Origin IGS: cccgatgaaacaagctatcggctgcaaggattttctcctatctttgcctataaaaagaaggctggagtgctaaggttattgacaaactcccgtagactatcccctcgccgtatcctgagcagacgctgtgtccagctcggaacctccttcacctgcgttaattcgctgagtcgttgatggtgctaagggcaataaggctttgataaattctcctgtagagctggttttgagccatttagaggctctctgcaaaactatgcaagagcctcttgctttaattctaaagtataaagaataggacatgatagcgcaagaggatattataaaacaaatgactaaacttaccgacgtacatttttctttggtagcgtacatttgctatactaatgattgcatccagatagataaaagtcaaataatcaacttaagaatgaata .........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 tattcattcttaagttgattatttgacttttatctatctggatgcaatcattagtatagcaaatgtacgctaccaaagaaaaatgtacgtcggtaagtttagtcatttgttttataatatcctcttgcgctatcatgtcctattctttatactttagaattaaagcaagaggctcttgcatagttttgcagagagcctctaaatggctcaaaaccagctctacaggagaatttatcaaagccttattgcccttagcaccatcaacgactcagcgaattaacgcaggtgaaggaggttccgagctggacacagcgtctgctcaggatacggcgaggggatagtctacgggagtttgtcaataaccttagcactccagccttctttttataggcaaagataggagaaaatccttgcagccgatagcttgtttcatcggg Mask Tandem Repeat Region ================================================ cccgatgaaacaagctatcggctgcaaggattttctcctatctttgcctataaaaagaaggctggagtgctaaggttattgacaaactcccgtagactatcccctcgccgtatcctgagcagacgctgtgtccagctcggaacctccttcacctgcgttaattcgctgagtcgttgatggtgctaagggcaataaggctttgataaattctcctgtagagctggttttgagccatttagaggctctctgcaaaactatgcaagagcctcttgctttaattctaaagtataaagaataggacatgatagcgcaagaggatattataaaacaaatgactaaacttaccgacgtacatttttctttggtagcgtacatttgctatactaatgattgcatccagatagataaaagtcaaataatcaacttaagaatgaata Find is-nt database================================================ Query_seq: PG0838:PG0839|PG0838:PG0839:integrase:hypothetical protein:->->:896916..897352 437 cccgatgaaacaagctatcggctgcaaggattttctcctatctttgcctataaaaagaaggctggagtgctaaggttattgacaaactcccgtagactatcccctcgccgtatcctgagcagacgctgtgtccagctcggaacctccttcacctgcgttaattcgctgagtcgttgatggtgctaagggcaataaggctttgataaattctcctgtagagctggttttgagccatttagaggctctctgcaaaactatgcaagagcctcttgctttaattctaaagtataaagaataggacatgatagcgcaagaggatattataaaacaaatgactaaacttaccgacgtacatttttctttggtagcgtacatttgctatactaatgattgcatccagatagataaaagtcaaataatcaacttaagaatgaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0838:PG0839|PG0838:PG0839:integrase:hypothetical protein:->->:896916..897352 437 cccgatgaaacaagctatcggctgcaaggattttctcctatctttgcctataaaaagaaggctggagtgctaaggttattgacaaactcccgtagactatcccctcgccgtatcctgagcagacgctgtgtccagctcggaacctccttcacctgcgttaattcgctgagtcgttgatggtgctaagggcaataaggctttgataaattctcctgtagagctggttttgagccatttagaggctctctgcaaaactatgcaagagcctcttgctttaattctaaagtataaagaataggacatgatagcgcaagaggatattataaaacaaatgactaaacttaccgacgtacatttttctttggtagcgtacatttgctatactaatgattgcatccagatagataaaagtcaaataatcaacttaagaatgaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0838:PG0839|PG0838:PG0839:integrase:hypothetical protein:->->:896916..897352 437 cccgatgaaacaagctatcggctgcaaggattttctcctatctttgcctataaaaagaaggctggagtgctaaggttattgacaaactcccgtagactatcccctcgccgtatcctgagcagacgctgtgtccagctcggaacctccttcacctgcgttaattcgctgagtcgttgatggtgctaagggcaataaggctttgataaattctcctgtagagctggttttgagccatttagaggctctctgcaaaactatgcaagagcctcttgctttaattctaaagtataaagaataggacatgatagcgcaagaggatattataaaacaaatgactaaacttaccgacgtacatttttctttggtagcgtacatttgctatactaatgattgcatccagatagataaaagtcaaataatcaacttaagaatgaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cccgatgaaacaagctatcggctgcaaggattttctcctatctttgcctataaaaagaaggctggagtgctaaggttattgacaaactcccgtagactatcccctcgccgtatcctgagcagacgctgtgtccagctcggaacctccttcacctgcgttaattcgctgagtcgttgatggtgctaagggcaataaggctttgataaattctcctgtagagctggttttgagccatttagaggctctctgcaaaactatgcaagagcctcttgctttaattctaaagtataaagaataggacatgatagcgcaagaggatattataaaacaaatgactaaacttaccgacgtacatttttctttggtagcgtacatttgctatactaatgattgcatccagatagataaaagtcaaataatcaacttaagaatgaata Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 22 End: 174 ..................... M Q G F S P I F A Y K K K A G V L R L L T N S R R L S P R R I L S R R C V Q L G T S F T C V N S L S R ....................................................................................................................................................................................................................................................................... Protein_Len: 32 Strand: + Start: 200 End: 295 ....................................................................................................................................................................................................... M I N S P V E L V L S H L E A L C K T M Q E P L A L I L K Y K E .............................................................................................................................................. Protein_Len: 45 Strand: + Start: 302 End: 436 ............................................................................................................................................................................................................................................................................................................. M I A Q E D I I K Q M T K L T D V H F S L V A Y I C Y T N D C I Q I D K S Q I I N L R M N . Protein_Len: 44 Strand: - Start: 284 End: 415 ........................................................................................................................................................................................................................................................................................... L I F F L V H Y R L L I N Y F L H S F K G V Y M K R Q Y R V N A I S I I A D L Y I F T M ...................... Protein_Len: 60 Strand: - Start: 100 End: 375 ................................................................................................... A K I F E G T S S T K L W K S A R Q L V I C S G R A K I R F Y L S Y S M I A C S S I I F C I V L S V S T C K E K T A Y M .............................................................. Protein_Len: 34 Strand: - Start: 51 End: 152 .................................................. L F F A P T S L N N V F E R L S D G R R I R L L R Q T W S P V E K M ............................................................................................................................................................................................................................................................................................. cccgatgaaacaagctatcggctgcaaggattttctcctatctttgcctataaaaagaaggctggagtgctaaggttattgacaaactcccgtagactatcccctcgccgtatcctgagcagacgctgtgtccagctcggaacctccttcacctgcgttaattcgctgagtcgttgatggtgctaagggcaataaggctttgataaattctcctgtagagctggttttgagccatttagaggctctctgcaaaactatgcaagagcctcttgctttaattctaaagtataaagaataggacatgatagcgcaagaggatattataaaacaaatgactaaacttaccgacgtacatttttctttggtagcgtacatttgctatactaatgattgcatccagatagataaaagtcaaataatcaacttaagaatgaata 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: 82 Start: 285 End: 314 ............................................................................................................................................................................................................................................................................................CTTGCGCTATCATGTCCTATTCTTTATACT........................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 320 End: 349 ...............................................................................................................................................................................................................................................................................................................................GTCGGTAAGTTTAGTCATTTGTTTTATAAT........................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 387 End: 416 ..................................................................................................................................................................................................................................................................................................................................................................................................TTTGACTTTTATCTATCTGGATGCAATCAT..................