Origin IGS: taatattttgttaaaatcatgttgcaatattaatttgggtctatataatacgcacataccctagaaaaatataactcaaaatacattattcagcccttcccccttgaaagggctttttttcgtcttgtagaaagtagaattgagtaaaaaatacctttaagtatgctcacaattacctgctatttgtattgctaacagaaaccagcgcaatttctttttaatagattattcattccccttgagatcctccccaatccgcactagactaccgccctcttttttaaaccaaatattccatt .........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 aatggaatatttggtttaaaaaagagggcggtagtctagtgcggattggggaggatctcaaggggaatgaataatctattaaaaagaaattgcgctggtttctgttagcaatacaaatagcaggtaattgtgagcatacttaaaggtattttttactcaattctactttctacaagacgaaaaaaagccctttcaagggggaagggctgaataatgtattttgagttatatttttctagggtatgtgcgtattatatagacccaaattaatattgcaacatgattttaacaaaatatta Mask Tandem Repeat Region ================================================ taatattttgttaaaatcatgttgcaatattaatttgggtctatataatacgcacataccctagaaaaatataactcaaaatacattattcagcccttcccccttgaaagggctttttttcgtcttgtagaaagtagaattgagtaaaaaatacctttaagtatgctcacaattacctgctatttgtattgctaacagaaaccagcgcaatttctttttaatagattattcattccccttgagatcctccccaatccgcactagactaccgccctcttttttaaaccaaatattccatt Find is-nt database================================================ Query_seq: AA02774:AA02775|AA02774:AA02775:collagenase prtC homolog, possible protease:S-adenosylmethionine:tRNA ribosyltransferase-isomerase (Queuosine biosynthesis protein queA):->->:1938396..1938694 299 taatattttgttaaaatcatgttgcaatattaatttgggtctatataatacgcacataccctagaaaaatataactcaaaatacattattcagcccttcccccttgaaagggctttttttcgtcttgtagaaagtagaattgagtaaaaaatacctttaagtatgctcacaattacctgctatttgtattgctaacagaaaccagcgcaatttctttttaatagattattcattccccttgagatcctccccaatccgcactagactaccgccctcttttttaaaccaaatattccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02774:AA02775|AA02774:AA02775:collagenase prtC homolog, possible protease:S-adenosylmethionine:tRNA ribosyltransferase-isomerase (Queuosine biosynthesis protein queA):->->:1938396..1938694 299 taatattttgttaaaatcatgttgcaatattaatttgggtctatataatacgcacataccctagaaaaatataactcaaaatacattattcagcccttcccccttgaaagggctttttttcgtcttgtagaaagtagaattgagtaaaaaatacctttaagtatgctcacaattacctgctatttgtattgctaacagaaaccagcgcaatttctttttaatagattattcattccccttgagatcctccccaatccgcactagactaccgccctcttttttaaaccaaatattccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02774:AA02775|AA02774:AA02775:collagenase prtC homolog, possible protease:S-adenosylmethionine:tRNA ribosyltransferase-isomerase (Queuosine biosynthesis protein queA):->->:1938396..1938694 299 taatattttgttaaaatcatgttgcaatattaatttgggtctatataatacgcacataccctagaaaaatataactcaaaatacattattcagcccttcccccttgaaagggctttttttcgtcttgtagaaagtagaattgagtaaaaaatacctttaagtatgctcacaattacctgctatttgtattgctaacagaaaccagcgcaatttctttttaatagattattcattccccttgagatcctccccaatccgcactagactaccgccctcttttttaaaccaaatattccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatattttgttaaaatcatgttgcaatattaatttgggtctatataatacgcacataccctagaaaaatataactcaaaatacattattcagcccttcccccttgaaagggctttttttcgtcttgtagaaagtagaattgagtaaaaaatacctttaagtatgctcacaattacctgctatttgtattgctaacagaaaccagcgcaatttctttttaatagattattcattccccttgagatcctccccaatccgcactagactaccgccctcttttttaaaccaaatattccatt Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 182 End: 298 ..................................................................................................................................................................................... M C I A N R N Q R N F F L I D Y S F P L R S S P I R T R L P P S F L N Q I F H . taatattttgttaaaatcatgttgcaatattaatttgggtctatataatacgcacataccctagaaaaatataactcaaaatacattattcagcccttcccccttgaaagggctttttttcgtcttgtagaaagtagaattgagtaaaaaatacctttaagtatgctcacaattacctgctatttgtattgctaacagaaaccagcgcaatttctttttaatagattattcattccccttgagatcctccccaatccgcactagactaccgccctcttttttaaaccaaatattccatt 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: 82 Start: 238 End: 267 .............................................................................................................................................................................................................................................CTTGAGATCCTCCCCAATCCGCACTAGACT................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatattttgttaaaatcatgttgcaatattaatttgggtctatataatacgcacataccctagaaaaatataactcaaaatacattattcagcccttcccccttgaaagggctttttttcgtcttgtagaaagtagaattgagtaaaaaatacctttaagtatgctcacaattacctgctatttgtattgctaacagaaaccagcgcaatttctttttaatagattattcattccccttgagatcctccccaatccgcactagactaccgccctcttttttaaaccaaatattccatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -6.8 Tail_Score: -5.6473 Start: 93 End: 113 Full_Region: AAAATACATTATTCA GCCCTTCC CCCTT GAAAGGGC TTTTTTTCGTCTTGT ............................................................................................GCCCTTCCCCCTTGAAAGGGC.......................................................................................................................................................................................... Find igs database================================================ Query_seq: AA02774:AA02775|AA02774:AA02775:collagenase prtC homolog, possible protease:S-adenosylmethionine:tRNA ribosyltransferase-isomerase (Queuosine biosynthesis protein queA):->->:1938396..1938694 299 taatattttgttaaaatcatgttgcaatattaatttgggtctatataatacgcacataccctagaaaaatataactcaaaatacattattcagcccttcccccttgaaagggctttttttcgtcttgtagaaagtagaattgagtaaaaaatacctttaagtatgctcacaattacctgctatttgtattgctaacagaaaccagcgcaatttctttttaatagattattcattccccttgagatcctccccaatccgcactagactaccgccctcttttttaaaccaaatattccatt Intra-Species Hit: Count: 1 Min: 1 Max: 299 Len: 299 Subject: aact_AA02774_AA02775|collagenase prtC homolog, possible protease:S-adenosylmethionine:tRNA ribosyltransferase-isomerase (Queuosine biosynthesis protein queA)|POSITIVE:POSITIVE|[1938396,1938694]|299 HSP 1 e-value: 1.0E-156 bit: 551.0 Len: 299 Query Start:1 Query End:299 Subject Strand: POSITIVE Subject Start: 1 Subject End: 299 taatattttgttaaaatcatgttgcaatattaatttgggtctatataatacgcacataccctagaaaaatataactcaaaatacattattcagcccttcccccttgaaagggcnnnnnnncgtcttgtagaaagtagaattgagtaaaaaatacctttaagtatgctcacaattacctgctatttgtattgctaacagaaaccagcgcaatttctttttaatagattattcattccccttgagatcctccccaatccgcactagactaccgccctcttttttaaaccaaatattccatt taatattttgttaaaatcatgttgcaatattaatttgggtctatataatacgcacataccctagaaaaatataactcaaaatacattattcagcccttcccccttgaaagggctttttttcgtcttgtagaaagtagaattgagtaaaaaatacctttaagtatgctcacaattacctgctatttgtattgctaacagaaaccagcgcaatttctttttaatagattattcattccccttgagatcctccccaatccgcactagactaccgccctcttttttaaaccaaatattccatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUUUUGUUAAAAUCAUGUUGCAAUAUUAAUUUGGGUCUAUAUAAUACGCACAUACCCUAGAAAAAUAUAACUCAAAAUACAUUAUUCAGCCCUUCCCCCUUGAAAGGGCUUUUUUUCGUCUUGUAGAAAGUAGAAUUGAGUAAAAAAUACCUUUAAGUAUGCUCACAAUUACCUGCUAUUUGUAUUGCUAACAGAAACCAGCGCAAUUUCUUUUUAAUAGAUUAUUCAUUCCCCUUGAGAUCCUCCCCAAUCCGCACUAGACUACCGCCCUCUUUUUUAAACCAAAUAUUCCAUU .(((((((.(((....((.(((((((((((.(((..((((.................................((((((..(((.......(((((((.(.....).)))))))...((((........)))))))...)))))).....((((......))))..........))))...))).))))))).)))))).....(((.....(((.......)))...((((.......)))).............)))........................))).)))))))..... (-41.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGGAAUAUUUGGUUUAAAAAAGAGGGCGGUAGUCUAGUGCGGAUUGGGGAGGAUCUCAAGGGGAAUGAAUAAUCUAUUAAAAAGAAAUUGCGCUGGUUUCUGUUAGCAAUACAAAUAGCAGGUAAUUGUGAGCAUACUUAAAGGUAUUUUUUACUCAAUUCUACUUUCUACAAGACGAAAAAAAGCCCUUUCAAGGGGGAAGGGCUGAAUAAUGUAUUUUGAGUUAUAUUUUUCUAGGGUAUGUGCGUAUUAUAUAGACCCAAAUUAAUAUUGCAACAUGAUUUUAACAAAAUAUUA .....(((((((...((((((.....(((((....(((((((((.(((((......)))))..(((........)))............)))))))))...))))).((((((..(((....(((...(((((((((((((((((((((.....((((((...(((.(((........)))....(((((((((.....))))))))).......)))..)))))).))))))))...)))))))).....)))))...)))...)))..)))))).......))))))..))))))). (-64.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 276 231 202 155 aact:AA01635|5end_ribonucleoside_diphosphate_reductase,_beta_chain_1104615..1104845_POSITIVE 352 276 233 231 182 aact:AA01692|5end_hexulose-6-phosphate_synthase_1149178..1149408_POSITIVE 340 287 245 160 100 aact:AA02047|5end_galactitol-1-phosphate_5-dehydrogenase_1393633..1393863_POSITIVE 328 275 238 53 13 aact:AA00804|5end_fumarate_reductase_flavoprotein_subunit_A_549770..550000_POSITIVE 308 285 246 150 100 aact:AA01295|5end_3-dehydroquinate_synthase_877272..877502_POSITIVE 282 135 91 161 118 aact:AA01991|5end_conserved_hypothetical_protein_(possible_nitroreductase)_1352372..1352602_POSITIVE 281 273 231 164 116 aact:AA01957|5end_conserved_hypothetical_protein_1323211..1323441_POSITIVE 281 282 249 224 181 aact:AA01905|5end_hypothetical_protein_1285306..1285536_POSITIVE 278 276 232 214 161 aact:AA01874|5end_conserved_hypothetical_protein_1262036..1262266_POSITIVE 276 276 232 131 81 aact:AA01565|5end_conserved_hypothetical_protein_1050711..1050941_POSITIVE 270 273 234 192 146 aact:AA01299|5end_competence_protein_C_880946..881176_POSITIVE 268 276 239 179 147 aact:AA01981|5end_4-alpha-glucanotransferase_1337202..1337432_POSITIVE 267 140 91 189 122 aact:AA02983|5end_formate_acetyltransferase_2085195..2085425_POSITIVE 267 99 53 225 185 aact:AA01925|5end_conserved_hypothetical_protein_1299961..1300191_POSITIVE 266 276 250 32 6 aact:AA01978|5end_hypothetical_protein_1337055..1337285_POSITIVE 265 123 91 168 133 aact:AA00856|5end_arginine_ABC_transporter,_periplasmic-binding_protein_590251..590481_POSITIVE 262 275 238 190 141 aact:AA02025|5end_hypothetical_protein_1378667..1378897_POSITIVE 261 273 231 230 189 aact:AA01286|5end_5,10-methylenetetrahydrofolate_dehydrogenase_(bifunctional_protein)_870309..870539_POSITIVE 260 288 256 202 155 aact:AA01967|5end_hypothetical_protein_1331511..1331741_POSITIVE 259 126 85 131 95 aact:AA00805|5end_fumarate_reductase_iron-sulfur_protein_551583..551813_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 276 233 115 66 aact:AA01690|3end_penicillin-binding_protein_1C_1149142..1149292_POSITIVE 340 287 245 134 74 aact:AA02046|3end_PTS_system_galactitol-specific_enzyme_IIC_1393687..1393837_POSITIVE 314 272 231 62 19 aact:AA02480|3end_excinuclease_ABC_subunit_B_1718442..1718592_POSITIVE 272 260 226 121 83 aact:AA01402|3end_beta_1-4_glucosyltransferase_948382..948532_POSITIVE 267 99 53 120 80 aact:AA01923|3end_type_III_restriction-modification_system_methylation_subunit_1299936..1300086_POSITIVE 266 276 250 29 3 aact:AA01976|3end_colicin_V_production_protein_1337132..1337282_POSITIVE 262 274 240 118 92 aact:AA01113|3end_transcriptional_regulator_(merR_family)_765249..765399_POSITIVE 261 273 231 135 94 aact:AA01284|3end_heat_shock_protein_(hsp60)_870294..870444_POSITIVE 260 288 256 125 78 aact:AA01966|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_1331514..1331664_POSITIVE 259 126 85 123 87 aact:AA00804|3end_fumarate_reductase_flavoprotein_subunit_A_551655..551805_POSITIVE 257 287 241 116 67 aact:AA00987|3end_tetracenomycin_polyketide_synthesis_O-methyltransferase_690586..690736_POSITIVE 256 210 164 150 104 aact:AA01603|3end_oligopeptidase_A_1085014..1085164_POSITIVE 255 279 250 46 11 aact:AA01817|3end_hypothetical_protein_1224400..1224550_POSITIVE 255 276 234 71 30 aact:AA00978|3end_conserved_hypothetical_protein_684585..684735_POSITIVE 253 136 91 59 4 aact:AA02564|3end_transketolase_N-terminal_section_1786783..1786933_POSITIVE 253 207 175 44 8 aact:AA00806|3end_fumarate_reductase_15_kD_hydrophobic_protein_552834..552984_POSITIVE 252 127 85 124 88 aact:AA00894|3end_selenium_transferase_(Cysteinyl-tRNA(Sec)_selenium_transferase)_621350..621500_POSITIVE 249 140 98 54 10 aact:AA01799|3end_polysacharide_biosynthesis_protein_(Orf14_of_cluster)_1213276..1213426_POSITIVE 249 272 233 141 98 aact:AA01608|3end_conserved_hypothetical_protein_1087977..1088127_POSITIVE 249 265 234 69 31 aact:AA01555|3end_ABC_transporter,_ATP-binding_protein_1044323..1044473_POSITIVE