Origin IGS: gctctaatgtatttaataatctaacgtttcaaaaatagtatataaatatatacaaaaaaaaaagttttgtatatatttacattttttatgtaataaatattattttaaacagacctgattttgattgtcataaaaattcaaaaccagtaattatctacatgaaaatcatgcttgccacagcttgcaagaagactaaaccacaacgtgtttttacactatctcttgcatttttgaataaatgatatttaacggctgtaaatccataaaaaatcactctgttgagagtattgcatgaaaaaattaacgaggcgtcattcctgctttacacgaaaattgcattacctttgtcgggcaattatcaaaaaacttacgt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 acgtaagttttttgataattgcccgacaaaggtaatgcaattttcgtgtaaagcaggaatgacgcctcgttaattttttcatgcaatactctcaacagagtgattttttatggatttacagccgttaaatatcatttattcaaaaatgcaagagatagtgtaaaaacacgttgtggtttagtcttcttgcaagctgtggcaagcatgattttcatgtagataattactggttttgaatttttatgacaatcaaaatcaggtctgtttaaaataatatttattacataaaaaatgtaaatatatacaaaacttttttttttgtatatatttatatactatttttgaaacgttagattattaaatacattagagc Mask Tandem Repeat Region ================================================ gctctaatgtatttaataatctaacgtttcaaaaatagtatataaatatatacaaaaaaaaaagttttgtatatatttacattttttatgtaataaatattattttaaacagacctgattttgattgtcataaaaattcaaaaccagtaattatctacatgaaaatcatgcttgccacagcttgcaagaagactaaaccacaacgtgtttttacactatctcttgcatttttgaataaatgatatttaacggctgtaaatccataaaaaatcactctgttgagagtattgcatgaaaaaattaacgaggcgtcattcctgctttacacgaaaattgcattacctttgtcgggcaattatcaaaaaacttacgt Find is-nt database================================================ Query_seq: TF0966:TF0967|TF0966:TF0967:hypothetical protein:alpha glycan phosphorylase:->->:1015998..1016370 373 gctctaatgtatttaataatctaacgtttcaaaaatagtatataaatatatacaaaaaaaaaagttttgtatatatttacattttttatgtaataaatattattttaaacagacctgattttgattgtcataaaaattcaaaaccagtaattatctacatgaaaatcatgcttgccacagcttgcaagaagactaaaccacaacgtgtttttacactatctcttgcatttttgaataaatgatatttaacggctgtaaatccataaaaaatcactctgttgagagtattgcatgaaaaaattaacgaggcgtcattcctgctttacacgaaaattgcattacctttgtcgggcaattatcaaaaaacttacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0966:TF0967|TF0966:TF0967:hypothetical protein:alpha glycan phosphorylase:->->:1015998..1016370 373 gctctaatgtatttaataatctaacgtttcaaaaatagtatataaatatatacaaaaaaaaaagttttgtatatatttacattttttatgtaataaatattattttaaacagacctgattttgattgtcataaaaattcaaaaccagtaattatctacatgaaaatcatgcttgccacagcttgcaagaagactaaaccacaacgtgtttttacactatctcttgcatttttgaataaatgatatttaacggctgtaaatccataaaaaatcactctgttgagagtattgcatgaaaaaattaacgaggcgtcattcctgctttacacgaaaattgcattacctttgtcgggcaattatcaaaaaacttacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0966:TF0967|TF0966:TF0967:hypothetical protein:alpha glycan phosphorylase:->->:1015998..1016370 373 gctctaatgtatttaataatctaacgtttcaaaaatagtatataaatatatacaaaaaaaaaagttttgtatatatttacattttttatgtaataaatattattttaaacagacctgattttgattgtcataaaaattcaaaaccagtaattatctacatgaaaatcatgcttgccacagcttgcaagaagactaaaccacaacgtgtttttacactatctcttgcatttttgaataaatgatatttaacggctgtaaatccataaaaaatcactctgttgagagtattgcatgaaaaaattaacgaggcgtcattcctgctttacacgaaaattgcattacctttgtcgggcaattatcaaaaaacttacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctctaatgtatttaataatctaacgtttcaaaaatagtatataaatatatacaaaaaaaaaagttttgtatatatttacattttttatgtaataaatattattttaaacagacctgattttgattgtcataaaaattcaaaaccagtaattatctacatgaaaatcatgcttgccacagcttgcaagaagactaaaccacaacgtgtttttacactatctcttgcatttttgaataaatgatatttaacggctgtaaatccataaaaaatcactctgttgagagtattgcatgaaaaaattaacgaggcgtcattcctgctttacacgaaaattgcattacctttgtcgggcaattatcaaaaaacttacgt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 42 End: 239 ......................................... M N I Y K K K S F V Y I Y I F Y V I N I I L N R P D F D C H K N S K P V I I Y M K I M L A T A C K K T K P Q R V F T L S ...................................................................................................................................... Protein_Len: 34 Strand: + Start: 270 End: 371 ............................................................................................................................................................................................................................................................................. M T L L R V L H E K I N E A S F L L Y T K I A L P L S G N Y Q K T Y .. Protein_Len: 48 Strand: - Start: 158 End: 301 ............................................................................................................................................................. M F I M S A V A Q L F V L G C R T K V S D R A N K F L H Y K V A T F G Y F I V R N L T N C S F M ........................................................................ gctctaatgtatttaataatctaacgtttcaaaaatagtatataaatatatacaaaaaaaaaagttttgtatatatttacattttttatgtaataaatattattttaaacagacctgattttgattgtcataaaaattcaaaaccagtaattatctacatgaaaatcatgcttgccacagcttgcaagaagactaaaccacaacgtgtttttacactatctcttgcatttttgaataaatgatatttaacggctgtaaatccataaaaaatcactctgttgagagtattgcatgaaaaaattaacgaggcgtcattcctgctttacacgaaaattgcattacctttgtcgggcaattatcaaaaaacttacgt 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================================================ gctctaatgtatttaataatctaacgtttcaaaaatagtatataaatatatacaaaaaaaaaagttttgtatatatttacattttttatgtaataaatattattttaaacagacctgattttgattgtcataaaaattcaaaaccagtaattatctacatgaaaatcatgcttgccacagcttgcaagaagactaaaccacaacgtgtttttacactatctcttgcatttttgaataaatgatatttaacggctgtaaatccataaaaaatcactctgttgagagtattgcatgaaaaaattaacgaggcgtcattcctgctttacacgaaaattgcattacctttgtcgggcaattatcaaaaaacttacgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -7.3 Tail_Score: -5.39721 Start: 41 End: 81 Full_Region: GTTTCAAAAATAGTA TATAAATATATACAAAA AAAAAAG TTTTGTATATATTTACA TTTTTTATGTAATAA ........................................TATAAATATATACAAAAAAAAAAGTTTTGTATATATTTACA.................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 79 HP_score: -9.9 Tail_Score: -2.88564 Start: 43 End: 79 Full_Region: TTCAAAAATAGTATA TAAATATATACAAAA AAAAAAG TTTTGTATATATTTA CATTTTTTATGTAAT ..........................................TAAATATATACAAAAAAAAAAGTTTTGTATATATTTA...................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 79 HP_score: -9.9 Tail_Score: -3.05832 Start: 43 End: 79 Full_Region: attacataaaaaatg taaatatatacaaaa ctttttt ttttgtatatattta tatactatttttgaa ..........................................taaatatatacaaaacttttttttttgtatatattta...................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 70 HP_score: -6.3 Tail_Score: -4.16101 Start: 47 End: 75 Full_Region: cataaaaaatgtaaa tatatacaaaa ctttttt ttttgtatata tttatatactatttt ..............................................tatatacaaaacttttttttttgtatata.......................