Origin IGS: ggatgggtaaaaatattttagtgaaatgataaaaacgcatcctatcaggtttgagtgagtctgataggatgcgttttatcatgtaaagatgttagttgagtttgaagttgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcaacttcaaactcaactaacatctttacatgataaaacgcatcctatcagactcactcaaacctgataggatgcgtttttatcatttcactaaaatatttttacccatcc Mask Tandem Repeat Region ================================================ ggatgggtaaaaatattttagtgaaatgataaaaacgcatcctatcaggtttgagtgagtctgataggatgcgttttatcatgtaaagatgttagttgagtttgaagttgc Find is-nt database================================================ Query_seq: SMT_1614:SMT_1615|SMT_1614:SMT_1615:K08998 hypothetical protein:K02016 iron complex transport system substrate-binding protein:-><-:1601713..1601823 111 ggatgggtaaaaatattttagtgaaatgataaaaacgcatcctatcaggtttgagtgagtctgataggatgcgttttatcatgtaaagatgttagttgagtttgaagttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1614:SMT_1615|SMT_1614:SMT_1615:K08998 hypothetical protein:K02016 iron complex transport system substrate-binding protein:-><-:1601713..1601823 111 ggatgggtaaaaatattttagtgaaatgataaaaacgcatcctatcaggtttgagtgagtctgataggatgcgttttatcatgtaaagatgttagttgagtttgaagttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1614:SMT_1615|SMT_1614:SMT_1615:K08998 hypothetical protein:K02016 iron complex transport system substrate-binding protein:-><-:1601713..1601823 111 ggatgggtaaaaatattttagtgaaatgataaaaacgcatcctatcaggtttgagtgagtctgataggatgcgttttatcatgtaaagatgttagttgagtttgaagttgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggatgggtaaaaatattttagtgaaatgataaaaacgcatcctatcaggtttgagtgagtctgataggatgcgttttatcatgtaaagatgttagttgagtttgaagttgc Predict ORF larger than 30AA ================================================ ggatgggtaaaaatattttagtgaaatgataaaaacgcatcctatcaggtttgagtgagtctgataggatgcgttttatcatgtaaagatgttagttgagtttgaagttgc 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================================================ ggatgggtaaaaatattttagtgaaatgataaaaacgcatcctatcaggtttgagtgagtctgataggatgcgttttatcatgtaaagatgttagttgagtttgaagttgc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.6 Tail_Score: -2.63479 Start: 31 End: 78 Full_Region: TTTTAGTGAAATGAT AAAAACGCATCCTATCAGGTTT GAGT GAGTCTGATAGGATGCGTTTTA TCATGTAAAGATGTT ..............................AAAAACGCATCCTATCAGGTTTGAGTGAGTCTGATAGGATGCGTTTTA................................. TransTerm Strand: + Conf: 100 HP_score: -16.5 Tail_Score: -4.50976 Start: 36 End: 73 Full_Region: GTGAAATGATAAAAA CGCATCCTATCAGGTTT GAGT GAGTCTGATAGGATGCG TTTTATCATGTAAAG ...................................CGCATCCTATCAGGTTTGAGTGAGTCTGATAGGATGCG...................................... TransTerm Strand: - Conf: 100 HP_score: -11.5 Tail_Score: -5.04325 Start: 36 End: 73 Full_Region: ctttacatgataaaa cgcatcctatcag actcactcaaac ctgataggatgcg tttttatcatttcac ...................................cgcatcctatcagactcactcaaacctgataggatgcg...................................... Find igs database================================================ Query_seq: SMT_1614:SMT_1615|SMT_1614:SMT_1615:K08998 hypothetical protein:K02016 iron complex transport system substrate-binding protein:-><-:1601713..1601823 111 ggatgggtaaaaatattttagtgaaatgataaaaacgcatcctatcaggtttgagtgagtctgataggatgcgttttatcatgtaaagatgttagttgagtttgaagttgc Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: smit_SMT_1614_SMT_1615|K08998 hypothetical protein:K02016 iron complex transport system substrate-binding protein|POSITIVE:NEGATIVE|[1601713,1601823]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 ggatgggtaaaaatattttagtgaaatgataaaaacgcatcctatcaggtttgagtgagtctgataggatgcgttttatcatgtaaagatgttagttgagtttgaagttgc ggatgggtaaaaatattttagtgaaatgataaaaacgcatcctatcaggtttgagtgagtctgataggatgcgttttatcatgtaaagatgttagttgagtttgaagttgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAUGGGUAAAAAUAUUUUAGUGAAAUGAUAAAAACGCAUCCUAUCAGGUUUGAGUGAGUCUGAUAGGAUGCGUUUUAUCAUGUAAAGAUGUUAGUUGAGUUUGAAGUUGC ...........((((((((......(((((((((.(((((((((((((..((....))..))))))))))))))))))))))...)))))))).................. (-36.