Origin IGS: tctatttctccttttattcctttaaaatacttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatcatcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaagactcttttagcatttttttgaaagattcaaaaacttcccctatagaaaagaggaagtttgataggca .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgcctatcaaacttcctcttttctataggggaagtttttgaatctttcaaaaaaatgctaaaagagtcttgacaagtagttgaaaaatgatataatttaaccattcagaaaagtaatcataataaactttttagagagtctgtggtagctgaaaacagataagtgtgatgatgaaaattgggctgaatggtatttagaatttgaaatcataaaaattcggtgagcacaccttacagtgcatctcgttattgcgagacagagcgatagggaaattccctataattgaggtggtaccgcgcatcgacgtcctcacacaagttttttgtgtgaggacttttttgatggaggttagtatggaaagaaaacgatggcgtagcttgttgagataagtgaagtattttaaaggaataaaaggagaaataga Mask Tandem Repeat Region ================================================ tctatttctccttttattcctttaaaatacttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatcatcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaagactcttttagcatttttttgaaagattcaaaaacttcccctatagaaaagaggaagtttgataggca Find is-nt database================================================ Query_seq: SMT_1339:SMT_1340|SMT_1339:SMT_1340:hypothetical protein:phosphoenolpyruvate carboxylase:<-<-:1314837..1315260 424 tctatttctccttttattcctttaaaatacttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatcatcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaagactcttttagcatttttttgaaagattcaaaaacttcccctatagaaaagaggaagtttgataggca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1339:SMT_1340|SMT_1339:SMT_1340:hypothetical protein:phosphoenolpyruvate carboxylase:<-<-:1314837..1315260 424 tctatttctccttttattcctttaaaatacttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatcatcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaagactcttttagcatttttttgaaagattcaaaaacttcccctatagaaaagaggaagtttgataggca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1339:SMT_1340|SMT_1339:SMT_1340:hypothetical protein:phosphoenolpyruvate carboxylase:<-<-:1314837..1315260 424 tctatttctccttttattcctttaaaatacttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatcatcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaagactcttttagcatttttttgaaagattcaaaaacttcccctatagaaaagaggaagtttgataggca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctatttctccttttattcctttaaaatacttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatcatcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaagactcttttagcatttttttgaaagattcaaaaacttcccctatagaaaagaggaagtttgataggca Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 27 End: 176 .......................... M L H L S Q Q A T P S F S F H T N L H Q K S P H T K N L C E D V D A R Y H L N Y R E F P Y R S V S Q ........................................................................................................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 4 End: 228 ... M S P F I P L K Y F T Y L N K L R H R F L S I L T S I K K V L T Q K T C V R T S M R G T T S I I G N F P I A L S R N N E .................................................................................................................................................................................................... Protein_Len: 58 Strand: + Start: 152 End: 325 ....................................................................................................................................................... M S L S L C L A I T R C T V R C A H R I F M I S N S K Y H S A Q F S S S H L S V F S Y H R L S K K F I M I T F L N G ................................................................................................... Protein_Len: 34 Strand: + Start: 321 End: 422 ................................................................................................................................................................................................................................................................................................................................ M V K L Y H F S T T C Q D S F S I F L K D S K T S P I E K R K F D R .. Protein_Len: 49 Strand: - Start: 39 End: 185 ...................................... R L L S R W R K R E M S V E M L F T R V C F V Q T L V D I R P V V E I I P F K G I A R D R L L S M ............................................................................................................................................................................................................................................... tctatttctccttttattcctttaaaatacttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatcatcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaagactcttttagcatttttttgaaagattcaaaaacttcccctatagaaaagaggaagtttgataggca 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================================================ tctatttctccttttattcctttaaaatacttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatcatcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaagactcttttagcatttttttgaaagattcaaaaacttcccctatagaaaagaggaagtttgataggca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -16.9 Tail_Score: -5.14965 Start: 91 End: 119 Full_Region: gtaccgcgcatcgac gtcctcacacaag ttt tttgtgtgaggac ttttttgatggaggt ..........................................................................................gtcctcacacaagttttttgtgtgaggac................................................................................................