Origin IGS: tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggtttgga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tccaaacctcttggcacccattataccataataaccaccaaaaagcgactttttaaaagtgtaatcagtaattctatcaattataagaaaaaggaggtttacaattcagtaaaccttcctttacacatattgaaa Mask Tandem Repeat Region ================================================ tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggtttgga Find is-nt database================================================ Query_seq: SMT_1285:SMT_1286|SMT_1285:SMT_1286:ribosomal subunit interface protein:hypothetical protein:->->:1248393..1248527 135 tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggtttgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1285:SMT_1286|SMT_1285:SMT_1286:ribosomal subunit interface protein:hypothetical protein:->->:1248393..1248527 135 tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggtttgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1285:SMT_1286|SMT_1285:SMT_1286:ribosomal subunit interface protein:hypothetical protein:->->:1248393..1248527 135 tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggtttgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggtttgga Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 31 End: 135 .............................. M V N L L F L I I D R I T D Y T F K K S L F G G Y Y G I M G A K R F G Protein_Len: 36 Strand: - Start: 1 End: 108 K L I H L P L N V S N Y V E K K K Y N I S N S I V S K F L R K K T T I M ........................... tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggtttgga 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: 82 Start: 79 End: 108 ..............................................................................TTTAAAAAGTCGCTTTTTGGTGGTTATTAT........................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggtttgga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 62 HP_score: -6.0 Tail_Score: -3.6106 Start: 17 End: 43 Full_Region: caattataagaaaaa ggaggtttac aattca gtaaaccttcc tttacacatattgaa ................ggaggtttacaattcagtaaaccttcc............................................................................................ TransTerm Strand: - Conf: 70 HP_score: -8.4 Tail_Score: -2.76315 Start: 18 End: 43 Full_Region: caattataagaaaaa ggaggtttac aattca gtaaaccttc ctttacacatattga .................ggaggtttacaattcagtaaaccttc............................................................................................ Find igs database================================================ Query_seq: SMT_1285:SMT_1286|SMT_1285:SMT_1286:ribosomal subunit interface protein:hypothetical protein:->->:1248393..1248527 135 tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggtttgga Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: smit_SMT_1285_SMT_1286|ribosomal subunit interface protein:hypothetical protein|POSITIVE:POSITIVE|[1248393,1248527]|135 HSP 1 e-value: 4.0E-71 bit: 268.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggtttgga tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggtttgga Inter-species Hit: Count: 3 Min: 1 Max: 132 Len: 132 Subject: NC_008533_SPD_2032_SPD_2033|DHH subfamily 1 protein:ribosomal subunit interface protein|NEGATIVE:NEGATIVE|[2012034,2012168]|135 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 132 Query Start:1 Query End:132 Subject Strand: NEGATIVE Subject Start: 4 Subject End: 135 tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggttt... tttcaatatgtgtaaaggtaggtttactgaattgtaaactacctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttgaggggtattatggtataatgggtgccaagaggttt... Subject: NC_003098_spr2010_spr2011|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2004534,2004668]|135 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 132 Query Start:1 Query End:132 Subject Strand: NEGATIVE Subject Start: 4 Subject End: 135 tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggttt... tttcaatatgtgtaaaggtaggtttactgaattgtaaactacctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttgaggggtattatggtataatgggtgccaagaggttt... Subject: NC_003028_SP_2205_SP_2206|DHH subfamily 1 protein:ribosomal subunit interface protein|NEGATIVE:NEGATIVE|[2126982,2127116]|135 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 132 Query Start:1 Query End:132 Subject Strand: NEGATIVE Subject Start: 4 Subject End: 135 tttcaatatgtgtaaaggaaggtttactgaattgtaaacctcctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttggtggttattatggtataatgggtgccaagaggttt... tttcaatatgtgtaaaggtaggtttactgaattgtaaactacctttttcttataattgatagaattactgattacacttttaaaaagtcgctttttgaggggtattatggtataatgggtgccaagaggttt... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCAAUAUGUGUAAAGGAAGGUUUACUGAAUUGUAAACCUCCUUUUUCUUAUAAUUGAUAGAAUUACUGAUUACACUUUUAAAAAGUCGCUUUUUGGUGGUUAUUAUGGUAUAAUGGGUGCCAAGAGGUUU ..(((((.((((.((((((.(((((((......)))))))))))))....)))))))))..............................(((((((((((.(((((((...))))))).))))))))))).. (-34.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACCUCUUGGCACCCAUUAUACCAUAAUAACCACCAAAAAGCGACUUUUUAAAAGUGUAAUCAGUAAUUCUAUCAAUUAUAAGAAAAAGGAGGUUUACAAUUCAGUAAACCUUCCUUUACACAUAUUGAAA .......((((.....(((((...))))).....)))).................((((((...((((((.....))))))........((((((((((......))))))))))..))))))......... (-21.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 130 86 205 165 smit:SMT_1736|5end_acetyltransferase,_GNAT_family_1719522..1719752_POSITIVE 280 130 86 48 8 smit:SMT_1735|5end_K03596_GTP-binding_protein_LepA_1719365..1719595_POSITIVE 276 120 75 207 148 smit:SMT_821|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_732775..733005_POSITIVE 270 126 85 71 16 smit:SMT_1469|5end_GTP_pyrophosphokinase_1450582..1450812_POSITIVE 241 129 86 124 84 smit:SMT_996|5end_K03309_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter,_DAACS_family_936859..937089_POSITIVE 239 123 86 129 93 smit:SMT_1351|5end_dephospho-CoA_kinase_1329817..1330047_NEGATIVE 236 129 85 130 90 smit:SMT_2044|5end_transcriptional_activator_TipA,_putative_1955885..1956115_NEGATIVE 234 130 94 157 119 smit:SMT_2142|5end_hypothetical_protein_predicted_by_Glimmer/Critica_2019999..2020229_POSITIVE 234 125 86 194 168 smit:SMT_1475|5end_K02004_1455873..1456103_POSITIVE 233 77 40 138 102 smit:SMT_1559|5end_6-phosphofructokinase_1545429..1545659_NEGATIVE 229 125 84 61 21 smit:SMT_1641|5end_arginyl-tRNA_synthetase_1628253..1628483_NEGATIVE 229 54 12 115 58 smit:SMT_1600|5end_malolactic_enzyme_1589941..1590171_POSITIVE 225 124 86 79 32 smit:SMT_1912|5end_D-alanyl-D-alanine_carboxypeptidase_1857920..1858150_NEGATIVE 223 130 85 155 105 smit:SMT_2114|5end_x-prolyl-dipeptidyl_aminopeptidase_2001484..2001714_POSITIVE 221 100 63 188 154 smit:SMT_1947|5end_lysine_decarboxylase_1883113..1883343_NEGATIVE 221 114 86 152 121 smit:SMT_856|5end_peroxide_resistance_protein,non-heme_iron-containing_ferritin_800648..800878_NEGATIVE 220 111 74 69 24 smit:SMT_1212|5end_acyl_carrier_protein,_putative_1171657..1171887_NEGATIVE 219 109 64 142 90 smit:SMT_2059|5end_hypothetical_protein_1967881..1968111_POSITIVE 218 124 85 90 33 smit:SMT_1071|5end_hypothetical_protein_1010058..1010288_POSITIVE 218 61 36 118 96 smit:SMT_981|5end_hypothetical_protein_928709..928939_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 129 86 151 112 smit:SMT_1735|3end_K03596_GTP-binding_protein_LepA_1719549..1719699_POSITIVE 254 46 3 77 32 smit:SMT_1285|3end_ribosomal_subunit_interface_protein_1248332..1248482_POSITIVE 254 129 86 122 80 smit:SMT_1019|3end_K03295_cation_efflux_system_protein,_CDF_family_954782..954932_NEGATIVE 248 130 89 108 72 smit:SMT_183|3end_30S_ribosomal_protein_S14_121279..121429_POSITIVE 239 123 86 129 93 smit:SMT_1352|3end_formamidopyrimidine-DNA_glycosylase_1329817..1329967_NEGATIVE 237 126 86 106 53 smit:SMT_1902|3end_proton-translocating_NADH-quinone_oxidoreductase,_chain_L_1852028..1852178_NEGATIVE 233 77 40 56 20 smit:SMT_1560|3end_DNA_polymerase_III_alpha_subunit_1545511..1545661_NEGATIVE 223 129 87 62 18 smit:SMT_2070|3end_K02035_peptide/nickel_transport_system_substrate-binding_protein_1975627..1975777_POSITIVE 220 111 74 63 18 smit:SMT_1213|3end_fatty_acid/phospholipid_synthesis_protein_PlsX_1171663..1171813_NEGATIVE 220 130 86 49 3 smit:SMT_706|3end_hypothetical_protein_615317..615467_NEGATIVE 218 44 16 45 11 smit:SMT_438|3end_hypothetical_protein_predicted_by_Glimmer/Critica_379377..379527_POSITIVE 217 110 71 75 39 smit:SMT_1541|3end_isopentenyl-diphosphate_delta-isomerase_1525083..1525233_NEGATIVE 213 123 85 59 23 smit:SMT_2074|3end_dTDP-glucose_4,6-dehydratase_1977802..1977952_POSITIVE 210 123 87 151 116 smit:SMT_758|3end_hypothetical_protein_664041..664191_POSITIVE 209 127 86 63 26 smit:SMT_916|3end_3-hydroxy-3-methylglutaryl-CoA_reductase_868730..868880_NEGATIVE 209 128 88 151 108 smit:SMT_622|3end_methionine_aminopeptidase_529441..529591_POSITIVE 208 60 14 131 76 smit:SMT_1504|3end_topology_modulation_protein_1487808..1487958_POSITIVE 205 130 87 113 50 smit:SMT_1244|3end_putative_repressor_protein_1205149..1205299_POSITIVE 205 124 87 66 23 smit:SMT_898|3end_polyribonucleotide_nucleotidyltransferase_844648..844798_NEGATIVE 203 129 94 38 2 smit:SMT_753|3end_chorismate_synthase_656801..656951_NEGATIVE