Origin IGS: tgatcctcttcttgttttgatatccaatgttgttttttgctcttttttctcgagattatttggatttctttaaaaaatctattatatttgcagacaaagaagaatgagtaaagccgcattgttagattgggaaactcatcagataaaatacaattccgagacacgctcttggcgctgatggcgggctgcaattccttgtgaatgcttcggcacagcagattacaaaggcgtcaaaggcactcaaaacctgtcatacggagtttgttcatatcggcagtgcggcctcccataaaagaggatgtgtcaaaacgtaatgttggggcgcatcctctttaattaatccgtatttt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatacggattaattaaagaggatgcgccccaacattacgttttgacacatcctcttttatgggaggccgcactgccgatatgaacaaactccgtatgacaggttttgagtgcctttgacgcctttgtaatctgctgtgccgaagcattcacaaggaattgcagcccgccatcagcgccaagagcgtgtctcggaattgtattttatctgatgagtttcccaatctaacaatgcggctttactcattcttctttgtctgcaaatataatagattttttaaagaaatccaaataatctcgagaaaaaagagcaaaaaacaacattggatatcaaaacaagaagaggatca Mask Tandem Repeat Region ================================================ tgatcctcttcttgttttgatatccaatgttgttttttgctcttttttctcgagattatttggatttctttaaaaaatctattatatttgcagacaaagaagaatgagtaaagccgcattgttagattgggaaactcatcagataaaatacaattccgagacacgctcttggcgctgatggcgggctgcaattccttgtgaatgcttcggcacagcagattacaaaggcgtcaaaggcactcaaaacctgtcatacggagtttgttcatatcggcagtgcggcctcccataaaagaggatgtgtcaaaacgtaatgttggggcgcatcctctttaattaatccgtatttt Find is-nt database================================================ Query_seq: TF2946:TF2947|TF2946:TF2947:conserved hypothetical protein; possible ATPase:isochorismate synthase:->->:3153423..3153772 350 tgatcctcttcttgttttgatatccaatgttgttttttgctcttttttctcgagattatttggatttctttaaaaaatctattatatttgcagacaaagaagaatgagtaaagccgcattgttagattgggaaactcatcagataaaatacaattccgagacacgctcttggcgctgatggcgggctgcaattccttgtgaatgcttcggcacagcagattacaaaggcgtcaaaggcactcaaaacctgtcatacggagtttgttcatatcggcagtgcggcctcccataaaagaggatgtgtcaaaacgtaatgttggggcgcatcctctttaattaatccgtatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2946:TF2947|TF2946:TF2947:conserved hypothetical protein; possible ATPase:isochorismate synthase:->->:3153423..3153772 350 tgatcctcttcttgttttgatatccaatgttgttttttgctcttttttctcgagattatttggatttctttaaaaaatctattatatttgcagacaaagaagaatgagtaaagccgcattgttagattgggaaactcatcagataaaatacaattccgagacacgctcttggcgctgatggcgggctgcaattccttgtgaatgcttcggcacagcagattacaaaggcgtcaaaggcactcaaaacctgtcatacggagtttgttcatatcggcagtgcggcctcccataaaagaggatgtgtcaaaacgtaatgttggggcgcatcctctttaattaatccgtatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2946:TF2947|TF2946:TF2947:conserved hypothetical protein; possible ATPase:isochorismate synthase:->->:3153423..3153772 350 tgatcctcttcttgttttgatatccaatgttgttttttgctcttttttctcgagattatttggatttctttaaaaaatctattatatttgcagacaaagaagaatgagtaaagccgcattgttagattgggaaactcatcagataaaatacaattccgagacacgctcttggcgctgatggcgggctgcaattccttgtgaatgcttcggcacagcagattacaaaggcgtcaaaggcactcaaaacctgtcatacggagtttgttcatatcggcagtgcggcctcccataaaagaggatgtgtcaaaacgtaatgttggggcgcatcctctttaattaatccgtatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatcctcttcttgttttgatatccaatgttgttttttgctcttttttctcgagattatttggatttctttaaaaaatctattatatttgcagacaaagaagaatgagtaaagccgcattgttagattgggaaactcatcagataaaatacaattccgagacacgctcttggcgctgatggcgggctgcaattccttgtgaatgcttcggcacagcagattacaaaggcgtcaaaggcactcaaaacctgtcatacggagtttgttcatatcggcagtgcggcctcccataaaagaggatgtgtcaaaacgtaatgttggggcgcatcctctttaattaatccgtatttt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 77 End: 175 ............................................................................ M Y Y I C R Q R R M S K A A L L D W E T H Q I K Y N S E T R S W R ............................................................................................................................................................................... Protein_Len: 33 Strand: + Start: 191 End: 289 .............................................................................................................................................................................................. M P C E C F G T A D Y K G V K G T Q N L S Y G V C S Y R Q C G L P ............................................................. Protein_Len: 53 Strand: + Start: 153 End: 311 ........................................................................................................................................................ M P R H A L G A D G G L Q F L V N A S A Q Q I T K A S K A L K T C H T E F V H I G S A A S H K R G C V K T ....................................... Protein_Len: 44 Strand: + Start: 202 End: 333 ......................................................................................................................................................................................................... M L R H S R L Q R R Q R H S K P V I R S L F I S A V R P P I K E D V S K R N V G A H P L ................. Protein_Len: 40 Strand: - Start: 125 End: 244 ............................................................................................................................ I P F S M L Y F V I G L C A R P A S P P S C N R T F A E A C C I V F A D F A S M .......................................................................................................... Protein_Len: 60 Strand: - Start: 3 End: 218 .. S K K R S I I Q I E K F F R N Y K C V F F F S Y L R M T L N P F E D S L I C N R S V S K A S I A P Q L E K H I S R C L M .................................................................................................................................... tgatcctcttcttgttttgatatccaatgttgttttttgctcttttttctcgagattatttggatttctttaaaaaatctattatatttgcagacaaagaagaatgagtaaagccgcattgttagattgggaaactcatcagataaaatacaattccgagacacgctcttggcgctgatggcgggctgcaattccttgtgaatgcttcggcacagcagattacaaaggcgtcaaaggcactcaaaacctgtcatacggagtttgttcatatcggcagtgcggcctcccataaaagaggatgtgtcaaaacgtaatgttggggcgcatcctctttaattaatccgtatttt 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================================================ tgatcctcttcttgttttgatatccaatgttgttttttgctcttttttctcgagattatttggatttctttaaaaaatctattatatttgcagacaaagaagaatgagtaaagccgcattgttagattgggaaactcatcagataaaatacaattccgagacacgctcttggcgctgatggcgggctgcaattccttgtgaatgcttcggcacagcagattacaaaggcgtcaaaggcactcaaaacctgtcatacggagtttgttcatatcggcagtgcggcctcccataaaagaggatgtgtcaaaacgtaatgttggggcgcatcctctttaattaatccgtatttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 80 HP_score: -8.7 Tail_Score: -3.96298 Start: 295 End: 331 Full_Region: CGGCCTCCCATAAAA GAGGATGTGTCAAAACG TAA TGTTGGGGCGCATCCTC TTTAATTAATCCGTA ......................................................................................................................................................................................................................................................................................................GAGGATGTGTCAAAACGTAATGTTGGGGCGCATCCTC................... Find igs database================================================ Query_seq: TF2946:TF2947|TF2946:TF2947:conserved hypothetical protein; possible ATPase:isochorismate synthase:->->:3153423..3153772 350 tgatcctcttcttgttttgatatccaatgttgttttttgctcttttttctcgagattatttggatttctttaaaaaatctattatatttgcagacaaagaagaatgagtaaagccgcattgttagattgggaaactcatcagataaaatacaattccgagacacgctcttggcgctgatggcgggctgcaattccttgtgaatgcttcggcacagcagattacaaaggcgtcaaaggcactcaaaacctgtcatacggagtttgttcatatcggcagtgcggcctcccataaaagaggatgtgtcaaaacgtaatgttggggcgcatcctctttaattaatccgtatttt