Origin IGS: ataaaaatcttgttagttaaattaggtaatggactttttgcccattattttaatagttaatatttaattcattcatcatttacgcatcttttctttagatgcaaatagcttgtattattcgttgcaaagttaaacaaaatatatggaagagcaaaatatttctaagctattgtgttataaaataaaggcttacacgttgttagcatcgtgtaagcctttatttggatagatggaacggtgtttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaacaccgttccatctatccaaataaaggcttacacgatgctaacaacgtgtaagcctttattttataacacaatagcttagaaatattttgctcttccatatattttgtttaactttgcaacgaataatacaagctatttgcatctaaagaaaagatgcgtaaatgatgaatgaattaaatattaactattaaaataatgggcaaaaagtccattacctaatttaactaacaagatttttat Mask Tandem Repeat Region ================================================ ataaaaatcttgttagttaaattaggtaatggactttttgcccattattttaatagttaatatttaattcattcatcatttacgcatcttttctttagatgcaaatagcttgtattattcgttgcaaagttaaacaaaatatatggaagagcaaaatatttctaagctattgtgttataaaataaaggcttacacgttgttagcatcgtgtaagcctttatttggatagatggaacggtgtttta Find is-nt database================================================ Query_seq: PI0856:PI0858|PI0856:PI0858:hypothetical protein:carbamyl phosphate synthase, large subunit:->->:789988..790232 245 ataaaaatcttgttagttaaattaggtaatggactttttgcccattattttaatagttaatatttaattcattcatcatttacgcatcttttctttagatgcaaatagcttgtattattcgttgcaaagttaaacaaaatatatggaagagcaaaatatttctaagctattgtgttataaaataaaggcttacacgttgttagcatcgtgtaagcctttatttggatagatggaacggtgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0856:PI0858|PI0856:PI0858:hypothetical protein:carbamyl phosphate synthase, large subunit:->->:789988..790232 245 ataaaaatcttgttagttaaattaggtaatggactttttgcccattattttaatagttaatatttaattcattcatcatttacgcatcttttctttagatgcaaatagcttgtattattcgttgcaaagttaaacaaaatatatggaagagcaaaatatttctaagctattgtgttataaaataaaggcttacacgttgttagcatcgtgtaagcctttatttggatagatggaacggtgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0856:PI0858|PI0856:PI0858:hypothetical protein:carbamyl phosphate synthase, large subunit:->->:789988..790232 245 ataaaaatcttgttagttaaattaggtaatggactttttgcccattattttaatagttaatatttaattcattcatcatttacgcatcttttctttagatgcaaatagcttgtattattcgttgcaaagttaaacaaaatatatggaagagcaaaatatttctaagctattgtgttataaaataaaggcttacacgttgttagcatcgtgtaagcctttatttggatagatggaacggtgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaaaatcttgttagttaaattaggtaatggactttttgcccattattttaatagttaatatttaattcattcatcatttacgcatcttttctttagatgcaaatagcttgtattattcgttgcaaagttaaacaaaatatatggaagagcaaaatatttctaagctattgtgttataaaataaaggcttacacgttgttagcatcgtgtaagcctttatttggatagatggaacggtgtttta Predict ORF larger than 30AA ================================================ ataaaaatcttgttagttaaattaggtaatggactttttgcccattattttaatagttaatatttaattcattcatcatttacgcatcttttctttagatgcaaatagcttgtattattcgttgcaaagttaaacaaaatatatggaagagcaaaatatttctaagctattgtgttataaaataaaggcttacacgttgttagcatcgtgtaagcctttatttggatagatggaacggtgtttta 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================================================ ataaaaatcttgttagttaaattaggtaatggactttttgcccattattttaatagttaatatttaattcattcatcatttacgcatcttttctttagatgcaaatagcttgtattattcgttgcaaagttaaacaaaatatatggaagagcaaaatatttctaagctattgtgttataaaataaaggcttacacgttgttagcatcgtgtaagcctttatttggatagatggaacggtgtttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -18.7 Tail_Score: -4.3739 Start: 183 End: 220 Full_Region: ttccatctatccaaa taaaggcttacacgatg ctaa caacgtgtaagccttta ttttataacacaata ......................................................................................................................................................................................taaaggcttacacgatgctaacaacgtgtaagccttta......................... TransTerm