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cccgatgaaacaagctatcggctgcaaggattttctcctatctttgcctataaaaagaaggctggagtgctaaggttattgacaaactcccgtagactatcccctcgccgtatcctgagcagacgctgtgtccagctcggaacctccttcacctgcgttaattcgctgagtcgttgatggtgctaagggcaataaggctttgataaattctcctgtagagctggttttgagccatttagaggctctctgcaaaactatgcaagagcctcttgctttaattctaaagtataaagaataggacatgatagcgcaagaggatattataaaacaaatgactaaacttaccgacgtacatttttctttggtagcgtacatttgctatactaatgattgcatccagatagataaaagtcaaataatcaacttaagaatgaata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 82 HP_score: -10.6 Tail_Score: -3.63655 Start: 239 End: 269 Full_Region: GTTTTGAGCCATTTA GAGGCTCTCTGCA AAACTA TGCAAGAGCCTC TTGCTTTAATTCTAA ..............................................................................................................................................................................................................................................GAGGCTCTCTGCAAAACTATGCAAGAGCCTC........................................................................................................................................................................ TransTerm Strand: + Conf: 77 HP_score: -8.6 Tail_Score: -4.00124 Start: 259 End: 273 Full_Region: TCTCTGCAAAACTAT GCAAGA GCC TCTTGC TTTAATTCTAAAGTA ..................................................................................................................................................................................................................................................................GCAAGAGCCTCTTGC.................................................................................................................................................................... Find igs database================================================ Query_seq: PG0838:PG0839|PG0838:PG0839:integrase:hypothetical protein:->->:896916..897352 437 cccgatgaaacaagctatcggctgcaaggattttctcctatctttgcctataaaaagaaggctggagtgctaaggttattgacaaactcccgtagactatcccctcgccgtatcctgagcagacgctgtgtccagctcggaacctccttcacctgcgttaattcgctgagtcgttgatggtgctaagggcaataaggctttgataaattctcctgtagagctggttttgagccatttagaggctctctgcaaaactatgcaagagcctcttgctttaattctaaagtataaagaataggacatgatagcgcaagaggatattataaaacaaatgactaaacttaccgacgtacatttttctttggtagcgtacatttgctatactaatgattgcatccagatagataaaagtcaaataatcaacttaagaatgaata Intra-Species Hit: Count: 1 Min: 1 Max: 437 Len: 437 Subject: NC_002950_PG0838_PG0839|integrase:hypothetical protein|POSITIVE:POSITIVE|[896916,897352]|437 HSP 1 e-value: 0.0 bit: 866.0 Len: 437 Query Start:1 Query End:437 Subject Strand: POSITIVE Subject Start: 1 Subject End: 437 cccgatgaaacaagctatcggctgcaaggattttctcctatctttgcctataaaaagaaggctggagtgctaaggttattgacaaactcccgtagactatcccctcgccgtatcctgagcagacgctgtgtccagctcggaacctccttcacctgcgttaattcgctgagtcgttgatggtgctaagggcaataaggctttgataaattctcctgtagagctggttttgagccatttagaggctctctgcaaaactatgcaagagcctcttgctttaattctaaagtataaagaataggacatgatagcgcaagaggatattataaaacaaatgactaaacttaccgacgtacatttttctttggtagcgtacatttgctatactaatgattgcatccagatagataaaagtcaaataatcaacttaagaatgaata cccgatgaaacaagctatcggctgcaaggattttctcctatctttgcctataaaaagaaggctggagtgctaaggttattgacaaactcccgtagactatcccctcgccgtatcctgagcagacgctgtgtccagctcggaacctccttcacctgcgttaattcgctgagtcgttgatggtgctaagggcaataaggctttgataaattctcctgtagagctggttttgagccatttagaggctctctgcaaaactatgcaagagcctcttgctttaattctaaagtataaagaataggacatgatagcgcaagaggatattataaaacaaatgactaaacttaccgacgtacatttttctttggtagcgtacatttgctatactaatgattgcatccagatagataaaagtcaaataatcaacttaagaatgaata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCGAUGAAACAAGCUAUCGGCUGCAAGGAUUUUCUCCUAUCUUUGCCUAUAAAAAGAAGGCUGGAGUGCUAAGGUUAUUGACAAACUCCCGUAGACUAUCCCCUCGCCGUAUCCUGAGCAGACGCUGUGUCCAGCUCGGAACCUCCUUCACCUGCGUUAAUUCGCUGAGUCGUUGAUGGUGCUAAGGGCAAUAAGGCUUUGAUAAAUUCUCCUGUAGAGCUGGUUUUGAGCCAUUUAGAGGCUCUCUGCAAAACUAUGCAAGAGCCUCUUGCUUUAAUUCUAAAGUAUAAAGAAUAGGACAUGAUAGCGCAAGAGGAUAUUAUAAAACAAAUGACUAAACUUACCGACGUACAUUUUUCUUUGGUAGCGUACAUUUGCUAUACUAAUGAUUGCAUCCAGAUAGAUAAAAGUCAAAUAAUCAACUUAAGAAUGAAUA .((((((........))))))..((((((((........)))))))).......(((..(((......)))..((((((((((..((....))...(((((.....((.(((((((.....(.((((((((((.((((((((((.((((((((.(((......)))...(((...)))))))..)))).......((((((.(((........))))))))))))))))))).....(((((((((.((((......)))))))))))))(((((((....))))))).........))))))...)))))...))))))).......((((((((.....(((((((.(.........).))))))).)).))))))..............)).....)))))......))).)))))))..)))........... (-109.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUCAUUCUUAAGUUGAUUAUUUGACUUUUAUCUAUCUGGAUGCAAUCAUUAGUAUAGCAAAUGUACGCUACCAAAGAAAAAUGUACGUCGGUAAGUUUAGUCAUUUGUUUUAUAAUAUCCUCUUGCGCUAUCAUGUCCUAUUCUUUAUACUUUAGAAUUAAAGCAAGAGGCUCUUGCAUAGUUUUGCAGAGAGCCUCUAAAUGGCUCAAAACCAGCUCUACAGGAGAAUUUAUCAAAGCCUUAUUGCCCUUAGCACCAUCAACGACUCAGCGAAUUAACGCAGGUGAAGGAGGUUCCGAGCUGGACACAGCGUCUGCUCAGGAUACGGCGAGGGGAUAGUCUACGGGAGUUUGUCAAUAACCUUAGCACUCCAGCCUUCUUUUUAUAGGCAAAGAUAGGAGAAAAUCCUUGCAGCCGAUAGCUUGUUUCAUCGGG .............