Origin IGS: aggtgcgtcttttgcgatatattaacattttaaacatttattacaaatttaaatcctaataaatgaggataaactattgacagcttgcataaatttaactatctttgcccccataaggttaataattgaaattattataataaaaaaacatatcacaatgaatctgcgaaagcttacatcatggtttcccgaactgacttatcgccaaaaggtggtatcgcttgttatatcgggtgtcattgtgggattaggaggattgtttttctatcttctgcgtatgcacacttatatt .........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 aatataagtgtgcatacgcagaagatagaaaaacaatcctcctaatcccacaatgacacccgatataacaagcgataccaccttttggcgataagtcagttcgggaaaccatgatgtaagctttcgcagattcattgtgatatgtttttttattataataatttcaattattaaccttatgggggcaaagatagttaaatttatgcaagctgtcaatagtttatcctcatttattaggatttaaatttgtaataaatgtttaaaatgttaatatatcgcaaaagacgcacct Mask Tandem Repeat Region ================================================ aggtgcgtcttttgcgatatattaacattttaaacatttattacaaatttaaatcctaataaatgaggataaactattgacagcttgcataaatttaactatctttgcccccataaggttaataattgaaattattataataaaaaaacatatcacaatgaatctgcgaaagcttacatcatggtttcccgaactgacttatcgccaaaaggtggtatcgcttgttatatcgggtgtcattgtgggattaggaggattgtttttctatcttctgcgtatgcacacttatatt Find is-nt database================================================ Query_seq: PI1007:PI1008|PI1007:PI1008:conserved hypothetical protein:cytochrome c nitrite reductase, small subunit:->->:928632..928923 292 aggtgcgtcttttgcgatatattaacattttaaacatttattacaaatttaaatcctaataaatgaggataaactattgacagcttgcataaatttaactatctttgcccccataaggttaataattgaaattattataataaaaaaacatatcacaatgaatctgcgaaagcttacatcatggtttcccgaactgacttatcgccaaaaggtggtatcgcttgttatatcgggtgtcattgtgggattaggaggattgtttttctatcttctgcgtatgcacacttatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1007:PI1008|PI1007:PI1008:conserved hypothetical protein:cytochrome c nitrite reductase, small subunit:->->:928632..928923 292 aggtgcgtcttttgcgatatattaacattttaaacatttattacaaatttaaatcctaataaatgaggataaactattgacagcttgcataaatttaactatctttgcccccataaggttaataattgaaattattataataaaaaaacatatcacaatgaatctgcgaaagcttacatcatggtttcccgaactgacttatcgccaaaaggtggtatcgcttgttatatcgggtgtcattgtgggattaggaggattgtttttctatcttctgcgtatgcacacttatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1007:PI1008|PI1007:PI1008:conserved hypothetical protein:cytochrome c nitrite reductase, small subunit:->->:928632..928923 292 aggtgcgtcttttgcgatatattaacattttaaacatttattacaaatttaaatcctaataaatgaggataaactattgacagcttgcataaatttaactatctttgcccccataaggttaataattgaaattattataataaaaaaacatatcacaatgaatctgcgaaagcttacatcatggtttcccgaactgacttatcgccaaaaggtggtatcgcttgttatatcgggtgtcattgtgggattaggaggattgtttttctatcttctgcgtatgcacacttatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggtgcgtcttttgcgatatattaacattttaaacatttattacaaatttaaatcctaataaatgaggataaactattgacagcttgcataaatttaactatctttgcccccataaggttaataattgaaattattataataaaaaaacatatcacaatgaatctgcgaaagcttacatcatggtttcccgaactgacttatcgccaaaaggtggtatcgcttgttatatcgggtgtcattgtgggattaggaggattgtttttctatcttctgcgtatgcacacttatatt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 178 End: 291 ................................................................................................................................................................................. M M V S R T D L S P K G G I A C Y I G C H C G I R R I V F L S S A Y A H L Y . Protein_Len: 60 Strand: + Start: 53 End: 292 .................................................... M L I N E D K L L T A C I N L T I F A P I R L I I E I I I I K K H I T M N L R K L T S W F P E L T Y R Q K V V S L V I S Protein_Len: 36 Strand: - Start: 52 End: 159 ................................................... I R I F S S L S N V A Q M F K V I K A G M L N I I S I I I I F F C I V M ..................................................................................................................................... aggtgcgtcttttgcgatatattaacattttaaacatttattacaaatttaaatcctaataaatgaggataaactattgacagcttgcataaatttaactatctttgcccccataaggttaataattgaaattattataataaaaaaacatatcacaatgaatctgcgaaagcttacatcatggtttcccgaactgacttatcgccaaaaggtggtatcgcttgttatatcgggtgtcattgtgggattaggaggattgtttttctatcttctgcgtatgcacacttatatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 76 End: 105 ...........................................................................ATTGACAGCTTGCATAAATTTAACTATCTT........................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 134 End: 163 .....................................................................................................................................ATTCATTGTGATATGTTTTTTTATTATAAT................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggtgcgtcttttgcgatatattaacattttaaacatttattacaaatttaaatcctaataaatgaggataaactattgacagcttgcataaatttaactatctttgcccccataaggttaataattgaaattattataataaaaaaacatatcacaatgaatctgcgaaagcttacatcatggtttcccgaactgacttatcgccaaaaggtggtatcgcttgttatatcgggtgtcattgtgggattaggaggattgtttttctatcttctgcgtatgcacacttatatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1007:PI1008|PI1007:PI1008:conserved hypothetical protein:cytochrome c nitrite reductase, small subunit:->->:928632..928923 292 aggtgcgtcttttgcgatatattaacattttaaacatttattacaaatttaaatcctaataaatgaggataaactattgacagcttgcataaatttaactatctttgcccccataaggttaataattgaaattattataataaaaaaacatatcacaatgaatctgcgaaagcttacatcatggtttcccgaactgacttatcgccaaaaggtggtatcgcttgttatatcgggtgtcattgtgggattaggaggattgtttttctatcttctgcgtatgcacacttatatt Intra-Species Hit: Count: 1 Min: 1 Max: 292 Len: 292 Subject: pint_PI1007_PI1008|conserved hypothetical protein:cytochrome c nitrite reductase, small subunit|POSITIVE:POSITIVE|[928632,928923]|292 HSP 1 e-value: 1.0E-152 bit: 537.0 Len: 292 Query Start:1 Query End:292 Subject Strand: POSITIVE Subject Start: 1 Subject End: 292 aggtgcgtcttttgcgatatattaacattttaaacatttattacaaatttaaatcctaataaatgaggataaactattgacagcttgcataaatttaactatctttgcccccataaggttaataattgaaattattataatnnnnnnncatatcacaatgaatctgcgaaagcttacatcatggtttcccgaactgacttatcgccaaaaggtggtatcgcttgttatatcgggtgtcattgtgggattaggaggattgtttttctatcttctgcgtatgcacacttatatt aggtgcgtcttttgcgatatattaacattttaaacatttattacaaatttaaatcctaataaatgaggataaactattgacagcttgcataaatttaactatctttgcccccataaggttaataattgaaattattataataaaaaaacatatcacaatgaatctgcgaaagcttacatcatggtttcccgaactgacttatcgccaaaaggtggtatcgcttgttatatcgggtgtcattgtgggattaggaggattgtttttctatcttctgcgtatgcacacttatatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUGCGUCUUUUGCGAUAUAUUAACAUUUUAAACAUUUAUUACAAAUUUAAAUCCUAAUAAAUGAGGAUAAACUAUUGACAGCUUGCAUAAAUUUAACUAUCUUUGCCCCCAUAAGGUUAAUAAUUGAAAUUAUUAUAAUAAAAAAACAUAUCACAAUGAAUCUGCGAAAGCUUACAUCAUGGUUUCCCGAACUGACUUAUCGCCAAAAGGUGGUAUCGCUUGUUAUAUCGGGUGUCAUUGUGGGAUUAGGAGGAUUGUUUUUCUAUCUUCUGCGUAUGCACACUUAUAUU ..((((((....(((.....................(((((((.........(((((........)))))....(((((((.....(((................))).........))))))).............)))))))........(((((((((....((....))..............(((((..((((.(((((((....)))))))......))))..)))))..))))))))).....(((((((.(.....).)))))))))).))))))......... (-58.03) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUAAGUGUGCAUACGCAGAAGAUAGAAAAACAAUCCUCCUAAUCCCACAAUGACACCCGAUAUAACAAGCGAUACCACCUUUUGGCGAUAAGUCAGUUCGGGAAACCAUGAUGUAAGCUUUCGCAGAUUCAUUGUGAUAUGUUUUUUUAUUAUAAUAAUUUCAAUUAUUAACCUUAUGGGGGCAAAGAUAGUUAAAUUUAUGCAAGCUGUCAAUAGUUUAUCCUCAUUUAUUAGGAUUUAAAUUUGUAAUAAAUGUUUAAAAUGUUAAUAUAUCGCAAAAGACGCACCU .......((((((....((....((((((........(((((......((((((((....(((......((((..(((......(((((.....)))))...((....)).....))).))))))).....))))))))................(((((((....))))))).......)))))....(((((((...........))))))).....))))))..(((((((((.((.......)).)))))))))...................))....).))))).. (-56.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 250 202 215 162 pint:PI1744|5end_chromosome_partitioning_protein_1665635..1665865_POSITIVE 342 239 193 87 38 pint:PI0945|5end_sodium:solute_symporter_family_protein_876249..876479_POSITIVE 310 278 231 55 9 pint:PI0230|5end_hypothetical_protein_228590..228820_POSITIVE 303 246 202 39 3 pint:PI0690|5end_uracil_permease_626025..626255_POSITIVE 301 211 172 73 33 pint:PI1640|5end_hypothetical_protein_1558062..1558292_POSITIVE 301 220 171 158 98 pint:PI1039|5end_conserved_hypothetical_protein_957721..957951_POSITIVE 296 260 211 76 25 pint:PI1895|5end_penicillin-binding_protein_2_1838460..1838690_POSITIVE 295 197 154 133 87 pint:PI1381|5end_conserved_hypothetical_protein_1303060..1303290_POSITIVE 292 252 211 199 150 pint:PI0490|5end_DNA_primase_449070..449300_POSITIVE 291 236 199 35 4 pint:PI1937|5end_hypothetical_protein_1889411..1889641_POSITIVE 289 289 241 150 95 pint:PI1635|5end_hypothetical_protein_1553948..1554178_POSITIVE 288 285 258 47 21 pint:PI1312|5end_conserved_hypothetical_protein_1228851..1229081_POSITIVE 282 237 193 70 23 pint:PI0577|5end_conserved_hypothetical_protein_521811..522041_POSITIVE 281 233 194 209 166 pint:PI1626|5end_hypothetical_protein_1550194..1550424_POSITIVE 281 247 204 49 17 pint:PI0805|5end_conserved_hypothetical_protein_742729..742959_POSITIVE 280 226 185 72 35 pint:PI1832|5end_conserved_hypothetical_protein_1773161..1773391_POSITIVE 275 258 211 106 59 pint:PI1432|5end_DNA_methylase_1353011..1353241_POSITIVE 275 246 204 114 74 pint:PI0264|5end_transfer_region-related_protein,_TraN_256494..256724_POSITIVE 274 240 194 223 175 pint:PI1185|5end_hypothetical_protein_1106076..1106306_POSITIVE 274 238 191 70 27 pint:PI0572|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_516382..516612_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 394 206 165 73 28 pint:PI0634|3end_conserved_hypothetical_protein_581121..581271_POSITIVE 346 236 191 143 95 pint:PI2041|3end_conserved_hypothetical_protein_1994660..1994810_POSITIVE 310 191 163 49 22 pint:PI1649|3end_hypothetical_protein_1563441..1563591_POSITIVE 301 211 172 64 24 pint:PI1639|3end_conserved_hypothetical_protein_1558133..1558283_POSITIVE 301 220 171 106 46 pint:PI1037|3end_probable_methyltransferase_957749..957899_POSITIVE 291 236 199 32 1 pint:PI1936|3end_conserved_hypothetical_protein;_possible_serine-type_protease_1889488..1889638_POSITIVE 288 257 211 65 4 pint:PI0247|3end_conjugative_transposon_protein,_TraA_246232..246382_POSITIVE 286 278 232 94 52 pint:PI2113|3end_hypothetical_protein_2064278..2064428_POSITIVE 285 220 172 124 85 pint:PI0428|3end_hypothetical_protein_396321..396471_POSITIVE 284 207 165 113 79 pint:PI1730|3end_hypothetical_protein_1650367..1650517_POSITIVE 280 219 171 108 50 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 277 246 202 95 46 pint:PI1794|3end_conserved_hypothetical_protein_1726696..1726846_POSITIVE 274 238 191 57 14 pint:PI0571|3end_conserved_hypothetical_protein;_possible_permease_516449..516599_POSITIVE 273 222 182 118 66 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 272 215 180 140 105 pint:PI1833|3end_bacterioferritin_comigratory_protein_1774495..1774645_POSITIVE 270 290 242 60 10 pint:PI0914|3end_ATPase,_AAA_family_844992..845142_POSITIVE 270 248 211 149 108 pint:PI0489|3end_probable_cardiolipin_synthetase_449108..449258_POSITIVE 269 244 202 57 17 pint:PI0758|3end_hypothetical_protein_690506..690656_POSITIVE 267 277 238 65 10 pint:PI0742|3end_hypothetical_protein_672749..672899_POSITIVE 266 206 172 111 74 pint:PI0813|3end_conserved_hypothetical_protein_752938..753088_POSITIVE