Origin IGS: cttaccttattaataacttattataggggcaaagttaaagaaaaaaacggaaagaagcaaagaatatcctctccttctttccgttttcaactcaattttctgcaagcccttcagatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatctgaagggcttgcagaaaattgagttgaaaacggaaagaaggagaggatattctttgcttctttccgtttttttctttaactttgcccctataataagttattaataaggtaag Mask Tandem Repeat Region ================================================ cttaccttattaataacttattataggggcaaagttaaagaaaaaaacggaaagaagcaaagaatatcctctccttctttccgttttcaactcaattttctgcaagcccttcagatta Find is-nt database================================================ Query_seq: PI2017:PI2018|PI2017:PI2018:conserved hypothetical protein:50S ribosomal protein L34:->->:1975779..1975896 118 cttaccttattaataacttattataggggcaaagttaaagaaaaaaacggaaagaagcaaagaatatcctctccttctttccgttttcaactcaattttctgcaagcccttcagatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2017:PI2018|PI2017:PI2018:conserved hypothetical protein:50S ribosomal protein L34:->->:1975779..1975896 118 cttaccttattaataacttattataggggcaaagttaaagaaaaaaacggaaagaagcaaagaatatcctctccttctttccgttttcaactcaattttctgcaagcccttcagatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2017:PI2018|PI2017:PI2018:conserved hypothetical protein:50S ribosomal protein L34:->->:1975779..1975896 118 cttaccttattaataacttattataggggcaaagttaaagaaaaaaacggaaagaagcaaagaatatcctctccttctttccgttttcaactcaattttctgcaagcccttcagatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttaccttattaataacttattataggggcaaagttaaagaaaaaaacggaaagaagcaaagaatatcctctccttctttccgttttcaactcaattttctgcaagcccttcagatta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 13 End: 117 ............ M T Y Y R G K V K E K N G K K Q R I S S P S F R F Q L N F L Q A L Q I . Protein_Len: 33 Strand: + Start: 20 End: 118 ................... M I G A K L K K K T E R S K E Y P L L L S V F N S I F C K P F R L Protein_Len: 34 Strand: - Start: 13 End: 114 ............ Y S I I P A F N F F F V S L L L S Y G R R R E T K L E I K Q L G K M .... cttaccttattaataacttattataggggcaaagttaaagaaaaaaacggaaagaagcaaagaatatcctctccttctttccgttttcaactcaattttctgcaagcccttcagatta 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================================================ cttaccttattaataacttattataggggcaaagttaaagaaaaaaacggaaagaagcaaagaatatcctctccttctttccgttttcaactcaattttctgcaagcccttcagatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -12.0 Tail_Score: -5.96894 Start: 48 End: 83 Full_Region: aaattgagttgaaaa cggaaagaaggagagg atat tctttgcttctttccg tttttttctttaact ...............................................cggaaagaaggagaggatattctttgcttctttccg................................... Find igs database================================================ Query_seq: PI2017:PI2018|PI2017:PI2018:conserved hypothetical protein:50S ribosomal protein L34:->->:1975779..1975896 118 cttaccttattaataacttattataggggcaaagttaaagaaaaaaacggaaagaagcaaagaatatcctctccttctttccgttttcaactcaattttctgcaagcccttcagatta Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: pint_PI2017_PI2018|conserved hypothetical protein:50S ribosomal protein L34|POSITIVE:POSITIVE|[1975779,1975896]|118 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 cttaccttattaataacttattataggggcaaagttaaagnnnnnnncggaaagaagcaaagaatatcctctccttctttccgttttcaactcaattttctgcaagcccttcagatta cttaccttattaataacttattataggggcaaagttaaagaaaaaaacggaaagaagcaaagaatatcctctccttctttccgttttcaactcaattttctgcaagcccttcagatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUACCUUAUUAAUAACUUAUUAUAGGGGCAAAGUUAAAGAAAAAAACGGAAAGAAGCAAAGAAUAUCCUCUCCUUCUUUCCGUUUUCAACUCAAUUUUCUGCAAGCCCUUCAGAUUA ........................((((((...((...(((((((((((((((((((...(((......))).))))))))))))).........))))))))..))))))....... (-27.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCUGAAGGGCUUGCAGAAAAUUGAGUUGAAAACGGAAAGAAGGAGAGGAUAUUCUUUGCUUCUUUCCGUUUUUUUCUUUAACUUUGCCCCUAUAAUAAGUUAUUAAUAAGGUAAG ..((((..((((...(((((.....(((..(((((((((((((((.(((((....))))).)))))))))))))))..)))....))))))))).(((((...)))))...))))... (-37.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 108 67 144 100 pint:PI0333|5end_hypothetical_protein_313478..313708_POSITIVE 250 70 23 173 126 pint:PI0067|5end_hypothetical_protein_66273..66503_POSITIVE 247 110 61 192 132 pint:PI0809|5end_hypothetical_protein_746630..746860_POSITIVE 242 108 69 189 151 pint:PI1646|5end_hypothetical_protein_1561954..1562184_POSITIVE 238 107 69 225 191 pint:PI0659|5end_hypothetical_protein_603203..603433_POSITIVE 235 89 47 175 133 pint:PI0336|5end_hypothetical_protein_314499..314729_POSITIVE 229 108 67 157 105 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 229 79 48 110 79 pint:PI0041|5end_hypothetical_protein_41785..42015_POSITIVE 228 106 69 57 31 pint:PI1075|5end_pyruvate_phosphate_dikinase_995828..996058_POSITIVE 223 110 67 156 115 pint:PI1845|5end_hypothetical_protein_1791457..1791687_POSITIVE 223 96 53 143 92 pint:PI1083|5end_TPR-repeat-containing_protein_1001975..1002205_POSITIVE 223 107 61 171 122 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 221 106 73 44 16 pint:PI2063|5end_conserved_hypothetical_protein_2023946..2024176_POSITIVE 218 109 68 199 158 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 218 90 53 138 100 pint:PI0877|5end_hypothetical_protein_811378..811608_POSITIVE 217 84 48 167 133 pint:PI2076|5end_hypothetical_protein_2035403..2035633_POSITIVE 215 88 47 182 128 pint:PI0328|5end_conserved_hypothetical_protein_309476..309706_POSITIVE 215 104 61 213 178 pint:PI0313|5end_conserved_hypothetical_protein_294833..295063_POSITIVE 215 104 61 101 66 pint:PI0311|5end_hypothetical_protein_294721..294951_POSITIVE 215 107 62 121 80 pint:PI0129|5end_hypothetical_protein_121709..121939_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 87 44 47 4 pint:PI2017|3end_conserved_hypothetical_protein_1975718..1975868_POSITIVE 278 94 68 118 94 pint:PI0513|3end_ion_transporter_472371..472521_POSITIVE 267 108 67 138 94 pint:PI0332|3end_conserved_hypothetical_protein_313552..313702_POSITIVE 261 97 67 70 41 pint:PI1153|3end_histidine_kinase_sensor_protein_1078638..1078788_POSITIVE 244 110 67 139 103 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 233 110 61 70 28 pint:PI0082|3end_conserved_hypothetical_protein_(possible_phosphoglycerol_transferase)_82711..82861_POSITIVE 229 79 48 117 86 pint:PI0040|3end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41872..42022_POSITIVE 227 109 78 141 110 pint:PI2122|3end_conserved_hypothetical_protein_2070480..2070630_POSITIVE 223 107 69 149 101 pint:PI0764|3end_permease_699145..699295_POSITIVE 218 90 53 117 79 pint:PI0875|3end_conserved_hypothetical_protein_811437..811587_POSITIVE 217 84 48 39 5 pint:PI2075|3end_conserved_hypothetical_protein_2035355..2035505_POSITIVE 212 88 45 68 22 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 209 100 57 138 95 pint:PI0944|3end_hypothetical_protein_875249..875399_POSITIVE 207 107 69 73 34 pint:PI0067|3end_hypothetical_protein_66586..66736_POSITIVE 206 108 61 109 68 pint:PI0945|3end_sodium:solute_symporter_family_protein_877624..877774_POSITIVE 206 107 67 58 14 pint:PI0593|3end_NAD-specific_glutamate_dehydrogenase_544369..544519_POSITIVE 205 107 69 121 92 pint:PI1653|3end_hypothetical_protein_1565714..1565864_POSITIVE 204 110 61 134 88 pint:PI1432|3end_DNA_methylase_1353771..1353921_POSITIVE 203 108 63 120 67 pint:PI1558|3end_conserved_hypothetical_protein_1476106..1476256_POSITIVE 202 105 64 88 47 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE