Origin IGS: actcaggggtaccgagctcgaattctggcgtaatagcgaagaggccnnnnnttaattaattaannnnntgctggaaagagcgaatgcagcaaaaacagcaatccataatgcaacaacaaacgtagca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgctacgtttgttgttgcattatggattgctgtttttgctgcattcgctctttccagcannnnnttaattaattaannnnnggcctcttcgctattacgccagaattcgagctcggtacccctgagt Mask Tandem Repeat Region ================================================ actcaggggtaccgagctcgaattctggcgtaatagcgaagaggccnnnnnttaattaattaannnnntgctggaaagagcgaatgcagcaaaaacagcaatccataatgcaacaacaaacgtagca Find is-nt database================================================ Query_seq: SMT_1464:SMT_1465|SMT_1464:SMT_1465:K02030 polar amino acid transport system substrate-binding protein:hypothetical protein:->->:1445422..1445548 127 actcaggggtaccgagctcgaattctggcgtaatagcgaagaggccnnnnnttaattaattaannnnntgctggaaagagcgaatgcagcaaaaacagcaatccataatgcaacaacaaacgtagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1464:SMT_1465|SMT_1464:SMT_1465:K02030 polar amino acid transport system substrate-binding protein:hypothetical protein:->->:1445422..1445548 127 actcaggggtaccgagctcgaattctggcgtaatagcgaagaggccnnnnnttaattaattaannnnntgctggaaagagcgaatgcagcaaaaacagcaatccataatgcaacaacaaacgtagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1464:SMT_1465|SMT_1464:SMT_1465:K02030 polar amino acid transport system substrate-binding protein:hypothetical protein:->->:1445422..1445548 127 actcaggggtaccgagctcgaattctggcgtaatagcgaagaggccnnnnnttaattaattaannnnntgctggaaagagcgaatgcagcaaaaacagcaatccataatgcaacaacaaacgtagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actcaggggtaccgagctcgaattctggcgtaatagcgaagaggccnnnnnttaattaattaannnnntgctggaaagagcgaatgcagcaaaaacagcaatccataatgcaacaacaaacgtagca Predict ORF larger than 30AA ================================================ actcaggggtaccgagctcgaattctggcgtaatagcgaagaggccnnnnnttaattaattaannnnntgctggaaagagcgaatgcagcaaaaacagcaatccataatgcaacaacaaacgtagca 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================================================ actcaggggtaccgagctcgaattctggcgtaatagcgaagaggccnnnnnttaattaattaannnnntgctggaaagagcgaatgcagcaaaaacagcaatccataatgcaacaacaaacgtagca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1464:SMT_1465|SMT_1464:SMT_1465:K02030 polar amino acid transport system substrate-binding protein:hypothetical protein:->->:1445422..1445548 127 actcaggggtaccgagctcgaattctggcgtaatagcgaagaggccnnnnnttaattaattaannnnntgctggaaagagcgaatgcagcaaaaacagcaatccataatgcaacaacaaacgtagca Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: smit_SMT_1464_SMT_1465|K02030 polar amino acid transport system substrate-binding protein:hypothetical protein|POSITIVE:POSITIVE|[1445422,1445548]|127 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 actcaggggtaccgagctcgaattctggcgtaatagcgaagaggccnnnnnttaattaattaannnnntgctggaaagagcgaatgcagcaaaaacagcaatccataatgcaacaacaaacgtagca actcaggggtaccgagctcgaattctggcgtaatagcgaagaggccnnnnnttaattaattaannnnntgctggaaagagcgaatgcagcaaaaacagcaatccataatgcaacaacaaacgtagca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCAGGGGUACCGAGCUCGAAUUCUGGCGUAAUAGCGAAGAGGCCNNNNNUUAAUUAAUUAANNNNNUGCUGGAAAGAGCGAAUGCAGCAAAAACAGCAAUCCAUAAUGCAACAACAAACGUAGCA ......((((.....((((...(((..((......((......)).......(((....))).......))..))).)))).......((.......)).))))....(((.((.......)).))) (-19.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUACGUUUGUUGUUGCAUUAUGGAUUGCUGUUUUUGCUGCAUUCGCUCUUUCCAGCANNNNNUUAAUUAAUUAANNNNNGGCCUCUUCGCUAUUACGCCAGAAUUCGAGCUCGGUACCCCUGAGU (((.(((.....))).)))....(((((.(((....(((((.............)))))......................(((......))).......))))))))..((((((.....)))))) (-19.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 978 46 1 178 133 smit:SMT_2002|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1924405..1924635_NEGATIVE 978 46 1 217 172 smit:SMT_1966|5end_DNA_polymerase_III_alpha_subunit_1897934..1898164_POSITIVE 978 46 1 178 133 smit:SMT_1942|5end_zinc_metalloprotease_ZmpB,_truncated_1877882..1878112_POSITIVE 978 46 1 218 173 smit:SMT_1926|5end_mevalonate_kinase_1867692..1867922_POSITIVE 978 46 1 199 154 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 795 39 1 231 193 smit:SMT_2030|5end_chromosomal_replication_initiator_protein_DnaA_1945167..1945397_NEGATIVE 638 31 1 231 201 smit:SMT_1672|5end_hypothetical_protein_1660051..1660281_NEGATIVE 365 46 5 67 23 smit:SMT_1414|5end_hypothetical_protein_1398446..1398676_NEGATIVE 323 17 1 161 145 smit:SMT_1914|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1859486..1859716_POSITIVE 313 37 3 191 154 smit:SMT_952|5end_hypothetical_protein_900912..901142_NEGATIVE 308 45 4 223 184 smit:SMT_857|5end_endo-beta-N-acetylglucosaminidase_802491..802721_NEGATIVE 292 46 11 229 187 smit:SMT_1982|5end_conserved_hypothetical_protein_1913036..1913266_POSITIVE 292 46 11 202 160 smit:SMT_1972|5end_uncharacterized_conserved_phage_related_protein_1903662..1903892_POSITIVE 292 46 11 217 175 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 292 46 11 180 138 smit:SMT_325|5end_K02029_polar_amino_acid_transport_system_permease_protein_263023..263253_NEGATIVE 289 16 1 231 216 smit:SMT_1927|5end_cell_division_protein_FtsH_1868779..1869009_NEGATIVE 289 118 75 69 33 smit:SMT_521|5end_K02005_HlyD_family_secretion_protein_445566..445796_POSITIVE 287 45 1 222 168 smit:SMT_861|5end_adenine_phosphoribosyltransferase_805705..805935_NEGATIVE 286 45 6 200 160 smit:SMT_1887|5end_LicC_protein_1841445..1841675_POSITIVE 280 45 2 128 79 smit:SMT_1850|5end_K01421_putative_membrane_protein_1815062..1815292_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 475 25 1 77 53 smit:SMT_1630|3end_hypothetical_protein_1618141..1618291_POSITIVE 365 46 5 70 26 smit:SMT_1415|3end_carboxynorspermidine_decarboxylase_1398443..1398593_NEGATIVE 281 46 2 150 101 smit:SMT_779|3end_ribonuclease_BN,_putative_687883..688033_NEGATIVE 271 46 4 120 73 smit:SMT_1853|3end_1,4-alpha-glucan_branching_enzyme_1817687..1817837_NEGATIVE 271 41 1 45 4 smit:SMT_1695|3end_ribulose-phosphate_3-epimerase_1678299..1678449_POSITIVE 268 46 3 57 14 smit:SMT_1874|3end_hypothetical_protein_1832623..1832773_NEGATIVE 266 99 71 30 3 smit:SMT_1225|3end_50S_ribosomal_protein_L13_1188798..1188948_POSITIVE 261 46 13 146 106 smit:SMT_327|3end_hypothetical_protein_264704..264854_POSITIVE 257 46 2 87 39 smit:SMT_2089|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_related_enzyme_1985270..1985420_POSITIVE 256 117 76 51 20 smit:SMT_1621|3end_K09134_hypothetical_protein_1607256..1607406_NEGATIVE 253 46 5 53 9 smit:SMT_822|3end_putative_mucus_binding_protein_734047..734197_NEGATIVE 251 45 12 40 2 smit:SMT_1594|3end_oligopeptide_transport_system_permease_protein_OppB_1585048..1585198_POSITIVE 251 46 6 46 1 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 249 45 2 45 5 smit:SMT_917|3end_hydroxymethylglutaryl-CoA_synthase_870004..870154_NEGATIVE 248 60 13 91 39 smit:SMT_987|3end_N-acetylmannosamine_kinase_/_transcriptional_regulator_931655..931805_NEGATIVE 245 26 2 149 127 smit:SMT_1926|3end_mevalonate_kinase_1868062..1868212_POSITIVE 245 100 52 102 51 smit:SMT_227|3end_hypothetical_protein_164418..164568_POSITIVE 241 46 4 90 38 smit:SMT_1115|3end_K02245_competence_protein_ComGC_1052473..1052623_NEGATIVE 241 60 12 99 50 smit:SMT_481|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_417641..417791_NEGATIVE 240 120 95 27 2 smit:SMT_2092|3end_malolactic_enzyme_1987040..1987190_NEGATIVE