Origin IGS: gacttaaagaacatagacaacagcgtagaatggttcgtgcggaactggcaaaagaaatctaaacgattgtacgtagtatcagccgttggggaaattgtgagactgatatgcttttgtgaacagctattcagttggctaagttttttgaagtaagtttggatgagtttgtaggataaaatgttcttgacagaattctcgaattattttatactttaaatgcgtatgaacagattctatggcttagcgtttcgtaagtcgttctccctctagcagggggatatagcaagttactttagcttcctagaggtctagttgacttgtctgttgcattttgcgtaatgagttttcatacgcttttttattattcttaggagaaaaca .........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 tgttttctcctaagaataataaaaaagcgtatgaaaactcattacgcaaaatgcaacagacaagtcaactagacctctaggaagctaaagtaacttgctatatccccctgctagagggagaacgacttacgaaacgctaagccatagaatctgttcatacgcatttaaagtataaaataattcgagaattctgtcaagaacattttatcctacaaactcatccaaacttacttcaaaaaacttagccaactgaatagctgttcacaaaagcatatcagtctcacaatttccccaacggctgatactacgtacaatcgtttagatttcttttgccagttccgcacgaaccattctacgctgttgtctatgttctttaagtc Mask Tandem Repeat Region ================================================ gacttaaagaacatagacaacagcgtagaatggttcgtgcggaactggcaaaagaaatctaaacgattgtacgtagtatcagccgttggggaaattgtgagactgatatgcttttgtgaacagctattcagttggctaagttttttgaagtaagtttggatgagtttgtaggataaaatgttcttgacagaattctcgaattattttatactttaaatgcgtatgaacagattctatggcttagcgtttcgtaagtcgttctccctctagcagggggatatagcaagttactttagcttcctagaggtctagttgacttgtctgttgcattttgcgtaatgagttttcatacgcttttttattattcttaggagaaaaca Find is-nt database================================================ Query_seq: SMT_1240:SMT_1241|SMT_1240:SMT_1241:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:1200800..1201179 380 gacttaaagaacatagacaacagcgtagaatggttcgtgcggaactggcaaaagaaatctaaacgattgtacgtagtatcagccgttggggaaattgtgagactgatatgcttttgtgaacagctattcagttggctaagttttttgaagtaagtttggatgagtttgtaggataaaatgttcttgacagaattctcgaattattttatactttaaatgcgtatgaacagattctatggcttagcgtttcgtaagtcgttctccctctagcagggggatatagcaagttactttagcttcctagaggtctagttgacttgtctgttgcattttgcgtaatgagttttcatacgcttttttattattcttaggagaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1240:SMT_1241|SMT_1240:SMT_1241:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:1200800..1201179 380 gacttaaagaacatagacaacagcgtagaatggttcgtgcggaactggcaaaagaaatctaaacgattgtacgtagtatcagccgttggggaaattgtgagactgatatgcttttgtgaacagctattcagttggctaagttttttgaagtaagtttggatgagtttgtaggataaaatgttcttgacagaattctcgaattattttatactttaaatgcgtatgaacagattctatggcttagcgtttcgtaagtcgttctccctctagcagggggatatagcaagttactttagcttcctagaggtctagttgacttgtctgttgcattttgcgtaatgagttttcatacgcttttttattattcttaggagaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1240:SMT_1241|SMT_1240:SMT_1241:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:1200800..1201179 380 gacttaaagaacatagacaacagcgtagaatggttcgtgcggaactggcaaaagaaatctaaacgattgtacgtagtatcagccgttggggaaattgtgagactgatatgcttttgtgaacagctattcagttggctaagttttttgaagtaagtttggatgagtttgtaggataaaatgttcttgacagaattctcgaattattttatactttaaatgcgtatgaacagattctatggcttagcgtttcgtaagtcgttctccctctagcagggggatatagcaagttactttagcttcctagaggtctagttgacttgtctgttgcattttgcgtaatgagttttcatacgcttttttattattcttaggagaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacttaaagaacatagacaacagcgtagaatggttcgtgcggaactggcaaaagaaatctaaacgattgtacgtagtatcagccgttggggaaattgtgagactgatatgcttttgtgaacagctattcagttggctaagttttttgaagtaagtttggatgagtttgtaggataaaatgttcttgacagaattctcgaattattttatactttaaatgcgtatgaacagattctatggcttagcgtttcgtaagtcgttctccctctagcagggggatatagcaagttactttagcttcctagaggtctagttgacttgtctgttgcattttgcgtaatgagttttcatacgcttttttattattcttaggagaaaaca Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 13 End: 150 ............ M D N S V E W F V R N W Q K K S K R L Y V V S A V G E I V R L I C F C E Q L F S W L S F L K ...................................................................................................................................................................................................................................... Protein_Len: 33 Strand: - Start: 139 End: 237 .......................................................................................................................................... T K Q L L N P H T Q L I F H E Q C F E R I I K Y K L H T H V S E M ............................................................................................................................................... Protein_Len: 59 Strand: - Start: 3 End: 179 .. K F F M S L L T S H N T R F Q C F F D L R N Y T T D A T P S I T L S I H K Q S C S N L Q S L K K F Y T Q I L K Y S L M ......................................................................................................................................................................................................... gacttaaagaacatagacaacagcgtagaatggttcgtgcggaactggcaaaagaaatctaaacgattgtacgtagtatcagccgttggggaaattgtgagactgatatgcttttgtgaacagctattcagttggctaagttttttgaagtaagtttggatgagtttgtaggataaaatgttcttgacagaattctcgaattattttatactttaaatgcgtatgaacagattctatggcttagcgtttcgtaagtcgttctccctctagcagggggatatagcaagttactttagcttcctagaggtctagttgacttgtctgttgcattttgcgtaatgagttttcatacgcttttttattattcttaggagaaaaca 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: 88 Start: 183 End: 212 ......................................................................................................................................................................................CTTGACAGAATTCTCGAATTATTTTATACT........................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacttaaagaacatagacaacagcgtagaatggttcgtgcggaactggcaaaagaaatctaaacgattgtacgtagtatcagccgttggggaaattgtgagactgatatgcttttgtgaacagctattcagttggctaagttttttgaagtaagtttggatgagtttgtaggataaaatgttcttgacagaattctcgaattattttatactttaaatgcgtatgaacagattctatggcttagcgtttcgtaagtcgttctccctctagcagggggatatagcaagttactttagcttcctagaggtctagttgacttgtctgttgcattttgcgtaatgagttttcatacgcttttttattattcttaggagaaaaca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 93 HP_score: -4.8 Tail_Score: -5.70522 Start: 334 End: 354 Full_Region: TGTCTGTTGCATTTT GCGTAATGA GTTT TCATACGC TTTTTTATTATTCTT .............................................................................................................................................................................................................................................................................................................................................GCGTAATGAGTTTTCATACGC.......................... Find igs database================================================ Query_seq: SMT_1240:SMT_1241|SMT_1240:SMT_1241:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:1200800..1201179 380 gacttaaagaacatagacaacagcgtagaatggttcgtgcggaactggcaaaagaaatctaaacgattgtacgtagtatcagccgttggggaaattgtgagactgatatgcttttgtgaacagctattcagttggctaagttttttgaagtaagtttggatgagtttgtaggataaaatgttcttgacagaattctcgaattattttatactttaaatgcgtatgaacagattctatggcttagcgtttcgtaagtcgttctccctctagcagggggatatagcaagttactttagcttcctagaggtctagttgacttgtctgttgcattttgcgtaatgagttttcatacgcttttttattattcttaggagaaaaca Intra-Species Hit: Count: 2 Min: 1 Max: 380 Len: 380 Subject: smit_SMT_1629_SMT_1630|hypothetical protein predicted by Glimmer/Critica:hypothetical protein|POSITIVE:POSITIVE|[1617051,1617430]|380 HSP 1 e-value: 0.0 bit: 753.0 Len: 380 Query Start:1 Query End:380 Subject Strand: POSITIVE Subject Start: 1 Subject End: 380 gacttaaagaacatagacaacagcgtagaatggttcgtgcggaactggcaaaagaaatctaaacgattgtacgtagtatcagccgttggggaaattgtgagactgatatgcttttgtgaacagctattcagttggctaagttttttgaagtaagtttggatgagtttgtaggataaaatgttcttgacagaattctcgaattattttatactttaaatgcgtatgaacagattctatggcttagcgtttcgtaagtcgttctccctctagcagggggatatagcaagttactttagcttcctagaggtctagttgacttgtctgttgcattttgcgtaatgagttttcatacgcttttttattattcttaggagaaaaca gacttaaagaacatagacaacagcgtagaatggttcgtgcggaactggcaaaagaaatctaaacgattgtacgtagtatcagccgttggggaaattgtgagactgatatgcttttgtgaacagctattcagttggctaagttttttgaagtaagtttggatgagtttgtaggataaaatgttcttgacagaattctcgaattattttatactttaaatgcgtatgaacagattctatggcttagcgtttcgtaagtcgttctccctctagcagggggatatagcaagttactttagcttcctagaggtctagttgacttgtctgttgcattttgcgtaatgagttttcatacgcttttttattattcttaggagaaaaca Subject: smit_SMT_1240_SMT_1241|hypothetical protein predicted by Glimmer/Critica:hypothetical protein|POSITIVE:POSITIVE|[1200800,1201179]|380 HSP 1 e-value: 0.0 bit: 753.0 Len: 380 Query Start:1 Query End:380 Subject Strand: POSITIVE Subject Start: 1 Subject End: 380 gacttaaagaacatagacaacagcgtagaatggttcgtgcggaactggcaaaagaaatctaaacgattgtacgtagtatcagccgttggggaaattgtgagactgatatgcttttgtgaacagctattcagttggctaagttttttgaagtaagtttggatgagtttgtaggataaaatgttcttgacagaattctcgaattattttatactttaaatgcgtatgaacagattctatggcttagcgtttcgtaagtcgttctccctctagcagggggatatagcaagttactttagcttcctagaggtctagttgacttgtctgttgcattttgcgtaatgagttttcatacgcttttttattattcttaggagaaaaca gacttaaagaacatagacaacagcgtagaatggttcgtgcggaactggcaaaagaaatctaaacgattgtacgtagtatcagccgttggggaaattgtgagactgatatgcttttgtgaacagctattcagttggctaagttttttgaagtaagtttggatgagtttgtaggataaaatgttcttgacagaattctcgaattattttatactttaaatgcgtatgaacagattctatggcttagcgtttcgtaagtcgttctccctctagcagggggatatagcaagttactttagcttcctagaggtctagttgacttgtctgttgcattttgcgtaatgagttttcatacgcttttttattattcttaggagaaaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUUAAAGAACAUAGACAACAGCGUAGAAUGGUUCGUGCGGAACUGGCAAAAGAAAUCUAAACGAUUGUACGUAGUAUCAGCCGUUGGGGAAAUUGUGAGACUGAUAUGCUUUUGUGAACAGCUAUUCAGUUGGCUAAGUUUUUUGAAGUAAGUUUGGAUGAGUUUGUAGGAUAAAAUGUUCUUGACAGAAUUCUCGAAUUAUUUUAUACUUUAAAUGCGUAUGAACAGAUUCUAUGGCUUAGCGUUUCGUAAGUCGUUCUCCCUCUAGCAGGGGGAUAUAGCAAGUUACUUUAGCUUCCUAGAGGUCUAGUUGACUUGUCUGUUGCAUUUUGCGUAAUGAGUUUUCAUACGCUUUUUUAUUAUUCUUAGGAGAAAACA ((((((..((((...(....)..((((((((.(((((((((.(((((((........(((.((((..(((((...))).))..))))..)))........((((((...(((...(....))))...)))))).))).)))).((((((((((((((((..((((((.(((((........)))))...)))))))))))))......)))))))))..)))))))))..)))))))).......))))..)))))).((((((.....((((.((......((((((((..((((((((...)))).)))).)))))))))).)))).....(((((.((......)))))))................)))))).... (-98.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUCUCCUAAGAAUAAUAAAAAAGCGUAUGAAAACUCAUUACGCAAAAUGCAACAGACAAGUCAACUAGACCUCUAGGAAGCUAAAGUAACUUGCUAUAUCCCCCUGCUAGAGGGAGAACGACUUACGAAACGCUAAGCCAUAGAAUCUGUUCAUACGCAUUUAAAGUAUAAAAUAAUUCGAGAAUUCUGUCAAGAACAUUUUAUCCUACAAACUCAUCCAAACUUACUUCAAAAAACUUAGCCAACUGAAUAGCUGUUCACAAAAGCAUAUCAGUCUCACAAUUUCCCCAACGGCUGAUACUACGUACAAUCGUUUAGAUUUCUUUUGCCAGUUCCGCACGAACCAUUCUACGCUGUUGUCUAUGUUCUUUAAGUC .(..(((((....((((.........((((((((....))).))))).((((((((((((...(((.....))).((((((.(((....((((.(((.....((((.(.....).))))...))).)))).....)))...)).)))).)))))).....)))))).............)))))))))..)....((((((((......................................((((((.(((((...(((.........)))...))))).................))))))......(.(((((.((.((((....((((((.......))).)))....)))).)).)))))).))))))))