Strand: + Conf: 100 HP_score: -15.1 Tail_Score: -4.46514 Start: 187 End: 216 Full_Region: GTGTTATAAAATAAA GGCTTACACGTTG TTAG CATCGTGTAAGCC TTTATTTGGATAGAT ..........................................................................................................................................................................................GGCTTACACGTTGTTAGCATCGTGTAAGCC............................. Find igs database================================================ Query_seq: PI0856:PI0858|PI0856:PI0858:hypothetical protein:carbamyl phosphate synthase, large subunit:->->:789988..790232 245 ataaaaatcttgttagttaaattaggtaatggactttttgcccattattttaatagttaatatttaattcattcatcatttacgcatcttttctttagatgcaaatagcttgtattattcgttgcaaagttaaacaaaatatatggaagagcaaaatatttctaagctattgtgttataaaataaaggcttacacgttgttagcatcgtgtaagcctttatttggatagatggaacggtgtttta Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: pint_PI0856_PI0858|hypothetical protein:carbamyl phosphate synthase, large subunit|POSITIVE:POSITIVE|[789988,790232]|245 HSP 1 e-value: 1.0E-136 bit: 486.0 Len: 245 Query Start:1 Query End:245 Subject Strand: POSITIVE Subject Start: 1 Subject End: 245 ataaaaatcttgttagttaaattaggtaatggactttttgcccattattttaatagttaatatttaattcattcatcatttacgcatcttttctttagatgcaaatagcttgtattattcgttgcaaagttaaacaaaatatatggaagagcaaaatatttctaagctattgtgttataaaataaaggcttacacgttgttagcatcgtgtaagcctttatttggatagatggaacggtgtttta ataaaaatcttgttagttaaattaggtaatggactttttgcccattattttaatagttaatatttaattcattcatcatttacgcatcttttctttagatgcaaatagcttgtattattcgttgcaaagttaaacaaaatatatggaagagcaaaatatttctaagctattgtgttataaaataaaggcttacacgttgttagcatcgtgtaagcctttatttggatagatggaacggtgtttta HSP 2 e-value: 6.0E-7 bit: 56.0 Len: 44 Query Start:180 Query End:223 Subject Strand: NEGATIVE Subject Start: 180 Subject End: 223 ...................................................................................................................................................................................aaataaaggcttacacgttgttagcatcgtgtaagcctttattt...................... ...................................................................................................................................................................................aaataaaggcttacacgatgctaacaacgtgtaagcctttattt...................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAAUCUUGUUAGUUAAAUUAGGUAAUGGACUUUUUGCCCAUUAUUUUAAUAGUUAAUAUUUAAUUCAUUCAUCAUUUACGCAUCUUUUCUUUAGAUGCAAAUAGCUUGUAUUAUUCGUUGCAAAGUUAAACAAAAUAUAUGGAAGAGCAAAAUAUUUCUAAGCUAUUGUGUUAUAAAAUAAAGGCUUACACGUUGUUAGCAUCGUGUAAGCCUUUAUUUGGAUAGAUGGAACGGUGUUUUA ...(((((.(((((.........(((((((((.(.....).)))))))))(((((((((((((((..(((.(((((.......((((((.......))))))...(((((((((........))).))))))..........))))).)))..)))))))....))))))))..((((.(((((((((((((((((.((....)).)))))))))))))))))..))))....))))).))))). (-62.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACACCGUUCCAUCUAUCCAAAUAAAGGCUUACACGAUGCUAACAACGUGUAAGCCUUUAUUUUAUAACACAAUAGCUUAGAAAUAUUUUGCUCUUCCAUAUAUUUUGUUUAACUUUGCAACGAAUAAUACAAGCUAUUUGCAUCUAAAGAAAAGAUGCGUAAAUGAUGAAUGAAUUAAAUAUUAACUAUUAAAAUAAUGGGCAAAAAGUCCAUUACCUAAUUUAACUAACAAGAUUUUUAU ........(((((.(((.....(((((((((((((((((.((....)).)))))))))))))))))........((((((((.....((((((((.........................)))..)))))....)))))))).((((((.......))))))......))))))))......................((((((((.....)))))))).......................... (-54.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 204 165 189 148 pint:PI0471|5end_50S_ribosomal_protein_L24_437736..437966_POSITIVE 280 127 83 104 52 pint:PI0729|5end_integrase_661428..661658_POSITIVE 275 239 193 211 166 pint:PI1603|5end_hypothetical_protein_1533779..1534009_POSITIVE 271 236 195 228 171 pint:PI0080|5end_hypothetical_protein_79047..79277_POSITIVE 266 158 112 153 107 pint:PI1336|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_1253839..1254069_POSITIVE 264 225 188 62 29 pint:PI0576|5end_helicase,_UvrD/Rep_520226..520456_POSITIVE 259 239 195 206 159 pint:PI1459|5end_ribonucleotide_reductase,_alpha_subunit,_C-terminal_region_1381569..1381799_POSITIVE 258 239 193 162 112 pint:PI1453|5end_probable_thiamine_pyrophosphokinase_1375982..1376212_POSITIVE 257 238 194 212 170 pint:PI1187|5end_conserved_hypothetical_protein_1106692..1106922_POSITIVE 255 240 191 201 143 pint:PI0490|5end_DNA_primase_449070..449300_POSITIVE 251 229 185 148 103 pint:PI0085|5end_RNase_P_protein_component_84440..84670_POSITIVE 250 217 191 205 169 pint:PI2155|5end_hypothetical_protein_2100664..2100894_POSITIVE 250 133 107 64 38 pint:PI1451|5end_outer_membrane_receptor_proteins,_tonB_dependent_(possibly_iron_transport_related)_1372931..1373161_POSITIVE 244 218 171 49 1 pint:PI0839|5end_conserved_hypothetical_protein_773843..774073_POSITIVE 241 240 194 199 157 pint:PI1386|5end_sugar_phosphate_isomerase_1307004..1307234_POSITIVE 241 238 193 220 168 pint:PI0753|5end_hypothetical_protein_683391..683621_POSITIVE 240 233 191 167 127 pint:PI1693|5end_possible_RmuC_domain_protein_1608183..1608413_POSITIVE 239 209 166 192 136 pint:PI1803|5end_conserved_hypothetical_protein_1735081..1735311_POSITIVE 239 208 184 87 62 pint:PI0434|5end_possible_beta-lactamase_405692..405922_POSITIVE 237 240 198 193 147 pint:PI1311|5end_large_protein_related_to_C.hutchinsonii_large_proteins_1226625..1226855_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 127 83 104 52 pint:PI0728|3end_integrase_661508..661658_POSITIVE 251 229 185 148 103 pint:PI0084|3end_conserved_hypothetical_protein_84520..84670_POSITIVE 244 218 171 53 5 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 237 240 198 93 47 pint:PI1309|3end_excinuclease_ABC,_A_subunit_1226605..1226755_POSITIVE 230 125 81 135 91 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 230 228 184 139 95 pint:PI1577|3end_conserved_hypothetical_protein_1503879..1504029_POSITIVE 230 216 186 73 47 pint:PI0999|3end_hypothetical_protein_922812..922962_POSITIVE 229 219 172 125 82 pint:PI0133|3end_hypothetical_protein_124632..124782_POSITIVE 227 240 195 133 89 pint:PI0864|3end_dihydrodipicolinate_synthase_801458..801608_POSITIVE 226 163 122 141 98 pint:PI1553|3end_hypothetical_protein_1470170..1470320_POSITIVE 225 240 203 83 48 pint:PI0753|3end_hypothetical_protein_683851..684001_POSITIVE 223 211 188 145 121 pint:PI1692|3end_alanine_racemase_1608248..1608398_POSITIVE 222 237 192 84 35 pint:PI1178|3end_histidyl-tRNA_synthetase_1100564..1100714_POSITIVE 220 236 196 54 14 pint:PI0317|3end_possible_kinase;_TPR_repeat?_300746..300896_POSITIVE 219 209 177 105 67 pint:PI1933|3end_hypothetical_protein_1880463..1880613_POSITIVE 219 229 193 148 112 pint:PI1452|3end_possible_nicotinamide_mononucleotide_transporter_1376062..1376212_POSITIVE 218 240 192 103 59 pint:PI0979|3end_transcriptional_regulator,_tetR_family_905678..905828_POSITIVE 217 232 193 145 100 pint:PI0710|3end_hypothetical_protein_648004..648154_POSITIVE 216 240 204 99 61 pint:PI1716|3end_hypothetical_protein_1632006..1632156_POSITIVE 216 217 179 151 114 pint:PI0491|3end_hypothetical_protein_451227..451377_POSITIVE