Origin IGS: ctctgccatctcctcaatataattgagttgaagcgaaagaagggcaaggaacgagagtcccattatgattgcaattgtccaaatcgtctttttattcatattatttacctacaacttacatagaaagcgttaaactacgcccacgtaatacttatatttgttttaactgaaagcaaaggtaatgaaattcttaagctattaacaatcaaaagttaattatcaccactttatttatttatattaactataaaatgaaattataattaatatttatcaatctaaaaggatgaaacagatgctaatattaccctaaaaagaacttaaaagaagaaaaatagccttcttttgatttgtaagttagtatagatttcatacaaaaatgcttatctttgcacgcattataaaaacagcagt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actgctgtttttataatgcgtgcaaagataagcatttttgtatgaaatctatactaacttacaaatcaaaagaaggctatttttcttcttttaagttctttttagggtaatattagcatctgtttcatccttttagattgataaatattaattataatttcattttatagttaatataaataaataaagtggtgataattaacttttgattgttaatagcttaagaatttcattacctttgctttcagttaaaacaaatataagtattacgtgggcgtagtttaacgctttctatgtaagttgtaggtaaataatatgaataaaaagacgatttggacaattgcaatcataatgggactctcgttccttgcccttctttcgcttcaactcaattatattgaggagatggcagag Mask Tandem Repeat Region ================================================ ctctgccatctcctcaatataattgagttgaagcgaaagaagggcaaggaacgagagtcccattatgattgcaattgtccaaatcgtctttttattcatattatttacctacaacttacatagaaagcgttaaactacgcccacgtaatacttatatttgttttaactgaaagcaaaggtaatgaaattcttaagctattaacaatcaaaagttaattatcaccactttatttatttatattaactataaaatgaaattataattaatatttatcaatctaaaaggatgaaacagatgctaatattaccctaaaaagaacttaaaagaagaaaaatagccttcttttgatttgtaagttagtatagatttcatacaaaaatgcttatctttgcacgcattataaaaacagcagt Find is-nt database================================================ Query_seq: PI1153:PI1154|PI1153:PI1154:histidine kinase sensor protein:conserved hypothetical protein; possible periplasmic solute-binding protein:->->:1078699..1079112 414 ctctgccatctcctcaatataattgagttgaagcgaaagaagggcaaggaacgagagtcccattatgattgcaattgtccaaatcgtctttttattcatattatttacctacaacttacatagaaagcgttaaactacgcccacgtaatacttatatttgttttaactgaaagcaaaggtaatgaaattcttaagctattaacaatcaaaagttaattatcaccactttatttatttatattaactataaaatgaaattataattaatatttatcaatctaaaaggatgaaacagatgctaatattaccctaaaaagaacttaaaagaagaaaaatagccttcttttgatttgtaagttagtatagatttcatacaaaaatgcttatctttgcacgcattataaaaacagcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1153:PI1154|PI1153:PI1154:histidine kinase sensor protein:conserved hypothetical protein; possible periplasmic solute-binding protein:->->:1078699..1079112 414 ctctgccatctcctcaatataattgagttgaagcgaaagaagggcaaggaacgagagtcccattatgattgcaattgtccaaatcgtctttttattcatattatttacctacaacttacatagaaagcgttaaactacgcccacgtaatacttatatttgttttaactgaaagcaaaggtaatgaaattcttaagctattaacaatcaaaagttaattatcaccactttatttatttatattaactataaaatgaaattataattaatatttatcaatctaaaaggatgaaacagatgctaatattaccctaaaaagaacttaaaagaagaaaaatagccttcttttgatttgtaagttagtatagatttcatacaaaaatgcttatctttgcacgcattataaaaacagcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1153:PI1154|PI1153:PI1154:histidine kinase sensor protein:conserved hypothetical protein; possible periplasmic solute-binding protein:->->:1078699..1079112 414 ctctgccatctcctcaatataattgagttgaagcgaaagaagggcaaggaacgagagtcccattatgattgcaattgtccaaatcgtctttttattcatattatttacctacaacttacatagaaagcgttaaactacgcccacgtaatacttatatttgttttaactgaaagcaaaggtaatgaaattcttaagctattaacaatcaaaagttaattatcaccactttatttatttatattaactataaaatgaaattataattaatatttatcaatctaaaaggatgaaacagatgctaatattaccctaaaaagaacttaaaagaagaaaaatagccttcttttgatttgtaagttagtatagatttcatacaaaaatgcttatctttgcacgcattataaaaacagcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctctgccatctcctcaatataattgagttgaagcgaaagaagggcaaggaacgagagtcccattatgattgcaattgtccaaatcgtctttttattcatattatttacctacaacttacatagaaagcgttaaactacgcccacgtaatacttatatttgttttaactgaaagcaaaggtaatgaaattcttaagctattaacaatcaaaagttaattatcaccactttatttatttatattaactataaaatgaaattataattaatatttatcaatctaaaaggatgaaacagatgctaatattaccctaaaaagaacttaaaagaagaaaaatagccttcttttgatttgtaagttagtatagatttcatacaaaaatgcttatctttgcacgcattataaaaacagcagt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 19 End: 120 .................. M I E L K R K K G K E R E S H Y D C N C P N R L F I H I I Y L Q L T ...................................................................................................................................................................................................................................................................................................... Protein_Len: 33 Strand: + Start: 69 End: 167 .................................................................... M Q L S K S S F Y S Y Y L P T T Y I E S V K L R P R N T Y I C F N ....................................................................................................................................................................................................................................................... Protein_Len: 33 Strand: - Start: 1 End: 99 E A M E E I Y N L Q L S L L A L F S L G M I I A I T W I T K K N M ........................................................................................................................................................................................................................................................................................................................... ctctgccatctcctcaatataattgagttgaagcgaaagaagggcaaggaacgagagtcccattatgattgcaattgtccaaatcgtctttttattcatattatttacctacaacttacatagaaagcgttaaactacgcccacgtaatacttatatttgttttaactgaaagcaaaggtaatgaaattcttaagctattaacaatcaaaagttaattatcaccactttatttatttatattaactataaaatgaaattataattaatatttatcaatctaaaaggatgaaacagatgctaatattaccctaaaaagaacttaaaagaagaaaaatagccttcttttgatttgtaagttagtatagatttcatacaaaaatgcttatctttgcacgcattataaaaacagcagt 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================================================ ctctgccatctcctcaatataattgagttgaagcgaaagaagggcaaggaacgagagtcccattatgattgcaattgtccaaatcgtctttttattcatattatttacctacaacttacatagaaagcgttaaactacgcccacgtaatacttatatttgttttaactgaaagcaaaggtaatgaaattcttaagctattaacaatcaaaagttaattatcaccactttatttatttatattaactataaaatgaaattataattaatatttatcaatctaaaaggatgaaacagatgctaatattaccctaaaaagaacttaaaagaagaaaaatagccttcttttgatttgtaagttagtatagatttcatacaaaaatgcttatctttgcacgcattataaaaacagcagt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 51 HP_score: -2.6 Tail_Score: -3.99228 Start: 321 End: 349 Full_Region: TACCCTAAAAAGAAC TTAAAAGAAG AAAAATAGC CTTCTTTTGA TTTGTAAGTTAGTAT ................................................................................................................................................................................................................................................................................................................................TTAAAAGAAGAAAAATAGCCTTCTTTTGA................................................................. Find igs database================================================ Query_seq: PI1153:PI1154|PI1153:PI1154:histidine kinase sensor protein:conserved hypothetical protein; possible periplasmic solute-binding protein:->->:1078699..1079112 414 ctctgccatctcctcaatataattgagttgaagcgaaagaagggcaaggaacgagagtcccattatgattgcaattgtccaaatcgtctttttattcatattatttacctacaacttacatagaaagcgttaaactacgcccacgtaatacttatatttgttttaactgaaagcaaaggtaatgaaattcttaagctattaacaatcaaaagttaattatcaccactttatttatttatattaactataaaatgaaattataattaatatttatcaatctaaaaggatgaaacagatgctaatattaccctaaaaagaacttaaaagaagaaaaatagccttcttttgatttgtaagttagtatagatttcatacaaaaatgcttatctttgcacgcattataaaaacagcagt Intra-Species Hit: Count: 1 Min: 1 Max: 414 Len: 414 Subject: pint_PI1153_PI1154|histidine kinase sensor protein:conserved hypothetical protein; possible periplasmic solute-binding protein|POSITIVE:POSITIVE|[1078699,1079112]|414 HSP 1 e-value: 1.0E-116 bit: 420.0 Len: 212 Query Start:1 Query End:212 Subject Strand: POSITIVE Subject Start: 1 Subject End: 212 ctctgccatctcctcaatataattgagttgaagcgaaagaagggcaaggaacgagagtcccattatgattgcaattgtccaaatcgtctttttattcatattatttacctacaacttacatagaaagcgttaaactacgcccacgtaatacttatatttgttttaactgaaagcaaaggtaatgaaattcttaagctattaacaatcaaaag.......................................................................................................................................................................................................... ctctgccatctcctcaatataattgagttgaagcgaaagaagggcaaggaacgagagtcccattatgattgcaattgtccaaatcgtctttttattcatattatttacctacaacttacatagaaagcgttaaactacgcccacgtaatacttatatttgttttaactgaaagcaaaggtaatgaaattcttaagctattaacaatcaaaag.......................................................................................................................................................................................................... HSP 2 e-value: 1.0E-73 bit: 278.0 Len: 140 Query Start:275 Query End:414 Subject Strand: POSITIVE Subject Start: 275 Subject End: 414 ..................................................................................................................................................................................................................................................................................caatctaaaaggatgaaacagatgctaatattaccctaaaaagaacttaaaagaagaaaaatagccttcttttgatttgtaagttagtatagatttcatacaaaaatgcttatctttgcacgcattataaaaacagcagt ..................................................................................................................................................................................................................................................................................caatctaaaaggatgaaacagatgctaatattaccctaaaaagaacttaaaagaagaaaaatagccttcttttgatttgtaagttagtatagatttcatacaaaaatgcttatctttgcacgcattataaaaacagcagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUGCCAUCUCCUCAAUAUAAUUGAGUUGAAGCGAAAGAAGGGCAAGGAACGAGAGUCCCAUUAUGAUUGCAAUUGUCCAAAUCGUCUUUUUAUUCAUAUUAUUUACCUACAACUUACAUAGAAAGCGUUAAACUACGCCCACGUAAUACUUAUAUUUGUUUUAACUGAAAGCAAAGGUAAUGAAAUUCUUAAGCUAUUAACAAUCAAAAGUUAAUUAUCACCACUUUAUUUAUUUAUAUUAACUAUAAAAUGAAAUUAUAAUUAAUAUUUAUCAAUCUAAAAGGAUGAAACAGAUGCUAAUAUUACCCUAAAAAGAACUUAAAAGAAGAAAAAUAGCCUUCUUUUGAUUUGUAAGUUAGUAUAGAUUUCAUACAAAAAUGCUUAUCUUUGCACGCAUUAUAAAAACAGCAGU ..((((..((..((((((...))))))..)).((((((((..((((.((.((....)).))..(((((.(((((((...((((((.((((((((................................((((......))))....((((((.((((((((((((((............(((.((((.............(((((........))))))))).))).(((((((.((..(((((((.(((((.......))))).)))))))..)).)))...))))..))))))))))).)))))))))..))))))))....((((((((.........))))))))))))))..)))).)))......)))))......))))..)))))...)))............)))). (-74.51) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGCUGUUUUUAUAAUGCGUGCAAAGAUAAGCAUUUUUGUAUGAAAUCUAUACUAACUUACAAAUCAAAAGAAGGCUAUUUUUCUUCUUUUAAGUUCUUUUUAGGGUAAUAUUAGCAUCUGUUUCAUCCUUUUAGAUUGAUAAAUAUUAAUUAUAAUUUCAUUUUAUAGUUAAUAUAAAUAAAUAAAGUGGUGAUAAUUAACUUUUGAUUGUUAAUAGCUUAAGAAUUUCAUUACCUUUGCUUUCAGUUAAAACAAAUAUAAGUAUUACGUGGGCGUAGUUUAACGCUUUCUAUGUAAGUUGUAGGUAAAUAAUAUGAAUAAAAAGACGAUUUGGACAAUUGCAAUCAUAAUGGGACUCUCGUUCCUUGCCCUUCUUUCGCUUCAACUCAAUUAUAUUGAGGAGAUGGCAGAG .((((((((((..((((((((((((((((....))))))))))).......................(((((((((.......)))))))))((((.......((((((......(((..(((((.(((.((((..(((.(((.(((((((((((((.......))))))))))))).........((((..(((((((((.....)))))))))...))))..........((((((.(((((...(((......)))..)))))((((((((((((......))))...)))))))).....))))))....))).)))...)))).)))..)))))..))).........(((((....))))).))))))......))))...........)))))..)))))))))).. (-87.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 78 38 74 30 pint:PI1781|5end_membrane-associated_zinc_metalloprotease_1713074..1713304_POSITIVE 305 50 1 61 9 pint:PI1323|5end_conserved_hypothetical_protein_1241810..1242040_POSITIVE 298 68 32 108 62 pint:PI1542|5end_mobilization_protein_1461728..1461958_POSITIVE 286 90 42 103 58 pint:PI0727|5end_integrase_659261..659491_POSITIVE 275 50 9 68 19 pint:PI0253|5end_conjugative_transposon_protein,_TraD_248294..248524_POSITIVE 273 60 24 182 132 pint:PI0272|5end_conserved_hypothetical_protein_262621..262851_POSITIVE 267 89 41 218 164 pint:PI1707|5end_GTP-binding_protein_1623795..1624025_POSITIVE 266 87 42 138 90 pint:PI1541|5end_hypothetical_protein_1461604..1461834_POSITIVE 265 50 2 63 12 pint:PI0949|5end_endonuclease_882264..882494_POSITIVE 265 80 33 79 36 pint:PI0861|5end_glucosamine--fructose-6-phosphate_aminotransferase_(glutamine-fructose-6-phosphate_transaminase_(isomerizing))_796346..796576_POSITIVE 263 57 17 130 89 pint:PI2140|5end_conserved_hypothetical_protein_2086773..2087003_POSITIVE 263 64 23 76 36 pint:PI1816|5end_acid_phosphatase_1754646..1754876_POSITIVE 262 400 351 145 91 pint:PI1779|5end_16S_rRNA_processing_protein_1711335..1711565_POSITIVE 262 90 41 64 24 pint:PI0051|5end_hypothetical_protein_52607..52837_POSITIVE 261 60 12 96 39 pint:PI2172|5end_hypothetical_protein_2113819..2114049_POSITIVE 261 60 12 72 15 pint:PI2173|5end_hypothetical_protein_2113795..2114025_POSITIVE 261 50 21 143 113 pint:PI2018|5end_50S_ribosomal_protein_L34_1975757..1975987_POSITIVE 261 59 11 89 46 pint:PI0451|5end_serine_proteases,__S51_group_424343..424573_POSITIVE 259 88 42 214 156 pint:PI0275|5end_hypothetical_protein_263138..263368_POSITIVE 253 79 32 119 63 pint:PI0223|5end_topoisomerase_IA_218377..218607_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 68 32 71 25 pint:PI1540|3end_hypothetical_protein_1461771..1461921_POSITIVE 275 50 9 77 28 pint:PI0252|3end_conserved_hypothetical_protein_248383..248533_POSITIVE 273 336 292 105 48 pint:PI2055|3end_hypothetical_protein_2013405..2013555_POSITIVE 265 61 24 128 92 pint:PI2075|3end_conserved_hypothetical_protein_2035355..2035505_POSITIVE 264 89 41 80 28 pint:PI0743|3end_hypothetical_protein_673026..673176_POSITIVE 262 400 351 129 75 pint:PI1778|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1711399..1711549_POSITIVE 262 90 41 92 52 pint:PI0052|3end_hypothetical_protein_52715..52865_POSITIVE 262 90 41 48 8 pint:PI0050|3end_conserved_hypothetical_protein_52671..52821_POSITIVE 258 89 41 109 52 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 257 62 22 102 58 pint:PI0199|3end_phosphate_acetyltransferase_190923..191073_POSITIVE 255 78 33 143 103 pint:PI1973|3end_conserved_hypothetical_protein_1931171..1931321_POSITIVE 254 79 31 112 54 pint:PI0058|3end_conserved_hypothetical_protein_57044..57194_POSITIVE 253 79 32 104 48 pint:PI0222|3end_conserved_hypothetical_protein_218442..218592_POSITIVE 252 85 42 58 27 pint:PI1766|3end_sugar_transporter,_possible_glucose/galactose_transporter_1694350..1694500_POSITIVE 248 90 43 140 93 pint:PI0114|3end_hypothetical_protein_108527..108677_POSITIVE 246 87 43 39 7 pint:PI0266|3end_DNA_primase_(bacterial_type)_258802..258952_POSITIVE 243 74 32 53 6 pint:PI1730|3end_hypothetical_protein_1650367..1650517_POSITIVE 242 90 44 47 2 pint:PI0645|3end_hypothetical_protein_586807..586957_POSITIVE 240 79 32 111 65 pint:PI0964|3end_conserved_hypothetical_protein_894187..894337_POSITIVE 239 89 51 81 39 pint:PI2103|3end_hypothetical_protein_2057934..2058084_POSITIVE