Intra-Species Hit: Count: 1 Min: 1 Max: 350 Len: 350 Subject: tfor_TF2946_TF2947|conserved hypothetical protein; possible ATPase:isochorismate synthase|POSITIVE:POSITIVE|[3153423,3153772]|350 HSP 1 e-value: 1.0E-170 bit: 599.0 Len: 302 Query Start:49 Query End:350 Subject Strand: POSITIVE Subject Start: 49 Subject End: 350 ................................................ctcgagattatttggatttctttaaaaaatctattatatttgcagacaaagaagaatgagtaaagccgcattgttagattgggaaactcatcagataaaatacaattccgagacacgctcttggcgctgatggcgggctgcaattccttgtgaatgcttcggcacagcagattacaaaggcgtcaaaggcactcaaaacctgtcatacggagtttgttcatatcggcagtgcggcctcccataaaagaggatgtgtcaaaacgtaatgttggggcgcatcctctttaattaatccgtatttt ................................................ctcgagattatttggatttctttaaaaaatctattatatttgcagacaaagaagaatgagtaaagccgcattgttagattgggaaactcatcagataaaatacaattccgagacacgctcttggcgctgatggcgggctgcaattccttgtgaatgcttcggcacagcagattacaaaggcgtcaaaggcactcaaaacctgtcatacggagtttgttcatatcggcagtgcggcctcccataaaagaggatgtgtcaaaacgtaatgttggggcgcatcctctttaattaatccgtatttt HSP 2 e-value: 3.0E-9 bit: 63.9 Len: 32 Query Start:1 Query End:32 Subject Strand: POSITIVE Subject Start: 1 Subject End: 32 tgatcctcttcttgttttgatatccaatgttg.............................................................................................................................................................................................................................................................................................................................. tgatcctcttcttgttttgatatccaatgttg.............................................................................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCCUCUUCUUGUUUUGAUAUCCAAUGUUGUUUUUUGCUCUUUUUUCUCGAGAUUAUUUGGAUUUCUUUAAAAAAUCUAUUAUAUUUGCAGACAAAGAAGAAUGAGUAAAGCCGCAUUGUUAGAUUGGGAAACUCAUCAGAUAAAAUACAAUUCCGAGACACGCUCUUGGCGCUGAUGGCGGGCUGCAAUUCCUUGUGAAUGCUUCGGCACAGCAGAUUACAAAGGCGUCAAAGGCACUCAAAACCUGUCAUACGGAGUUUGUUCAUAUCGGCAGUGCGGCCUCCCAUAAAAGAGGAUGUGUCAAAACGUAAUGUUGGGGCGCAUCCUCUUUAAUUAAUCCGUAUUUU .............(..(((((.....(((......(((((((.((((((...(((((.((((((....)))))).)))))......((((....)))))))))).)))))))((((((((((..(((.((....)).))).((((....(((((((((.((((.((..((((((((..((.....((((.((((.....))))((....))...))))....))..))))))))..))..........))))...))))).))))...)))).))))))))))....))).((((((((((((((..(((.....)))..)))))))))))))).)))))..)....... (-102.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUACGGAUUAAUUAAAGAGGAUGCGCCCCAACAUUACGUUUUGACACAUCCUCUUUUAUGGGAGGCCGCACUGCCGAUAUGAACAAACUCCGUAUGACAGGUUUUGAGUGCCUUUGACGCCUUUGUAAUCUGCUGUGCCGAAGCAUUCACAAGGAAUUGCAGCCCGCCAUCAGCGCCAAGAGCGUGUCUCGGAAUUGUAUUUUAUCUGAUGAGUUUCCCAAUCUAACAAUGCGGCUUUACUCAUUCUUCUUUGUCUGCAAAUAUAAUAGAUUUUUUAAAGAAAUCCAAAUAAUCUCGAGAAAAAAGAGCAAAAAACAACAUUGGAUAUCAAAACAAGAAGAGGAUCA ........((((....((((((((((.(.(..(((.....)))..).).)))))))))).(((((((((((((.((..((((.((((((..((((...((((.(((((..((((...((.((...(((((((((...((((....))))......)).)))))))..)).))...))))..))))).)))).)))).)))).)).)))).(((..........)))...)).))))))))..)))))(((((((.(((((.........)))))........((.((((((.....(((.........)))............)))))).)).....))))))).)))). (-82.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 583 335 293 164 119 tfor:TF0476|5end_conserved_hypothetical_protein_494944..495174_POSITIVE 527 334 291 228 185 tfor:TF0184|5end_dihydroneopterin_aldolase_195629..195859_POSITIVE 511 334 295 171 132 tfor:TF2536|5end_subtilisin-like_serine_protease_2719286..2719516_POSITIVE 496 218 172 56 6 tfor:TF0987|5end_DNA_repair_protein_1043090..1043320_POSITIVE 441 210 164 69 13 tfor:TF2248|5end_transfer_region-related_protein,_TraB_2422551..2422781_POSITIVE 430 332 294 229 186 tfor:TF1454|5end_sugar_phosphate_epimerase/isomerase_1539696..1539926_POSITIVE 426 333 291 203 161 tfor:TF2289|5end_secretion_protein,_possible_HlyD_family_2442725..2442955_POSITIVE 424 200 153 202 146 tfor:TF2020|5end_muconate_cycloisomerase_2176321..2176551_POSITIVE 415 220 171 121 50 tfor:TF2499|5end_possible_thioesterase_family_protein_2673903..2674133_POSITIVE 413 335 294 167 122 tfor:TF0792|5end_pyruvate_ferredoxin;_flavodoxin_oxidoreductase_846454..846684_POSITIVE 412 335 293 203 161 tfor:TF2320|5end_hypothetical_protein_2476654..2476884_POSITIVE 401 210 163 191 148 tfor:TF2047|5end_hypothetical_protein_2210057..2210287_POSITIVE 400 328 289 159 120 tfor:TF0702|5end_possible_peptidyl-prolyl_isomerase_744977..745207_POSITIVE 392 335 294 158 114 tfor:TF1284|5end_glyceraldehyde_3-phosphate_dehydrogenase_1367939..1368169_POSITIVE 390 334 293 214 173 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 388 200 156 218 173 tfor:TF0529|5end_transposase_554776..555006_POSITIVE 387 328 290 151 113 tfor:TF1024|5end_50S_ribosomal_protein_L19_1081948..1082178_POSITIVE 384 334 292 204 161 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 382 210 163 83 34 tfor:TF2759|5end_xylose_repressor,_ROK_family_2943568..2943798_POSITIVE 382 210 166 61 14 tfor:TF1933|5end_methionyl-tRNA_synthetase_2079675..2079905_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 527 334 291 47 4 tfor:TF0182|3end_DNA-binding_protein,_HU-related_195528..195678_POSITIVE 444 210 162 110 57 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 441 210 164 63 7 tfor:TF2247|3end_transfer_region-related_protein,_TraA_2422625..2422775_POSITIVE 430 332 294 110 67 tfor:TF1452|3end_conserved_hypothetical_protein;_possible_transglutaminase-like_enzyme_1539657..1539807_POSITIVE 412 335 293 57 15 tfor:TF2319|3end_acyl_carrier_protein_2476588..2476738_POSITIVE 410 335 295 114 74 tfor:TF2413|3end_hypothetical_protein_2590680..2590830_POSITIVE 388 200 156 141 96 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 384 334 292 49 6 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 382 210 166 61 14 tfor:TF1932|3end_pigmentation_and_extracellular_proteinase_regulator_2079755..2079905_POSITIVE 381 335 293 64 22 tfor:TF0105|3end_DNA-binding_stress_protein,_Dps_family_113907..114057_POSITIVE 380 189 156 66 26 tfor:TF1165|3end_conserved_hypothetical_protein_1245921..1246071_POSITIVE 379 200 151 142 102 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 377 335 292 46 1 tfor:TF3144|3end_phosphomannomutase/phosphoglucomutase_3381184..3381334_POSITIVE 375 198 166 140 96 tfor:TF1865|3end_conserved_hypothetical_protein;_possible_transposase_2022406..2022556_POSITIVE 374 219 171 68 17 tfor:TF3009|3end_RNA_polymerase_ECF-type_sigma_factor_3229709..3229859_POSITIVE 373 216 173 151 103 tfor:TF1954|3end_long-chain-fatty-acid--CoA_ligase_2106940..2107090_POSITIVE 371 210 162 86 30 tfor:TF0960|3end_beta-galactosidase_1010506..1010656_POSITIVE 369 331 295 64 28 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 369 217 172 73 24 tfor:TF1322|3end_conserved_hypothetical_protein;_possible_surface_protein_1402567..1402717_POSITIVE 368 331 291 49 9 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE