Origin IGS: aaaggcgaggaatttactcctcttttcggaataaaacccctcgccaattgtgtttttatgtactgttctgtacttatctgtcattaattaacttgatgtgaaatcaaaattaataatgtcgtaaactta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagtttacgacattattaattttgatttcacatcaagttaattaatgacagataagtacagaacagtacataaaaacacaattggcgaggggttttattccgaaaagaggagtaaattcctcgccttt Mask Tandem Repeat Region ================================================ aaaggcgaggaatttactcctcttttcggaataaaacccctcgccaattgtgtttttatgtactgttctgtacttatctgtcattaattaacttgatgtgaaatcaaaattaataatgtcgtaaactta Find is-nt database================================================ Query_seq: PI0771:PI0772|PI0771:PI0772:conserved hypothetical protein:conserved hypothetical protein:->->:707168..707296 129 aaaggcgaggaatttactcctcttttcggaataaaacccctcgccaattgtgtttttatgtactgttctgtacttatctgtcattaattaacttgatgtgaaatcaaaattaataatgtcgtaaactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0771:PI0772|PI0771:PI0772:conserved hypothetical protein:conserved hypothetical protein:->->:707168..707296 129 aaaggcgaggaatttactcctcttttcggaataaaacccctcgccaattgtgtttttatgtactgttctgtacttatctgtcattaattaacttgatgtgaaatcaaaattaataatgtcgtaaactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0771:PI0772|PI0771:PI0772:conserved hypothetical protein:conserved hypothetical protein:->->:707168..707296 129 aaaggcgaggaatttactcctcttttcggaataaaacccctcgccaattgtgtttttatgtactgttctgtacttatctgtcattaattaacttgatgtgaaatcaaaattaataatgtcgtaaactta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaggcgaggaatttactcctcttttcggaataaaacccctcgccaattgtgtttttatgtactgttctgtacttatctgtcattaattaacttgatgtgaaatcaaaattaataatgtcgtaaactta Predict ORF larger than 30AA ================================================ aaaggcgaggaatttactcctcttttcggaataaaacccctcgccaattgtgtttttatgtactgttctgtacttatctgtcattaattaacttgatgtgaaatcaaaattaataatgtcgtaaactta 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================================================ aaaggcgaggaatttactcctcttttcggaataaaacccctcgccaattgtgtttttatgtactgttctgtacttatctgtcattaattaacttgatgtgaaatcaaaattaataatgtcgtaaactta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0771:PI0772|PI0771:PI0772:conserved hypothetical protein:conserved hypothetical protein:->->:707168..707296 129 aaaggcgaggaatttactcctcttttcggaataaaacccctcgccaattgtgtttttatgtactgttctgtacttatctgtcattaattaacttgatgtgaaatcaaaattaataatgtcgtaaactta Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: pint_PI0771_PI0772|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[707168,707296]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 aaaggcgaggaatttactcctcttttcggaataaaacccctcgccaattgtgtttttatgtactgttctgtacttatctgtcattaattaacttgatgtgaaatcaaaattaataatgtcgtaaactta aaaggcgaggaatttactcctcttttcggaataaaacccctcgccaattgtgtttttatgtactgttctgtacttatctgtcattaattaacttgatgtgaaatcaaaattaataatgtcgtaaactta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGGCGAGGAAUUUACUCCUCUUUUCGGAAUAAAACCCCUCGCCAAUUGUGUUUUUAUGUACUGUUCUGUACUUAUCUGUCAUUAAUUAACUUGAUGUGAAAUCAAAAUUAAUAAUGUCGUAAACUUA ...(((((((..((((.(((.......))).))))...)))))))......((((....((((......))))......(.(((((.((((.(((((.....)))))..))))))))).)..))))... (-29.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUUUACGACAUUAUUAAUUUUGAUUUCACAUCAAGUUAAUUAAUGACAGAUAAGUACAGAACAGUACAUAAAAACACAAUUGGCGAGGGGUUUUAUUCCGAAAAGAGGAGUAAAUUCCUCGCCUUU ...((((....((((((((((((.(((.....)))))))))).)))))........((((......))))....))))......((((((((((((.(((((.......)))))))))))))))))... (-36.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 89 41 95 42 pint:PI1397|5end_histidine_ammonia-lyase_1317879..1318109_POSITIVE 263 74 36 157 118 pint:PI0871|5end_hypothetical_protein_806834..807064_POSITIVE 257 49 1 74 14 pint:PI2014|5end_conserved_hypothetical_protein_1971471..1971701_POSITIVE 247 79 37 230 179 pint:PI1635|5end_hypothetical_protein_1553948..1554178_POSITIVE 247 83 42 182 135 pint:PI1158|5end_1,4-alpha-glucan_branching_enzyme,_C-terminal_region_1082675..1082905_POSITIVE 245 46 1 187 126 pint:PI2011|5end_hypothetical_protein_1970429..1970659_POSITIVE 245 38 1 57 11 pint:PI0281|5end_conserved_hypothetical_protein_266309..266539_POSITIVE 244 45 7 161 113 pint:PI1264|5end_hypothetical_protein_1184806..1185036_POSITIVE 242 50 2 119 63 pint:PI0268|5end_lysozyme-related_protein_259198..259428_POSITIVE 241 70 21 74 35 pint:PI1401|5end_TPR-repeat-containing_protein_1322027..1322257_POSITIVE 241 65 21 209 157 pint:PI0626|5end_penicillin-binding_protein,_D-alanyl-D-alanine_carboxypeptidase_574305..574535_POSITIVE 241 65 21 107 55 pint:PI0624|5end_hypothetical_protein_574203..574433_POSITIVE 239 85 41 92 43 pint:PI1658|5end_conserved_hypothetical_protein_1573607..1573837_POSITIVE 236 80 36 109 66 pint:PI1550|5end_conserved_hypothetical_protein_1467360..1467590_POSITIVE 232 53 27 41 10 pint:PI0577|5end_conserved_hypothetical_protein_521811..522041_POSITIVE 228 45 3 209 169 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 227 85 42 71 15 pint:PI1632|5end_hypothetical_protein_1552819..1553049_POSITIVE 227 47 4 223 177 pint:PI0486|5end_DNA-directed_RNA_polymerase,_alpha_subunit_445073..445303_POSITIVE 227 44 5 206 156 pint:PI0359|5end_hypothetical_protein_328339..328569_POSITIVE 227 46 2 147 97 pint:PI0058|5end_conserved_hypothetical_protein_56398..56628_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 74 36 137 98 pint:PI0870|3end_branched-chain_amino_acid_aminotransferase_806894..807044_POSITIVE 257 49 1 78 18 pint:PI2012|3end_hypothetical_protein_1971555..1971705_POSITIVE 244 45 7 81 33 pint:PI1263|3end_probable_integrase_1184806..1184956_POSITIVE 242 50 2 132 76 pint:PI0267|3end_conjugative_transposon_protein,_TraQ_259291..259441_POSITIVE 239 85 41 76 27 pint:PI1657|3end_hypothetical_protein_1573671..1573821_POSITIVE 236 80 36 51 8 pint:PI1549|3end_conserved_hypothetical_protein_1467382..1467532_POSITIVE 236 78 42 151 105 pint:PI1157|3end_hypothetical_protein_1082725..1082875_POSITIVE 229 70 26 139 95 pint:PI1623|3end_hypothetical_protein_1549261..1549411_POSITIVE 227 85 42 127 71 pint:PI1633|3end_hypothetical_protein_1552955..1553105_POSITIVE 226 73 38 51 15 pint:PI1637|3end_hypothetical_protein_1555284..1555434_POSITIVE 222 70 28 109 71 pint:PI0771|3end_conserved_hypothetical_protein_707107..707257_POSITIVE 219 44 1 69 28 pint:PI0268|3end_lysozyme-related_protein_259790..259940_POSITIVE 217 46 6 134 93 pint:PI0260|3end_conjugative_transposon_protein,_TraJ_254122..254272_POSITIVE 216 41 2 81 47 pint:PI0241|3end_possible_tetracycline_resistance_element_/mobilization_regulatory_protein_240036..240186_POSITIVE 213 75 39 150 114 pint:PI1548|3end_conserved_hypothetical_protein_1466886..1467036_POSITIVE 213 81 42 45 2 pint:PI0512|3end_conserved_hypothetical_protein_471440..471590_POSITIVE 210 50 2 121 49 pint:PI1444|3end_protease_ClpB_1368137..1368287_POSITIVE 209 46 3 87 35 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 208 46 3 112 48 pint:PI0217|3end_conserved_hypothetical_protein;_possible_lipoprotein_210794..210944_POSITIVE 207 70 25 98 63 pint:PI0225|3end_conserved_hypothetical_protein_222759..222909_POSITIVE