Origin IGS: atattttttatcaacatattttttcaatgttttcccaattccaaaatgtgctgcatctaaacaccattctaatgacgtattttttagtgaggaagataattcttttatatcccatatttctcttctggaatttttcctcacttttaaataatctgagaaaaatataattcttctaaaatataagacaaatctgttaattaaataattttttaatattgctattctgatatattccttccatt .........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 aatggaaggaatatatcagaatagcaatattaaaaaattatttaattaacagatttgtcttatattttagaagaattatatttttctcagattatttaaaagtgaggaaaaattccagaagagaaatatgggatataaaagaattatcttcctcactaaaaaatacgtcattagaatggtgtttagatgcagcacattttggaattgggaaaacattgaaaaaatatgttgataaaaaatat Mask Tandem Repeat Region ================================================ atattttttatcaacatattttttcaatgttttcccaattccaaaatgtgctgcatctaaacaccattctaatgacgtattttttagtgaggaagataattcttttatatcccatatttctcttctggaatttttcctcacttttaaataatctgagaaaaatataattcttctaaaatataagacaaatctgttaattaaataattttttaatattgctattctgatatattccttccatt Find is-nt database================================================ Query_seq: FN1690:FN1691|FN1690:FN1691:hypothetical protein:Hypothetical membrane-spanning protein:<-<-:186480..186721 242 atattttttatcaacatattttttcaatgttttcccaattccaaaatgtgctgcatctaaacaccattctaatgacgtattttttagtgaggaagataattcttttatatcccatatttctcttctggaatttttcctcacttttaaataatctgagaaaaatataattcttctaaaatataagacaaatctgttaattaaataattttttaatattgctattctgatatattccttccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1690:FN1691|FN1690:FN1691:hypothetical protein:Hypothetical membrane-spanning protein:<-<-:186480..186721 242 atattttttatcaacatattttttcaatgttttcccaattccaaaatgtgctgcatctaaacaccattctaatgacgtattttttagtgaggaagataattcttttatatcccatatttctcttctggaatttttcctcacttttaaataatctgagaaaaatataattcttctaaaatataagacaaatctgttaattaaataattttttaatattgctattctgatatattccttccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1690:FN1691|FN1690:FN1691:hypothetical protein:Hypothetical membrane-spanning protein:<-<-:186480..186721 242 atattttttatcaacatattttttcaatgttttcccaattccaaaatgtgctgcatctaaacaccattctaatgacgtattttttagtgaggaagataattcttttatatcccatatttctcttctggaatttttcctcacttttaaataatctgagaaaaatataattcttctaaaatataagacaaatctgttaattaaataattttttaatattgctattctgatatattccttccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atattttttatcaacatattttttcaatgttttcccaattccaaaatgtgctgcatctaaacaccattctaatgacgtattttttagtgaggaagataattcttttatatcccatatttctcttctggaatttttcctcacttttaaataatctgagaaaaatataattcttctaaaatataagacaaatctgttaattaaataattttttaatattgctattctgatatattccttccatt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 38 End: 148 ..................................... M P K C A A S K H H S N D V F F S E E D N S F I S H I S L L E F F L T F K .............................................................................................. Protein_Len: 54 Strand: + Start: 3 End: 164 .. M F Y Q H I F S M F S Q F Q N V L H L N T I L M T Y F L V R K I I L L Y P I F L F W N F S S L L N N L R K I .............................................................................. Protein_Len: 50 Strand: - Start: 14 End: 163 ............. C I K E I N E W N W F T S C R F V M R I V Y K K T L F I I R K Y G M N R K Q F K E E S K F L R L F M ............................................................................... Protein_Len: 60 Strand: - Start: 1 End: 228 A A D L C W E L S T N K L S S S L E K I D W I E R R S N K R V K L Y D S F F I I R R F Y L V F R N I L Y N K L I A I R M .............. atattttttatcaacatattttttcaatgttttcccaattccaaaatgtgctgcatctaaacaccattctaatgacgtattttttagtgaggaagataattcttttatatcccatatttctcttctggaatttttcctcacttttaaataatctgagaaaaatataattcttctaaaatataagacaaatctgttaattaaataattttttaatattgctattctgatatattccttccatt 