Origin IGS: ttttcttgttcgttacattatattcttatttattcttttcaaaagaaaaaagaaaatagtagtatgataggctgtggatagcgtttataagttttttatcaattccttgcatatttggttatcaactcgtgaataaaagttatccacacttctatgctttgctttattattgatattcaacctatattagcagttatccacatttccactctatcctgcaaagataataagtttatatcttttatcttacaaaagctgtgtaaaacttctataaaagcacgttaataactctgtgtttatcctctataactttgttccgtcttgtttgttgtggataagtcggaggttattttaaagttattaaccgagttatccataaagttatccacatttgaaaattctcaatgcctacttttcaacaataaaaagaaaagtcgtttctaccaataagcttctattgaatacgaattatcacttta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaagtgataattcgtattcaatagaagcttattggtagaaacgacttttctttttattgttgaaaagtaggcattgagaattttcaaatgtggataactttatggataactcggttaataactttaaaataacctccgacttatccacaacaaacaagacggaacaaagttatagaggataaacacagagttattaacgtgcttttatagaagttttacacagcttttgtaagataaaagatataaacttattatctttgcaggatagagtggaaatgtggataactgctaatataggttgaatatcaataataaagcaaagcatagaagtgtggataacttttattcacgagttgataaccaaatatgcaaggaattgataaaaaacttataaacgctatccacagcctatcatactactattttcttttttcttttgaaaagaataaataagaatataatgtaacgaacaagaaaa Mask Tandem Repeat Region ================================================ ttttcttgttcgttacattatattcttatttattcttttcaaaagaaaaaagaaaatagtagtatgataggctgtggatagcgtttataagttttttatcaattccttgcatatttggttatcaactcgtgaataaaagttatccacacttctatgctttgctttattattgatattcaacctatattagcagttatccacatttccactctatcctgcaaagataataagtttatatcttttatcttacaaaagctgtgtaaaacttctataaaagcacgttaataactctgtgtttatcctctataactttgttccgtcttgtttgttgtggataagtcggaggttattttaaagttattaaccgagttatccataaagttatccacatttgaaaattctcaatgcctacttttcaacaataaaaagaaaagtcgtttctaccaataagcttctattgaatacgaattatcacttta Find is-nt database================================================ Query_seq: PI0002:PI0003|PI0002:PI0003:conserved hypothetical protein:pseudouridylate synthase:->->:3931..4409 479 ttttcttgttcgttacattatattcttatttattcttttcaaaagaaaaaagaaaatagtagtatgataggctgtggatagcgtttataagttttttatcaattccttgcatatttggttatcaactcgtgaataaaagttatccacacttctatgctttgctttattattgatattcaacctatattagcagttatccacatttccactctatcctgcaaagataataagtttatatcttttatcttacaaaagctgtgtaaaacttctataaaagcacgttaataactctgtgtttatcctctataactttgttccgtcttgtttgttgtggataagtcggaggttattttaaagttattaaccgagttatccataaagttatccacatttgaaaattctcaatgcctacttttcaacaataaaaagaaaagtcgtttctaccaataagcttctattgaatacgaattatcacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0002:PI0003|PI0002:PI0003:conserved hypothetical protein:pseudouridylate synthase:->->:3931..4409 479 ttttcttgttcgttacattatattcttatttattcttttcaaaagaaaaaagaaaatagtagtatgataggctgtggatagcgtttataagttttttatcaattccttgcatatttggttatcaactcgtgaataaaagttatccacacttctatgctttgctttattattgatattcaacctatattagcagttatccacatttccactctatcctgcaaagataataagtttatatcttttatcttacaaaagctgtgtaaaacttctataaaagcacgttaataactctgtgtttatcctctataactttgttccgtcttgtttgttgtggataagtcggaggttattttaaagttattaaccgagttatccataaagttatccacatttgaaaattctcaatgcctacttttcaacaataaaaagaaaagtcgtttctaccaataagcttctattgaatacgaattatcacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0002:PI0003|PI0002:PI0003:conserved hypothetical protein:pseudouridylate synthase:->->:3931..4409 479 ttttcttgttcgttacattatattcttatttattcttttcaaaagaaaaaagaaaatagtagtatgataggctgtggatagcgtttataagttttttatcaattccttgcatatttggttatcaactcgtgaataaaagttatccacacttctatgctttgctttattattgatattcaacctatattagcagttatccacatttccactctatcctgcaaagataataagtttatatcttttatcttacaaaagctgtgtaaaacttctataaaagcacgttaataactctgtgtttatcctctataactttgttccgtcttgtttgttgtggataagtcggaggttattttaaagttattaaccgagttatccataaagttatccacatttgaaaattctcaatgcctacttttcaacaataaaaagaaaagtcgtttctaccaataagcttctattgaatacgaattatcacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcttgttcgttacattatattcttatttattcttttcaaaagaaaaaagaaaatagtagtatgataggctgtggatagcgtttataagttttttatcaattccttgcatatttggttatcaactcgtgaataaaagttatccacacttctatgctttgctttattattgatattcaacctatattagcagttatccacatttccactctatcctgcaaagataataagtttatatcttttatcttacaaaagctgtgtaaaacttctataaaagcacgttaataactctgtgtttatcctctataactttgttccgtcttgtttgttgtggataagtcggaggttattttaaagttattaaccgagttatccataaagttatccacatttgaaaattctcaatgcctacttttcaacaataaaaagaaaagtcgtttctaccaataagcttctattgaatacgaattatcacttta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 72 End: 170 ....................................................................... M W I A F I S F L S I P C I F G Y Q L V N K S Y P H F Y A L L Y Y ..................................................................................................................................................................................................................................................................................................................... Protein_Len: 50 Strand: + Start: 133 End: 282 .................................................................................................................................... M K V I H T S M L C F I I D I Q P I L A V I H I S T L S C K D N K F I S F I L Q K L C K T S I K A R ..................................................................................................................................................................................................... Protein_Len: 42 Strand: + Start: 322 End: 447 ................................................................................................................................................................................................................................................................................................................................. M F V V D K S E V I L K L L T E L S I K L S T F E N S Q C L L F N N K K K S R F Y Q ................................ Protein_Len: 30 Strand: - Start: 300 End: 389 ........................................................................................................................................................................................................................................................................................................... G R Y S Q E T K N T T S L D S T I K F N N V S N D M F N D M .......................................................................................... Protein_Len: 31 Strand: - Start: 180 End: 272 ................................................................................................................................................................................... G I N A T I W M E V R D Q L S L L N I D K I K C F S H L V E M ............................................................................................................................................................................................................... Protein_Len: 31 Strand: - Start: 88 End: 180 ....................................................................................... L N K I L E K C I Q N D V R S Y F N D V S R H K A K N N I N M ........................................................................................................................................................................................................................................................................................................... ttttcttgttcgttacattatattcttatttattcttttcaaaagaaaaaagaaaatagtagtatgataggctgtggatagcgtttataagttttttatcaattccttgcatatttggttatcaactcgtgaataaaagttatccacacttctatgctttgctttattattgatattcaacctatattagcagttatccacatttccactctatcctgcaaagataataagtttatatcttttatcttacaaaagctgtgtaaaacttctataaaagcacgttaataactctgtgtttatcctctataactttgttccgtcttgtttgttgtggataagtcggaggttattttaaagttattaaccgagttatccataaagttatccacatttgaaaattctcaatgcctacttttcaacaataaaaagaaaagtcgtttctaccaataagcttctattgaatacgaattatcacttta 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: 83 Start: 224 End: 253 ...............................................................................................................................................................................................................................TTTGTAAGATAAAAGATATAAACTTATTAT.................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttcttgttcgttacattatattcttatttattcttttcaaaagaaaaaagaaaatagtagtatgataggctgtggatagcgtttataagttttttatcaattccttgcatatttggttatcaactcgtgaataaaagttatccacacttctatgctttgctttattattgatattcaacctatattagcagttatccacatttccactctatcctgcaaagataataagtttatatcttttatcttacaaaagctgtgtaaaacttctataaaagcacgttaataactctgtgtttatcctctataactttgttccgtcttgtttgttgtggataagtcggaggttattttaaagttattaaccgagttatccataaagttatccacatttgaaaattctcaatgcctacttttcaacaataaaaagaaaagtcgtttctaccaataagcttctattgaatacgaattatcacttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0002:PI0003|PI0002:PI0003:conserved hypothetical protein:pseudouridylate synthase:->->:3931..4409 479 ttttcttgttcgttacattatattcttatttattcttttcaaaagaaaaaagaaaatagtagtatgataggctgtggatagcgtttataagttttttatcaattccttgcatatttggttatcaactcgtgaataaaagttatccacacttctatgctttgctttattattgatattcaacctatattagcagttatccacatttccactctatcctgcaaagataataagtttatatcttttatcttacaaaagctgtgtaaaacttctataaaagcacgttaataactctgtgtttatcctctataactttgttccgtcttgtttgttgtggataagtcggaggttattttaaagttattaaccgagttatccataaagttatccacatttgaaaattctcaatgcctacttttcaacaataaaaagaaaagtcgtttctaccaataagcttctattgaatacgaattatcacttta Intra-Species Hit: Count: 1 Min: 1 Max: 479 Len: 479 Subject: pint_PI0002_PI0003|conserved hypothetical protein:pseudouridylate synthase|POSITIVE:POSITIVE|[3931,4409]|479 HSP 1 e-value: 0.0 bit: 839.0 Len: 423 Query Start:57 Query End:479 Subject Strand: POSITIVE Subject Start: 57 Subject End: 479 ........................................................tagtagtatgataggctgtggatagcgtttataagttttttatcaattccttgcatatttggttatcaactcgtgaataaaagttatccacacttctatgctttgctttattattgatattcaacctatattagcagttatccacatttccactctatcctgcaaagataataagtttatatcttttatcttacaaaagctgtgtaaaacttctataaaagcacgttaataactctgtgtttatcctctataactttgttccgtcttgtttgttgtggataagtcggaggttattttaaagttattaaccgagttatccataaagttatccacatttgaaaattctcaatgcctacttttcaacaataaaaagaaaagtcgtttctaccaataagcttctattgaatacgaattatcacttta ........................................................tagtagtatgataggctgtggatagcgtttataagttttttatcaattccttgcatatttggttatcaactcgtgaataaaagttatccacacttctatgctttgctttattattgatattcaacctatattagcagttatccacatttccactctatcctgcaaagataataagtttatatcttttatcttacaaaagctgtgtaaaacttctataaaagcacgttaataactctgtgtttatcctctataactttgttccgtcttgtttgttgtggataagtcggaggttattttaaagttattaaccgagttatccataaagttatccacatttgaaaattctcaatgcctacttttcaacaataaaaagaaaagtcgtttctaccaataagcttctattgaatacgaattatcacttta HSP 2 e-value: 8.0E-14 bit: 79.8 Len: 40 Query Start:1 Query End:40 Subject Strand: POSITIVE Subject Start: 1 Subject End: 40 ttttcttgttcgttacattatattcttatttattcttttc....................................................................................................................................................................................................................................................................................................................................................................................................................................................... ttttcttgttcgttacattatattcttatttattcttttc....................................................................................................................................................................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUUGUUCGUUACAUUAUAUUCUUAUUUAUUCUUUUCAAAAGAAAAAAGAAAAUAGUAGUAUGAUAGGCUGUGGAUAGCGUUUAUAAGUUUUUUAUCAAUUCCUUGCAUAUUUGGUUAUCAACUCGUGAAUAAAAGUUAUCCACACUUCUAUGCUUUGCUUUAUUAUUGAUAUUCAACCUAUAUUAGCAGUUAUCCACAUUUCCACUCUAUCCUGCAAAGAUAAUAAGUUUAUAUCUUUUAUCUUACAAAAGCUGUGUAAAACUUCUAUAAAAGCACGUUAAUAACUCUGUGUUUAUCCUCUAUAACUUUGUUCCGUCUUGUUUGUUGUGGAUAAGUCGGAGGUUAUUUUAAAGUUAUUAACCGAGUUAUCCAUAAAGUUAUCCACAUUUGAAAAUUCUCAAUGCCUACUUUUCAACAAUAAAAAGAAAAGUCGUUUCUACCAAUAAGCUUCUAUUGAAUACGAAUUAUCACUUUA ..(((.((((((....((((((((.((((((.((.(((((....))))).)).)))))).)))))))).((.(((((((((((((((((.(((...(((((((.....(((.....(((.........(((.(((.....))).)))........))).)))......)))))))...))).))))..))).))))))))))...)).............(((((((.(((.......))))))))))....(((((..(((((((..........((..((..((((((.((((..((..(((.((((((((((((((.(((((((.....))))))).))))).......))))))))).....))).))..)))).))))))..))..((((......)))).))..(((((((...........))))))).)))).))).....)))))....)))))).)))........... (-89.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGUGAUAAUUCGUAUUCAAUAGAAGCUUAUUGGUAGAAACGACUUUUCUUUUUAUUGUUGAAAAGUAGGCAUUGAGAAUUUUCAAAUGUGGAUAACUUUAUGGAUAACUCGGUUAAUAACUUUAAAAUAACCUCCGACUUAUCCACAACAAACAAGACGGAACAAAGUUAUAGAGGAUAAACACAGAGUUAUUAACGUGCUUUUAUAGAAGUUUUACACAGCUUUUGUAAGAUAAAAGAUAUAAACUUAUUAUCUUUGCAGGAUAGAGUGGAAAUGUGGAUAACUGCUAAUAUAGGUUGAAUAUCAAUAAUAAAGCAAAGCAUAGAAGUGUGGAUAACUUUUAUUCACGAGUUGAUAACCAAAUAUGCAAGGAAUUGAUAAAAAACUUAUAAACGCUAUCCACAGCCUAUCAUACUACUAUUUUCUUUUUUCUUUUGAAAAGAAUAAAUAAGAAUAUAAUGUAACGAACAAGAAAA ...........(((((...((.((....(((((((((((.....(((((((...........)))))))((((.......(((((((..((((...(((((((((((..((...((((((((((((....((.((((.(((((.(((..............)))...)))))...)))).)).....))))))))))))))...))))).))))))...))))..((((((((((((((((.......))).))))).)))))))).....)))))))(((((((...((...((((((((...(((((((.......(...(((((....((((((((.....))))))))..(((.....))).)))))...).)))))))...))))))))...))))))))).))))......)))))...((((((((......))))))))..))))))....)).))..)))))........ (-101.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 347 301 209 164 pint:PI0268|5end_lysozyme-related_protein_259198..259428_POSITIVE 303 349 306 69 27 pint:PI0163|5end_conserved_hypothetical_protein_157116..157346_POSITIVE 290 194 151 175 119 pint:PI0934|5end_hypothetical_protein_865855..866085_POSITIVE 285 366 322 59 12 pint:PI0732|5end_conserved_hypothetical_protein_663598..663828_POSITIVE 283 337 291 163 112 pint:PI0132|5end_hypothetical_protein_123783..124013_POSITIVE 275 326 289 85 46 pint:PI1632|5end_hypothetical_protein_1552819..1553049_POSITIVE 271 348 304 197 152 pint:PI1783|5end_possible_4-diphosphocytidyl-2c-methyl-D-erythritol_synthase_1715362..1715592_POSITIVE 269 348 310 110 72 pint:PI0038|5end_transcriptional_regulator,_LysR_family_39578..39808_POSITIVE 264 109 69 59 18 pint:PI0468|5end_50S_ribosomal_protein_L29_436905..437135_POSITIVE 261 332 294 98 42 pint:PI0746|5end_hypothetical_protein_675971..676201_POSITIVE 260 159 117 57 1 pint:PI1539|5end_3-phosphoshikimate_1-carboxyvinyltransferase_1459804..1460034_POSITIVE 258 109 61 130 75 pint:PI1570|5end_succinyl-diaminopimelate_desuccinylase_1493280..1493510_POSITIVE 257 346 313 82 45 pint:PI0264|5end_transfer_region-related_protein,_TraN_256494..256724_POSITIVE 253 347 302 58 5 pint:PI0429|5end_hypothetical_protein_396418..396648_POSITIVE 252 346 312 62 30 pint:PI2157|5end_xanthosine_triphosphate_pyrophosphatase,_HAM1_family_2103736..2103966_POSITIVE 252 350 304 218 164 pint:PI0169|5end_hypothetical_protein_163645..163875_POSITIVE 251 346 301 225 168 pint:PI1627|5end_hypothetical_protein_1550445..1550675_POSITIVE 250 318 275 87 52 pint:PI0968|5end_hypothetical_protein_895946..896176_POSITIVE 249 119 71 63 11 pint:PI0034|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_37151..37381_POSITIVE 248 347 312 216 177 pint:PI1845|5end_hypothetical_protein_1791457..1791687_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 349 301 100 43 pint:PI0547|3end_fructose-bisphosphate_aldolase_499466..499616_POSITIVE 290 194 151 124 68 pint:PI0933|3end_hypothetical_protein_865884..866034_POSITIVE 285 366 322 54 7 pint:PI0731|3end_conserved_hypothetical_protein_663673..663823_POSITIVE 275 326 289 141 102 pint:PI1633|3end_hypothetical_protein_1552955..1553105_POSITIVE 271 348 304 150 105 pint:PI1782|3end_possible_LPS_biosynthesis_protein_1715395..1715545_POSITIVE 269 348 310 68 30 pint:PI0037|3end_hypothetical_protein_39616..39766_POSITIVE 264 109 69 50 9 pint:PI0467|3end_50S_ribosomal_protein_L16_436976..437126_POSITIVE 262 346 308 136 86 pint:PI0292|3end_ISPg-3_transposase_fragment_275904..276054_POSITIVE 256 326 293 134 101 pint:PI0950|3end_50S_ribosomal_protein_L31_883655..883805_POSITIVE 252 346 312 123 91 pint:PI2156|3end_conserved_hypothetical_protein;_possible_permease_2103877..2104027_POSITIVE 252 82 44 144 107 pint:PI0590|3end_ribosomal_large_subunit_pseudouridine_synthase_B_538545..538695_POSITIVE 251 346 313 94 60 pint:PI0230|3end_hypothetical_protein_228906..229056_POSITIVE 250 350 309 66 15 pint:PI1653|3end_hypothetical_protein_1565714..1565864_POSITIVE 250 218 188 89 48 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 247 338 293 134 92 pint:PI0269|3end_conserved_hypothetical_protein_261480..261630_POSITIVE 245 101 62 124 85 pint:PI1880|3end_phosphoenolpyruvate_carboxykinase_(ATP)_1823300..1823450_POSITIVE 242 350 314 144 96 pint:PI1658|3end_conserved_hypothetical_protein_1574736..1574886_POSITIVE 241 92 63 125 90 pint:PI1230|3end_probable_metallo-beta-lactamase_family_protein_1152729..1152879_POSITIVE 239 105 67 131 84 pint:PI0999|3end_hypothetical_protein_922812..922962_POSITIVE 238 345 301 70 13 pint:PI0758|3end_hypothetical_protein_690506..690656_POSITIVE