Origin IGS: aatgaattttgtttttaagtttgataaatgcgtaaaaaagaatttctatacttcacttttctctatatgaaaacgagggtgtgccatttctacacaccctcgcttttatataaaagttactttatttttttgtctataaaatcataataaacttaattatagcaactctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagagttgctataattaagtttattatgattttatagacaaaaaaataaagtaacttttatataaaagcgagggtgtgtagaaatggcacaccctcgttttcatatagagaaaagtgaagtatagaaattcttttttacgcatttatcaaacttaaaaacaaaattcatt Mask Tandem Repeat Region ================================================ aatgaattttgtttttaagtttgataaatgcgtaaaaaagaatttctatacttcacttttctctatatgaaaacgagggtgtgccatttctacacaccctcgcttttatataaaagttactttatttttttgtctataaaatcataataaacttaattatagcaactctta Find is-nt database================================================ Query_seq: PI1938:PI1940|PI1938:PI1940:hypothetical protein:conserved hypothetical protein; possible outer membrane protein:->->:1895699..1895869 171 aatgaattttgtttttaagtttgataaatgcgtaaaaaagaatttctatacttcacttttctctatatgaaaacgagggtgtgccatttctacacaccctcgcttttatataaaagttactttatttttttgtctataaaatcataataaacttaattatagcaactctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1938:PI1940|PI1938:PI1940:hypothetical protein:conserved hypothetical protein; possible outer membrane protein:->->:1895699..1895869 171 aatgaattttgtttttaagtttgataaatgcgtaaaaaagaatttctatacttcacttttctctatatgaaaacgagggtgtgccatttctacacaccctcgcttttatataaaagttactttatttttttgtctataaaatcataataaacttaattatagcaactctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1938:PI1940|PI1938:PI1940:hypothetical protein:conserved hypothetical protein; possible outer membrane protein:->->:1895699..1895869 171 aatgaattttgtttttaagtttgataaatgcgtaaaaaagaatttctatacttcacttttctctatatgaaaacgagggtgtgccatttctacacaccctcgcttttatataaaagttactttatttttttgtctataaaatcataataaacttaattatagcaactctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgaattttgtttttaagtttgataaatgcgtaaaaaagaatttctatacttcacttttctctatatgaaaacgagggtgtgccatttctacacaccctcgcttttatataaaagttactttatttttttgtctataaaatcataataaacttaattatagcaactctta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 28 End: 144 ........................... M R K K E F L Y F T F L Y M K T R V C H F Y T P S L L Y K S Y F I F L S I K S ........................... aatgaattttgtttttaagtttgataaatgcgtaaaaaagaatttctatacttcacttttctctatatgaaaacgagggtgtgccatttctacacaccctcgcttttatataaaagttactttatttttttgtctataaaatcataataaacttaattatagcaactctta 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================================================ aatgaattttgtttttaagtttgataaatgcgtaaaaaagaatttctatacttcacttttctctatatgaaaacgagggtgtgccatttctacacaccctcgcttttatataaaagttactttatttttttgtctataaaatcataataaacttaattatagcaactctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -8.3 Tail_Score: -4.53705 Start: 73 End: 103 Full_Region: TTTCTCTATATGAAA ACGAGGGTGTG CCATTTCTA CACACCCTCGC TTTTATATAAAAGTT ........................................................................ACGAGGGTGTGCCATTTCTACACACCCTCGC.................................................................... TransTerm Strand: - Conf: 100 HP_score: -12.5 Tail_Score: -4.34402 Start: 74 End: 102 Full_Region: acttttatataaaag cgagggtgtgt agaaatg gcacaccctcg ttttcatatagagaa .........................................................................cgagggtgtgtagaaatggcacaccctcg..................................................................... Find igs database================================================ Query_seq: PI1938:PI1940|PI1938:PI1940:hypothetical protein:conserved hypothetical protein; possible outer membrane protein:->->:1895699..1895869 171 aatgaattttgtttttaagtttgataaatgcgtaaaaaagaatttctatacttcacttttctctatatgaaaacgagggtgtgccatttctacacaccctcgcttttatataaaagttactttatttttttgtctataaaatcataataaacttaattatagcaactctta Intra-Species Hit: Count: 1 Min: 1 Max: 171 Len: 171 Subject: pint_PI1938_PI1940|hypothetical protein:conserved hypothetical protein; possible outer membrane protein|POSITIVE:POSITIVE|[1895699,1895869]|171 HSP 1 e-value: 6.0E-80 bit: 297.0 Len: 171 Query Start:1 Query End:171 Subject Strand: POSITIVE Subject Start: 1 Subject End: 171 aatgaattttgtttttaagtttgataaatgcgtaaaaaagaatttctatacttcacttttctctatatgaaaacgagggtgtgccatttctacacaccctcgcttttatataaaagttactttannnnnnngtctataaaatcataataaacttaattatagcaactctta aatgaattttgtttttaagtttgataaatgcgtaaaaaagaatttctatacttcacttttctctatatgaaaacgagggtgtgccatttctacacaccctcgcttttatataaaagttactttatttttttgtctataaaatcataataaacttaattatagcaactctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAAUUUUGUUUUUAAGUUUGAUAAAUGCGUAAAAAAGAAUUUCUAUACUUCACUUUUCUCUAUAUGAAAACGAGGGUGUGCCAUUUCUACACACCCUCGCUUUUAUAUAAAAGUUACUUUAUUUUUUUGUCUAUAAAAUCAUAAUAAACUUAAUUAUAGCAACUCUUA ........