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TF0966:TF0967|TF0966:TF0967:hypothetical protein:alpha glycan phosphorylase:->->:1015998..1016370 373 gctctaatgtatttaataatctaacgtttcaaaaatagtatataaatatatacaaaaaaaaaagttttgtatatatttacattttttatgtaataaatattattttaaacagacctgattttgattgtcataaaaattcaaaaccagtaattatctacatgaaaatcatgcttgccacagcttgcaagaagactaaaccacaacgtgtttttacactatctcttgcatttttgaataaatgatatttaacggctgtaaatccataaaaaatcactctgttgagagtattgcatgaaaaaattaacgaggcgtcattcctgctttacacgaaaattgcattacctttgtcgggcaattatcaaaaaacttacgt Intra-Species Hit: Count: 1 Min: 1 Max: 373 Len: 373 Subject: tfor_TF0966_TF0967|hypothetical protein:alpha glycan phosphorylase|POSITIVE:POSITIVE|[1015998,1016370]|373 HSP 1 e-value: 0.0 bit: 680.0 Len: 373 Query Start:1 Query End:373 Subject Strand: POSITIVE Subject Start: 1 Subject End: 373 gctctaatgtatttaataatctaacgtttcaaaaatagtatataaatatatacnnnnnnnnnngttttgtatatatttacattttttatgtaataaatattattttaaacagacctgattttgattgtcataaaaattcaaaaccagtaattatctacatgaaaatcatgcttgccacagcttgcaagaagactaaaccacaacgtgtttttacactatctcttgcatttttgaataaatgatatttaacggctgtaaatccataaaaaatcactctgttgagagtattgcatgaaaaaattaacgaggcgtcattcctgctttacacgaaaattgcattacctttgtcgggcaattatcaaaaaacttacgt gctctaatgtatttaataatctaacgtttcaaaaatagtatataaatatatacaaaaaaaaaagttttgtatatatttacattttttatgtaataaatattattttaaacagacctgattttgattgtcataaaaattcaaaaccagtaattatctacatgaaaatcatgcttgccacagcttgcaagaagactaaaccacaacgtgtttttacactatctcttgcatttttgaataaatgatatttaacggctgtaaatccataaaaaatcactctgttgagagtattgcatgaaaaaattaacgaggcgtcattcctgctttacacgaaaattgcattacctttgtcgggcaattatcaaaaaacttacgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUCUAAUGUAUUUAAUAAUCUAACGUUUCAAAAAUAGUAUAUAAAUAUAUACAAAAAAAAAAGUUUUGUAUAUAUUUACAUUUUUUAUGUAAUAAAUAUUAUUUUAAACAGACCUGAUUUUGAUUGUCAUAAAAAUUCAAAACCAGUAAUUAUCUACAUGAAAAUCAUGCUUGCCACAGCUUGCAAGAAGACUAAACCACAACGUGUUUUUACACUAUCUCUUGCAUUUUUGAAUAAAUGAUAUUUAACGGCUGUAAAUCCAUAAAAAAUCACUCUGUUGAGAGUAUUGCAUGAAAAAAUUAACGAGGCGUCAUUCCUGCUUUACACGAAAAUUGCAUUACCUUUGUCGGGCAAUUAUCAAAAAACUUACGU ......(((((............(((((((............(((((((((((((((.......)))))))))))))))..((((((((((((((.......((((((.((((..(((((((...((..............................((((.....))))......(((((((((((((.(.......).....((((....))))....)))))))...(((((((.....))))))).)))))).....))...))))))).)))))))))).))))))))))))))......)))))))................((.((((((...((....))...)))))).))........))))) (-72.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGUAAGUUUUUUGAUAAUUGCCCGACAAAGGUAAUGCAAUUUUCGUGUAAAGCAGGAAUGACGCCUCGUUAAUUUUUUCAUGCAAUACUCUCAACAGAGUGAUUUUUUAUGGAUUUACAGCCGUUAAAUAUCAUUUAUUCAAAAAUGCAAGAGAUAGUGUAAAAACACGUUGUGGUUUAGUCUUCUUGCAAGCUGUGGCAAGCAUGAUUUUCAUGUAGAUAAUUACUGGUUUUGAAUUUUUAUGACAAUCAAAAUCAGGUCUGUUUAAAAUAAUAUUUAUUACAUAAAAAAUGUAAAUAUAUACAAAACUUUUUUUUUUGUAUAUAUUUAUAUACUAUUUUUGAAACGUUAGAUUAUUAAAUACAUUAGAGC ......((..((((((((((...((.((((((((......((((..(((((.(((((((.((((((.((.......((((.((((..(((((....)))))(((.(((.((((........)))).))).))).............)))).))))..((((....))))..)).)))...)))))))))).(((...(((..(((((.....))))).........((((((((((.............))))))))))))).)))..............)))))..))))((((((((((((((((((.......))))))))))))))))))..))))))))...))...)))))))))).))........ (-83.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 337 305 36 4 tfor:TF2832|5end_possible_proton/sodium:glutamate_symporter_protein_3022660..3022890_POSITIVE 307 339 294 176 130 tfor:TF2245|5end_conserved_hypothetical_protein_2420654..2420884_POSITIVE 303 350 306 93 44 tfor:TF0406|5end_monofunctional_biosynthetic_peptidoglycan_transglycosylase_424245..424475_POSITIVE 287 361 327 41 8 tfor:TF0219|5end_threonyl-tRNA_synthetase_243843..244073_POSITIVE 286 354 311 167 126 tfor:TF0962|5end_possible_amidohydrolase_1011593..1011823_POSITIVE 283 350 305 85 57 tfor:TF2487|5end_transposase_2663010..2663240_POSITIVE 281 350 309 144 109 tfor:TF2045|5end_aminoacyl-histidine_dipeptidase_2206114..2206344_POSITIVE 279 214 176 220 180 tfor:TF0100|5end_conserved_hypothetical_protein_111135..111365_POSITIVE 277 208 161 220 172 tfor:TF2963|5end_type_I_restriction_enzyme_3174523..3174753_POSITIVE 276 185 143 144 106 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 276 350 305 162 114 tfor:TF2093|5end_conserved_hypothetical_protein_2261972..2262202_POSITIVE 275 326 281 55 10 tfor:TF1603|5end_RNA_polymerase_ECF-type_sigma_factor_1717176..1717406_POSITIVE 270 192 153 78 36 tfor:TF2188|5end_conserved_hypothetical_protein_2362652..2362882_POSITIVE 270 354 311 231 173 tfor:TF1651|5end_integrase_1761296..1761526_POSITIVE 270 207 168 41 2 tfor:TF1409|5end_outer_membrane_protein_TolC_1485479..1485709_POSITIVE 268 353 311 199 155 tfor:TF0127|5end_conserved_hypothetical_protein_138026..138256_POSITIVE 267 337 294 120 70 tfor:TF0183|5end_conserved_hypothetical_protein_195954..196184_POSITIVE 266 350 308 210 170 tfor:TF2261|5end_transfer_region-related_protein,_TraM_2430496..2430726_POSITIVE 266 220 176 55 12 tfor:TF2218|5end_two-component_system_response_regulator_2390162..2390392_POSITIVE 266 350 305 100 45 tfor:TF0888|5end_transfer_region-related_protein,_TraN_938392..938622_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 209 169 55 2 tfor:TF0908|3end_integrase_fragment_951024..951174_POSITIVE 305 185 150 79 44 tfor:TF2302|3end_conserved_hypothetical_protein;_possible_outer_membrane_protein_2458063..2458213_POSITIVE 303 350 306 76 27 tfor:TF0405|3end_conserved_hypothetical_protein_424308..424458_POSITIVE 281 350 309 113 78 tfor:TF2044|3end_excinuclease_ABC,_subunit_A_2206163..2206313_POSITIVE 279 214 176 129 89 tfor:TF0099|3end_glycosyltransferase_of_PMT_family_111124..111274_POSITIVE 277 350 305 100 56 tfor:TF0598|3end_hypothetical_protein_629500..629650_POSITIVE 276 185 143 122 84 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 270 192 153 66 24 tfor:TF2187|3end_conserved_hypothetical_protein_2362720..2362870_POSITIVE 267 337 294 148 98 tfor:TF0184|3end_dihydroneopterin_aldolase_196062..196212_POSITIVE 260 340 292 58 10 tfor:TF2581|3end_50S_ribosomal_protein_L17_2749370..2749520_POSITIVE 259 354 311 56 1 tfor:TF3133|3end_conserved_hypothetical_protein_3369913..3370063_POSITIVE 257 315 271 116 75 tfor:TF0562|3end_2-methylthioadenine_synthetase_595291..595441_POSITIVE 254 213 172 74 27 tfor:TF2321|3end_hypothetical_protein_2482657..2482807_POSITIVE 254 350 306 142 86 tfor:TF1285|3end_hypothetical_protein_1369245..1369395_POSITIVE 252 219 172 57 15 tfor:TF1064|3end_ampG_permease_1135382..1135532_POSITIVE 252 349 309 111 66 tfor:TF0913|3end_conserved_hypothetical_protein;_possible_lipoprotein_955344..955494_POSITIVE 250 329 281 92 55 tfor:TF2394|3end_integrase/recombinase_XerD_2566590..2566740_POSITIVE 249 207 167 78 37 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 245 354 314 42 1 tfor:TF3022|3end_chorismate_synthase_3247301..3247451_POSITIVE 242 206 171 121 80 tfor:TF1951|3end_xanthosine_triphosphate_pyrophosphatase,_Ham1-like_protein_2101447..2101597_POSITIVE