Origin IGS: ctgtttgttccttttcagtgggtattccatacctttcgttttgtttcttttctactatgaaaaagcagttcgagagtcttctttaaatcgctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatctttttggagtctgttcggtatctttcgtttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaacgaaagataccgaacagactccaaaaagataccgagcgaactccaaaaagatatcgagcaatctgcgaaaagataccgagcgatttaaagaagactctcgaactgctttttcatagtagaaaagaaacaaaacgaaaggtatggaatacccactgaaaaggaacaaacag Mask Tandem Repeat Region ================================================ ctgtttgttccttttcagtgggtattccatacctttcgttttgtttcttttctactatgaaaaagcagttcgagagtcttctttaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgtttta Find is-nt database================================================ Query_seq: PI1952:PI1953|PI1952:PI1953:hypothetical protein:possible ABC-type permease:->->:1907100..1907274 175 ctgtttgttccttttcagtgggtattccatacctttcgttttgtttcttttctactatgaaaaagcagttcgagagtcttctttaaatcgctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatctttttggagtctgttcggtatctttcgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1952:PI1953|PI1952:PI1953:hypothetical protein:possible ABC-type permease:->->:1907100..1907274 175 ctgtttgttccttttcagtgggtattccatacctttcgttttgtttcttttctactatgaaaaagcagttcgagagtcttctttaaatcgctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatctttttggagtctgttcggtatctttcgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1952:PI1953|PI1952:PI1953:hypothetical protein:possible ABC-type permease:->->:1907100..1907274 175 ctgtttgttccttttcagtgggtattccatacctttcgttttgtttcttttctactatgaaaaagcagttcgagagtcttctttaaatcgctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatctttttggagtctgttcggtatctttcgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgtttgttccttttcagtgggtattccatacctttcgttttgtttcttttctactatgaaaaagcagttcgagagtcttctttaaatcgctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatctttttggagtctgttcggtatctttcgtttta Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 5 End: 175 .... M F L F S G Y S I P F V L F L F Y Y E K A V R E S S L N R S V S F R R L L D I F L E F A R Y L F G V C S V S F V L Protein_Len: 49 Strand: - Start: 18 End: 164 ................. H T N W V K R K T E K R S H F L L E L T K K L D S P I K E C I A R Y R K P T R E T D K Q L R N P M ........... ctgtttgttccttttcagtgggtattccatacctttcgttttgtttcttttctactatgaaaaagcagttcgagagtcttctttaaatcgctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatctttttggagtctgttcggtatctttcgtttta 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================================================ ctgtttgttccttttcagtgggtattccatacctttcgttttgtttcttttctactatgaaaaagcagttcgagagtcttctttaaatcgctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatctttttggagtctgttcggtatctttcgtttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1952:PI1953|PI1952:PI1953:hypothetical protein:possible ABC-type permease:->->:1907100..1907274 175 ctgtttgttccttttcagtgggtattccatacctttcgttttgtttcttttctactatgaaaaagcagttcgagagtcttctttaaatcgctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatctttttggagtctgttcggtatctttcgtttta Intra-Species Hit: Count: 1 Min: 1 Max: 175 Len: 175 Subject: pint_PI1952_PI1953|hypothetical protein:possible ABC-type permease|POSITIVE:POSITIVE|[1907100,1907274]|175 HSP 1 e-value: 8.0E-95 bit: 347.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 ctgtttgttccttttcagtgggtattccatacctttcgttttgtttcttttctactatgaaaaagcagttcgagagtcttctttaaatcgctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatctttttggagtctgttcggtatctttcgtttta ctgtttgttccttttcagtgggtattccatacctttcgttttgtttcttttctactatgaaaaagcagttcgagagtcttctttaaatcgctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatctttttggagtctgttcggtatctttcgtttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUUGUUCCUUUUCAGUGGGUAUUCCAUACCUUUCGUUUUGUUUCUUUUCUACUAUGAAAAAGCAGUUCGAGAGUCUUCUUUAAAUCGCUCGGUAUCUUUUCGCAGAUUGCUCGAUAUCUUUUUGGAGUUCGCUCGGUAUCUUUUUGGAGUCUGUUCGGUAUCUUUCGUUUUA .................((((.....))))..((((((..((((((..((((......))))))))))..)))))).......((((.((...((((((.....(((((((.(..((((((......(((....))))))))).....).)))))))..))))))...)).)))) (-34.