Origin IGS: agcgtaatgatgatttaattagaatgtaaagttaatactttaaaacgagaccaacaactttttggtaaagaaaatgaaaagagggagccaaactccctctttcctatattctgctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagcagaatataggaaagagggagtttggctccctcttttcattttctttaccaaaaagttgttggtctcgttttaaagtattaactttacattctaattaaatcatcattacgct Mask Tandem Repeat Region ================================================ agcgtaatgatgatttaattagaatgtaaagttaatactttaaaacgagaccaacaactttttggtaaagaaaatgaaaagagggagccaaactccctctttcctatattctgctta Find is-nt database================================================ Query_seq: PI1420:PI1422|PI1420:PI1422:probable membrane protein:hypothetical protein:->->:1340713..1340829 117 agcgtaatgatgatttaattagaatgtaaagttaatactttaaaacgagaccaacaactttttggtaaagaaaatgaaaagagggagccaaactccctctttcctatattctgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1420:PI1422|PI1420:PI1422:probable membrane protein:hypothetical protein:->->:1340713..1340829 117 agcgtaatgatgatttaattagaatgtaaagttaatactttaaaacgagaccaacaactttttggtaaagaaaatgaaaagagggagccaaactccctctttcctatattctgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1420:PI1422|PI1420:PI1422:probable membrane protein:hypothetical protein:->->:1340713..1340829 117 agcgtaatgatgatttaattagaatgtaaagttaatactttaaaacgagaccaacaactttttggtaaagaaaatgaaaagagggagccaaactccctctttcctatattctgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcgtaatgatgatttaattagaatgtaaagttaatactttaaaacgagaccaacaactttttggtaaagaaaatgaaaagagggagccaaactccctctttcctatattctgctta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 18 End: 107 ................. N S H L T L V K F R S W C S K P L S F S F L S G F E R K G M .......... agcgtaatgatgatttaattagaatgtaaagttaatactttaaaacgagaccaacaactttttggtaaagaaaatgaaaagagggagccaaactccctctttcctatattctgctta 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================================================ agcgtaatgatgatttaattagaatgtaaagttaatactttaaaacgagaccaacaactttttggtaaagaaaatgaaaagagggagccaaactccctctttcctatattctgctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 93 HP_score: -10.3 Tail_Score: -3.95449 Start: 81 End: 99 Full_Region: TAAAGAAAATGAAAA GAGGGAG CCAAA CTCCCTC TTTCCTATATTCTGC ................................................................................GAGGGAGCCAAACTCCCTC.................. Find igs database================================================ Query_seq: PI1420:PI1422|PI1420:PI1422:probable membrane protein:hypothetical protein:->->:1340713..1340829 117 agcgtaatgatgatttaattagaatgtaaagttaatactttaaaacgagaccaacaactttttggtaaagaaaatgaaaagagggagccaaactccctctttcctatattctgctta Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: pint_PI1420_PI1422|probable membrane protein:hypothetical protein|POSITIVE:POSITIVE|[1340713,1340829]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 agcgtaatgatgatttaattagaatgtaaagttaatactttaaaacgagaccaacaactttttggtaaagaaaatgaaaagagggagccaaactccctctttcctatattctgctta agcgtaatgatgatttaattagaatgtaaagttaatactttaaaacgagaccaacaactttttggtaaagaaaatgaaaagagggagccaaactccctctttcctatattctgctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGUAAUGAUGAUUUAAUUAGAAUGUAAAGUUAAUACUUUAAAACGAGACCAACAACUUUUUGGUAAAGAAAAUGAAAAGAGGGAGCCAAACUCCCUCUUUCCUAUAUUCUGCUUA ..(((..((((......)))).....((((((....))))))..)))..(((((.......)))))..((((.(((.((((((((((.....))))))))))..))).))))..... (-26.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCAGAAUAUAGGAAAGAGGGAGUUUGGCUCCCUCUUUUCAUUUUCUUUACCAAAAAGUUGUUGGUCUCGUUUUAAAGUAUUAACUUUACAUUCUAAUUAAAUCAUCAUUACGCU ..(((.(((.((.((((((((((((.....)))))))))))))).)))...(((((.......))))).......((((((....)))))).......................))) (-28.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 110 70 106 50 pint:PI1314|5end_hypothetical_protein_1231188..1231418_POSITIVE 237 108 63 225 168 pint:PI0846|5end_transcription_regulator,_CRP_family_780435..780665_POSITIVE 233 106 61 155 116 pint:PI0781|5end_UDP-glucose/GDP-mannose_dehydrogenase_family;_probable__UDP-glucose_6-dehydrogenase_719260..719490_POSITIVE 232 100 51 231 165 pint:PI0161|5end_possible_TonB_receptor_153364..153594_POSITIVE 228 102 66 206 149 pint:PI0489|5end_probable_cardiolipin_synthetase_447610..447840_POSITIVE 227 109 61 138 87 pint:PI1018|5end_ISPg3-related_transposase,_N-terminal_region_937554..937784_POSITIVE 226 105 64 227 182 pint:PI1742|5end_SpoOJ_regulator_protein_1664826..1665056_POSITIVE 224 90 46 82 44 pint:PI1052|5end_fructose-1,6-bisphosphatase_970492..970722_POSITIVE 222 105 61 167 121 pint:PI0569|5end_phosphoglycerate_kinase_513297..513527_POSITIVE 219 97 57 53 1 pint:PI0257|5end_conjugative_transposon_protein,_TraF_249348..249578_POSITIVE 218 107 62 173 123 pint:PI0328|5end_conserved_hypothetical_protein_309476..309706_POSITIVE 212 90 44 142 103 pint:PI0189|5end_integrase_179623..179853_POSITIVE 211 84 46 32 4 pint:PI1408|5end_glucose-1-phosphate_thymidylyltransferase_1329055..1329285_POSITIVE 207 106 81 208 169 pint:PI1652|5end_hypothetical_protein_1564655..1564885_POSITIVE 205 86 45 104 48 pint:PI0861|5end_glucosamine--fructose-6-phosphate_aminotransferase_(glutamine-fructose-6-phosphate_transaminase_(isomerizing))_796346..796576_POSITIVE 205 110 61 78 29 pint:PI0124|5end_outer_membrane_protein/protective_antigen_OMA87_114487..114717_POSITIVE 204 90 58 90 63 pint:PI0042|5end_hypothetical_protein_42981..43211_POSITIVE 204 90 58 74 47 pint:PI0044|5end_thiamine_biosynthetic_enzyme_42965..43195_POSITIVE 203 108 72 188 151 pint:PI1768|5end_conserved_hypothetical_protein_1695456..1695686_POSITIVE 203 102 81 209 183 pint:PI0645|5end_hypothetical_protein_586419..586649_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 110 70 79 23 pint:PI1313|3end_possible_POT_family_(proton-dependent_oligopeptide_transport_family)_1231241..1231391_POSITIVE 239 110 61 60 3 pint:PI1828|3end_peptidase,_M23/M37_family,_C-terminal_1769089..1769239_POSITIVE 237 108 63 149 92 pint:PI0845|3end_peptidyl-dipeptidase_780439..780589_POSITIVE 233 105 64 57 23 pint:PI0282|3end_hypothetical_protein_266826..266976_POSITIVE 220 102 73 53 8 pint:PI0488|3end_conserved_hypothetical_protein_447537..447687_POSITIVE 218 105 62 89 49 pint:PI0846|3end_transcription_regulator,_CRP_family_781009..781159_POSITIVE 217 96 52 97 53 pint:PI0010|3end_conserved_hypothetical_protein_11679..11829_POSITIVE 214 88 46 129 92 pint:PI1475|3end_possible_short_chain_dehydrogenase_1397905..1398055_POSITIVE 212 90 44 109 70 pint:PI0188|3end_phosphomethylpyrimidine_kinase_179670..179820_POSITIVE 202 89 53 50 18 pint:PI1856|3end_nicotinate-nucleotide_adenylyltransferase_1803885..1804035_POSITIVE 202 109 74 57 5 pint:PI1370|3end_alkyl_hydroperoxide_reductase,_subunit_F_1292176..1292326_POSITIVE 202 105 73 61 14 pint:PI0160|3end_conserved_hypothetical_protein_153268..153418_POSITIVE 201 88 44 113 69 pint:PI1565|3end_conserved_hypothetical_protein;_possible_surface_antigen_1487357..1487507_POSITIVE 200 86 42 110 67 pint:PI0224|3end_conserved_hypothetical_protein_221979..222129_POSITIVE 199 110 74 73 28 pint:PI1602|3end_conserved_hypothetical_protein;_possible_internalin-related_protein_1533819..1533969_POSITIVE 198 90 44 81 32 pint:PI1921|3end_conserved_hypothetical_protein_1865100..1865250_POSITIVE 197 88 44 41 1 pint:PI1727|3end__ATP-dependent_Clp_protease,_ATP-binding_subunit_1646989..1647139_POSITIVE 195 84 45 89 50 pint:PI2035|3end_Holliday_junction_DNA_helicase_ruvB_1989323..1989473_POSITIVE 195 100 74 60 31 pint:PI0553|3end_recombination_protein_504383..504533_POSITIVE 192 94 69 111 85 pint:PI0281|3end_conserved_hypothetical_protein_266604..266754_POSITIVE