Origin IGS: aatttagtctgtcatttcaattgtgaaaactcttttggtcagtataattttataaagactgtgaagttttttatattctcaaaaaataagtgagttacaatatttgtaactcacatttttttctggttgggggaaggggaataatatcaatgaagcaagatataatgcagaaaaatcatataaaaaaat .........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 atttttttatatgatttttctgcattatatcttgcttcattgatattattccccttcccccaaccagaaaaaaatgtgagttacaaatattgtaactcacttattttttgagaatataaaaaacttcacagtctttataaaattatactgaccaaaagagttttcacaattgaaatgacagactaaatt Mask Tandem Repeat Region ================================================ aatttagtctgtcatttcaattgtgaaaactcttttggtcagtataattttataaagactgtgaagttttttatattctcaaaaaataagtgagttacaatatttgtaactcacatttttttctggttgggggaaggggaataatatcaatgaagcaagatataatgcagaaaaatcatataaaaaaat Find is-nt database================================================ Query_seq: FN0550:FN0551|FN0550:FN0551:Mannose-1-phosphate guanylyl transferase (GDP):Bacterial regulatory proteins, crp family:->->:1203227..1203415 189 aatttagtctgtcatttcaattgtgaaaactcttttggtcagtataattttataaagactgtgaagttttttatattctcaaaaaataagtgagttacaatatttgtaactcacatttttttctggttgggggaaggggaataatatcaatgaagcaagatataatgcagaaaaatcatataaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0550:FN0551|FN0550:FN0551:Mannose-1-phosphate guanylyl transferase (GDP):Bacterial regulatory proteins, crp family:->->:1203227..1203415 189 aatttagtctgtcatttcaattgtgaaaactcttttggtcagtataattttataaagactgtgaagttttttatattctcaaaaaataagtgagttacaatatttgtaactcacatttttttctggttgggggaaggggaataatatcaatgaagcaagatataatgcagaaaaatcatataaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0550:FN0551|FN0550:FN0551:Mannose-1-phosphate guanylyl transferase (GDP):Bacterial regulatory proteins, crp family:->->:1203227..1203415 189 aatttagtctgtcatttcaattgtgaaaactcttttggtcagtataattttataaagactgtgaagttttttatattctcaaaaaataagtgagttacaatatttgtaactcacatttttttctggttgggggaaggggaataatatcaatgaagcaagatataatgcagaaaaatcatataaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttagtctgtcatttcaattgtgaaaactcttttggtcagtataattttataaagactgtgaagttttttatattctcaaaaaataagtgagttacaatatttgtaactcacatttttttctggttgggggaaggggaataatatcaatgaagcaagatataatgcagaaaaatcatataaaaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 90 End: 188 ......................................................................................... M S Y N I C N S H F F L V G G R G I I S M K Q D I M Q K N H I K K . Protein_Len: 36 Strand: - Start: 82 End: 189 ................................................................................. F I L S N C Y K Y S V N K E P Q P F P F L I L S A L Y L A S F D Y L F M aatttagtctgtcatttcaattgtgaaaactcttttggtcagtataattttataaagactgtgaagttttttatattctcaaaaaataagtgagttacaatatttgtaactcacatttttttctggttgggggaaggggaataatatcaatgaagcaagatataatgcagaaaaatcatataaaaaaat 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================================================ aatttagtctgtcatttcaattgtgaaaactcttttggtcagtataattttataaagactgtgaagttttttatattctcaaaaaataagtgagttacaatatttgtaactcacatttttttctggttgggggaaggggaataatatcaatgaagcaagatataatgcagaaaaatcatataaaaaaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.0 Tail_Score: -5.71983 Start: 89 End: 115 Full_Region: TATTCTCAAAAAATA AGTGAGTTACAA TAT TTGTAACTCACA TTTTTTTCTGGTTGG ........................................................................................AGTGAGTTACAATATTTGTAACTCACA.......................................................................... TransTerm Strand: - Conf: 100 HP_score: -14.5 Tail_Score: -4.62085 Start: 90 End: 114 Full_Region: caaccagaaaaaaat gtgagttacaa ata ttgtaactcac ttattttttgagaat .........................................................................................gtgagttacaaatattgtaactcac........................................................................... Find igs database================================================ Query_seq: FN0550:FN0551|FN0550:FN0551:Mannose-1-phosphate guanylyl transferase (GDP):Bacterial regulatory proteins, crp family:->->:1203227..1203415 189 aatttagtctgtcatttcaattgtgaaaactcttttggtcagtataattttataaagactgtgaagttttttatattctcaaaaaataagtgagttacaatatttgtaactcacatttttttctggttgggggaaggggaataatatcaatgaagcaagatataatgcagaaaaatcatataaaaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: NC_003454_FN0550_FN0551|Mannose-1-phosphate guanylyl transferase (GDP):Bacterial regulatory proteins, crp family|POSITIVE:POSITIVE|[1203227,1203415]|189 HSP 1 e-value: 7.0E-86 bit: 317.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 aatttagtctgtcatttcaattgtgaaaactcttttggtcagtataattttataaagactgtgaagttttttatattctcaaaaaataagtgagttacaatatttgtaactcacannnnnnnctggttgggggaaggggaataatatcaatgaagcaagatataatgcagaaaaatcatat........ aatttagtctgtcatttcaattgtgaaaactcttttggtcagtataattttataaagactgtgaagttttttatattctcaaaaaataagtgagttacaatatttgtaactcacatttttttctggttgggggaaggggaataatatcaatgaagcaagatataatgcagaaaaatcatat........ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUAGUCUGUCAUUUCAAUUGUGAAAACUCUUUUGGUCAGUAUAAUUUUAUAAAGACUGUGAAGUUUUUUAUAUUCUCAAAAAAUAAGUGAGUUACAAUAUUUGUAACUCACAUUUUUUUCUGGUUGGGGGAAGGGGAAUAAUAUCAAUGAAGCAAGAUAUAAUGCAGAAAAAUCAUAU .......((((.((((....(((((((((((.((.(((((..((((....))))..))))).)))))))))..(((((((.........((((((((((.....))))))))))...(((..((....))..))).)))))))...........)))).....)))))))).......... (-42.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUGAUUUUUCUGCAUUAUAUCUUGCUUCAUUGAUAUUAUUCCCCUUCCCCCAACCAGAAAAAAAUGUGAGUUACAAAUAUUGUAACUCACUUAUUUUUUGAGAAUAUAAAAAACUUCACAGUCUUUAUAAAAUUAUACUGACCAAAAGAGUUUUCACAAUUGAAAUGACAGACUAAAUU ....(((((.((((((((..........((((((......................(((((((.((.((((((((((.....)))))))))))).))))))).........(((((((....(((..((((....))))..))).....)))))))..))).))))))).))))..))))) (-31.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 99 57 173 127 NC_003454:FN0117|5end_O6-methylguanine-DNA_methyltransferase_750338..750568_POSITIVE 229 80 32 84 30 NC_003454:FN1687|5end_Gluconate_5-dehydrogenase_183712..183942_NEGATIVE 225 168 135 96 56 NC_003454:FN2033|5end_Guanylate_kinase_537904..538134_NEGATIVE 215 78 39 211 169 NC_003454:FN1869|5end_hypothetical_protein_360839..361069_NEGATIVE 213 160 116 199 146 NC_003454:FN1348|5end_ABC_transporter_ATP-binding_protein_2001141..2001371_NEGATIVE 211 120 82 145 107 NC_003454:FN0932|5end_hypothetical_protein_1584678..1584908_POSITIVE 201 80 31 174 111 NC_003454:FN0952|5end_cobalamin_biosynthesis_protein_CbiG_1609502..1609732_NEGATIVE 200 168 125 231 195 