Origin IGS: acatgtccaactaattggatgaatttgtccagctcattagactcgtctgtccaacttattggacaagtgtgtccaatttgcacgaacgtcatacatgctgtaagccatatgctgttgctgtttgccataatcctttgcgagcgattggtgtaggggtatcattgccgttctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagaacggcaatgatacccctacaccaatcgctcgcaaaggattatggcaaacagcaacagcatatggcttacagcatgtatgacgttcgtgcaaattggacacacttgtccaataagttggacagacgagtctaatgagctggacaaattcatccaattagttggacatgt Mask Tandem Repeat Region ================================================ acatgtccaactaattggatgaatttgtccagctcattagactcgtctgtccaacttattggacaagtgtgtccaatttgcacgaacgtcatacatgctgtaagccatatgctgttgctgtttgccataatcctttgcgagcgattggtgtaggggtatcattgccgttctta Find is-nt database================================================ Query_seq: PI0733:PI0734|PI0733:PI0734:membrane protein; predicted exporter:ABC transporter, ATP-binding / permease:->->:667019..667191 173 acatgtccaactaattggatgaatttgtccagctcattagactcgtctgtccaacttattggacaagtgtgtccaatttgcacgaacgtcatacatgctgtaagccatatgctgttgctgtttgccataatcctttgcgagcgattggtgtaggggtatcattgccgttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0733:PI0734|PI0733:PI0734:membrane protein; predicted exporter:ABC transporter, ATP-binding / permease:->->:667019..667191 173 acatgtccaactaattggatgaatttgtccagctcattagactcgtctgtccaacttattggacaagtgtgtccaatttgcacgaacgtcatacatgctgtaagccatatgctgttgctgtttgccataatcctttgcgagcgattggtgtaggggtatcattgccgttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0733:PI0734|PI0733:PI0734:membrane protein; predicted exporter:ABC transporter, ATP-binding / permease:->->:667019..667191 173 acatgtccaactaattggatgaatttgtccagctcattagactcgtctgtccaacttattggacaagtgtgtccaatttgcacgaacgtcatacatgctgtaagccatatgctgttgctgtttgccataatcctttgcgagcgattggtgtaggggtatcattgccgttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acatgtccaactaattggatgaatttgtccagctcattagactcgtctgtccaacttattggacaagtgtgtccaatttgcacgaacgtcatacatgctgtaagccatatgctgttgctgtttgccataatcctttgcgagcgattggtgtaggggtatcattgccgttctta Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 19 End: 150 .................. M N L S S S L D S S V Q L I G Q V C P I C T N V I H A V S H M L L L F A I I L C E R L V ....................... Protein_Len: 53 Strand: + Start: 15 End: 173 .............. M D E F V Q L I R L V C P T Y W T S V S N L H E R H T C C K P Y A V A V C H N P L R A I G V G V S L P F L Protein_Len: 41 Strand: - Start: 40 End: 162 ....................................... V R R D L K N S L H T W N A R V D Y M S Y A M H Q Q Q K G Y D K A L S Q H L P I M ........... Protein_Len: 43 Strand: - Start: 3 End: 131 .. H G V L Q I F K D L E N S E D T W S I P C T H G I Q V F T M C A T L W I S N S N A M M .......................................... acatgtccaactaattggatgaatttgtccagctcattagactcgtctgtccaacttattggacaagtgtgtccaatttgcacgaacgtcatacatgctgtaagccatatgctgttgctgtttgccataatcctttgcgagcgattggtgtaggggtatcattgccgttctta 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================================================ acatgtccaactaattggatgaatttgtccagctcattagactcgtctgtccaacttattggacaagtgtgtccaatttgcacgaacgtcatacatgctgtaagccatatgctgttgctgtttgccataatcctttgcgagcgattggtgtaggggtatcattgccgttctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -8.5 Tail_Score: -3.53444 Start: 59 End: 76 Full_Region: CGTCTGTCCAACTTA TTGGACA AGTG TGTCCAA TTTGCACGAACGTCA ..........................................................TTGGACAAGTGTGTCCAA................................................................................................. Find igs database================================================ Query_seq: PI0733:PI0734|PI0733:PI0734:membrane protein; predicted exporter:ABC transporter, ATP-binding / permease:->->:667019..667191 173 acatgtccaactaattggatgaatttgtccagctcattagactcgtctgtccaacttattggacaagtgtgtccaatttgcacgaacgtcatacatgctgtaagccatatgctgttgctgtttgccataatcctttgcgagcgattggtgtaggggtatcattgccgttctta Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: pint_PI0733_PI0734|membrane protein; predicted exporter:ABC transporter, ATP-binding / permease|POSITIVE:POSITIVE|[667019,667191]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 acatgtccaactaattggatgaatttgtccagctcattagactcgtctgtccaacttattggacaagtgtgtccaatttgcacgaacgtcatacatgctgtaagccatatgctgttgctgtttgccataatcctttgcgagcgattggtgtaggggtatcattgccgttctta acatgtccaactaattggatgaatttgtccagctcattagactcgtctgtccaacttattggacaagtgtgtccaatttgcacgaacgtcatacatgctgtaagccatatgctgttgctgtttgccataatcctttgcgagcgattggtgtaggggtatcattgccgttctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUGUCCAACUAAUUGGAUGAAUUUGUCCAGCUCAUUAGACUCGUCUGUCCAACUUAUUGGACAAGUGUGUCCAAUUUGCACGAACGUCAUACAUGCUGUAAGCCAUAUGCUGUUGCUGUUUGCCAUAAUCCUUUGCGAGCGAUUGGUGUAGGGGUAUCAUUGCCGUUCUUA ....