Origin IGS: tgattttgcgtaaaagttcttttgcctcgtcggatatggcgacctttgccgtacaaacaaacctgtacaacaatgagaaaattatatctttcggcaccgcttccatttcagggacagaagcgg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccgcttctgtccctgaaatggaagcggtgccgaaagatataattttctcattgttgtacaggtttgtttgtacggcaaaggtcgccatatccgacgaggcaaaagaacttttacgcaaaatca Mask Tandem Repeat Region ================================================ tgattttgcgtaaaagttcttttgcctcgtcggatatggcgacctttgccgtacaaacaaacctgtacaacaatgagaaaattatatctttcggcaccgcttccatttcagggacagaagcgg Find is-nt database================================================ Query_seq: PI0369:PI0370|PI0369:PI0370:hypothetical protein:conserved hypothetical protein:->->:340470..340592 123 tgattttgcgtaaaagttcttttgcctcgtcggatatggcgacctttgccgtacaaacaaacctgtacaacaatgagaaaattatatctttcggcaccgcttccatttcagggacagaagcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0369:PI0370|PI0369:PI0370:hypothetical protein:conserved hypothetical protein:->->:340470..340592 123 tgattttgcgtaaaagttcttttgcctcgtcggatatggcgacctttgccgtacaaacaaacctgtacaacaatgagaaaattatatctttcggcaccgcttccatttcagggacagaagcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0369:PI0370|PI0369:PI0370:hypothetical protein:conserved hypothetical protein:->->:340470..340592 123 tgattttgcgtaaaagttcttttgcctcgtcggatatggcgacctttgccgtacaaacaaacctgtacaacaatgagaaaattatatctttcggcaccgcttccatttcagggacagaagcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgattttgcgtaaaagttcttttgcctcgtcggatatggcgacctttgccgtacaaacaaacctgtacaacaatgagaaaattatatctttcggcaccgcttccatttcagggacagaagcgg Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 3 End: 122 .. M L R K S S F A S S D M A T F A V Q T N L Y N N E K I I S F G T A S I S G T E A . Protein_Len: 34 Strand: + Start: 22 End: 123 ..................... M P R R I W R P L P Y K Q T C T T M R K L Y L S A P L P F Q G Q K R Protein_Len: 35 Strand: - Start: 2 End: 106 . I K R L L E K A E D S I A V K A T C V F R Y L L S F I I D K P V A E M ................. tgattttgcgtaaaagttcttttgcctcgtcggatatggcgacctttgccgtacaaacaaacctgtacaacaatgagaaaattatatctttcggcaccgcttccatttcagggacagaagcgg 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================================================ tgattttgcgtaaaagttcttttgcctcgtcggatatggcgacctttgccgtacaaacaaacctgtacaacaatgagaaaattatatctttcggcaccgcttccatttcagggacagaagcgg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0369:PI0370|PI0369:PI0370:hypothetical protein:conserved hypothetical protein:->->:340470..340592 123 tgattttgcgtaaaagttcttttgcctcgtcggatatggcgacctttgccgtacaaacaaacctgtacaacaatgagaaaattatatctttcggcaccgcttccatttcagggacagaagcgg Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: pint_PI0369_PI0370|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[340470,340592]|123 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 tgattttgcgtaaaagttcttttgcctcgtcggatatggcgacctttgccgtacaaacaaacctgtacaacaatgagaaaattatatctttcggcaccgcttccatttcagggacagaagcgg tgattttgcgtaaaagttcttttgcctcgtcggatatggcgacctttgccgtacaaacaaacctgtacaacaatgagaaaattatatctttcggcaccgcttccatttcagggacagaagcgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUUGCGUAAAAGUUCUUUUGCCUCGUCGGAUAUGGCGACCUUUGCCGUACAAACAAACCUGUACAACAAUGAGAAAAUUAUAUCUUUCGGCACCGCUUCCAUUUCAGGGACAGAAGCGG .........((((((....))))))...((((((...(((((...)))))(((((........))))).....................)))))).(((((((..((.....))..))))))) (-26.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGCUUCUGUCCCUGAAAUGGAAGCGGUGCCGAAAGAUAUAAUUUUCUCAUUGUUGUACAGGUUUGUUUGUACGGCAAAGGUCGCCAUAUCCGACGAGGCAAAAGAACUUUUACGCAAAAUCA ((((((((((.......))))))))))((((...................((((((((((((....))))))))))))..((((.......))))..))))...................... (-33.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 70 22 100 42 pint:PI1879|5end_uracil_phosphoribosyltransferase_1820671..1820901_POSITIVE 353 50 8 142 95 pint:PI1705|5end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_1621781..1622011_POSITIVE 329 52 24 156 124 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 329 52 24 82 50 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 323 68 31 63 19 pint:PI0482|5end_50S_ribosomal_protein_L36_443346..443576_POSITIVE 322 53 15 144 105 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 308 50 6 141 91 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 299 50 2 153 103 pint:PI0253|5end_conjugative_transposon_protein,_TraD_248294..248524_POSITIVE 298 67 21 56 1 pint:PI0539|5end_hypothetical_protein_493406..493636_POSITIVE 297 50 11 186 138 pint:PI0502|5end_conserved_hypothetical_protein;_possible_helicase_461798..462028_POSITIVE 295 69 22 231 187 pint:PI1937|5end_hypothetical_protein_1889411..1889641_POSITIVE 295 66 22 136 82 pint:PI0531|5end_ABC_transporter,_ATP-binding_protein;_possible_gliding_motility_related_484696..484926_POSITIVE 289 52 22 46 4 pint:PI1668|5end_conserved_hypothetical_protein_1580692..1580922_POSITIVE 288 50 4 88 45 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 288 68 29 229 183 pint:PI0959|5end_uridine_kinase_890495..890725_POSITIVE 288 114 84 180 147 pint:PI0336|5end_hypothetical_protein_314499..314729_POSITIVE 285 50 6 130 78 pint:PI1770|5end_4-alpha-glucanotransferase_1697336..1697566_POSITIVE 284 55 16 45 11 pint:PI1498|5end_probable_membrane_associated_lipoprotein_1418427..1418657_POSITIVE 284 56 29 105 78 pint:PI0536|5end_hypothetical_protein_492163..492393_POSITIVE 282 49 17 214 177 pint:PI0754|5end_possible_outer_membrane_receptor_683771..684001_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 68 31 46 2 pint:PI0481|3end_translation_initiation_factor_IF-1_443409..443559_POSITIVE 308 50 6 135 85 pint:PI0336|3end_hypothetical_protein_314806..314956_POSITIVE 307 49 8 150 113 pint:PI0092|3end_regulatory_protein_RecX_89651..89801_POSITIVE 295 66 22 117 63 pint:PI0530|3end_possible_membrane-fusion_protein_484757..484907_POSITIVE 290 42 6 142 94 pint:PI2123|3end_adenine_phosphoribosyltransferase_2072324..2072474_POSITIVE 289 52 22 46 4 pint:PI1667|3end_conserved_hypothetical_protein_1580772..1580922_POSITIVE 284 70 23 106 55 pint:PI2113|3end_hypothetical_protein_2064278..2064428_POSITIVE 282 49 1 149 89 pint:PI0482|3end_50S_ribosomal_protein_L36_443539..443689_POSITIVE 278 55 21 148 106 pint:PI0829|3end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_766539..766689_POSITIVE 276 61 25 134 97 pint:PI0428|3end_hypothetical_protein_396321..396471_POSITIVE 275 50 3 137 72 pint:PI0284|3end_flavoprotein_A_270157..270307_POSITIVE 273 43 4 119 67 pint:PI0560|3end_hypothetical_protein_508910..509060_POSITIVE 268 66 31 56 11 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 267 66 24 76 41 pint:PI0245|3end_possible_mobilization_protein_244258..244408_POSITIVE 265 50 3 150 104 pint:PI1650|3end_N-acetylmuramoyl-L-alanine_amidase_1563901..1564051_POSITIVE 265 52 22 55 24 pint:PI1008|3end_cytochrome_c_nitrite_reductase,_small_subunit_929331..929481_POSITIVE 264 45 13 89 56 pint:PI1947|3end_hypothetical_protein_1902865..1903015_POSITIVE 261 78 31 62 8 pint:PI0828|3end_GMP_synthase_(glutamine_amidotransferase)_765695..765845_POSITIVE 260 59 16 148 107 pint:PI0047|3end_phosphomethylpyrimidine_kinase_46781..46931_POSITIVE 259 50 3 139 90 pint:PI1412|3end_HD_superfamily_hydrolase_1333823..1333973_POSITIVE