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================================================ atattttttatcaacatattttttcaatgttttcccaattccaaaatgtgctgcatctaaacaccattctaatgacgtattttttagtgaggaagataattcttttatatcccatatttctcttctggaatttttcctcacttttaaataatctgagaaaaatataattcttctaaaatataagacaaatctgttaattaaataattttttaatattgctattctgatatattccttccatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1690:FN1691|FN1690:FN1691:hypothetical protein:Hypothetical membrane-spanning protein:<-<-:186480..186721 242 atattttttatcaacatattttttcaatgttttcccaattccaaaatgtgctgcatctaaacaccattctaatgacgtattttttagtgaggaagataattcttttatatcccatatttctcttctggaatttttcctcacttttaaataatctgagaaaaatataattcttctaaaatataagacaaatctgttaattaaataattttttaatattgctattctgatatattccttccatt Intra-Species Hit: Count: 1 Min: 1 Max: 242 Len: 242 Subject: NC_003454_FN1690_FN1691|hypothetical protein:Hypothetical membrane-spanning protein|NEGATIVE:NEGATIVE|[186480,186721]|242 HSP 1 e-value: 3.0E-76 bit: 285.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 atattttttatcaacatattttttcaatgttttcccaattccaaaatgtgctgcatctaaacaccattctaatgacgtattttttagtgaggaagataattcttttatatcccatatttctcttctggaatttttcctcacttt.................................................................................................. atattttttatcaacatattttttcaatgttttcccaattccaaaatgtgctgcatctaaacaccattctaatgacgtattttttagtgaggaagataattcttttatatcccatatttctcttctggaatttttcctcacttt.................................................................................................. HSP 2 e-value: 1.0E-11 bit: 71.9 Len: 36 Query Start:207 Query End:242 Subject Strand: POSITIVE Subject Start: 207 Subject End: 242 ..............................................................................................................................................................................................................tttttaatattgctattctgatatattccttccatt ..............................................................................................................................................................................................................tttttaatattgctattctgatatattccttccatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUUUUUAUCAACAUAUUUUUUCAAUGUUUUCCCAAUUCCAAAAUGUGCUGCAUCUAAACACCAUUCUAAUGACGUAUUUUUUAGUGAGGAAGAUAAUUCUUUUAUAUCCCAUAUUUCUCUUCUGGAAUUUUUCCUCACUUUUAAAUAAUCUGAGAAAAAUAUAAUUCUUCUAAAAUAUAAGACAAAUCUGUUAAUUAAAUAAUUUUUUAAUAUUGCUAUUCUGAUAUAUUCCUUCCAUU ........(((((.((((((((.....((......)).....))))))))..(((....((((...((((...((..(((((...(((((((((((..(((((.......................))))))))))))))))...))))).))..))))............(((........)))......)))).((((((......))))))..))).....)))))............. (-31.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGGAAGGAAUAUAUCAGAAUAGCAAUAUUAAAAAAUUAUUUAAUUAACAGAUUUGUCUUAUAUUUUAGAAGAAUUAUAUUUUUCUCAGAUUAUUUAAAAGUGAGGAAAAAUUCCAGAAGAGAAAUAUGGGAUAUAAAAGAAUUAUCUUCCUCACUAAAAAAUACGUCAUUAGAAUGGUGUUUAGAUGCAGCACAUUUUGGAAUUGGGAAAACAUUGAAAAAAUAUGUUGAUAAAAAAUAU ........(((((......((((....)))).......))))).((((((((((((.(((........))).)))))....((((((((((((((((...((((((((...((((((....(....).)))))).....(((....)))))))))))...))))).))).((((((((((((......))).).))))))))...)))))))).............)))))))......... (-40.