Origin IGS: tgaattgttaggtggtagggaaagggtgcagaaaatgaattttagcacctccgaaatgcctaaaacgcagaaaaaacagccaattatttggtagataggaaaataagccgtaattttgcacccgctaaagtggtgtaatgccgcttggcaaatgtttcacataattaataaataaaacaaacaagc .........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 gcttgtttgttttatttattaattatgtgaaacatttgccaagcggcattacaccactttagcgggtgcaaaattacggcttattttcctatctaccaaataattggctgttttttctgcgttttaggcatttcggaggtgctaaaattcattttctgcaccctttccctaccacctaacaattca Mask Tandem Repeat Region ================================================ tgaattgttaggtggtagggaaagggtgcagaaaatgaattttagcacctccgaaatgcctaaaacgcagaaaaaacagccaattatttggtagataggaaaataagccgtaattttgcacccgctaaagtggtgtaatgccgcttggcaaatgtttcacataattaataaataaaacaaacaagc Find is-nt database================================================ Query_seq: PI0434:PI0435|PI0434:PI0435:possible beta-lactamase:30S ribosomal protein S21:->->:406951..407136 186 tgaattgttaggtggtagggaaagggtgcagaaaatgaattttagcacctccgaaatgcctaaaacgcagaaaaaacagccaattatttggtagataggaaaataagccgtaattttgcacccgctaaagtggtgtaatgccgcttggcaaatgtttcacataattaataaataaaacaaacaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0434:PI0435|PI0434:PI0435:possible beta-lactamase:30S ribosomal protein S21:->->:406951..407136 186 tgaattgttaggtggtagggaaagggtgcagaaaatgaattttagcacctccgaaatgcctaaaacgcagaaaaaacagccaattatttggtagataggaaaataagccgtaattttgcacccgctaaagtggtgtaatgccgcttggcaaatgtttcacataattaataaataaaacaaacaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0434:PI0435|PI0434:PI0435:possible beta-lactamase:30S ribosomal protein S21:->->:406951..407136 186 tgaattgttaggtggtagggaaagggtgcagaaaatgaattttagcacctccgaaatgcctaaaacgcagaaaaaacagccaattatttggtagataggaaaataagccgtaattttgcacccgctaaagtggtgtaatgccgcttggcaaatgtttcacataattaataaataaaacaaacaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaattgttaggtggtagggaaagggtgcagaaaatgaattttagcacctccgaaatgcctaaaacgcagaaaaaacagccaattatttggtagataggaaaataagccgtaattttgcacccgctaaagtggtgtaatgccgcttggcaaatgtttcacataattaataaataaaacaaacaagc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 11 End: 121 .......... T T P F P H L F H I K A G G F H R F R L F F L W N N P L Y S F L G Y N Q M ................................................................. Protein_Len: 51 Strand: - Start: 1 End: 153 S N N P P L S L T C F I F K L V E S I G L V C F F C G I I Q Y I P F Y A T I K C G S F H H L A A Q C M ................................. tgaattgttaggtggtagggaaagggtgcagaaaatgaattttagcacctccgaaatgcctaaaacgcagaaaaaacagccaattatttggtagataggaaaataagccgtaattttgcacccgctaaagtggtgtaatgccgcttggcaaatgtttcacataattaataaataaaacaaacaagc 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================================================ tgaattgttaggtggtagggaaagggtgcagaaaatgaattttagcacctccgaaatgcctaaaacgcagaaaaaacagccaattatttggtagataggaaaataagccgtaattttgcacccgctaaagtggtgtaatgccgcttggcaaatgtttcacataattaataaataaaacaaacaagc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 42 HP_score: -2.8 Tail_Score: -2.78798 Start: 25 End: 49 Full_Region: tttaggcatttcgga ggtgctaaaa ttcat tttctgcacc ctttccctaccacct ........................ggtgctaaaattcattttctgcacc......................................................................................................................................... Find igs database================================================ Query_seq: PI0434:PI0435|PI0434:PI0435:possible beta-lactamase:30S ribosomal protein S21:->->:406951..407136 186 tgaattgttaggtggtagggaaagggtgcagaaaatgaattttagcacctccgaaatgcctaaaacgcagaaaaaacagccaattatttggtagataggaaaataagccgtaattttgcacccgctaaagtggtgtaatgccgcttggcaaatgtttcacataattaataaataaaacaaacaagc Intra-Species Hit: Count: 1 Min: 1 Max: 186 Len: 186 Subject: pint_PI0434_PI0435|possible beta-lactamase:30S ribosomal protein S21|POSITIVE:POSITIVE|[406951,407136]|186 HSP 1 e-value: 1.0E-101 bit: 369.0 Len: 186 Query Start:1 Query End:186 Subject Strand: POSITIVE Subject Start: 1 Subject End: 186 tgaattgttaggtggtagggaaagggtgcagaaaatgaattttagcacctccgaaatgcctaaaacgcagaaaaaacagccaattatttggtagataggaaaataagccgtaattttgcacccgctaaagtggtgtaatgccgcttggcaaatgtttcacataattaataaataaaacaaacaagc tgaattgttaggtggtagggaaagggtgcagaaaatgaattttagcacctccgaaatgcctaaaacgcagaaaaaacagccaattatttggtagataggaaaataagccgtaattttgcacccgctaaagtggtgtaatgccgcttggcaaatgtttcacataattaataaataaaacaaacaagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUUGUUAGGUGGUAGGGAAAGGGUGCAGAAAAUGAAUUUUAGCACCUCCGAAAUGCCUAAAACGCAGAAAAAACAGCCAAUUAUUUGGUAGAUAGGAAAAUAAGCCGUAAUUUUGCACCCGCUAAAGUGGUGUAAUGCCGCUUGGCAAAUGUUUCACAUAAUUAAUAAAUAAAACAAACAAGC (((((((((((((((((.(((...(((((.((((.....)))).))))))))....(((.......((((((......(((((....))))).....((........))....))))))..((((....)))).))).)))))))))))))....))))........................... (-44.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUGUUUGUUUUAUUUAUUAAUUAUGUGAAACAUUUGCCAAGCGGCAUUACACCACUUUAGCGGGUGCAAAAUUACGGCUUAUUUUCCUAUCUACCAAAUAAUUGGCUGUUUUUUCUGCGUUUUAGGCAUUUCGGAGGUGCUAAAAUUCAUUUUCUGCACCCUUUCCCUACCACCUAACAAUUCA (((((((((((((((.((.....)).))))))))..((((....))))............)))))))((((((..((((((.(((................))).))))))..))).)))...(((((......((((((((..(((.....)))..)))))...)))......)))))....... (-39.49) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 158 120 184 147 pint:PI0541|5end_GTP-binding_protein,_GTP1/OBG_family_493760..493990_POSITIVE 352 160 119 228 181 pint:PI0005|5end_hypothetical_protein_6984..7214_POSITIVE 334 166 122 62 13 pint:PI0571|5end_conserved_hypothetical_protein;_possible_permease_515161..515391_POSITIVE 324 150 106 105 46 pint:PI0098|5end_conserved_hypothetical_protein_(possible_glycosyl/glycerophosphate_transferase)_94622..94852_POSITIVE 321 149 108 224 181 pint:PI2102|5end_DNA_topoisomerase_IV,_subunit_B_2055706..2055936_POSITIVE 317 59 11 170 118 pint:PI0415|5end_malate_dehydrogenase_385358..385588_POSITIVE 316 150 107 53 2 pint:PI1836|5end_conserved_hypothetical_protein_1777308..1777538_POSITIVE 310 60 11 196 146 pint:PI0040|5end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41010..41240_POSITIVE 308 150 102 65 15 pint:PI1711|5end_ABC_transporter,_ATP-binding_protein_1627597..1627827_POSITIVE 308 150 110 43 7 pint:PI0087|5end_conserved_hypothetical_protein_85700..85930_POSITIVE 303 148 105 216 171 pint:PI1743|5end_stationary-phase_survival_protein_1663948..1664178_POSITIVE 302 120 77 183 144 pint:PI2085|5end_conserved_hypothetical_protein_2041100..2041330_POSITIVE 301 150 106 154 112 pint:PI0867|5end_hypothetical_protein_803859..804089_POSITIVE 301 150 106 71 29 pint:PI0866|5end_hypothetical_protein_803776..804006_POSITIVE 298 152 118 231 194 pint:PI1893|5end_phospho-N-acetylmuramoyl-pentapeptide-transferase__1835624..1835854_POSITIVE 298 149 107 159 102 pint:PI0930|5end_alpha-L-fucosidase_precursor_860977..861207_POSITIVE 297 147 104 185 138 pint:PI2053|5end_conserved_hypothetical_protein;_possible_outer_membrane_receptor_protein_2010673..2010903_POSITIVE 297 150 109 184 133 pint:PI0952|5end_conserved_hypothetical_protein_883718..883948_POSITIVE 292 149 106 105 64 pint:PI1618|5end_hypothetical_protein_1542670..1542900_POSITIVE 292 83 44 48 7 pint:PI0817|5end_glycosyl_transferase,_group_1_family_protein_756861..757091_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 383 59 12 78 36 pint:PI0572|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_517589..517739_POSITIVE 356 158 120 72 35 pint:PI0539|3end_hypothetical_protein_493728..493878_POSITIVE 332 149 108 77 32 pint:PI0327|3end_hypothetical_protein_309107..309257_POSITIVE 330 42 2 140 96 pint:PI1075|3end_pyruvate_phosphate_dikinase_998571..998721_POSITIVE 330 127 81 59 15 pint:PI0429|3end_hypothetical_protein_399602..399752_POSITIVE 324 150 106 85 26 pint:PI0097|3end_aspartate_aminotransferase_94682..94832_POSITIVE 302 120 77 72 33 pint:PI2084|3end_hypothetical_protein_2041069..2041219_POSITIVE 300 150 114 33 1 pint:PI0086|3end_possible_uroporphyrinogen-III_synthase_85770..85920_POSITIVE 298 152 118 74 37 pint:PI1892|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_1835547..1835697_POSITIVE 298 149 107 150 93 pint:PI0929|3end_copper_homeostasis_protein_861048..861198_POSITIVE 293 149 106 64 24 pint:PI0273|3end_hypothetical_protein_263284..263434_POSITIVE 287 150 107 136 95 pint:PI0595|3end_conserved_hypothetical_protein_546406..546556_POSITIVE 286 160 123 71 35 pint:PI0624|3end_hypothetical_protein_574471..574621_POSITIVE 282 166 121 75 29 pint:PI0571|3end_conserved_hypothetical_protein;_possible_permease_516449..516599_POSITIVE 281 59 15 94 43 pint:PI1953|3end_possible_ABC-type_permease_1908582..1908732_POSITIVE 281 68 23 138 86 pint:PI0535|3end_hypothetical_protein_489779..489929_POSITIVE 281 150 101 68 14 pint:PI0147|3end_HIT_family_protein_141308..141458_POSITIVE 280 146 105 125 77 pint:PI0936|3end_conserved_hypothetical_protein_869464..869614_POSITIVE 279 60 11 118 64 pint:PI1579|3end_penicillin-binding_protein_2_1507913..1508063_POSITIVE 275 157 111 54 9 pint:PI2018|3end_50S_ribosomal_protein_L34_1975989..1976139_POSITIVE