Origin IGS: gtttagcttttctcttgtagttcttcagtggtcatgtttttacttgacaagttctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttcttgtggccagactctctcactagcaaaggtaaaaggagaaacct .........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 aggtttctccttttacctttgctagtgagagagtctggccacaagaagccacgaaaaaaggaacctgccaacagcaaggttccacgaaaaatgggtagtctccaccctttcaccgtctaaccttagctgcctctctggactgctttaaaggttttttactattctattatttctactagaacttgtcaagtaaaaacatgaccactgaagaactacaagagaaaagctaaac Mask Tandem Repeat Region ================================================ gtttagcttttctcttgtagttcttcagtggtcatgtttttacttgacaagttctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttcttgtggccagactctctcactagcaaaggtaaaaggagaaacct Find is-nt database================================================ Query_seq: SMT_433:SMT_434|SMT_433:SMT_434:cell division protein DivIB:orotidine 5'-phosphate decarboxylase:->->:376015..376246 232 gtttagcttttctcttgtagttcttcagtggtcatgtttttacttgacaagttctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttcttgtggccagactctctcactagcaaaggtaaaaggagaaacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_433:SMT_434|SMT_433:SMT_434:cell division protein DivIB:orotidine 5'-phosphate decarboxylase:->->:376015..376246 232 gtttagcttttctcttgtagttcttcagtggtcatgtttttacttgacaagttctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttcttgtggccagactctctcactagcaaaggtaaaaggagaaacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_433:SMT_434|SMT_433:SMT_434:cell division protein DivIB:orotidine 5'-phosphate decarboxylase:->->:376015..376246 232 gtttagcttttctcttgtagttcttcagtggtcatgtttttacttgacaagttctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttcttgtggccagactctctcactagcaaaggtaaaaggagaaacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttagcttttctcttgtagttcttcagtggtcatgtttttacttgacaagttctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttcttgtggccagactctctcactagcaaaggtaaaaggagaaacct Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 120 End: 230 ....................................................................................................................... M K G W R L P I F R G T L L L A G S F F R G F L W P D S L T S K G K R R N .. Protein_Len: 33 Strand: - Start: 116 End: 214 ................................................................................................................... V T F P H L S G M K R P V K S N A P E K K R P K K H G S E R V L M .................. Protein_Len: 37 Strand: - Start: 88 End: 198 ....................................................................................... L L G S L C S L N S P S L T S V V W K E H F R A T P L N R K E H S R T A M .................................. gtttagcttttctcttgtagttcttcagtggtcatgtttttacttgacaagttctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttcttgtggccagactctctcactagcaaaggtaaaaggagaaacct 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: 86 Start: 43 End: 72 ..........................................CTTGACAAGTTCTAGTAGAAATAATAGAAT................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtttagcttttctcttgtagttcttcagtggtcatgtttttacttgacaagttctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttcttgtggccagactctctcactagcaaaggtaaaaggagaaacct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -8.2 Tail_Score: -5.18357 Start: 150 End: 173 Full_Region: CTACCCATTTTTCGT GGAACCTTGCT GTT GGCAGGTTCC TTTTTTCGTGGCTTC .....................................................................................................................................................GGAACCTTGCTGTTGGCAGGTTCC........................................................... Find