...... (-67.07) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 359 314 150 116 smit:SMT_1649|5end_GMP_reductase_1635002..1635232_POSITIVE 306 336 291 225 180 smit:SMT_1493|5end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1475737..1475967_POSITIVE 306 277 238 65 14 smit:SMT_110|5end_alpha-L-fucosidase_57445..57675_POSITIVE 302 348 303 44 7 smit:SMT_1190|5end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1148232..1148462_NEGATIVE 295 329 282 74 24 smit:SMT_567|5end_conserved_hypothetical_protein_484845..485075_POSITIVE 294 307 261 128 67 smit:SMT_1961|5end_K07485_transposase_1894206..1894436_POSITIVE 293 307 261 172 109 smit:SMT_1954|5end_6-phospho-beta-glucosidase_1888548..1888778_POSITIVE 290 307 263 207 147 smit:SMT_2044|5end_transcriptional_activator_TipA,_putative_1955885..1956115_NEGATIVE 290 277 238 54 9 smit:SMT_1652|5end_Cof_family_protein_1640534..1640764_POSITIVE 288 336 292 178 135 smit:SMT_1930|5end_peptide_chain_release_factor_1_1870765..1870995_NEGATIVE 287 290 244 224 181 smit:SMT_1677|5end_transcription-repair_coupling_factor_1662112..1662342_NEGATIVE 286 290 243 155 97 smit:SMT_192|5end_translation_initiation_factor_IF-1_126500..126730_POSITIVE 285 307 261 163 102 smit:SMT_1944|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1879494..1879724_NEGATIVE 284 298 253 223 171 smit:SMT_329|5end_hypothetical_protein_265240..265470_POSITIVE 283 278 233 100 37 smit:SMT_2000|5end_hypothetical_protein_1923108..1923338_NEGATIVE 283 280 238 123 84 smit:SMT_1617|5end_K02015_iron_complex_transport_system_permease_protein_1604500..1604730_NEGATIVE 282 116 71 64 15 smit:SMT_2098|5end_similar_to_CDP-ribitol_pyrophosphorylase_1991376..1991606_POSITIVE 282 330 297 91 55 smit:SMT_1854|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1818375..1818605_POSITIVE 281 106 64 86 48 smit:SMT_1214|5end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1173422..1173652_NEGATIVE 280 169 123 136 84 smit:SMT_1609|5end_hypothetical_protein_1598113..1598343_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 310 263 62 10 smit:SMT_1580|3end_MutT/NUDIX_family_protein_1573153..1573303_POSITIVE 307 284 243 149 101 smit:SMT_1530|3end_K07456_DNA_mismatch_repair_protein_MutS2_1513010..1513160_NEGATIVE 306 277 238 63 12 smit:SMT_109|3end_beta-galactosidase_57523..57673_POSITIVE 300 310 267 148 106 smit:SMT_111|3end_alpha-1,2-mannosidase,_putative_59223..59373_NEGATIVE 299 330 282 91 35 smit:SMT_984|3end_transcriptional_regulator_Spx_930497..930647_NEGATIVE 295 329 282 52 2 smit:SMT_566|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_484903..485053_POSITIVE 292 167 124 146 91 smit:SMT_1965|3end_hypothetical_protein_1897711..1897861_POSITIVE 290 277 238 57 12 smit:SMT_1651|3end_chromosome_segregation_SMC_protein_1640617..1640767_POSITIVE 288 336 292 147 104 smit:SMT_1931|3end_23S_rRNA_methyltransferase_1870796..1870946_NEGATIVE 283 280 238 133 94 smit:SMT_1618|3end_K02015_iron_complex_transport_system_permease_protein_1604490..1604640_NEGATIVE 282 303 263 93 48 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 281 106 64 89 51 smit:SMT_1215|3end_aromatic_amino_acid_aminotransferase_1173419..1173569_NEGATIVE 280 320 296 147 125 smit:SMT_1753|3end_tryptophan_synthase_beta_chain_1731652..1731802_POSITIVE 280 169 123 139 87 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 280 310 262 147 103 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 276 119 73 151 95 smit:SMT_2141|3end_hypothetical_protein_2018960..2019110_NEGATIVE 275 287 243 45 5 smit:SMT_450|3end_hydroxyethylthiazole_kinase_389022..389172_POSITIVE 273 285 250 149 111 smit:SMT_919|3end_hypothetical_protein_871741..871891_NEGATIVE 271 272 231 83 32 smit:SMT_1214|3end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1172652..1172802_NEGATIVE 271 309 262 53 8 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE