Origin IGS: acccctcgacgagaagaagagtacagcaaaaataagtgccataatatacaaccagttcatattgaactttggcatttttggcttgttgtttggattctgattgtccatttaattcatttgataaagataaataaaactgtttacgatgtggcaacagtctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagactgttgccacatcgtaaacagttttatttatctttatcaaatgaattaaatggacaatcagaatccaaacaacaagccaaaaatgccaaagttcaatatgaactggttgtatattatggcacttatttttgctgtactcttcttctcgtcgaggggt Mask Tandem Repeat Region ================================================ acccctcgacgagaagaagagtacagcaaaaataagtgccataatatacaaccagttcatattgaactttggcatttttggcttgttgtttggattctgattgtccatttaattcatttgataaagataaataaaactgtttacgatgtggcaacagtctta Find is-nt database================================================ Query_seq: PI1677:PI1678|PI1677:PI1678:cell division protein FtsH:conserved hypothetical protein:->->:1593862..1594023 162 acccctcgacgagaagaagagtacagcaaaaataagtgccataatatacaaccagttcatattgaactttggcatttttggcttgttgtttggattctgattgtccatttaattcatttgataaagataaataaaactgtttacgatgtggcaacagtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1677:PI1678|PI1677:PI1678:cell division protein FtsH:conserved hypothetical protein:->->:1593862..1594023 162 acccctcgacgagaagaagagtacagcaaaaataagtgccataatatacaaccagttcatattgaactttggcatttttggcttgttgtttggattctgattgtccatttaattcatttgataaagataaataaaactgtttacgatgtggcaacagtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1677:PI1678|PI1677:PI1678:cell division protein FtsH:conserved hypothetical protein:->->:1593862..1594023 162 acccctcgacgagaagaagagtacagcaaaaataagtgccataatatacaaccagttcatattgaactttggcatttttggcttgttgtttggattctgattgtccatttaattcatttgataaagataaataaaactgtttacgatgtggcaacagtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acccctcgacgagaagaagagtacagcaaaaataagtgccataatatacaaccagttcatattgaactttggcatttttggcttgttgtttggattctgattgtccatttaattcatttgataaagataaataaaactgtttacgatgtggcaacagtctta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 46 End: 162 ............................................. M Q P V H I E L W H F W L V V W I L I V H L I H L I K I N K T V Y D V A T V L Protein_Len: 52 Strand: - Start: 2 End: 157 . G E V L L L T C C F Y T G Y Y V V L E Y Q V K A N K A Q Q K S E S Q G N L E N S L S L Y F Q K R H P L M ..... Protein_Len: 36 Strand: - Start: 1 End: 108 G R S S F F L V A F I L A M I Y L W N M N F K P M K P K N N P N Q N D M ...................................................... acccctcgacgagaagaagagtacagcaaaaataagtgccataatatacaaccagttcatattgaactttggcatttttggcttgttgtttggattctgattgtccatttaattcatttgataaagataaataaaactgtttacgatgtggcaacagtctta 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================================================ acccctcgacgagaagaagagtacagcaaaaataagtgccataatatacaaccagttcatattgaactttggcatttttggcttgttgtttggattctgattgtccatttaattcatttgataaagataaataaaactgtttacgatgtggcaacagtctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1677:PI1678|PI1677:PI1678:cell division protein FtsH:conserved hypothetical protein:->->:1593862..1594023 162 acccctcgacgagaagaagagtacagcaaaaataagtgccataatatacaaccagttcatattgaactttggcatttttggcttgttgtttggattctgattgtccatttaattcatttgataaagataaataaaactgtttacgatgtggcaacagtctta Intra-Species Hit: Count: 1 Min: 1 Max: 162 Len: 162 Subject: pint_PI1677_PI1678|cell division protein FtsH:conserved hypothetical protein|POSITIVE:POSITIVE|[1593862,1594023]|162 HSP 1 e-value: 4.0E-87 bit: 321.0 Len: 162 Query Start:1 Query End:162 Subject Strand: POSITIVE Subject Start: 1 Subject End: 162 acccctcgacgagaagaagagtacagcaaaaataagtgccataatatacaaccagttcatattgaactttggcatttttggcttgttgtttggattctgattgtccatttaattcatttgataaagataaataaaactgtttacgatgtggcaacagtctta acccctcgacgagaagaagagtacagcaaaaataagtgccataatatacaaccagttcatattgaactttggcatttttggcttgttgtttggattctgattgtccatttaattcatttgataaagataaataaaactgtttacgatgtggcaacagtctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCCCUCGACGAGAAGAAGAGUACAGCAAAAAUAAGUGCCAUAAUAUACAACCAGUUCAUAUUGAACUUUGGCAUUUUUGGCUUGUUGUUUGGAUUCUGAUUGUCCAUUUAAUUCAUUUGAUAAAGAUAAAUAAAACUGUUUACGAUGUGGCAACAGUCUUA .......(((((..((((....(((((((....((((((((............(((((.....))))).)))))))).....))))))).....))))..)))))..........................(((.((((((..(.....)..)))))).))) (-32.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGACUGUUGCCACAUCGUAAACAGUUUUAUUUAUCUUUAUCAAAUGAAUUAAAUGGACAAUCAGAAUCCAAACAACAAGCCAAAAAUGCCAAAGUUCAAUAUGAACUGGUUGUAUAUUAUGGCACUUAUUUUUGCUGUACUCUUCUUCUCGUCGAGGGGU ((((((((((((......)).))))))))))............((((((......((((.........))))........((((((.((((...(((((.....)))))....)))).)).))))..)))))).......(((((((........))))))) (-31.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 40 1 80 37 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 267 105 61 191 142 pint:PI0309|5end_hypothetical_protein_291503..291733_POSITIVE 263 45 6 87 36 pint:PI2040|5end_conserved_hypothetical_protein;_possible_transporter_1993068..1993298_POSITIVE 261 120 79 200 155 pint:PI1166|5end_hypothetical_protein_1089305..1089535_POSITIVE 256 92 52 57 24 pint:PI0522|5end_50S_ribosomal_protein_L19_479004..479234_POSITIVE 253 99 52 182 123 pint:PI1945|5end_ribonuclease_HII_1901932..1902162_POSITIVE 253 42 2 225 169 pint:PI0025|5end_two_component_system_sensor_histidine_kinase_28682..28912_POSITIVE 252 43 1 53 6 pint:PI0647|5end_potassium_uptake_protein_587505..587735_POSITIVE 252 110 61 93 44 pint:PI0113|5end_arginyl-tRNA_synthetase_108371..108601_POSITIVE 247 108 79 91 67 pint:PI1602|5end_conserved_hypothetical_protein;_possible_internalin-related_protein_1531025..1531255_POSITIVE 247 107 67 61 11 pint:PI1549|5end_conserved_hypothetical_protein_1467021..1467251_POSITIVE 245 40 1 54 17 pint:PI1029|5end_seryl-tRNA_synthetase_945938..946168_POSITIVE 244 106 67 135 87 pint:PI1654|5end_hypothetical_protein_1567669..1567899_POSITIVE 240 54 15 122 85 pint:PI0152|5end_DNA_mismatch_endonuclease_vsr_145314..145544_POSITIVE 240 110 66 87 45 pint:PI0075|5end_uridine_kinase_73748..73978_POSITIVE 235 58 23 152 102 pint:PI0106|5end_ABC_transport_system,_ATP-binding/permease_101381..101611_POSITIVE 234 106 68 150 103 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 233 49 5 228 191 pint:PI0843|5end_carboxyl-terminal_protease_776145..776375_POSITIVE 229 57 11 162 119 pint:PI0349|5end_hypothetical_protein_323144..323374_POSITIVE 227 40 7 180 152 pint:PI1755|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1681930..1682160_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 106 69 147 113 pint:PI1855|3end_lipopolysaccharide_biosynthesis_protein_1803168..1803318_POSITIVE 280 47 5 91 49 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 256 92 52 34 1 pint:PI0521|3end_hypothetical_protein_479061..479211_POSITIVE 253 107 68 116 74 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 243 99 52 148 101 pint:PI1944|3end_hypothetical_protein_1901990..1902140_POSITIVE 239 107 68 44 2 pint:PI0881|3end_conserved_hypothetical_protein_815283..815433_POSITIVE 235 58 23 144 94 pint:PI0105|3end_possible_sulfatase_101453..101603_POSITIVE 229 90 48 140 105 pint:PI1796|3end_2-hydroxyhepta-2,4-diene-1,7-dioate_isomerase,_fumarylacetoacetate_hydrolase_family_protein_1731086..1731236_POSITIVE 229 57 11 149 106 pint:PI0348|3end_conserved_hypothetical_protein_323211..323361_POSITIVE 227 93 56 132 98 pint:PI0392|3end_possible_transcriptional_regulator_358735..358885_POSITIVE 225 110 78 98 65 pint:PI2071|3end_hypothetical_protein_2030308..2030458_POSITIVE 222 29 2 55 29 pint:PI0252|3end_conserved_hypothetical_protein_248383..248533_POSITIVE 222 115 71 74 28 pint:PI0245|3end_possible_mobilization_protein_244258..244408_POSITIVE 217 48 2 69 13 pint:PI0814|3end_conserved_hypothetical_protein_754426..754576_POSITIVE 216 89 50 131 98 pint:PI2152|3end_heptosyltransferase_2099296..2099446_POSITIVE 215 100 72 38 10 pint:PI0872|3end_hypothetical_protein_807807..807957_POSITIVE 215 100 72 146 118 pint:PI0871|3end_hypothetical_protein_807915..808065_POSITIVE 215 115 81 115 77 pint:PI0380|3end_conserved_hypothetical_protein_350541..350691_POSITIVE 213 99 54 67 17 pint:PI1997|3end_hypothetical_protein_1951884..1952034_POSITIVE 213 98 54 151 114 pint:PI0317|3end_possible_kinase;_TPR_repeat?_300746..300896_POSITIVE