Origin IGS: ttttatacctccagtatattttaatgaacaaattataacatttcttttttatatagtcaatagtttaaagagaaaactatctacatagtgggtttaataataatatctttcctcaggaaaagatatattattatcttggatatttaaaaaagctagttatcaataaaaattgcactgagtgtgacattaaaatactatttccactatctataaatt .........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 aatttatagatagtggaaatagtattttaatgtcacactcagtgcaatttttattgataactagcttttttaaatatccaagataataatatatcttttcctgaggaaagatattattattaaacccactatgtagatagttttctctttaaactattgactatataaaaaagaaatgttataatttgttcattaaaatatactggaggtataaaa Mask Tandem Repeat Region ================================================ ttttatacctccagtatattttaatgaacaaattataacatttcttttttatatagtcaatagtttaaagagaaaactatctacatagtgggtttaataataatatctttcctcaggaaaagatatattattatcttggatatttaaaaaagctagttatcaataaaaattgcactgagtgtgacattaaaatactatttccactatctataaatt Find is-nt database================================================ Query_seq: FN1670:FN1671|FN1670:FN1671:Choline kinase:ABC transporter ATP-binding protein:<-<-:168357..168572 216 ttttatacctccagtatattttaatgaacaaattataacatttcttttttatatagtcaatagtttaaagagaaaactatctacatagtgggtttaataataatatctttcctcaggaaaagatatattattatcttggatatttaaaaaagctagttatcaataaaaattgcactgagtgtgacattaaaatactatttccactatctataaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1670:FN1671|FN1670:FN1671:Choline kinase:ABC transporter ATP-binding protein:<-<-:168357..168572 216 ttttatacctccagtatattttaatgaacaaattataacatttcttttttatatagtcaatagtttaaagagaaaactatctacatagtgggtttaataataatatctttcctcaggaaaagatatattattatcttggatatttaaaaaagctagttatcaataaaaattgcactgagtgtgacattaaaatactatttccactatctataaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1670:FN1671|FN1670:FN1671:Choline kinase:ABC transporter ATP-binding protein:<-<-:168357..168572 216 ttttatacctccagtatattttaatgaacaaattataacatttcttttttatatagtcaatagtttaaagagaaaactatctacatagtgggtttaataataatatctttcctcaggaaaagatatattattatcttggatatttaaaaaagctagttatcaataaaaattgcactgagtgtgacattaaaatactatttccactatctataaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttatacctccagtatattttaatgaacaaattataacatttcttttttatatagtcaatagtttaaagagaaaactatctacatagtgggtttaataataatatctttcctcaggaaaagatatattattatcttggatatttaaaaaagctagttatcaataaaaattgcactgagtgtgacattaaaatactatttccactatctataaatt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 105 End: 215 ........................................................................................................ M F P Q E K I Y Y Y L G Y L K K L V I N K N C T E C D I K I L F P L S I N . ttttatacctccagtatattttaatgaacaaattataacatttcttttttatatagtcaatagtttaaagagaaaactatctacatagtgggtttaataataatatctttcctcaggaaaagatatattattatcttggatatttaaaaaagctagttatcaataaaaattgcactgagtgtgacattaaaatactatttccactatctataaatt 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: 90 Start: 32 End: 61 ...............................ATTGACTATATAAAAAAGAAATGTTATAAT........................