((((((..(((((......(((.((((...((........(((.((((((((.((((((((.................))).)))...)))))))))).))).........(((.(((((..(((...(((((.........)))))....)))(((((((((((((......)))).)))))))))..))))).))).....))....))))))).....))))).......(((.....)))..))))))......(((......))).(((((((.(((((((((((.((((.....)))))))).)))..((((..((((((..(((.(.((((((((..........))).))))).((((.........)))).......).)))..))))))...))))...)))).)))))))... (-112.73) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 148 103 68 14 NC_002950:PG2159|5end_protoporphyrinogen_oxidase_2264397..2264627_POSITIVE 397 141 102 70 20 NC_002950:PG1486|5end_conjugative_transposon_protein_TraA_1561166..1561396_NEGATIVE 386 178 131 87 29 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 386 157 113 140 104 NC_002950:PG0604|5end_4-hydroxy-3-methylbut-2-enyl_diphosphate_reductase_660262..660492_POSITIVE 386 190 150 172 131 NC_002950:PG0146|5end_hypothetical_protein_169115..169345_NEGATIVE 382 150 101 62 10 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 381 140 91 182 138 NC_002950:PG1485|5end_conjugative_transposon_protein_TraC_1560370..1560600_NEGATIVE 380 140 101 51 3 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 372 139 91 104 33 NC_002950:PG1172|5end_iron-sulfur_cluster_binding_protein,_putative_1251173..1251403_POSITIVE 369 150 104 176 127 NC_002950:PG0283|5end_efflux_transporter,_MFP_component,_RND_family_318245..318475_NEGATIVE 364 138 91 78 30 NC_002950:PG1391|5end_hypothetical_protein_1471670..1471900_POSITIVE 358 119 74 60 13 NC_002950:PG0212|5end_precorrin-6Y_C5,15-methyltransferase,_decarboxylating_249065..249295_NEGATIVE 357 250 201 74 30 NC_002950:PG1755|5end_fructose-bisphosphate_aldolase_1843278..1843508_NEGATIVE 357 160 115 180 133 NC_002950:PG0700|5end_hypothetical_protein_756595..756825_NEGATIVE 356 159 113 226 164 NC_002950:PG2029|5end_hypothetical_protein_2126543..2126773_POSITIVE 352 184 141 54 11 NC_002950:PG1232|5end_glutamate_dehydrogenase_1309611..1309841_NEGATIVE 350 180 131 212 165 NC_002950:PG2223|5end_glycosyl_transferase,_group_2_family_protein_2337713..2337943_POSITIVE 350 46 1 74 16 NC_002950:PG0291|5end_hypothetical_protein_325457..325687_POSITIVE 349 142 101 123 82 NC_002950:PG1409|5end_hypothetical_protein_1493265..1493495_NEGATIVE 348 198 151 181 134 NC_002950:PG0422|5end_hypothetical_protein_462302..462532_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 148 103 64 10 NC_002950:PG2158|3end_hypothetical_protein_2264473..2264623_POSITIVE 392 146 102 120 70 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 386 157 113 143 107 NC_002950:PG0603|3end_cytidylate_kinase_660345..660495_POSITIVE 363 140 91 47 5 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 358 119 74 67 20 NC_002950:PG0213|3end_precorrin-3_methylase/precorrin-8X_methylmutase_249058..249208_NEGATIVE 356 109 61 66 23 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 353 139 91 124 84 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 352 189 143 147 110 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 351 176 132 145 94 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 350 170 121 59 3 NC_002950:PG1622|3end_DNA_topoisomerase_IV_subunit_A_1701418..1701568_NEGATIVE 350 46 1 71 13 NC_002950:PG0290|3end_hypothetical_protein_325534..325684_POSITIVE 346 46 2 86 25 NC_002950:PG0575|3end_penicillin-binding_protein_2,_putative_631782..631932_POSITIVE 345 140 94 124 78 NC_002950:PG0658|3end_phosphatase,_YrbI_family_707798..707948_NEGATIVE 343 140 91 122 61 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 341 140 100 145 84 NC_002950:PG1303|3end_helicase,_putative_1382147..1382297_POSITIVE 338 147 101 86 23 NC_002950:PG2075|3end_hypothetical_protein_2176248..2176398_NEGATIVE 338 147 101 86 23 NC_002950:PG1671|3end_hypothetical_protein_1757440..1757590_NEGATIVE 338 147 101 86 23 NC_002950:PG1266|3end_hypothetical_protein_1346769..1346919_NEGATIVE 338 147 101 86 23 NC_002950:PG0101|3end_hypothetical_protein_119496..119646_POSITIVE 331 166 124 149 112 NC_002950:PG0713|3end_anthranilate_synthase_component_II_767153..767303_NEGATIVE