Origin IGS: cgtttttaaaaattaggaaacaaaaaaaggcactcgtttgagtgcctttaaatttagctagcggcaatagggcttatctaatttacggatttataattctatattcaatatatacttataaaattataaatatacttgcttacatagtgcttacataaataaaggggctgcttaaaataaacatccccttacattaaaaact .........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 agtttttaatgtaaggggatgtttattttaagcagcccctttatttatgtaagcactatgtaagcaagtatatttataattttataagtatatattgaatatagaattataaatccgtaaattagataagccctattgccgctagctaaatttaaaggcactcaaacgagtgcctttttttgtttcctaatttttaaaaacg Mask Tandem Repeat Region ================================================ cgtttttaaaaattaggaaacaaaaaaaggcactcgtttgagtgcctttaaatttagctagcggcaatagggcttatctaatttacggatttataattctatattcaatatatacttataaaattataaatatacttgcttacatagtgcttacataaataaaggggctgcttaaaataaacatccccttacattaaaaact Find is-nt database================================================ Query_seq: TDE1132:TDE1133|TDE1132:TDE1133:chorismate synthase:hypothetical protein:-><-:1164641..1164842 202 cgtttttaaaaattaggaaacaaaaaaaggcactcgtttgagtgcctttaaatttagctagcggcaatagggcttatctaatttacggatttataattctatattcaatatatacttataaaattataaatatacttgcttacatagtgcttacataaataaaggggctgcttaaaataaacatccccttacattaaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1132:TDE1133|TDE1132:TDE1133:chorismate synthase:hypothetical protein:-><-:1164641..1164842 202 cgtttttaaaaattaggaaacaaaaaaaggcactcgtttgagtgcctttaaatttagctagcggcaatagggcttatctaatttacggatttataattctatattcaatatatacttataaaattataaatatacttgcttacatagtgcttacataaataaaggggctgcttaaaataaacatccccttacattaaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1132:TDE1133|TDE1132:TDE1133:chorismate synthase:hypothetical protein:-><-:1164641..1164842 202 cgtttttaaaaattaggaaacaaaaaaaggcactcgtttgagtgcctttaaatttagctagcggcaatagggcttatctaatttacggatttataattctatattcaatatatacttataaaattataaatatacttgcttacatagtgcttacataaataaaggggctgcttaaaataaacatccccttacattaaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtttttaaaaattaggaaacaaaaaaaggcactcgtttgagtgcctttaaatttagctagcggcaatagggcttatctaatttacggatttataattctatattcaatatatacttataaaattataaatatacttgcttacatagtgcttacataaataaaggggctgcttaaaataaacatccccttacattaaaaact Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 42 End: 155 ......................................... M P L N L A S G N R A Y L I Y G F I I L Y S I Y T Y K I I N I L A Y I V L T ............................................... cgtttttaaaaattaggaaacaaaaaaaggcactcgtttgagtgcctttaaatttagctagcggcaatagggcttatctaatttacggatttataattctatattcaatatatacttataaaattataaatatacttgcttacatagtgcttacataaataaaggggctgcttaaaataaacatccccttacattaaaaact 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================================================ cgtttttaaaaattaggaaacaaaaaaaggcactcgtttgagtgcctttaaatttagctagcggcaatagggcttatctaatttacggatttataattctatattcaatatatacttataaaattataaatatacttgcttacatagtgcttacataaataaaggggctgcttaaaataaacatccccttacattaaaaact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.3 Tail_Score: -5.99154 Start: 29 End: 46 Full_Region: ctagctaaatttaaa ggcactc aaac gagtgcc tttttttgtttccta ............................ggcactcaaacgagtgcc............................................................................................................................................................ Find igs database================================================ Query_seq: TDE1132:TDE1133|TDE1132:TDE1133:chorismate synthase:hypothetical protein:-><-:1164641..1164842 202 cgtttttaaaaattaggaaacaaaaaaaggcactcgtttgagtgcctttaaatttagctagcggcaatagggcttatctaatttacggatttataattctatattcaatatatacttataaaattataaatatacttgcttacatagtgcttacataaataaaggggctgcttaaaataaacatccccttacattaaaaact Intra-Species Hit: Count: 1 Min: 1 Max: 202 Len: 202 Subject: NC_002967_TDE1132_TDE1133|chorismate synthase:hypothetical protein|POSITIVE:NEGATIVE|[1164641,1164842]|202 HSP 1 e-value: 4.0E-32 bit: 139.0 Len: 91 Query Start:1 Query End:91 Subject Strand: POSITIVE Subject Start: 1 Subject End: 91 cgtttttaaaaattaggaaacnnnnnnnggcactcgtttgagtgcctttaaatttagctagcggcaatagggcttatctaatttacggatt............................................................................................................... cgtttttaaaaattaggaaacaaaaaaaggcactcgtttgagtgcctttaaatttagctagcggcaatagggcttatctaatttacggatt............................................................................................................... HSP 2 e-value: 6.0E-31 bit: 135.0 Len: 68 Query Start:135 Query End:202 Subject Strand: POSITIVE Subject Start: 135 Subject End: 202 ......................................................................................................................................cttgcttacatagtgcttacataaataaaggggctgcttaaaataaacatccccttacattaaaaact ......................................................................................................................................cttgcttacatagtgcttacataaataaaggggctgcttaaaataaacatccccttacattaaaaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUUUUAAAAAUUAGGAAACAAAAAAAGGCACUCGUUUGAGUGCCUUUAAAUUUAGCUAGCGGCAAUAGGGCUUAUCUAAUUUACGGAUUUAUAAUUCUAUAUUCAAUAUAUACUUAUAAAAUUAUAAAUAUACUUGCUUACAUAGUGCUUACAUAAAUAAAGGGGCUGCUUAAAAUAAACAUCCCCUUACAUUAAAAACU .((((((((......(....)....((((((((((....)))))))))).......((((..(((((((((.....))))........((((((((((.((((.............)))).))))))))))....)))))....)))).............((((((.((.(((...))).)).))))))...)))))))). (-44.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUUUAAUGUAAGGGGAUGUUUAUUUUAAGCAGCCCCUUUAUUUAUGUAAGCACUAUGUAAGCAAGUAUAUUUAUAAUUUUAUAAGUAUAUAUUGAAUAUAGAAUUAUAAAUCCGUAAAUUAGAUAAGCCCUAUUGCCGCUAGCUAAAUUUAAAGGCACUCAAACGAGUGCCUUUUUUUGUUUCCUAAUUUUUAAAAACG .((((((((...((((((.((((((...)))))).))))))......(((((...((((((...((((((((((((((....))))))))))).))).))))))..))))).......(((((((...(((.........)))...((((...((((((((((....)))))))))).))))....))))))))))))))). (-51.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 88 43 225 179 NC_002967:TDE0566|5end_hypothetical_protein_597185..597415_POSITIVE 293 88 43 71 25 NC_002967:TDE0565|5end_hypothetical_protein_597031..597261_POSITIVE 285 65 26 169 133 NC_002967:TDE1414|5end_phosphonopyruvate_decarboxylase,_putative_1456812..1457042_POSITIVE 271 73 31 225 175 NC_002967:TDE0735|5end_hypothetical_protein_775003..775233_NEGATIVE 264 106 61 77 39 NC_002967:TDE2391|5end_peptidyl-prolyl_cis-trans_isomerase_2421550..2421780_NEGATIVE 261 49 9 49 5 NC_002967:TDE2148|5end_OmpA_family_protein_2185946..2186176_NEGATIVE 261 74 37 147 108 NC_002967:TDE0176|5end_hypothetical_protein_209798..210028_NEGATIVE 256 74 32 226 180 NC_002967:TDE0055|5end_flagellar_biosynthesis_protein_63565..63795_POSITIVE 253 78 34 71 15 NC_002967:TDE1895|5end_GTP-binding_protein_Era_1914963..1915193_POSITIVE 247 84 42 167 124 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 243 73 33 185 140 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 241 103 62 41 1 NC_002967:TDE1586|5end_hypothetical_protein_1633920..1634150_NEGATIVE 240 87 41 229 171 NC_002967:TDE0855|5end_DNA-binding_response_regulator_876536..876766_POSITIVE 239 193 157 205 167 NC_002967:TDE2524|5end_ABC_transporter,_ATP-binding_protein_2550456..2550686_POSITIVE 239 69 21 231 191 NC_002967:TDE2276|5end_hypothetical_protein_2312676..2312906_NEGATIVE 238 69 28 166 127 NC_002967:TDE1037|5end_hypothetical_protein_1064470..1064700_POSITIVE 238 87 46 184 142 NC_002967:TDE0365|5end_hypothetical_protein_412421..412651_NEGATIVE 237 74 32 224 183 NC_002967:TDE0199|5end_hypothetical_protein_234708..234938_NEGATIVE 236 74 32 133 93 NC_002967:TDE0474|5end_hypothetical_protein_530740..530970_POSITIVE 236 79 32 75 39 NC_002967:TDE0049|5end_hypothetical_protein_59089..59319_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 60 26 93 61 NC_002967:TDE1355|3end_hypothetical_protein_1395527..1395677_POSITIVE 274 49 26 65 42 NC_002967:TDE1132|3end_chorismate_synthase_1164580..1164730_POSITIVE 273 74 31 59 13 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 271 65 22 81 35 NC_002967:TDE1324|3end_hypothetical_protein_1360915..1361065_NEGATIVE 267 89 42 117 64 NC_002967:TDE0975|3end_hypothetical_protein_999879..1000029_POSITIVE 259 49 15 30 1 NC_002967:TDE2149|3end_transglycosylase,_SLT_family_2185965..2186115_NEGATIVE 257 76 33 49 13 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 255 75 37 87 38 NC_002967:TDE2724|3end_hypothetical_protein_2782282..2782432_POSITIVE 254 80 38 104 57 NC_002967:TDE0165|3end_hypothetical_protein_195056..195206_POSITIVE 253 92 57 42 4 NC_002967:TDE1980|3end_hypothetical_protein_1991960..1992110_NEGATIVE 253 78 34 69 13 NC_002967:TDE1894|3end_ferredoxin_1915041..1915191_POSITIVE 250 190 147 112 63 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 247 84 42 81 38 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 246 65 26 132 84 NC_002967:TDE0146|3end_amidohydrolase_family_protein_167435..167585_NEGATIVE 245 88 41 98 45 NC_002967:TDE0793|3end_hypothetical_protein_819205..819355_POSITIVE 243 73 33 141 96 NC_002967:TDE1782|3end_hypothetical_protein_1823304..1823454_NEGATIVE 242 187 144 76 24 NC_002967:TDE1066|3end_hypothetical_protein_1094335..1094485_NEGATIVE 240 73 32 149 110 NC_002967:TDE2710|3end_MATE_efflux_family_protein_2767974..2768124_POSITIVE 236 74 32 113 73 NC_002967:TDE0473|3end_heavy_metal_translocating_P-type_ATPase_530800..530950_POSITIVE 235 174 144 143 119 NC_002967:TDE2325|3end_hypothetical_protein_2361177..2361327_POSITIVE