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttatacctccagtatattttaatgaacaaattataacatttcttttttatatagtcaatagtttaaagagaaaactatctacatagtgggtttaataataatatctttcctcaggaaaagatatattattatcttggatatttaaaaaagctagttatcaataaaaattgcactgagtgtgacattaaaatactatttccactatctataaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1670:FN1671|FN1670:FN1671:Choline kinase:ABC transporter ATP-binding protein:<-<-:168357..168572 216 ttttatacctccagtatattttaatgaacaaattataacatttcttttttatatagtcaatagtttaaagagaaaactatctacatagtgggtttaataataatatctttcctcaggaaaagatatattattatcttggatatttaaaaaagctagttatcaataaaaattgcactgagtgtgacattaaaatactatttccactatctataaatt Intra-Species Hit: Count: 1 Min: 1 Max: 216 Len: 216 Subject: NC_003454_FN1670_FN1671|Choline kinase:ABC transporter ATP-binding protein|NEGATIVE:NEGATIVE|[168357,168572]|216 HSP 1 e-value: 1.0E-119 bit: 428.0 Len: 216 Query Start:1 Query End:216 Subject Strand: POSITIVE Subject Start: 1 Subject End: 216 ttttatacctccagtatattttaatgaacaaattataacatttcttttttatatagtcaatagtttaaagagaaaactatctacatagtgggtttaataataatatctttcctcaggaaaagatatattattatcttggatatttaaaaaagctagttatcaataaaaattgcactgagtgtgacattaaaatactatttccactatctataaatt ttttatacctccagtatattttaatgaacaaattataacatttcttttttatatagtcaatagtttaaagagaaaactatctacatagtgggtttaataataatatctttcctcaggaaaagatatattattatcttggatatttaaaaaagctagttatcaataaaaattgcactgagtgtgacattaaaatactatttccactatctataaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUACCUCCAGUAUAUUUUAAUGAACAAAUUAUAACAUUUCUUUUUUAUAUAGUCAAUAGUUUAAAGAGAAAACUAUCUACAUAGUGGGUUUAAUAAUAAUAUCUUUCCUCAGGAAAAGAUAUAUUAUUAUCUUGGAUAUUUAAAAAAGCUAGUUAUCAAUAAAAAUUGCACUGAGUGUGACAUUAAAAUACUAUUUCCACUAUCUAUAAAUU ............((((((((((((((.....((((((((....((((((((.(((..(((..................((((((...)))))).((((((((.(((((((((...)).)))))))))))))))..)))..))).))))))))...))))).))).....(..(((...)))..))))))))))).))))................. (-32.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUAUAGAUAGUGGAAAUAGUAUUUUAAUGUCACACUCAGUGCAAUUUUUAUUGAUAACUAGCUUUUUUAAAUAUCCAAGAUAAUAAUAUAUCUUUUCCUGAGGAAAGAUAUUAUUAUUAAACCCACUAUGUAGAUAGUUUUCUCUUUAAACUAUUGACUAUAUAAAAAAGAAAUGUUAUAAUUUGUUCAUUAAAAUAUACUGGAGGUAUAAAA ..((((((..((((.......(((((((((((..(((.((((((.......))))))((((...((((((((...........(((((((((((((((((....))))))))).))))))))..........((.((((((((.......)))))))).))....))))))))....)))).....))).)))))))))))))))....)))))). (-39.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 747 120 71 211 162 NC_003454:FN1670|5end_Choline_kinase_168266..168496_NEGATIVE 312 147 106 52 15 NC_003454:FN0599|5end_Transposase_1253833..1254063_POSITIVE 285 147 106 52 15 NC_003454:FN0275|5end_Transposase_901560..901790_NEGATIVE 209 199 151 64 5 NC_003454:FN0670|5end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1325702..1325932_POSITIVE 207 145 103 139 90 NC_003454:FN0600|5end_hypothetical_protein_1256019..1256249_NEGATIVE 200 173 135 145 100 NC_003454:FN1673|5end_hypothetical_protein_171858..172088_NEGATIVE 197 117 78 213 177 NC_003454:FN0273|5end_Butyrate-acetoacetate_CoA-transferase_subunit_B_899423..899653_POSITIVE 191 184 141 172 116 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 189 110 77 58 21 NC_003454:FN0008|5end_quinolinate_synthetase_648010..648240_POSITIVE 188 72 33 112 73 NC_003454:FN0745|5end_metal_dependent_phosphohydrolase_1403275..1403505_POSITIVE 187 210 167 148 98 NC_003454:FN2040|5end_LSU_ribosomal_protein_L11P_549043..549273_NEGATIVE 183 47 1 139 98 NC_003454:FN0592|5end_ATP-dependent_DNA_helicase_pcrA_1245712..1245942_POSITIVE 183 144 110 57 18 NC_003454:FN0430|5end_50S_ribosomal_protein_L19_1071361..1071591_POSITIVE 183 47 8 135 99 NC_003454:FN0174|5end_Enoyl-[acyl-carrier-protein]_reductase_799427..799657_POSITIVE 181 200 151 153 102 NC_003454:FN0727|5end_hypothetical_protein_1385507..1385737_NEGATIVE 181 206 161 118 76 NC_003454:FN1789|5end_Na+_driven_multidrug_efflux_pump_270120..270350_POSITIVE 180 140 103 69 35 NC_003454:FN0922|5end_Homoserine_kinase_1577526..1577756_NEGATIVE 178 43 6 140 96 NC_003454:FN0776|5end_asparagine_synthetase_AsnA_1431944..1432174_POSITIVE 178 99 69 76 44 NC_003454:FN0368|5end_adenylosuccinate_lyase_998471..998701_NEGATIVE 178 104 61 61 23 NC_003454:FN0281|5end_DNA_polymerase_III_alpha_subunit_912129..912359_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 95 55 81 39 NC_003454:FN0512|3end_Flavoprotein_1161386..1161536_NEGATIVE 220 149 107 85 42 NC_003454:FN1315|3end_hypothetical_protein_1968921..1969071_NEGATIVE 220 100 52 74 30 NC_003454:FN0749|3end_hypothetical_protein_1407712..1407862_NEGATIVE 207 145 103 56 7 NC_003454:FN0601|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1256102..1256252_NEGATIVE 195 134 91 64 16 NC_003454:FN0173|3end_hypothetical_protein_799304..799454_POSITIVE 188 72 33 115 76 NC_003454:FN0744|3end_metal_dependent_phosphohydrolase_1403358..1403508_POSITIVE 187 210 167 113 63 NC_003454:FN2041|3end_Transcription_antitermination_protein_nusG_549078..549228_NEGATIVE 181 206 161 151 109 NC_003454:FN1788|3end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_270233..270383_POSITIVE 180 140 103 57 23 NC_003454:FN0923|3end_Cardiolipin_synthetase_1577538..1577688_NEGATIVE 178 43 6 53 9 NC_003454:FN0775|3end_putative_aminopeptidase_2_1431937..1432087_POSITIVE 178 99 69 83 51 NC_003454:FN0369|3end_Ribosomal-protein-alanine_acetyltransferase_998464..998614_NEGATIVE 178 104 61 74 36 NC_003454:FN0282|3end_hypothetical_protein_912116..912266_NEGATIVE 178 78 33 133 91 NC_003454:FN2106|3end_Transporter_618094..618244_POSITIVE 176 49 8 128 84 NC_003454:FN0979|3end_hypothetical_protein_1632544..1632694_POSITIVE 175 190 147 61 11 NC_003454:FN1486|3end_Integral_membrane_protein_with_CBS_domains_2168019..2168169_NEGATIVE 170 45 2 67 20 NC_003454:FN1216|3end_RRF2_family_protein_1876171..1876321_NEGATIVE 168 143 106 135 99 NC_003454:FN1441|3end_PTS_system,_fructose-specific_IIABC_component_2110123..2110273_POSITIVE 168 137 100 97 49 NC_003454:FN0363|3end_ATP_synthase_C_chain,_sodium_ion_specific_993434..993584_NEGATIVE 168 83 45 110 66 NC_003454:FN1728|3end_Pyrrolidone-carboxylate_peptidase_227722..227872_NEGATIVE 165 50 1 103 54 NC_003454:FN1291|3end_hypothetical_protein_1947972..1948122_NEGATIVE