NC_003454:FN1412|5end_5-methylthioribose_kinase_2073206..2073436_NEGATIVE 197 125 90 69 28 NC_003454:FN1538|5end_Arsenical_pump-driving_ATPase_52299..52529_NEGATIVE 195 99 71 161 137 NC_003454:FN0070|5end_Glycyl-tRNA_synthetase_beta_chain_708902..709132_POSITIVE 189 108 65 170 132 NC_003454:FN0988|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1640968..1641198_NEGATIVE 187 122 82 165 121 NC_003454:FN1918|5end_SPO0B-associated_GTP-binding_protein_415026..415256_NEGATIVE 186 134 100 35 2 NC_003454:FN0933|5end_3-phosphoshikimate_1-carboxyvinyltransferase_1585182..1585412_POSITIVE 185 143 106 43 9 NC_003454:FN0561|5end_Proline_synthetase_associated_protein_1214155..1214385_POSITIVE 184 154 125 228 195 NC_003454:FN1018|5end_hypothetical_protein_1672369..1672599_NEGATIVE 183 100 77 167 143 NC_003454:FN0423|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit_1066328..1066558_POSITIVE 182 153 120 135 103 NC_003454:FN1751|5end_Pyruvate-flavodoxin_oxidoreductase_248067..248297_POSITIVE 181 80 32 59 1 NC_003454:FN2093|5end_General_secretion_pathway_protein_G_603551..603781_NEGATIVE 181 170 123 54 1 NC_003454:FN1503|5end_Nickel_transport_system_permease_protein_nikB_8441..8671_NEGATIVE 180 164 125 72 44 NC_003454:FN0051|5end_hypothetical_protein_688929..689159_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 123 81 87 45 NC_003454:FN0598|3end_Phospholipid-lipopolysaccharide_ABC_transporter_1253712..1253862_POSITIVE 255 172 131 71 28 NC_003454:FN1194|3end_hypothetical_protein_1855668..1855818_POSITIVE 229 80 32 99 45 NC_003454:FN1688|3end_Oxidoreductase_183697..183847_NEGATIVE 228 155 124 39 12 NC_003454:FN1464|3end_1-deoxy-D-xylulose-5-phosphate_synthase_2145954..2146104_NEGATIVE 225 168 135 83 43 NC_003454:FN2034|3end_Protein_yicC_537917..538067_NEGATIVE 214 141 116 127 106 NC_003454:FN0171|3end_Hypothetical_cytosolic_protein_796921..797071_POSITIVE 210 80 31 142 94 NC_003454:FN1421|3end_Pyruvate-flavodoxin_oxidoreductase_2086957..2087107_POSITIVE 209 80 31 142 94 NC_003454:FN1751|3end_Pyruvate-flavodoxin_oxidoreductase_248443..248593_POSITIVE 204 79 32 92 45 NC_003454:FN0788|3end_hypothetical_protein_1443940..1444090_NEGATIVE 187 122 82 58 14 NC_003454:FN1919|3end_Methyltransferase_415133..415283_NEGATIVE 186 134 100 34 1 NC_003454:FN0932|3end_hypothetical_protein_1585261..1585411_POSITIVE 184 157 124 40 2 NC_003454:FN1442|3end_Transposase_2110155..2110305_NEGATIVE 184 73 32 103 64 NC_003454:FN0209|3end_Hypothetical_cytosolic_protein_836800..836950_POSITIVE 183 100 77 42 18 NC_003454:FN0422|3end_carbamoyl-phosphate_synthase_large_subunit_1066283..1066433_POSITIVE 182 153 120 67 35 NC_003454:FN1750|3end_Pyruvate-flavodoxin_oxidoreductase_248079..248229_POSITIVE 181 124 81 90 33 NC_003454:FN1141|3end_Formate_transporter_1790493..1790643_NEGATIVE 178 58 28 60 34 NC_003454:FN0755|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_C_1414663..1414813_NEGATIVE 177 124 82 71 20 NC_003454:FN1985|3end_Inner_membrane_protein_487273..487423_NEGATIVE 176 96 57 65 30 NC_003454:FN0430|3end_50S_ribosomal_protein_L19_1071791..1071941_POSITIVE 175 132 111 135 110 NC_003454:FN1620|3end_30S_ribosomal_protein_S2_128719..128869_POSITIVE