Origin IGS: taatgccaatgtgtatcgctcaatgcaccaaagcgactgtttgccgatagcataagctttctttattcagcgaggtgagggattatagaatcggcaaagcgttgttatcggtttactaaagtgatgttatagattcaacaaagcgttgctgtcgatttattaagatgttattatagcttcagcaaatcagtattgttgatttgccaaagcgatataatagattcagtaaagcagctttgtagatttaccaaagcagtattacagatttactaaattgccattataaaccgtctgcaaacctccaacccataccgaataaagtctttcataaacataataaagcgcagaaataaaaaaagacgcaccgtttccgatgcgcctaccttgagttatttagtcggttgtagtggtgttttgccttttcttatttttgcgtcttccgacctttttatccttttctctttttccaattatcgtatattgtttcttccta .........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 taggaagaaacaatatacgataattggaaaaagagaaaaggataaaaaggtcggaagacgcaaaaataagaaaaggcaaaacaccactacaaccgactaaataactcaaggtaggcgcatcggaaacggtgcgtctttttttatttctgcgctttattatgtttatgaaagactttattcggtatgggttggaggtttgcagacggtttataatggcaatttagtaaatctgtaatactgctttggtaaatctacaaagctgctttactgaatctattatatcgctttggcaaatcaacaatactgatttgctgaagctataataacatcttaataaatcgacagcaacgctttgttgaatctataacatcactttagtaaaccgataacaacgctttgccgattctataatccctcacctcgctgaataaagaaagcttatgctatcggcaaacagtcgctttggtgcattgagcgatacacattggcatta Mask Tandem Repeat Region ================================================ taatgccaatgtgtatcgctcaatgcaccaaagcgactgtttgccgatagcataagctttctttattcagcgaggtgagggattatagaatcggcaaagcgttgttatcggtttactaaagtgatgttatagattcaacaaagcgttgctgtcgatttattaagatgttattatagcttcagcaaatcagtattgttgatttgccaaagcgatataatagattcagtaaagcagctttgtagatttaccaaagcagtattacagatttactaaattgccattataaaccgtctgcaaacctccaacccataccgaataaagtctttcataaacataataaagcgcagaaataaaaaaagacgcaccgtttccgatgcgcctaccttgagttatttagtcggttgtagtggtgttttgccttttcttatttttgcgtcttccgacctttttatccttttctctttttccaattatcgtatattgtttcttccta Find is-nt database================================================ Query_seq: PI0594:PI0595|PI0594:PI0595:possible rare lipoprotein A:conserved hypothetical protein:->->:545218..545710 493 taatgccaatgtgtatcgctcaatgcaccaaagcgactgtttgccgatagcataagctttctttattcagcgaggtgagggattatagaatcggcaaagcgttgttatcggtttactaaagtgatgttatagattcaacaaagcgttgctgtcgatttattaagatgttattatagcttcagcaaatcagtattgttgatttgccaaagcgatataatagattcagtaaagcagctttgtagatttaccaaagcagtattacagatttactaaattgccattataaaccgtctgcaaacctccaacccataccgaataaagtctttcataaacataataaagcgcagaaataaaaaaagacgcaccgtttccgatgcgcctaccttgagttatttagtcggttgtagtggtgttttgccttttcttatttttgcgtcttccgacctttttatccttttctctttttccaattatcgtatattgtttcttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0594:PI0595|PI0594:PI0595:possible rare lipoprotein A:conserved hypothetical protein:->->:545218..545710 493 taatgccaatgtgtatcgctcaatgcaccaaagcgactgtttgccgatagcataagctttctttattcagcgaggtgagggattatagaatcggcaaagcgttgttatcggtttactaaagtgatgttatagattcaacaaagcgttgctgtcgatttattaagatgttattatagcttcagcaaatcagtattgttgatttgccaaagcgatataatagattcagtaaagcagctttgtagatttaccaaagcagtattacagatttactaaattgccattataaaccgtctgcaaacctccaacccataccgaataaagtctttcataaacataataaagcgcagaaataaaaaaagacgcaccgtttccgatgcgcctaccttgagttatttagtcggttgtagtggtgttttgccttttcttatttttgcgtcttccgacctttttatccttttctctttttccaattatcgtatattgtttcttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0594:PI0595|PI0594:PI0595:possible rare lipoprotein A:conserved hypothetical protein:->->:545218..545710 493 taatgccaatgtgtatcgctcaatgcaccaaagcgactgtttgccgatagcataagctttctttattcagcgaggtgagggattatagaatcggcaaagcgttgttatcggtttactaaagtgatgttatagattcaacaaagcgttgctgtcgatttattaagatgttattatagcttcagcaaatcagtattgttgatttgccaaagcgatataatagattcagtaaagcagctttgtagatttaccaaagcagtattacagatttactaaattgccattataaaccgtctgcaaacctccaacccataccgaataaagtctttcataaacataataaagcgcagaaataaaaaaagacgcaccgtttccgatgcgcctaccttgagttatttagtcggttgtagtggtgttttgccttttcttatttttgcgtcttccgacctttttatccttttctctttttccaattatcgtatattgtttcttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatgccaatgtgtatcgctcaatgcaccaaagcgactgtttgccgatagcataagctttctttattcagcgaggtgagggattatagaatcggcaaagcgttgttatcggtttactaaagtgatgttatagattcaacaaagcgttgctgtcgatttattaagatgttattatagcttcagcaaatcagtattgttgatttgccaaagcgatataatagattcagtaaagcagctttgtagatttaccaaagcagtattacagatttactaaattgccattataaaccgtctgcaaacctccaacccataccgaataaagtctttcataaacataataaagcgcagaaataaaaaaagacgcaccgtttccgatgcgcctaccttgagttatttagtcggttgtagtggtgttttgccttttcttatttttgcgtcttccgacctttttatccttttctctttttccaattatcgtatattgtttcttccta Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 133 End: 270 .................................................................................................................................... M Q Q S V A V D L L R C Y Y S F S K S V L L I C Q S D I I D S V K Q L C R F T K A V L Q I Y ............................................................................................................................................................................................................................... Protein_Len: 36 Strand: + Start: 243 End: 350 .................................................................................................................................................................................................................................................. M Y Q S S I T D L L N C H Y K P S A N L Q P I P N K V F H K H N K A Q K ............................................................................................................................................... Protein_Len: 60 Strand: + Start: 274 End: 492 ................................................................................................................................................................................................................................................................................. M A I I N R L Q T S N P Y R I K S F I N I I K R R N K K R R T V S D A P T L S Y L V G C S G V L P F L I F A S S D L F I . Protein_Len: 31 Strand: - Start: 273 End: 365 ................................................................................................................................................................................................................................................................................ I A M I F R R C V E L G Y R I F D K M F M I F R L F L F L R M ................................................................................................................................ Protein_Len: 44 Strand: - Start: 262 End: 393 ..................................................................................................................................................................................................................................................................... L N V L N G N Y V T Q L G G V W V S Y L R E Y V Y Y L A S I F F S A G N G I R R G Q T M .................................................................................................... Protein_Len: 31 Strand: - Start: 174 End: 266 ............................................................................................................................................................................. L K L L D T N N I Q W L S I I S E T F C S Q L N V L A T N C M ................................................................................................................................................................................................................................... taatgccaatgtgtatcgctcaatgcaccaaagcgactgtttgccgatagcataagctttctttattcagcgaggtgagggattatagaatcggcaaagcgttgttatcggtttactaaagtgatgttatagattcaacaaagcgttgctgtcgatttattaagatgttattatagcttcagcaaatcagtattgttgatttgccaaagcgatataatagattcagtaaagcagctttgtagatttaccaaagcagtattacagatttactaaattgccattataaaccgtctgcaaacctccaacccataccgaataaagtctttcataaacataataaagcgcagaaataaaaaaagacgcaccgtttccgatgcgcctaccttgagttatttagtcggttgtagtggtgttttgccttttcttatttttgcgtcttccgacctttttatccttttctctttttccaattatcgtatattgtttcttccta 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================================================ taatgccaatgtgtatcgctcaatgcaccaaagcgactgtttgccgatagcataagctttctttattcagcgaggtgagggattatagaatcggcaaagcgttgttatcggtttactaaagtgatgttatagattcaacaaagcgttgctgtcgatttattaagatgttattatagcttcagcaaatcagtattgttgatttgccaaagcgatataatagattcagtaaagcagctttgtagatttaccaaagcagtattacagatttactaaattgccattataaaccgtctgcaaacctccaacccataccgaataaagtctttcataaacataataaagcgcagaaataaaaaaagacgcaccgtttccgatgcgcctaccttgagttatttagtcggttgtagtggtgttttgccttttcttatttttgcgtcttccgacctttttatccttttctctttttccaattatcgtatattgtttcttccta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 47 HP_score: -3.5 Tail_Score: -3.1552 Start: 166 End: 219 Full_Region: ctgctttactgaatc tattatatcgctttggcaaatca acaatac tgatttgctgaagctataataaca tcttaataaatcgac .....................................................................................................................................................................tattatatcgctttggcaaatcaacaatactgatttgctgaagctataataaca.................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 75 HP_score: -10.2 Tail_Score: -2.8092 Start: 176 End: 210 Full_Region: tgaatctattatatc gctttggcaaatca acaatac tgatttgctgaagc tataataacatctta ...............................................................................................................................................................................gctttggcaaatcaacaatactgatttgctgaagc........................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -10.1 Tail_Score: -6.02919 Start: 359 End: 380 Full_Region: aaataactcaaggta ggcgcatcg gaaa cggtgcgtc tttttttatttctgc ......................................................................................................................................................................................................................................................................................................................................................................ggcgcatcggaaacggtgcgtc................................................................................................................. Find igs database================================================ Query_seq: PI0594:PI0595|PI0594:PI0595:possible rare lipoprotein A:conserved hypothetical protein:->->:545218..545710 493 taatgccaatgtgtatcgctcaatgcaccaaagcgactgtttgccgatagcataagctttctttattcagcgaggtgagggattatagaatcggcaaagcgttgttatcggtttactaaagtgatgttatagattcaacaaagcgttgctgtcgatttattaagatgttattatagcttcagcaaatcagtattgttgatttgccaaagcgatataatagattcagtaaagcagctttgtagatttaccaaagcagtattacagatttactaaattgccattataaaccgtctgcaaacctccaacccataccgaataaagtctttcataaacataataaagcgcagaaataaaaaaagacgcaccgtttccgatgcgcctaccttgagttatttagtcggttgtagtggtgttttgccttttcttatttttgcgtcttccgacctttttatccttttctctttttccaattatcgtatattgtttcttccta Intra-Species Hit: Count: 1 Min: 1 Max: 412 Len: 412 Subject: pint_PI0594_PI0595|possible rare lipoprotein A:conserved hypothetical protein|POSITIVE:POSITIVE|[545218,545710]|493 HSP 1 e-value: 0.0 bit: 775.0 Len: 412 Query Start:1 Query End:412 Subject Strand: POSITIVE Subject Start: 1 Subject End: 412 taatgccaatgtgtatcgctcaatgcaccaaagcgactgtttgccgatagcataagctttctttattcagcgaggtgagggattatagaatcggcaaagcgttgttatcggtttactaaagtgatgttatagattcaacaaagcgttgctgtcgatttattaagatgttattatagcttcagcaaatcagtattgttgatttgccaaagcgatataatagattcagtaaagcagctttgtagatttaccaaagcagtattacagatttactaaattgccattataaaccgtctgcaaacctccaacccataccgaataaagtctttcataaacataataaagcgcagaaatnnnnnnngacgcaccgtttccgatgcgcctaccttgagttatttagtcggttgtagtggtg................................................................................. taatgccaatgtgtatcgctcaatgcaccaaagcgactgtttgccgatagcataagctttctttattcagcgaggtgagggattatagaatcggcaaagcgttgttatcggtttactaaagtgatgttatagattcaacaaagcgttgctgtcgatttattaagatgttattatagcttcagcaaatcagtattgttgatttgccaaagcgatataatagattcagtaaagcagctttgtagatttaccaaagcagtattacagatttactaaattgccattataaaccgtctgcaaacctccaacccataccgaataaagtctttcataaacataataaagcgcagaaataaaaaaagacgcaccgtttccgatgcgcctaccttgagttatttagtcggttgtagtggtg................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGCCAAUGUGUAUCGCUCAAUGCACCAAAGCGACUGUUUGCCGAUAGCAUAAGCUUUCUUUAUUCAGCGAGGUGAGGGAUUAUAGAAUCGGCAAAGCGUUGUUAUCGGUUUACUAAAGUGAUGUUAUAGAUUCAACAAAGCGUUGCUGUCGAUUUAUUAAGAUGUUAUUAUAGCUUCAGCAAAUCAGUAUUGUUGAUUUGCCAAAGCGAUAUAAUAGAUUCAGUAAAGCAGCUUUGUAGAUUUACCAAAGCAGUAUUACAGAUUUACUAAAUUGCCAUUAUAAACCGUCUGCAAACCUCCAACCCAUACCGAAUAAAGUCUUUCAUAAACAUAAUAAAGCGCAGAAAUAAAAAAAGACGCACCGUUUCCGAUGCGCCUACCUUGAGUUAUUUAGUCGGUUGUAGUGGUG ((((((...(((.(((((((...(((......)))...((..((((((((((...((((((((((((......)))))))((((....))))...)))))..))))))))))..))...)))))))...((((((..(((((((.((((((..(((((((((..(((....))).((((..(((((((((.....)))))))))..))))....)))))))))))))))....))))))).)))))).....)))))))))...............((((((((((.(((.(((.....(((...........(((........)))..............((((((((((...............)))))...))))).......))).....))).))))))))))))). (-99.66) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACCACUACAACCGACUAAAUAACUCAAGGUAGGCGCAUCGGAAACGGUGCGUCUUUUUUUAUUUCUGCGCUUUAUUAUGUUUAUGAAAGACUUUAUUCGGUAUGGGUUGGAGGUUUGCAGACGGUUUAUAAUGGCAAUUUAGUAAAUCUGUAAUACUGCUUUGGUAAAUCUACAAAGCUGCUUUACUGAAUCUAUUAUAUCGCUUUGGCAAAUCAACAAUACUGAUUUGCUGAAGCUAUAAUAACAUCUUAAUAAAUCGACAGCAACGCUUUGUUGAAUCUAUAACAUCACUUUAGUAAACCGAUAACAACGCUUUGCCGAUUCUAUAAUCCCUCACCUCGCUGAAUAAAGAAAGCUUAUGCUAUCGGCAAACAGUCGCUUUGGUGCAUUGAGCGAUACACAUUGGCAUUA ...........((((....((..(((((...((((((((((....))))))))))............(((((......(((((.(((....(((((((((((..((((((..(((((((...((((((((.......((((((((((...(((.....((((((.........))))))))))))))))))).(((((((..((((..((((((((.......))))))))..)))))))))))........)))))))).((((((....))))))...................)))))))..))))...........((((....)))).....))..)))))))))))..(((....))).)))..)))))........))))).)))))..)).....))))..... (-112.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 415 60 17 56 4 pint:PI0605|5end_chloromuconate_cycloisomerase_551912..552142_POSITIVE 383 104 61 108 62 pint:PI0555|5end_conserved_hypothetical_protein_504577..504807_POSITIVE 380 52 11 87 47 pint:PI0212|5end_surface_protein/internalin-related_protein_204417..204647_POSITIVE 365 390 346 140 93 pint:PI0826|5end_hypothetical_protein_763738..763968_POSITIVE 365 390 346 120 73 pint:PI0825|5end_hypothetical_protein_763718..763948_POSITIVE 363 378 334 199 149 pint:PI0168|5end_methionyl-tRNA_synthetase_(methionine--tRNA_ligase)_161181..161411_POSITIVE 363 378 334 104 54 pint:PI0166|5end_hypothetical_protein_161086..161316_POSITIVE 334 47 2 169 135 pint:PI2099|5end_D-alanyl-D-alanine_dipeptidase_2052409..2052639_POSITIVE 332 46 2 54 4 pint:PI0005|5end_hypothetical_protein_6984..7214_POSITIVE 330 46 5 68 29 pint:PI1600|5end_conserved_hypothetical_protein_1529269..1529499_POSITIVE 326 78 31 57 14 pint:PI0251|5end_hypothetical_protein_247551..247781_POSITIVE 318 63 25 197 154 pint:PI1620|5end__two-component_system_sensor_protein_1543956..1544186_POSITIVE 318 57 11 165 112 pint:PI1186|5end_conserved_hypothetical_protein_1106480..1106710_POSITIVE 307 48 1 92 42 pint:PI2100|5end_conserved_hypothetical_protein_2053351..2053581_POSITIVE 307 51 16 216 180 pint:PI0786|5end_conserved_hypothetical_protein;_possible_glycosyltransferase_723240..723470_POSITIVE 307 51 16 120 84 pint:PI0783|5end_hypothetical_protein_723144..723374_POSITIVE 306 391 359 123 85 pint:PI1496|5end_nucleoside_phosphorylase_1417116..1417346_POSITIVE 306 127 82 180 131 pint:PI1067|5end_thymidylate_synthase_983940..984170_POSITIVE 303 47 5 135 84 pint:PI1642|5end_conserved_hypothetical_protein_1558800..1559030_POSITIVE 303 52 17 75 28 pint:PI1139|5end_endopeptidase,_endothelin-converting_enzyme_1065216..1065446_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 383 104 61 50 4 pint:PI0554|3end_hypothetical_protein_504599..504749_POSITIVE 365 390 346 62 15 pint:PI0824|3end_large_conductance_mechanosensitive_channel_protein_763740..763890_POSITIVE 337 409 365 136 71 pint:PI0331|3end_hypothetical_protein_312575..312725_POSITIVE 337 409 365 106 41 pint:PI0330|3end_hypothetical_protein_312545..312695_POSITIVE 326 50 5 134 81 pint:PI0073|3end_dihydropteroate_synthase_71785..71935_POSITIVE 323 409 365 106 41 pint:PI1623|3end_hypothetical_protein_1549261..1549411_POSITIVE 321 384 341 146 102 pint:PI1891|3end_hypothetical_protein_1835917..1836067_POSITIVE 310 379 331 151 100 pint:PI1448|3end_hypothetical_protein_1371832..1371982_POSITIVE 306 89 45 106 54 pint:PI1879|3end_uracil_phosphoribosyltransferase_1821245..1821395_POSITIVE 306 127 82 92 43 pint:PI1066|3end_dihydrofolate_reductase_983932..984082_POSITIVE 303 47 5 138 87 pint:PI1641|3end_hypothetical_protein_1558883..1559033_POSITIVE 297 46 4 52 6 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 295 46 9 97 59 pint:PI0128|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_121826..121976_POSITIVE 295 46 3 77 18 pint:PI0091|3end_hypothetical_protein_89774..89924_POSITIVE 293 118 72 142 97 pint:PI1442|3end_radical-activating_enzyme_(pyruvate-formate_lyase-activating_enzyme)_1364649..1364799_POSITIVE 288 48 4 68 22 pint:PI1924|3end_cytidine_deaminase_1866495..1866645_POSITIVE 287 48 4 126 78 pint:PI0049|3end_outer_membrane_receptor_protein_(iron_transport)_51090..51240_POSITIVE 287 88 45 75 35 pint:PI0047|3end_phosphomethylpyrimidine_kinase_46781..46931_POSITIVE 285 95 55 87 29 pint:PI1649|3end_hypothetical_protein_1563441..1563591_POSITIVE 285 77 31 40 1 pint:PI1065|3end_hypothetical_protein_983650..983800_POSITIVE