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 832 80 31 171 122 NC_003454:FN1690|5end_hypothetical_protein_186389..186619_NEGATIVE 270 145 105 87 46 NC_003454:FN2078|5end_Transcriptional_regulator,_DeoR_family_590266..590496_NEGATIVE 263 59 28 57 29 NC_003454:FN1192|5end_hypothetical_protein_1854679..1854909_POSITIVE 259 145 101 226 179 NC_003454:FN1688|5end_Oxidoreductase_184569..184799_NEGATIVE 255 155 121 185 140 NC_003454:FN2008|5end_Glycine_betaine_transport_ATP-binding_protein_508319..508549_NEGATIVE 251 148 101 112 59 NC_003454:FN1286|5end_30S_ribosomal_protein_S13_1944074..1944304_NEGATIVE 242 140 91 136 69 NC_003454:FN1100|5end_Plasmid_addiction_system_poison_protein_1744177..1744407_POSITIVE 240 138 102 45 3 NC_003454:FN0197|5end_Methyltransferase_822664..822894_POSITIVE 230 68 21 137 91 NC_003454:FN0943|5end_Sensory_Transduction_Protein_Kinase_1596800..1597030_POSITIVE 228 178 135 106 65 NC_003454:FN1312|5end_Biopolymer_transport_exbB_protein_1966948..1967178_NEGATIVE 227 140 100 142 106 NC_003454:FN2034|5end_Protein_yicC_538795..539025_NEGATIVE 224 239 192 101 57 NC_003454:FN0150|5end_Acyl_carrier_protein_778453..778683_POSITIVE 219 44 5 211 161 NC_003454:FN0753|5end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_1413169..1413399_NEGATIVE 218 36 4 171 138 NC_003454:FN0279|5end_Lipoprotein_906479..906709_NEGATIVE 217 139 93 106 57 NC_003454:FN0936|5end_CapC_protein_1589107..1589337_NEGATIVE 216 141 116 36 10 NC_003454:FN1432|5end_Leucine-,_isoleucine-,_valine-,_threonine-,_and_alanine-binding_protein_2101580..2101810_NEGATIVE 216 80 33 93 50 NC_003454:FN1729|5end_4-amino-4-deoxychorismate_lyase_229087..229317_NEGATIVE 214 142 101 92 41 NC_003454:FN1067|5end_Tetratricopeptide_repeat_family_protein_1713086..1713316_POSITIVE 214 70 24 213 169 NC_003454:FN1861|5end_L-lysine_permease_352308..352538_NEGATIVE 213 154 112 124 88 NC_003454:FN0754|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A_1414646..1414876_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 158 113 119 78 NC_003454:FN0447|3end_NIFS_protein_1090574..1090724_POSITIVE 250 59 35 27 6 NC_003454:FN1191|3end_hypothetical_protein_1854729..1854879_POSITIVE 242 140 91 151 84 NC_003454:FN1099|3end_hypothetical_protein_1744272..1744422_POSITIVE 240 138 102 48 6 NC_003454:FN0196|3end_Transcriptional_regulator,_FUR_family_822747..822897_POSITIVE 230 68 21 147 101 NC_003454:FN0942|3end_Sensory_Transduction_Protein_Kinase_1596890..1597040_POSITIVE 227 140 100 115 79 NC_003454:FN2035|3end_DNA-directed_RNA_polymerase_beta'_chain_538822..538972_NEGATIVE 217 139 93 116 67 NC_003454:FN0937|3end_Gamma-polyglutamic_acid_synthetase_1589097..1589247_NEGATIVE 216 80 33 99 56 NC_003454:FN1730|3end_Anthranilate_synthase_component_I_229081..229231_NEGATIVE 214 142 101 72 21 NC_003454:FN1066|3end_Exodeoxyribonuclease_VII_large_subunit_1713146..1713296_POSITIVE 213 154 112 107 71 NC_003454:FN0755|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_C_1414663..1414813_NEGATIVE 213 79 43 72 42 NC_003454:FN1904|3end_Transcriptional_regulator,_MarR_family_393633..393783_POSITIVE 210 126 82 109 51 NC_003454:FN1101|3end_ATPase_1746039..1746189_POSITIVE 210 126 81 87 40 NC_003454:FN0338|3end_hypothetical_protein_972097..972247_POSITIVE 204 133 110 125 105 NC_003454:FN1899|3end_Hypothetical_lipoprotein_386714..386864_NEGATIVE 203 175 131 122 78 NC_003454:FN1726|3end_Na+_driven_multidrug_efflux_pump_224686..224836_NEGATIVE 202 143 101 72 33 NC_003454:FN0952|3end_cobalamin_biosynthesis_protein_CbiG_1608489..1608639_NEGATIVE 202 75 35 63 9 NC_003454:FN0780|3end_Hypothetical_membrane-spanning_protein_1436999..1437149_NEGATIVE 202 59 30 53 27 NC_003454:FN1608|3end_Ribosomal_protein_L11_methyltransferase_117909..118059_NEGATIVE 200 70 28 92 31 NC_003454:FN1841|3end_Dihydroxyacetone_kinase_331567..331717_POSITIVE 200 155 117 61 14 NC_003454:FN1765|3end_pyruvate_kinase_258023..258173_NEGATIVE