(((((.((((((((((((((...(((((..((.....)).......(((((....(((((((((.((((((((((.........)))))))))).))))))))))))))...)))))...))))))..............))))))))....)))))...... (-35.73) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAGUUGCUAUAAUUAAGUUUAUUAUGAUUUUAUAGACAAAAAAAUAAAGUAACUUUUAUAUAAAAGCGAGGGUGUGUAGAAAUGGCACACCCUCGUUUUCAUAUAGAGAAAAGUGAAGUAUAGAAAUUCUUUUUUACGCAUUUAUCAAACUUAAAAACAAAAUUCAUU ...(((((.......((((((((......(((((((..........)))))))...((((((((.(((((((((((((((.......))))))))))))))).))))))))....((((((..((((((....))))))..).))))).))))))))......)))))... (-43.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 109 75 156 123 pint:PI1075|5end_pyruvate_phosphate_dikinase_995828..996058_POSITIVE 319 112 77 208 172 pint:PI1463|5end_fumarate_hydratase,_class_I_1385349..1385579_POSITIVE 313 107 77 181 145 pint:PI0426|5end_conserved_hypothetical_protein_389345..389575_POSITIVE 308 110 67 104 54 pint:PI1314|5end_hypothetical_protein_1231188..1231418_POSITIVE 300 98 55 92 38 pint:PI0770|5end_hypothetical_protein_706170..706400_POSITIVE 292 107 67 150 98 pint:PI2040|5end_conserved_hypothetical_protein;_possible_transporter_1993068..1993298_POSITIVE 285 111 75 165 121 pint:PI1505|5end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_1424922..1425152_POSITIVE 283 110 65 111 66 pint:PI1603|5end_hypothetical_protein_1533779..1534009_POSITIVE 283 107 67 160 113 pint:PI0313|5end_conserved_hypothetical_protein_294833..295063_POSITIVE 283 107 67 48 1 pint:PI0311|5end_hypothetical_protein_294721..294951_POSITIVE 276 102 61 190 151 pint:PI0250|5end_hypothetical_protein_246946..247176_POSITIVE 275 110 62 186 124 pint:PI1635|5end_hypothetical_protein_1553948..1554178_POSITIVE 271 102 67 194 157 pint:PI1273|5end_anthranilate_synthase_component_II_1192285..1192515_POSITIVE 259 105 61 185 146 pint:PI0850|5end_conserved_hypothetical_protein_783231..783461_POSITIVE 259 105 61 147 108 pint:PI0849|5end_hypothetical_protein_783193..783423_POSITIVE 252 105 68 146 105 pint:PI0398|5end_hypothetical_protein_363378..363608_POSITIVE 250 103 66 229 189 pint:PI1707|5end_GTP-binding_protein_1623795..1624025_POSITIVE 248 106 73 34 1 pint:PI0853|5end_glycosyl_transferase,_group_2_family_protein_785515..785745_POSITIVE 247 107 74 85 43 pint:PI0345|5end_conserved_hypothetical_protein_319485..319715_POSITIVE 246 98 51 210 166 pint:PI0332|5end_conserved_hypothetical_protein_312600..312830_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 110 67 77 27 pint:PI1313|3end_possible_POT_family_(proton-dependent_oligopeptide_transport_family)_1231241..1231391_POSITIVE 285 111 75 67 23 pint:PI1504|3end_non-specific_DNA-binding_protein_1424904..1425054_POSITIVE 283 110 65 71 26 pint:PI1602|3end_conserved_hypothetical_protein;_possible_internalin-related_protein_1533819..1533969_POSITIVE 267 101 64 48 4 pint:PI1621|3end_hypothetical_protein_1545740..1545890_POSITIVE 267 101 64 48 4 pint:PI0327|3end_hypothetical_protein_309107..309257_POSITIVE 259 105 61 109 70 pint:PI0848|3end_glycosyl_transferase,_group_2_family_protein_783235..783385_POSITIVE 257 109 72 60 11 pint:PI0128|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_121826..121976_POSITIVE 247 120 72 132 83 pint:PI0331|3end_hypothetical_protein_312575..312725_POSITIVE 247 120 72 102 53 pint:PI0330|3end_hypothetical_protein_312545..312695_POSITIVE 245 109 74 114 81 pint:PI0304|3end_hypothetical_protein_289705..289855_POSITIVE 243 105 61 71 19 pint:PI0986|3end_conserved_hypothetical_protein_912366..912516_POSITIVE 242 102 64 74 36 pint:PI1733|3end_hypothetical_protein_1652437..1652587_POSITIVE 241 118 71 66 11 pint:PI1004|3end_conserved_hypothetical_protein_926217..926367_POSITIVE 240 109 64 125 76 pint:PI0173|3end_hypothetical_protein_165558..165708_POSITIVE 231 102 74 110 83 pint:PI1347|3end_DNA_damage-inducible_protein_1262178..1262328_POSITIVE 228 117 93 36 8 pint:PI1938|3end_hypothetical_protein_1895638..1895788_POSITIVE 226 119 74 130 69 pint:PI1790|3end_hypothetical_protein_1722762..1722912_POSITIVE 225 106 72 122 79 pint:PI0535|3end_hypothetical_protein_489779..489929_POSITIVE 223 103 61 46 6 pint:PI0084|3end_conserved_hypothetical_protein_84520..84670_POSITIVE 213 103 77 151 126 pint:PI1462|3end_hypothetical_protein_1385383..1385533_POSITIVE