((((((....))))))...........((..(((.(((.((..(((((((....)))))))..)).))).)))..))..(((((.((...(((((.(..((((...((....)).((((((...........))))))...))))...).)))))...)).)))))... (-46.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAACGGCAAUGAUACCCCUACACCAAUCGCUCGCAAAGGAUUAUGGCAAACAGCAACAGCAUAUGGCUUACAGCAUGUAUGACGUUCGUGCAAAUUGGACACACUUGUCCAAUAAGUUGGACAGACGAGUCUAAUGAGCUGGACAAAUUCAUCCAAUUAGUUGGACAUGU ...(((((((.(((((.((.....................))))))).))..(((((...(((.....)))....)).)))....)))))..((.(((((((.....(((((((....(((((((......)))))))....))))))).....))))))).))......... (-38.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 484 76 31 180 135 pint:PI0513|5end_ion_transporter_471530..471760_POSITIVE 437 158 112 60 14 pint:PI1650|5end_N-acetylmuramoyl-L-alanine_amidase_1563195..1563425_POSITIVE 389 158 111 216 173 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 368 143 105 48 1 pint:PI0010|5end_conserved_hypothetical_protein_10628..10858_POSITIVE 363 170 125 218 171 pint:PI1279|5end_RNA_polymerase_sigma_factor/ECF_subfamily_(sigma-70)_1195215..1195445_POSITIVE 355 140 91 83 31 pint:PI1971|5end_possible_IS1249-related_transposase_1928027..1928257_POSITIVE 355 140 91 83 31 pint:PI1533|5end_conserved_hypothetical_protein;_possible_transposase_1452667..1452897_POSITIVE 355 140 91 83 31 pint:PI0534|5end_conserved_hypothetical_protein;_possible_transposase_488568..488798_POSITIVE 353 159 113 157 92 pint:PI0756|5end_50S_ribosomal_protein_L7/L12_687146..687376_POSITIVE 352 157 111 209 163 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 351 170 127 48 3 pint:PI0034|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_37151..37381_POSITIVE 342 75 33 206 161 pint:PI0869|5end_possible_exodeoxyribonuclease_VII_(small_subunit)_805518..805748_POSITIVE 340 109 61 176 138 pint:PI0601|5end_hypothetical_protein_548758..548988_POSITIVE 336 127 83 214 168 pint:PI0652|5end_conserved_hypothetical_protein_592878..593108_POSITIVE 330 138 96 228 181 pint:PI1081|5end_probable_endonuclease/resolvase_1000806..1001036_POSITIVE 329 155 113 52 4 pint:PI0806|5end_heavy_metal_efflux_pump_743679..743909_POSITIVE 328 165 124 60 15 pint:PI0122|5end_outer_membrane_protein,_ompH_family_113319..113549_POSITIVE 324 158 115 193 155 pint:PI0036|5end_glutathione_peroxidase_38598..38828_POSITIVE 323 157 112 185 137 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 322 150 104 76 29 pint:PI0108|5end_L-lactate_permease_104892..105122_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 160 111 59 16 pint:PI0114|3end_hypothetical_protein_108527..108677_POSITIVE 340 109 61 135 97 pint:PI0600|3end_bifunctional_purine_biosynthesis_protein,_5-aminoimidazole-4-carboxamide_ribonucleotide(AICAR)_transformylase/IMP_cyclohydrolase_548797..548947_POSITIVE 337 169 132 70 39 pint:PI1585|3end_ampG_permease_1514260..1514410_POSITIVE 336 127 83 151 105 pint:PI0651|3end_HD_superfamily_hydrolase_592895..593045_POSITIVE 329 155 113 100 52 pint:PI0805|3end_conserved_hypothetical_protein_743807..743957_POSITIVE 320 139 92 75 25 pint:PI2148|3end_ribonuclease_III_2095541..2095691_POSITIVE 317 118 80 137 98 pint:PI0896|3end_2-oxoglutarate_oxidoreductase,_alpha_subunit_828276..828426_POSITIVE 315 158 111 136 95 pint:PI1566|3end_predicted_TPR-repeat-containing_protein_1489224..1489374_POSITIVE 314 158 112 96 42 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 314 160 111 148 80 pint:PI1504|3end_non-specific_DNA-binding_protein_1424904..1425054_POSITIVE 310 126 81 147 99 pint:PI1370|3end_alkyl_hydroperoxide_reductase,_subunit_F_1292176..1292326_POSITIVE 310 170 122 46 3 pint:PI0729|3end_integrase_661765..661915_POSITIVE 304 124 82 113 62 pint:PI1143|3end_hypothetical_protein_1070504..1070654_POSITIVE 304 140 96 74 26 pint:PI0056|3end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_55907..56057_POSITIVE 303 78 31 100 57 pint:PI0733|3end_membrane_protein;_predicted_exporter_666958..667108_POSITIVE 300 159 111 69 27 pint:PI1253|3end_hypothetical_protein_1175691..1175841_POSITIVE 295 157 111 66 22 pint:PI0578|3end_methyltransferase_523253..523403_POSITIVE 294 120 77 69 31 pint:PI0037|3end_hypothetical_protein_39616..39766_POSITIVE 293 127 81 46 14 pint:PI1653|3end_hypothetical_protein_1565714..1565864_POSITIVE 293 157 111 122 82 pint:PI1440|3end_conserved_hypothetical_protein_1363009..1363159_POSITIVE