igs database================================================ Query_seq: SMT_433:SMT_434|SMT_433:SMT_434:cell division protein DivIB:orotidine 5'-phosphate decarboxylase:->->:376015..376246 232 gtttagcttttctcttgtagttcttcagtggtcatgtttttacttgacaagttctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttcttgtggccagactctctcactagcaaaggtaaaaggagaaacct Intra-Species Hit: Count: 1 Min: 1 Max: 232 Len: 232 Subject: smit_SMT_433_SMT_434|cell division protein DivIB:orotidine 5'-phosphate decarboxylase|POSITIVE:POSITIVE|[376015,376246]|232 HSP 1 e-value: 1.0E-128 bit: 460.0 Len: 232 Query Start:1 Query End:232 Subject Strand: POSITIVE Subject Start: 1 Subject End: 232 gtttagcttttctcttgtagttcttcagtggtcatgtttttacttgacaagttctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttcttgtggccagactctctcactagcaaaggtaaaaggagaaacct gtttagcttttctcttgtagttcttcagtggtcatgtttttacttgacaagttctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttcttgtggccagactctctcactagcaaaggtaaaaggagaaacct Inter-species Hit: Count: 2 Min: 33 Max: 232 Len: 200 Subject: NC_008533_SPD_0606_SPD_0608|hypothetical protein:orotidine 5'-phosphate decarboxylase|POSITIVE:POSITIVE|[631210,631943]|734 HSP 1 e-value: 1.0E-100 bit: 365.0 Len: 200 Query Start:33 Query End:232 Subject Strand: POSITIVE Subject Start: 535 Subject End: 734 ................................catgtttttacttgacaagttctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttcttgtggccagactctctcactagcaaaggtaaaaggagaaacct ................................catgtttttacttgacaagtgctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttctgttggccagactctctcactagtaaaggtaaaaggagaaacct Subject: NC_003028_SP_0699_SP_0701|hypothetical protein:orotidine 5'-phosphate decarboxylase|POSITIVE:POSITIVE|[667515,668160]|646 HSP 1 e-value: 7.0E-99 bit: 361.0 Len: 198 Query Start:35 Query End:232 Subject Strand: POSITIVE Subject Start: 449 Subject End: 646 ..................................tgtttttacttgacaagttctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttcttgtggccagactctctcactagcaaaggtaaaaggagaaacct ..................................tgtttttacttgacaagtgctagtagaaataatagaatagtaaaaaacctttaaagcagtccagagaggcagctaaggttagacggtgaaagggtggagactacccatttttcgtggaaccttgctgttggcaggttccttttttcgtggcttctgttggccagactctctcactagtaaaggtaaaaggagaaacct Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUGUUUUUACUUGACAAGUUCUAGUAGAAAUAAUAGAAUAGUAAAAAACCUUUAAAGCAGUCCAGAGAGGCAGCUAAGGUUAGACGGUGAAAGGGUGGAGACUACCCAUUUUUCGUGGAACCUUGCUGUUGGCAGGUUCCUUUUUUCGUGGCUUCUUGUGGCCAGACUCUCUCACUAGCAAAGGUAAAAGGAGAAACCU ...((((((.(((.....((((((.((....)).))))))........((((((...(((((..(((((((((((.((((((..((((.(((.(((((....).)))).))).))))..)))))))))))...................(((((......)))))..)))))).))).))))))))..))).)))))).. (-60.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUUUCUCCUUUUACCUUUGCUAGUGAGAGAGUCUGGCCACAAGAAGCCACGAAAAAAGGAACCUGCCAACAGCAAGGUUCCACGAAAAAUGGGUAGUCUCCACCCUUUCACCGUCUAACCUUAGCUGCCUCUCUGGACUGCUUUAAAGGUUUUUUACUAUUCUAUUAUUUCUACUAGAACUUGUCAAGUAAAAACAUG ((((((((.(((((((........)))))))..((((((........)))).))....)))))))).....((((((((((..(((......((((.......))))......)))..)))))).))))((.....))..(((((...(((((((......................)))))))...)))))........ (-45.15) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 180 131 70 29 smit:SMT_683|5end_similar_to_CDP-ribitol_pyrophosphorylase_592572..592802_NEGATIVE 339 100 57 63 14 smit:SMT_186|5end_50S_ribosomal_protein_L18_122623..122853_POSITIVE 335 180 131 226 173 smit:SMT_868|5end_D-alanyl-D-alanine_carboxypeptidase_817225..817455_NEGATIVE 335 169 127 192 148 smit:SMT_360|5end_K07742_hypothetical_protein_295628..295858_POSITIVE 333 109 62 184 138 smit:SMT_400|5end_hypothetical_protein_329090..329320_POSITIVE 330 170 123 89 40 smit:SMT_296|5end_hypothetical_protein_predicted_by_Glimmer/Critica_238147..238377_POSITIVE 327 166 123 112 52 smit:SMT_116|5end_beta-N-acetylhexosaminidase_66396..66626_POSITIVE 308 120 71 81 30 smit:SMT_1622|5end_K03499_trk_system_potassium_uptake_protein_TrkA_1608243..1608473_POSITIVE 305 140 95 60 9 smit:SMT_1017|5end_transcriptional_regulator,_MerR_family_954448..954678_NEGATIVE 305 105 61 68 9 smit:SMT_435|5end_orotate_phosphoribosyltransferase_376842..377072_POSITIVE 304 140 92 184 126 smit:SMT_235|5end_hypothetical_protein_174081..174311_POSITIVE 301 130 87 154 110 smit:SMT_448|5end_K03707_transcriptional_activator_TenA_386789..387019_POSITIVE 300 128 83 213 175 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 300 141 103 62 23 smit:SMT_361|5end_hypothetical_protein_295914..296144_POSITIVE 300 150 108 91 55 smit:SMT_215|5end_leucyl-tRNA_synthetase_147045..147275_POSITIVE 300 140 94 210 154 smit:SMT_131|5end_phosphatase,_putative_83663..83893_NEGATIVE 299 173 131 95 59 smit:SMT_1873|5end_K02006_cobalt_transport_system_ATP-binding_protein_1831936..1832166_POSITIVE 295 108 64 176 112 smit:SMT_1978|5end_hypothetical_protein_1909566..1909796_NEGATIVE 295 167 124 208 158 smit:SMT_346|5end_K01992_ABC-2_type_transport_system_permease_protein_284720..284950_POSITIVE 294 107 63 99 46 smit:SMT_1322|5end_K02075_zinc/manganese_transport_system_permease_protein_1291371..1291601_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 166 123 118 58 smit:SMT_115|3end_hypothetical_protein_66482..66632_POSITIVE 300 141 103 69 30 smit:SMT_360|3end_K07742_hypothetical_protein_296001..296151_POSITIVE 298 110 65 151 105 smit:SMT_355|3end_hypothetical_protein_292313..292463_POSITIVE 297 151 117 33 3 smit:SMT_214|3end_leucyl-tRNA_synthetase_147066..147216_POSITIVE 296 105 61 127 72 smit:SMT_1774|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1750151..1750301_NEGATIVE 294 107 63 106 53 smit:SMT_1321|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1291458..1291608_POSITIVE 293 108 61 128 69 smit:SMT_1454|3end_cytidine_deaminase_1437497..1437647_NEGATIVE 292 123 85 150 112 smit:SMT_234|3end_aminopeptidase_PepS_174151..174301_POSITIVE 290 137 93 66 22 smit:SMT_1827|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1797722..1797872_POSITIVE 289 106 62 55 2 smit:SMT_1001|3end_aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_A_943707..943857_POSITIVE 287 150 107 76 9 smit:SMT_1272|3end_K02006_cobalt_transport_system_ATP-binding_protein_1237004..1237154_POSITIVE 281 98 57 87 44 smit:SMT_939|3end_phosphomethylpyrimidine_kinase_891252..891402_NEGATIVE 281 168 121 114 64 smit:SMT_833|3end_hypothetical_protein_predicted_by_Glimmer/Critica_775183..775333_NEGATIVE 280 169 121 140 86 smit:SMT_889|3end_K02029_polar_amino_acid_transport_system_permease_protein_837023..837173_POSITIVE 277 175 131 69 25 smit:SMT_541|3end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457120..457270_NEGATIVE 275 155 111 65 17 smit:SMT_2046|3end_choline_binding_protein_C_1957280..1957430_NEGATIVE 275 157 111 61 22 smit:SMT_1538|3end_two-component_response_regulator_YvqC_1522669..1522819_NEGATIVE 274 138 91 56 5 smit:SMT_83|3end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_14543..14693_NEGATIVE 273 169 124 83 38 smit:SMT_1438|3end_hypothetical_protein_1422260..1422410_NEGATIVE 273 167 126 127 73 smit:SMT_929|3end_hypothetical_protein_883202..883352_NEGATIVE