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: SMT_1339:SMT_1340|SMT_1339:SMT_1340:hypothetical protein:phosphoenolpyruvate carboxylase:<-<-:1314837..1315260 424 tctatttctccttttattcctttaaaatacttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatcatcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaagactcttttagcatttttttgaaagattcaaaaacttcccctatagaaaagaggaagtttgataggca Intra-Species Hit: Count: 1 Min: 1 Max: 424 Len: 424 Subject: smit_SMT_1339_SMT_1340|hypothetical protein:phosphoenolpyruvate carboxylase|NEGATIVE:NEGATIVE|[1314837,1315260]|424 HSP 1 e-value: 0.0 bit: 799.0 Len: 424 Query Start:1 Query End:424 Subject Strand: POSITIVE Subject Start: 1 Subject End: 424 tctatttctccttttattcctttaaaatacttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatcatcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaagactcttttagcannnnnnngaaagattcaaaaacttcccctatagaaaagaggaagtttgataggca tctatttctccttttattcctttaaaatacttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatcatcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaagactcttttagcatttttttgaaagattcaaaaacttcccctatagaaaagaggaagtttgataggca Inter-species Hit: Count: 3 Min: 31 Max: 356 Len: 326 Subject: NC_008533_SPD_0953_SPD_0954|phosphoenolpyruvate carboxylase:hypothetical protein|POSITIVE:POSITIVE|[967853,968234]|382 HSP 1 e-value: 1.0E-149 bit: 529.0 Len: 326 Query Start:31 Query End:356 Subject Strand: NEGATIVE Subject Start: 55 Subject End: 380 ..............................ttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatca-tcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaa.................................................................... ..............................ttcacttatctaaacaagcgacgccatcgttttctttccatactaacctccatcaaaaaaatcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctcagtctcgcaataacgagatgcactgtaaggtgtgcttaccgaatttttataatttcaaattctaaatagcattcagcccaattttcatcattgccacttatctgttttcagctaccacagactctctaaaaagttt-gtatgattacttttctgaatggttaaattatatcatttttaaactacttgtcaa.................................................................... Subject: NC_003098_spr0974_spr0975|phosphoenolpyruvate carboxylase:ABC transporter substrate-binding protein - unknown substrate|POSITIVE:POSITIVE|[960322,960703]|382 HSP 1 e-value: 1.0E-149 bit: 529.0 Len: 326 Query Start:31 Query End:356 Subject Strand: NEGATIVE Subject Start: 55 Subject End: 380 ..............................ttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatca-tcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaa.................................................................... ..............................ttcacttatctaaacaagcgacgccatcgttttctttccatactaacctccatcaaaaaaatcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctcagtctcgcaataacgagatgcactgtaaggtgtgcttaccgaatttttataatttcaaattctaaatagcattcagcccaattttcatcattgccacttatctgttttcagctaccacagactctctaaaaagttt-gtatgattacttttctgaatggttaaattatatcatttttaaactacttgtcaa.................................................................... Subject: NC_003028_SP_1068_SP_1069|phosphoenolpyruvate carboxylase:hypothetical protein|POSITIVE:POSITIVE|[1005224,1005605]|382 HSP 1 e-value: 1.0E-149 bit: 529.0 Len: 326 Query Start:31 Query End:356 Subject Strand: NEGATIVE Subject Start: 55 Subject End: 380 ..............................ttcacttatctcaacaagctacgccatcgttttctttccatactaacctccatcaaaaaagtcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctctgtctcgcaataacgagatgcactgtaaggtgtgctcaccgaatttttatgatttcaaattctaaataccattcagcccaattttcatca-tcacacttatctgttttcagctaccacagactctctaaaaagtttattatgattacttttctgaatggttaaattatatcatttttcaactacttgtcaa.................................................................... ..............................ttcacttatctaaacaagcgacgccatcgttttctttccatactaacctccatcaaaaaaatcctcacacaaaaaacttgtgtgaggacgtcgatgcgcggtaccacctcaattatagggaatttccctatcgctcagtctcgcaataacgagatgcactgtaaggtgtgcttaccgaatttttataatttcaaattctaaatagcattcagcccaattttcatcattgccacttatctgttttcagctaccacagactctctaaaaagttt-gtatgattacttttctgaatggttaaattatatcatttttaaactacttgtcaa.................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCACUUAUCUCAACAAGCUACGCCAUCGUUUUCUUUCCAUACUAACCUCCAUCAAAAAAGUCCUCACACAAAAAACUUGUGUGAGGACGUCGAUGCGCGGUACCACCUCAAUUAUAGGGAAUUUCCCUAUCGCUCUGUCUCGCAAUAACGAGAUGCACUGUAAGGUGUGCUCACCGAAUUUUUAUGAUUUCAAAUUCUAAAUACCAUUCAGCCCAAUUUUCAUCAUCACACUUAUCUGUUUUCAGCUACCACAGACUCUCUAAAAAGUUUAUUAUGAUUACUUUUCUGAAUGGUUAAAUUAUAUCAUUUUUCAACUACUUGUCAA .............(((((...((((((((.....((........))..............((((((((((((.....))))))))))))..))))).)))((((.((((.....((((((.....)))))).((...((((((......))))))))......)))))))).....(((....((((((((............(((((((((........((((............(((....))).......(((((........)))))...))))........))))))))).))))))))......))).....)))))... (-72.31) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGACAAGUAGUUGAAAAAUGAUAUAAUUUAACCAUUCAGAAAAGUAAUCAUAAUAAACUUUUUAGAGAGUCUGUGGUAGCUGAAAACAGAUAAGUGUGAUGAUGAAAAUUGGGCUGAAUGGUAUUUAGAAUUUGAAAUCAUAAAAAUUCGGUGAGCACACCUUACAGUGCAUCUCGUUAUUGCGAGACAGAGCGAUAGGGAAAUUCCCUAUAAUUGAGGUGGUACCGCGCAUCGACGUCCUCACACAAGUUUUUUGUGUGAGGACUUUUUUGAUGGAGGUUAGUAUGGAAAGAAAACGAUGGCGUAGCUUGUUGAGAUAAGUGAA ....(((((.(((....)))...........(((((((((...(((..((((.((..((((........((((((...........))))))))))...)).))))..)))...))))))))).......)))))...((((.....(((((..(((.(((((((..((...((((((....))))))....)).((((((.....))))))...)))))))....(((.(((((..(((((((((((((...)))))))))))))((((((.(((........))).))))))...))))))))..)))..)))))....)))). (-95.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1015 110 61 231 182 smit:SMT_1339|5end_hypothetical_protein_1314746..1314976_NEGATIVE 372 110 61 102 41 smit:SMT_894|5end_hypothetical_protein_841701..841931_NEGATIVE 360 140 97 202 160 smit:SMT_370|5end_acetyltransferase,_GNAT_family_304688..304918_POSITIVE 354 108 64 132 86 smit:SMT_1685|5end_phenylalanyl-tRNA_synthetase_alpha_chain_1668845..1669075_NEGATIVE 330 138 92 80 31 smit:SMT_607|5end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520119..520349_POSITIVE 320 153 111 135 86 smit:SMT_1531|5end_hypothetical_protein_1515997..1516227_NEGATIVE 320 109 63 155 97 smit:SMT_765|5end_hypothetical_protein_672620..672850_NEGATIVE 311 139 97 64 1 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 305 102 61 72 28 smit:SMT_1364|5end_50S_ribosomal_protein_L35_1343865..1344095_NEGATIVE 301 170 122 162 103 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 300 129 83 59 17 smit:SMT_452|5end_phosphomethylpyrimidine_kinase_390568..390798_NEGATIVE 299 114 77 74 25 smit:SMT_1085|5end_sensor_histidine_kinase_(homolog_to_HK11_Spn)_1022267..1022497_NEGATIVE 299 200 155 98 44 smit:SMT_151|5end_K02073_D-methionine_transport_system_substrate-binding_protein_99474..99704_POSITIVE 296 176 131 194 143 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 296 130 81 174 134 smit:SMT_1190|5end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1148232..1148462_NEGATIVE 289 176 131 89 37 smit:SMT_1800|5end_exonuclease_RexA_1773788..1774018_NEGATIVE 289 146 101 58 18 smit:SMT_460|5end_6-phospho-beta-glucosidase_397819..398049_POSITIVE 282 109 69 219 174 smit:SMT_970|5end_threonyl-tRNA_synthetase_915772..916002_POSITIVE 279 176 133 204 154 smit:SMT_1264|5end_oligoendopeptidase_F_1228858..1229088_POSITIVE 274 103 78 50 18 smit:SMT_1015|5end_galactose_operon_repressor_951938..952168_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 110 61 109 48 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE 320 153 111 138 89 smit:SMT_1532|3end_hypothetical_protein_1515994..1516144_NEGATIVE 287 110 62 63 6 smit:SMT_780|3end_peptidase_family_U32_688752..688902_NEGATIVE 273 260 212 57 9 smit:SMT_1958|3end_tryptophan_synthase,_beta_subunit_1892052..1892202_POSITIVE 271 166 126 43 3 smit:SMT_1738|3end_peptidyl-prolyl_cis-trans_isomerase_1721341..1721491_POSITIVE 270 102 75 39 4 smit:SMT_1365|3end_translation_initiation_factor_IF-3_1343898..1344048_NEGATIVE 270 98 51 80 30 smit:SMT_629|3end_glycogen_synthase_535480..535630_POSITIVE 268 108 79 147 105 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 266 159 115 64 4 smit:SMT_1321|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1291458..1291608_POSITIVE 265 129 81 69 13 smit:SMT_628|3end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_534050..534200_POSITIVE 264 190 141 92 29 smit:SMT_1442|3end_hypothetical_protein_1425762..1425912_NEGATIVE 264 137 91 140 91 smit:SMT_978|3end_hypothetical_protein_925765..925915_NEGATIVE 261 129 89 107 67 smit:SMT_1185|3end_beta-galactosidase_1142034..1142184_NEGATIVE 261 258 221 135 96 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE 261 258 221 135 96 smit:SMT_370|3end_acetyltransferase,_GNAT_family_305328..305478_POSITIVE 257 108 76 129 97 smit:SMT_798|3end_hypothetical_protein_707106..707256_POSITIVE 255 178 139 69 21 smit:SMT_1324|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1294036..1294186_POSITIVE 253 130 84 66 11 smit:SMT_2040|3end_transcription-repair_coupling_factor_1950463..1950613_NEGATIVE 250 144 104 40 2 smit:SMT_147|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_98016..98166_POSITIVE 249 177 133 82 29 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE