52 15 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 266 277 238 212 165 NC_002950:PG0672|5end_iron_compound_ABC_transporter,_ATP-binding_protein_723002..723232_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 230 181 70 6 NC_002950:PG0660|3end_nitroreductase_family_protein_709141..709291_NEGATIVE 301 218 184 151 115 NC_002950:PG2109|3end_thiamine-phosphate_pyrophosphorylase_2217509..2217659_NEGATIVE 281 279 243 63 11 NC_002950:PG1735|3end_MutT/nudix_family_protein_1822528..1822678_NEGATIVE 278 299 251 51 4 NC_002950:PG1388|3end_hypothetical_protein_1470095..1470245_NEGATIVE 278 110 62 78 33 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE 272 98 62 47 2 NC_002950:PG1809|3end_2-oxoglutarate_oxidoreductase,_gamma_subunit_1905491..1905641_NEGATIVE 270 298 251 58 14 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 269 213 172 80 41 NC_002950:PG0163|3end_diphosphate--fructose-6-phosphate_1-phosphotransferase_185236..185386_NEGATIVE 264 187 144 75 26 NC_002950:PG1035|3end_hypothetical_protein_1098445..1098595_POSITIVE 261 230 185 145 93 NC_002950:PG0308|3end_electron_transport_complex,_RnfABCDGE_type,_A_subunit_343827..343977_POSITIVE 260 189 143 116 73 NC_002950:PG2068|3end_glycerol-3-phosphate_cytidylyltransferase_2164872..2165022_POSITIVE 259 287 248 64 17 NC_002950:PG1004|3end_prolyl_oligopeptidase_family_protein_1060433..1060583_NEGATIVE 257 286 241 62 22 NC_002950:PG1630|3end_hypothetical_protein_1712142..1712292_POSITIVE 257 289 255 71 34 NC_002950:PG0196|3end_peptidase,_M16_family_235808..235958_POSITIVE 255 218 172 68 19 NC_002950:PG1195|3end_8-amino-7-oxononanoate_synthase_1275207..1275357_POSITIVE 255 95 54 67 29 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 254 239 191 73 32 NC_002950:PG1824|3end_phosphopyruvate_hydratase_1918153..1918303_NEGATIVE 251 270 225 49 12 NC_002950:PG1823|3end_hypothetical_protein_1918050..1918200_POSITIVE 251 285 247 64 27 NC_002950:PG0607|3end_hypothetical_protein_662994..663144_POSITIVE 251 105 61 50 2 NC_002950:PG0264|3end_glycosyl_transferase,_group_2_family_protein_298122..298272_POSITIVE