Origin IGS: aaactttaccgaaagaaataaaaattaagagttgattttcatagtgaaaaccaactcttaatttttatcagtgaaatatcaaatagccctatcaagtcctctgcttggattgtgttcgcctattaaagaagcaaaaaactcatttctcctaccaacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagttggtaggagaaatgagttttttgcttctttaataggcgaacacaatccaagcagaggacttgatagggctatttgatatttcactgataaaaattaagagttggttttcactatgaaaatcaactcttaatttttatttctttcggtaaagttt Mask Tandem Repeat Region ================================================ aaactttaccgaaagaaataaaaattaagagttgattttcatagtgaaaaccaactcttaatttttatcagtgaaatatcaaatagccctatcaagtcctctgcttggattgtgttcgcctattaaagaagcaaaaaactcatttctcctaccaacta Find is-nt database================================================ Query_seq: PI1804:PI1805|PI1804:PI1805:hypothetical protein:TPR repeat containing protein:->->:1738351..1738508 158 aaactttaccgaaagaaataaaaattaagagttgattttcatagtgaaaaccaactcttaatttttatcagtgaaatatcaaatagccctatcaagtcctctgcttggattgtgttcgcctattaaagaagcaaaaaactcatttctcctaccaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1804:PI1805|PI1804:PI1805:hypothetical protein:TPR repeat containing protein:->->:1738351..1738508 158 aaactttaccgaaagaaataaaaattaagagttgattttcatagtgaaaaccaactcttaatttttatcagtgaaatatcaaatagccctatcaagtcctctgcttggattgtgttcgcctattaaagaagcaaaaaactcatttctcctaccaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1804:PI1805|PI1804:PI1805:hypothetical protein:TPR repeat containing protein:->->:1738351..1738508 158 aaactttaccgaaagaaataaaaattaagagttgattttcatagtgaaaaccaactcttaatttttatcagtgaaatatcaaatagccctatcaagtcctctgcttggattgtgttcgcctattaaagaagcaaaaaactcatttctcctaccaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaactttaccgaaagaaataaaaattaagagttgattttcatagtgaaaaccaactcttaatttttatcagtgaaatatcaaatagccctatcaagtcctctgcttggattgtgttcgcctattaaagaagcaaaaaactcatttctcctaccaacta Predict ORF larger than 30AA ================================================ aaactttaccgaaagaaataaaaattaagagttgattttcatagtgaaaaccaactcttaatttttatcagtgaaatatcaaatagccctatcaagtcctctgcttggattgtgttcgcctattaaagaagcaaaaaactcatttctcctaccaacta 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================================================ aaactttaccgaaagaaataaaaattaagagttgattttcatagtgaaaaccaactcttaatttttatcagtgaaatatcaaatagccctatcaagtcctctgcttggattgtgttcgcctattaaagaagcaaaaaactcatttctcctaccaacta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -17.7 Tail_Score: -5.5454 Start: 25 End: 61 Full_Region: tttcactgataaaaa ttaagagttggttttca cta tgaaaatcaactcttaa tttttatttctttcg ........................ttaagagttggttttcactatgaaaatcaactcttaa................................................................................................. Find igs database================================================ Query_seq: PI1804:PI1805|PI1804:PI1805:hypothetical protein:TPR repeat containing protein:->->:1738351..1738508 158 aaactttaccgaaagaaataaaaattaagagttgattttcatagtgaaaaccaactcttaatttttatcagtgaaatatcaaatagccctatcaagtcctctgcttggattgtgttcgcctattaaagaagcaaaaaactcatttctcctaccaacta Intra-Species Hit: Count: 1 Min: 1 Max: 158 Len: 158 Subject: pint_PI1804_PI1805|hypothetical protein:TPR repeat containing protein|POSITIVE:POSITIVE|[1738351,1738508]|158 HSP 1 e-value: 9.0E-85 bit: 313.0 Len: 158 Query Start:1 Query End:158 Subject Strand: POSITIVE Subject Start: 1 Subject End: 158 aaactttaccgaaagaaataaaaattaagagttgattttcatagtgaaaaccaactcttaatttttatcagtgaaatatcaaatagccctatcaagtcctctgcttggattgtgttcgcctattaaagaagcaaaaaactcatttctcctaccaacta aaactttaccgaaagaaataaaaattaagagttgattttcatagtgaaaaccaactcttaatttttatcagtgaaatatcaaatagccctatcaagtcctctgcttggattgtgttcgcctattaaagaagcaaaaaactcatttctcctaccaacta HSP 2 e-value: 6.0E-9 bit: 61.9 Len: 51 Query Start:18 Query End:68 Subject Strand: NEGATIVE Subject Start: 18 Subject End: 68 .................ataaaaattaagagttgattttcatagtgaaaaccaactcttaatttttat.......................................................................................... .................ataaaaattaagagttggttttcactatgaaaatcaactcttaatttttat.......................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUUUACCGAAAGAAAUAAAAAUUAAGAGUUGAUUUUCAUAGUGAAAACCAACUCUUAAUUUUUAUCAGUGAAAUAUCAAAUAGCCCUAUCAAGUCCUCUGCUUGGAUUGUGUUCGCCUAUUAAAGAAGCAAAAAACUCAUUUCUCCUACCAACUA ...(((((.(....)..(((((((((((((((((.(((((.....))))).)))))))))))))))))..(((((..(((....(((...............)))..)))....)))))....))))).............................. (-31.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUGGUAGGAGAAAUGAGUUUUUUGCUUCUUUAAUAGGCGAACACAAUCCAAGCAGAGGACUUGAUAGGGCUAUUUGAUAUUUCACUGAUAAAAAUUAAGAGUUGGUUUUCACUAUGAAAAUCAACUCUUAAUUUUUAUUUCUUUCGGUAAAGUUU ...(((.(..((((...(((((((((((((......................)))))))))))))........................((((((((((((((((((((((((.....))))))))))))))))))))))))))))..).)))..... (-43.05) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 140 97 147 106 pint:PI0779|5end_predicted_TPR-repeat-containing_protein_714554..714784_POSITIVE 308 140 97 138 97 pint:PI0778|5end_hypothetical_protein_714545..714775_POSITIVE 298 129 86 190 149 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 285 120 86 58 10 pint:PI1711|5end_ABC_transporter,_ATP-binding_protein_1627597..1627827_POSITIVE 283 122 83 144 92 pint:PI1705|5end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_1621781..1622011_POSITIVE 276 121 98 161 139 pint:PI0743|5end_hypothetical_protein_672728..672958_POSITIVE 268 121 85 227 190 pint:PI1697|5end_conserved_hypothetical_protein_1612217..1612447_POSITIVE 268 130 86 52 17 pint:PI0514|5end_possible_cell_filamentation_protein_472408..472638_POSITIVE 262 119 79 106 70 pint:PI1104|5end_GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-redu_ctase_1027749..1027979_POSITIVE 260 114 72 220 178 pint:PI2052|5end_hypothetical_protein_2008594..2008824_POSITIVE 260 121 86 47 5 pint:PI0351|5end_hypothetical_protein_324317..324547_POSITIVE 258 119 71 160 98 pint:PI1332|5end_aminotransferase,_possible_pyridoxal-phosphate-dependent_aminotransferase_1249374..1249604_POSITIVE 248 120 85 141 102 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 247 150 103 102 57 pint:PI0915|5end_hypothetical_protein_845183..845413_POSITIVE 246 148 101 215 155 pint:PI1945|5end_ribonuclease_HII_1901932..1902162_POSITIVE 246 134 96 160 107 pint:PI1747|5end_membrane-bound_lytic_murein_transglycosylase_D_1667483..1667713_POSITIVE 246 129 94 148 116 pint:PI0859|5end_carbamoyl-phosphate_synthase,_small_subunit_793317..793547_POSITIVE 239 126 85 221 180 pint:PI0334|5end_hypothetical_protein_313234..313464_POSITIVE 238 128 85 50 11 pint:PI0308|5end_conserved_hypothetical_protein_290587..290817_POSITIVE 237 107 86 124 102 pint:PI1267|5end_probable_integrase_1186105..1186335_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 380 68 21 73 26 pint:PI1804|3end_hypothetical_protein_1738290..1738440_POSITIVE 276 121 98 102 80 pint:PI0742|3end_hypothetical_protein_672749..672899_POSITIVE 269 147 101 50 5 pint:PI0321|3end_conserved_hypothetical_protein_303286..303436_POSITIVE 256 149 101 51 3 pint:PI0948|3end_hypothetical_protein_881978..882128_POSITIVE 248 120 85 144 105 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 246 129 94 145 113 pint:PI0858|3end_carbamyl_phosphate_synthase,_large_subunit_793394..793544_POSITIVE 246 120 83 96 57 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 245 130 86 48 6 pint:PI1944|3end_hypothetical_protein_1901990..1902140_POSITIVE 238 128 85 50 11 pint:PI0307|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_290667..290817_POSITIVE 237 134 92 145 107 pint:PI0203|3end_conserved_hypothetical_protein_196064..196214_POSITIVE 235 118 85 135 104 pint:PI0735|3end_ABC_transporter,_ATP-binding_/_permease_670591..670741_POSITIVE 229 119 86 112 53 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE 220 120 85 58 26 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 220 121 88 139 110 pint:PI0632|3end_NusB_family_protein_(N_utilization_substance_protein_B)_579731..579881_POSITIVE 219 107 67 142 106 pint:PI1448|3end_hypothetical_protein_1371832..1371982_POSITIVE 218 121 84 131 80 pint:PI0496|3end_heat_shock_protein_hsp70_(chaperone_protein_dnaK)_458610..458760_POSITIVE 217 108 61 151 110 pint:PI1237|3end_ATP-dependent_DNA_helicase_1161480..1161630_POSITIVE 217 122 86 128 96 pint:PI0019|3end_conserved_hypothetical_protein_24454..24604_POSITIVE 216 144 101 82 41 pint:PI0805|3end_conserved_hypothetical_protein_743807..743957_POSITIVE 212 149 101 54 2 pint:PI0901|3end_hypothetical_protein_832207..832357_POSITIVE