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAACUUCAAACUCAACUAACAUCUUUACAUGAUAAAACGCAUCCUAUCAGACUCACUCAAACCUGAUAGGAUGCGUUUUUAUCAUUUCACUAAAAUAUUUUUACCCAUCC .............................((((((((((((((((((((((............))))))))))))).)))))))))......................... (-29.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 108 61 67 18 smit:SMT_338|5end_heat-inducible_transcription_repressor_HrcA_276825..277055_POSITIVE 264 79 35 147 94 smit:SMT_1059|5end_NAD(P)H-flavin_oxidoreductase_997379..997609_POSITIVE 262 72 37 65 34 smit:SMT_1876|5end_transcriptional_regulator,_MarR_family_1833594..1833824_POSITIVE 245 77 32 174 130 smit:SMT_1012|5end_xanthine_permease_949154..949384_POSITIVE 244 77 36 81 35 smit:SMT_871|5end_K03311_branched-chain_amino_acid:cation_transporter,_LIVCS_family_820160..820390_NEGATIVE 244 77 36 81 35 smit:SMT_386|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_320353..320583_POSITIVE 240 69 23 124 77 smit:SMT_864|5end_K07485_transposase_814322..814552_POSITIVE 239 74 36 46 2 smit:SMT_453|5end_CopAB_ATPase_metal-fist_type_repressor_390883..391113_POSITIVE 231 84 49 93 59 smit:SMT_1192|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase_/_IMP_cyclohydrolase_1151406..1151636_NEGATIVE 228 84 42 84 51 smit:SMT_1914|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1859486..1859716_POSITIVE 228 74 31 104 53 smit:SMT_142|5end_hypothetical_protein_95088..95318_NEGATIVE 226 77 37 183 133 smit:SMT_1839|5end_6-phosphogluconate_dehydrogenase,_decarboxylating_1805999..1806229_NEGATIVE 225 77 36 201 153 smit:SMT_2067|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1973432..1973662_POSITIVE 225 76 37 189 145 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 221 90 41 181 131 smit:SMT_1642|5end_K03497_chromosome_partitioning_protein,_ParB_family_1628996..1629226_NEGATIVE 221 89 47 212 165 smit:SMT_1334|5end_hypothetical_protein_1309077..1309307_NEGATIVE 220 76 36 66 26 smit:SMT_316|5end_acetyl-CoA_carboxylase_carboxyl_transferase_subunit_alpha_256544..256774_POSITIVE 220 61 35 55 23 smit:SMT_270|5end_ATP-binding_subunit_of_Clp_protease_and_DnaK/DnaJ_chaperones_209040..209270_POSITIVE 219 76 36 162 119 smit:SMT_1832|5end_tagatose-6-phosphate_kinase_1800438..1800668_POSITIVE 218 108 63 158 107 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 568 80 32 63 14 smit:SMT_1614|3end_K08998_hypothetical_protein_1601652..1601802_POSITIVE 399 77 32 78 32 smit:SMT_778|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_687834..687984_POSITIVE 359 79 31 67 20 smit:SMT_937|3end_dipeptidase_890741..890891_POSITIVE 293 77 31 71 24 smit:SMT_779|3end_ribonuclease_BN,_putative_687883..688033_NEGATIVE 277 77 31 124 77 smit:SMT_1018|3end_hypothetical_protein_predicted_by_Glimmer/Critica_954739..954889_POSITIVE 275 77 32 73 27 smit:SMT_130|3end_capsular_polysaccharide_biosynthesis_protein_82925..83075_POSITIVE 264 79 35 150 97 smit:SMT_1058|3end_primosomal_protein_DnaI_997462..997612_POSITIVE 263 58 22 146 114 smit:SMT_716|3end_50S_ribosomal_protein_L31_622732..622882_POSITIVE 246 64 22 68 24 smit:SMT_735|3end_putative_transposase,_ISSmu1_641395..641545_POSITIVE 242 85 42 143 98 smit:SMT_1514|3end_methylenetetrahydrofolate_dehydrogenase_(NADP+)_/_methenyltetrahydrofolate_cyclohydrolase_1495720..1495870_NEGATIVE 235 90 43 65 19 smit:SMT_638|3end_hypothetical_protein_543180..543330_NEGATIVE 234 74 34 146 93 smit:SMT_519|3end_glutathione_reductase_443940..444090_NEGATIVE 231 110 68 47 3 smit:SMT_298|3end_penicillin-binding_protein_1A_240719..240869_NEGATIVE 228 74 31 102 51 smit:SMT_143|3end_hypothetical_protein_95090..95240_NEGATIVE 221 73 32 55 13 smit:SMT_1308|3end_hypothetical_protein_1273854..1274004_POSITIVE 220 76 36 69 29 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 219 77 31 67 22 smit:SMT_1977|3end_endopeptidase_O_1908454..1908604_POSITIVE 219 76 36 151 108 smit:SMT_1831|3end_galactose-6-phosphate_isomerase_1800507..1800657_POSITIVE 218 107 66 56 8 smit:SMT_1919|3end_aspartate_kinase_1862769..1862919_POSITIVE 217 76 36 51 8 smit:SMT_1954|3end_6-phospho-beta-glucosidase_1888831..1888981_POSITIVE