Origin IGS: tgatcgcgtctttccgactctccttttttatggcggaatgtcactcgagatgagatcaacatcttaaaaaaaacgccaaaatgtcagaaattatgacagtcttcgctttcatcatttttggcacactatttgctgcttgtcaatcaacgtgtttaacacatagaggatattgaagcaaataaaacattaatatagaataaat .........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 atttattctatattaatgttttatttgcttcaatatcctctatgtgttaaacacgttgattgacaagcagcaaatagtgtgccaaaaatgatgaaagcgaagactgtcataatttctgacattttggcgttttttttaagatgttgatctcatctcgagtgacattccgccataaaaaaggagagtcggaaagacgcgatca Mask Tandem Repeat Region ================================================ tgatcgcgtctttccgactctccttttttatggcggaatgtcactcgagatgagatcaacatcttaaaaaaaacgccaaaatgtcagaaattatgacagtcttcgctttcatcatttttggcacactatttgctgcttgtcaatcaacgtgtttaacacatagaggatattgaagcaaataaaacattaatatagaataaat Find is-nt database================================================ Query_seq: TF1689:TF1690|TF1689:TF1690:conserved hypothetical protein:chaperone protein dnaK:->->:1806675..1806876 202 tgatcgcgtctttccgactctccttttttatggcggaatgtcactcgagatgagatcaacatcttaaaaaaaacgccaaaatgtcagaaattatgacagtcttcgctttcatcatttttggcacactatttgctgcttgtcaatcaacgtgtttaacacatagaggatattgaagcaaataaaacattaatatagaataaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1689:TF1690|TF1689:TF1690:conserved hypothetical protein:chaperone protein dnaK:->->:1806675..1806876 202 tgatcgcgtctttccgactctccttttttatggcggaatgtcactcgagatgagatcaacatcttaaaaaaaacgccaaaatgtcagaaattatgacagtcttcgctttcatcatttttggcacactatttgctgcttgtcaatcaacgtgtttaacacatagaggatattgaagcaaataaaacattaatatagaataaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1689:TF1690|TF1689:TF1690:conserved hypothetical protein:chaperone protein dnaK:->->:1806675..1806876 202 tgatcgcgtctttccgactctccttttttatggcggaatgtcactcgagatgagatcaacatcttaaaaaaaacgccaaaatgtcagaaattatgacagtcttcgctttcatcatttttggcacactatttgctgcttgtcaatcaacgtgtttaacacatagaggatattgaagcaaataaaacattaatatagaataaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatcgcgtctttccgactctccttttttatggcggaatgtcactcgagatgagatcaacatcttaaaaaaaacgccaaaatgtcagaaattatgacagtcttcgctttcatcatttttggcacactatttgctgcttgtcaatcaacgtgtttaacacatagaggatattgaagcaaataaaacattaatatagaataaat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 81 End: 170 ................................................................................ M S E I M T V F A F I I F G T L F A A C Q S T C L T H R G Y ................................ tgatcgcgtctttccgactctccttttttatggcggaatgtcactcgagatgagatcaacatcttaaaaaaaacgccaaaatgtcagaaattatgacagtcttcgctttcatcatttttggcacactatttgctgcttgtcaatcaacgtgtttaacacatagaggatattgaagcaaataaaacattaatatagaataaat 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: 81 Start: 169 End: 198 ........................................................................................................................................................................ATTGAAGCAAATAAAACATTAATATAGAAT.... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: + Score: 92 Start: 118 End: 134 .....................................................................................................................TTGGCACACTATTTGCT.................................................................... tgatcgcgtctttccgactctccttttttatggcggaatgtcactcgagatgagatcaacatcttaaaaaaaacgccaaaatgtcagaaattatgacagtcttcgctttcatcatttttggcacactatttgctgcttgtcaatcaacgtgtttaacacatagaggatattgaagcaaataaaacattaatatagaataaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1689:TF1690|TF1689:TF1690:conserved hypothetical protein:chaperone protein dnaK:->->:1806675..1806876 202 tgatcgcgtctttccgactctccttttttatggcggaatgtcactcgagatgagatcaacatcttaaaaaaaacgccaaaatgtcagaaattatgacagtcttcgctttcatcatttttggcacactatttgctgcttgtcaatcaacgtgtttaacacatagaggatattgaagcaaataaaacattaatatagaataaat Intra-Species Hit: Count: 1 Min: 1 Max: 202 Len: 202 Subject: tfor_TF1689_TF1690|conserved hypothetical protein:chaperone protein dnaK|POSITIVE:POSITIVE|[1806675,1806876]|202 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 202 Query Start:1 Query End:202 Subject Strand: POSITIVE Subject Start: 1 Subject End: 202 tgatcgcgtctttccgactctccttttttatggcggaatgtcactcgagatgagatcaacatcttnnnnnnnncgccaaaatgtcagaaattatgacagtcttcgctttcatcatttttggcacactatttgctgcttgtcaatcaacgtgtttaacacatagaggatattgaagcaaataaaacattaatatagaataaat tgatcgcgtctttccgactctccttttttatggcggaatgtcactcgagatgagatcaacatcttaaaaaaaacgccaaaatgtcagaaattatgacagtcttcgctttcatcatttttggcacactatttgctgcttgtcaatcaacgtgtttaacacatagaggatattgaagcaaataaaacattaatatagaataaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCGCGUCUUUCCGACUCUCCUUUUUUAUGGCGGAAUGUCACUCGAGAUGAGAUCAACAUCUUAAAAAAAACGCCAAAAUGUCAGAAAUUAUGACAGUCUUCGCUUUCAUCAUUUUUGGCACACUAUUUGCUGCUUGUCAAUCAACGUGUUUAACACAUAGAGGAUAUUGAAGCAAAUAAAACAUUAAUAUAGAAUAAAU (((((.((((((...(((..(((...........)))..)))....)))))).)))))...(((.................((((((((((.((((.(((....))).)))).))))))))))...((((((((...((((..((...(((.....)))...)).))))....))))))))............)))...... (-45.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUAUUCUAUAUUAAUGUUUUAUUUGCUUCAAUAUCCUCUAUGUGUUAAACACGUUGAUUGACAAGCAGCAAAUAGUGUGCCAAAAAUGAUGAAAGCGAAGACUGUCAUAAUUUCUGACAUUUUGGCGUUUUUUUUAAGAUGUUGAUCUCAUCUCGAGUGACAUUCCGCCAUAAAAAAGGAGAGUCGGAAAGACGCGAUCA ....................((((((((((((((.......(((((.....)))))..))))).....))))))))).(((.((.((((.((((.((......)).)))).)))).)).)))....((((((((((..(((((.......)))))..)..(((.((((...........)))).))).)))))))))..... (-39.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 49 1 185 114 tfor:TF0646|5end_conserved_hypothetical_protein;_possible_adenylate_cyclase_689059..689289_POSITIVE 313 46 1 188 134 tfor:TF1768|5end_conserved_hypothetical_protein;_possible_transposase_1906526..1906756_POSITIVE 305 43 5 176 123 tfor:TF1841|5end_hypothetical_protein_1991936..1992166_POSITIVE 305 48 1 193 137 tfor:TF0307|5end_conserved_hypothetical_protein_332783..333013_POSITIVE 299 43 4 90 48 tfor:TF2889|5end_50S_ribosomal_protein_L27_3078333..3078563_POSITIVE 297 47 6 222 179 tfor:TF0944|5end_TonB-dependent_receptor_986340..986570_POSITIVE 296 49 1 165 91 tfor:TF0292|5end_conserved_hypothetical_protein_320087..320317_POSITIVE 295 144 104 58 13 tfor:TF1784|5end_conserved_hypothetical_protein;_possible_formiminotransferase-cyclodeaminase_1923850..1924080_POSITIVE 293 50 3 226 184 tfor:TF2918|5end_hypothetical_protein_3114084..3114314_POSITIVE 287 50 2 76 23 tfor:TF0190|5end_cell_division_protein_FtsH_204029..204259_POSITIVE 285 155 121 226 189 tfor:TF1292|5end_sensor_histidine_protein_kinase_1372567..1372797_POSITIVE 281 47 5 199 149 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 281 50 2 50 10 tfor:TF2256|5end_transfer_region-related_protein,_TraI_2427908..2428138_POSITIVE 279 48 6 209 173 tfor:TF2380|5end_hemagglutinin_2545012..2545242_POSITIVE 279 54 16 212 168 tfor:TF0594|5end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_626971..627201_POSITIVE 278 42 3 50 9 tfor:TF2394|5end_integrase/recombinase_XerD_2565608..2565838_POSITIVE 278 47 1 198 132 tfor:TF0988|5end_conserved_hypothetical_protein;_possible_nucleotidyltransferase_1044463..1044693_POSITIVE 277 45 4 226 175 tfor:TF1703|5end_conserved_hypothetical_protein_1822065..1822295_POSITIVE 277 48 6 42 2 tfor:TF1600|5end_uroporphyrinogen-III_synthase_1713964..1714194_POSITIVE 276 47 5 149 105 tfor:TF0340|5end_hypothetical_protein_363893..364123_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 48 1 79 23 tfor:TF0306|3end_transglutaminase-like_enzyme/cysteine_protease_332749..332899_POSITIVE 303 38 1 151 110 tfor:TF2937|3end_translation_elongation_factor_Tu_3140502..3140652_POSITIVE 299 43 4 66 24 tfor:TF2888|3end_50S_ribosomal_protein_L21_3078389..3078539_POSITIVE 298 50 3 113 57 tfor:TF0419|3end_conserved_hypothetical_protein_435794..435944_POSITIVE 296 49 1 129 55 tfor:TF0291|3end_triose-phosphate_isomerase_320131..320281_POSITIVE 287 50 2 57 4 tfor:TF0189|3end_phosphatidate_cytidylytransferase_(CDP-diglyceride_synthetase)_204090..204240_POSITIVE 284 48 1 52 8 tfor:TF1599|3end_ribonuclease_P_protein_component_1714054..1714204_POSITIVE 276 48 1 61 4 tfor:TF2807|3end_possible_chloride_channel_protein_2998534..2998684_POSITIVE 276 25 1 144 114 tfor:TF0645|3end_hypothetical_protein_689139..689289_POSITIVE 276 138 93 125 65 tfor:TF0099|3end_glycosyltransferase_of_PMT_family_111124..111274_POSITIVE 273 57 13 117 60 tfor:TF2911|3end_hypothetical_protein_3106640..3106790_POSITIVE 272 50 4 115 58 tfor:TF2990|3end_nicotinate-nucleotide_pyrophosphorylase_3206389..3206539_POSITIVE 269 50 6 138 84 tfor:TF1581|3end_hypothetical_protein_1689467..1689617_POSITIVE 268 60 14 74 30 tfor:TF3109|3end_hypothetical_protein_3342803..3342953_POSITIVE 267 57 11 53 11 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 264 50 1 62 9 tfor:TF1592|3end_hypothetical_protein_1708557..1708707_POSITIVE 263 50 1 110 61 tfor:TF2893|3end_conserved_hypothetical_protein;_possible_phosphoesterase_3082039..3082189_POSITIVE 262 59 11 129 76 tfor:TF2638|3end_cation_transport_protein_2809051..2809201_POSITIVE 261 150 104 60 16 tfor:TF0143|3end_aspartate--ammonia_ligase_152501..152651_POSITIVE 260 50 3 98 38 tfor:TF3008|3end_zinc_protease_3228837..3228987_POSITIVE