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACGAAAGAUACCGAACAGACUCCAAAAAGAUACCGAGCGAACUCCAAAAAGAUAUCGAGCAAUCUGCGAAAAGAUACCGAGCGAUUUAAAGAAGACUCUCGAACUGCUUUUUCAUAGUAGAAAAGAAACAAAACGAAAGGUAUGGAAUACCCACUGAAAAGGAACAAACAG .....(....)...((...(((...........(((((...((..(((............)))...(((((((((((....((((.(.(((....))).).)))).....))))))....)))))............))...)))))((.....)).)))....))......... (-24.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 555 160 111 196 147 pint:PI1709|5end_ABC_transporter,_ATP-binding_protein_1625843..1626073_POSITIVE 339 161 121 172 121 pint:PI1998|5end_hypothetical_protein_1951770..1952000_POSITIVE 331 155 114 60 6 pint:PI0116|5end_conserved_hypothetical_protein_110213..110443_POSITIVE 322 169 121 221 176 pint:PI1646|5end_hypothetical_protein_1561954..1562184_POSITIVE 315 109 61 173 127 pint:PI0592|5end_DNA_mismatch_repair_protein_540795..541025_POSITIVE 312 56 17 109 62 pint:PI0713|5end_hypothetical_protein_650294..650524_POSITIVE 310 148 108 231 192 pint:PI1596|5end_conserved_hypothetical_protein_1525088..1525318_POSITIVE 300 165 125 117 68 pint:PI0439|5end_conserved_hypothetical_protein;_possible_preprotein_translocase_subunit_SecE_410319..410549_POSITIVE 297 136 104 84 56 pint:PI0361|5end_hypothetical_protein_333062..333292_POSITIVE 296 159 113 63 5 pint:PI1851|5end_conserved_hypothetical_protein_1796847..1797077_POSITIVE 295 141 101 220 174 pint:PI0751|5end_conserved_hypothetical_protein_680623..680853_POSITIVE 292 149 104 133 95 pint:PI0092|5end_regulatory_protein_RecX_89080..89310_POSITIVE 288 140 93 220 159 pint:PI2066|5end_hypothetical_protein_2027179..2027409_POSITIVE 288 70 26 132 87 pint:PI0886|5end_hypothetical_protein_817640..817870_POSITIVE 285 169 121 154 95 pint:PI0128|5end_dipeptidase,_pathogenicity_island-encoded_protein_D_120532..120762_POSITIVE 282 140 91 123 74 pint:PI1684|5end_dimethyladenosine_transferase_1601073..1601303_POSITIVE 282 140 91 120 41 pint:PI0415|5end_malate_dehydrogenase_385358..385588_POSITIVE 280 138 93 59 13 pint:PI0692|5end_iron_compound_ABC_transporter,_permease_protein_627350..627580_POSITIVE 278 150 102 146 85 pint:PI1914|5end_RNA_polymerase,_ECF-type_sigma_factor_1858025..1858255_POSITIVE 278 160 112 203 156 pint:PI0135|5end_internalin-related_protein_125849..126079_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 146 105 144 103 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 312 56 17 92 45 pint:PI0712|3end_conserved_hypothetical_protein;_possible_xylanase_650357..650507_POSITIVE 295 141 101 150 104 pint:PI0750|3end_zinc_protease_680633..680783_POSITIVE 292 149 104 133 95 pint:PI0090|3end_amidophosphoribosyltransferase_89160..89310_POSITIVE 291 138 95 151 93 pint:PI0036|3end_glutathione_peroxidase_39289..39439_POSITIVE 288 107 64 148 101 pint:PI1153|3end_histidine_kinase_sensor_protein_1078638..1078788_POSITIVE 288 70 26 150 105 pint:PI0887|3end_hypothetical_protein_817738..817888_POSITIVE 288 70 26 81 36 pint:PI0884|3end_hypothetical_protein_817669..817819_POSITIVE 276 170 125 122 71 pint:PI0681|3end_hypothetical_protein_619256..619406_POSITIVE 275 138 92 148 113 pint:PI1855|3end_lipopolysaccharide_biosynthesis_protein_1803168..1803318_POSITIVE 272 137 93 74 25 pint:PI2037|3end_TIM-barrel_protein,_NifR3_family_1990369..1990519_POSITIVE 269 169 121 109 42 pint:PI1942|3end_hypothetical_protein_1901269..1901419_POSITIVE 267 144 105 68 22 pint:PI0624|3end_hypothetical_protein_574471..574621_POSITIVE 267 139 95 67 32 pint:PI0313|3end_conserved_hypothetical_protein_295530..295680_POSITIVE 265 156 116 65 20 pint:PI1106|3end_conserved_hypothetical_protein_1030869..1031019_POSITIVE 264 49 2 96 55 pint:PI1777|3end_conserved_hypothetical_protein_1710081..1710231_POSITIVE 263 155 112 52 3 pint:PI1518|3end_outer_membrane_protein_oprM_precursor,_multidrug_resistance_protein_1440378..1440528_POSITIVE 263 170 121 61 8 pint:PI0616|3end_electron_transfer_flavoprotein,_beta-subunit_566440..566590_POSITIVE 262 159 120 48 10 pint:PI1530|3end_conserved_hypothetical_protein_1450908..1451058_POSITIVE 261 124 81 90 53 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE