Origin IGS: acttggtgttttgttgggtgattatgatgaattgcttgtttcttcggtggtatcggacaggaaggagaggaccattggattctgccgatagcgacgacaagattagaaaaatatgctgacatattctattcaaaagtagtgccccgatcggtaaggtcgtcctaacagctcagtaacgtcgtcctaacagatcggtaaggtcgtcctaacaggttggtaacgtcgtcctaacagctcagtaacgtcgccctaacggctcagtaaggtcgtcctattccgatgtgagggtcatcccttctgcttatatggg .........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 cccatataagcagaagggatgaccctcacatcggaataggacgaccttactgagccgttagggcgacgttactgagctgttaggacgacgttaccaacctgttaggacgaccttaccgatctgttaggacgacgttactgagctgttaggacgaccttaccgatcggggcactacttttgaatagaatatgtcagcatatttttctaatcttgtcgtcgctatcggcagaatccaatggtcctctccttcctgtccgataccaccgaagaaacaagcaattcatcataatcacccaacaaaacaccaagt Mask Tandem Repeat Region ================================================ acttggtgttttgttgggtgattatgatgaattgcttgtttcttcggtggtatcggacaggaaggagaggaccattggattctgccgatagcgacgacaagattagaaaaatatgctgacatattctattcaaaagtagtgccccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttccgatgtgagggtcatcccttctgcttatatggg Find is-nt database================================================ Query_seq: PG1004:PG1005|PG1004:PG1005:prolyl oligopeptidase family protein:lipoprotein, putative:<-<-:1062803..1063112 310 acttggtgttttgttgggtgattatgatgaattgcttgtttcttcggtggtatcggacaggaaggagaggaccattggattctgccgatagcgacgacaagattagaaaaatatgctgacatattctattcaaaagtagtgccccgatcggtaaggtcgtcctaacagctcagtaacgtcgtcctaacagatcggtaaggtcgtcctaacaggttggtaacgtcgtcctaacagctcagtaacgtcgccctaacggctcagtaaggtcgtcctattccgatgtgagggtcatcccttctgcttatatggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1004:PG1005|PG1004:PG1005:prolyl oligopeptidase family protein:lipoprotein, putative:<-<-:1062803..1063112 310 acttggtgttttgttgggtgattatgatgaattgcttgtttcttcggtggtatcggacaggaaggagaggaccattggattctgccgatagcgacgacaagattagaaaaatatgctgacatattctattcaaaagtagtgccccgatcggtaaggtcgtcctaacagctcagtaacgtcgtcctaacagatcggtaaggtcgtcctaacaggttggtaacgtcgtcctaacagctcagtaacgtcgccctaacggctcagtaaggtcgtcctattccgatgtgagggtcatcccttctgcttatatggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1004:PG1005|PG1004:PG1005:prolyl oligopeptidase family protein:lipoprotein, putative:<-<-:1062803..1063112 310 acttggtgttttgttgggtgattatgatgaattgcttgtttcttcggtggtatcggacaggaaggagaggaccattggattctgccgatagcgacgacaagattagaaaaatatgctgacatattctattcaaaagtagtgccccgatcggtaaggtcgtcctaacagctcagtaacgtcgtcctaacagatcggtaaggtcgtcctaacaggttggtaacgtcgtcctaacagctcagtaacgtcgccctaacggctcagtaaggtcgtcctattccgatgtgagggtcatcccttctgcttatatggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acttggtgttttgttgggtgattatgatgaattgcttgtttcttcggtggtatcggacaggaaggagaggaccattggattctgccgatagcgacgacaagattagaaaaatatgctgacatattctattcaaaagtagtgccccgatcggtaaggtcgtcctaacagctcagtaacgtcgtcctaacagatcggtaaggtcgtcctaacaggttggtaacgtcgtcctaacagctcagtaacgtcgccctaacggctcagtaaggtcgtcctattccgatgtgagggtcatcccttctgcttatatggg Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 3 End: 116 .. M V F C W V I M M N C L F L R W Y R T G R R G P L D S A D S D D K I R K I C .................................................................................................................................................................................................. Protein_Len: 44 Strand: + Start: 31 End: 162 .............................. M A C F F G G I G Q E G E D H W I L P I A T T R L E K Y A D I F Y S K V V P R S V R S S .................................................................................................................................................... Protein_Len: 40 Strand: - Start: 3 End: 122 .. Q H K T P H N H H I A Q K K P P I P C S P S S W Q I R G I A V V L N S F Y A S M ............................................................................................................................................................................................ Protein_Len: 49 Strand: - Start: 2 End: 148 . K T N Q Q T I I I F Q K N R R H Y R V P L L P G N S E A S L S S L I L F I H Q C I R N L L L A G M .................................................................................................................................................................. acttggtgttttgttgggtgattatgatgaattgcttgtttcttcggtggtatcggacaggaaggagaggaccattggattctgccgatagcgacgacaagattagaaaaatatgctgacatattctattcaaaagtagtgccccgatcggtaaggtcgtcctaacagctcagtaacgtcgtcctaacagatcggtaaggtcgtcctaacaggttggtaacgtcgtcctaacagctcagtaacgtcgccctaacggctcagtaaggtcgtcctattccgatgtgagggtcatcccttctgcttatatggg 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================================================ acttggtgttttgttgggtgattatgatgaattgcttgtttcttcggtggtatcggacaggaaggagaggaccattggattctgccgatagcgacgacaagattagaaaaatatgctgacatattctattcaaaagtagtgccccgatcggtaaggtcgtcctaacagctcagtaacgtcgtcctaacagatcggtaaggtcgtcctaacaggttggtaacgtcgtcctaacagctcagtaacgtcgccctaacggctcagtaaggtcgtcctattccgatgtgagggtcatcccttctgcttatatggg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -3.0 Tail_Score: -4.9934 Start: 112 End: 123 Full_Region: tacttttgaatagaa tatg tcag cata tttttctaatcttgt ...............................................................................................................tatgtcagcata........................................................................................................................................................................................... TransTerm Strand: + Conf: 39 HP_score: -2.3 Tail_Score: -2.7555 Start: 246 End: 269 Full_Region: ACAGCTCAGTAACGT CGCCCTAAC GGCTCA GTAAGGTCG TCCTATTCCGATGTG .....................................................................................................................................................................................................................................................CGCCCTAACGGCTCAGTAAGGTCG......................................... Find igs database================================================ Query_seq: PG1004:PG1005|PG1004:PG1005:prolyl oligopeptidase family protein:lipoprotein, putative:<-<-:1062803..1063112 310 acttggtgttttgttgggtgattatgatgaattgcttgtttcttcggtggtatcggacaggaaggagaggaccattggattctgccgatagcgacgacaagattagaaaaatatgctgacatattctattcaaaagtagtgccccgatcggtaaggtcgtcctaacagctcagtaacgtcgtcctaacagatcggtaaggtcgtcctaacaggttggtaacgtcgtcctaacagctcagtaacgtcgccctaacggctcagtaaggtcgtcctattccgatgtgagggtcatcccttctgcttatatggg Intra-Species Hit: Count: 1 Min: 1 Max: 310 Len: 310 Subject: NC_002950_PG1004_PG1005|prolyl oligopeptidase family protein:lipoprotein, putative|NEGATIVE:NEGATIVE|[1062803,1063112]|310 HSP 1 e-value: 1.0E-175 bit: 615.0 Len: 310 Query Start:1 Query End:310 Subject Strand: POSITIVE Subject Start: 1 Subject End: 310 acttggtgttttgttgggtgattatgatgaattgcttgtttcttcggtggtatcggacaggaaggagaggaccattggattctgccgatagcgacgacaagattagaaaaatatgctgacatattctattcaaaagtagtgccccgatcggtaaggtcgtcctaacagctcagtaacgtcgtcctaacagatcggtaaggtcgtcctaacaggttggtaacgtcgtcctaacagctcagtaacgtcgccctaacggctcagtaaggtcgtcctattccgatgtgagggtcatcccttctgcttatatggg acttggtgttttgttgggtgattatgatgaattgcttgtttcttcggtggtatcggacaggaaggagaggaccattggattctgccgatagcgacgacaagattagaaaaatatgctgacatattctattcaaaagtagtgccccgatcggtaaggtcgtcctaacagctcagtaacgtcgtcctaacagatcggtaaggtcgtcctaacaggttggtaacgtcgtcctaacagctcagtaacgtcgccctaacggctcagtaaggtcgtcctattccgatgtgagggtcatcccttctgcttatatggg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUGGUGUUUUGUUGGGUGAUUAUGAUGAAUUGCUUGUUUCUUCGGUGGUAUCGGACAGGAAGGAGAGGACCAUUGGAUUCUGCCGAUAGCGACGACAAGAUUAGAAAAAUAUGCUGACAUAUUCUAUUCAAAAGUAGUGCCCCGAUCGGUAAGGUCGUCCUAACAGCUCAGUAACGUCGUCCUAACAGAUCGGUAAGGUCGUCCUAACAGGUUGGUAACGUCGUCCUAACAGCUCAGUAACGUCGCCCUAACGGCUCAGUAAGGUCGUCCUAUUCCGAUGUGAGGGUCAUCCCUUCUGCUUAUAUGGG .((((.((..((((((((((((.....(((.((((((.(((((((.(......).)).))))).)))(((((...((...((.(((..(((.((((((..((.((((...(((((....))))))))).))............((((((.((.(((.((.(...((......))...).)).))).)).))))))....)))))))))...))).))...))..)))))..))).))).....))))))).)))))..)).)))).....(((((........(((((....)))))........))))) (-87.59) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCAUAUAAGCAGAAGGGAUGACCCUCACAUCGGAAUAGGACGACCUUACUGAGCCGUUAGGGCGACGUUACUGAGCUGUUAGGACGACGUUACCAACCUGUUAGGACGACCUUACCGAUCUGUUAGGACGACGUUACUGAGCUGUUAGGACGACCUUACCGAUCGGGGCACUACUUUUGAAUAGAAUAUGUCAGCAUAUUUUUCUAAUCUUGUCGUCGCUAUCGGCAGAAUCCAAUGGUCCUCUCCUUCCUGUCCGAUACCACCGAAGAAACAAGCAAUUCAUCAUAAUCACCCAACAAAACACCAAGU ...............(((.(((.......((((((..((((.((((.......((((.(((((..(((((.((((....))))...)))))..))..........((((((....((((((.((.(((....((((.((((....)))))))).))).)).))))))............((.(((((((((....)))))...)))).))..)))))).))).))))..........))))...)))).....))))))......((.(((........))).))....))))))............... (-76.53) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1022 100 51 191 142 NC_002950:PG1004|5end_prolyl_oligopeptidase_family_protein_1062712..1062942_NEGATIVE 472 88 41 186 120 NC_002950:PG0124|5end_hypothetical_protein_146234..146464_NEGATIVE 395 88 43 157 107 NC_002950:PG1500|5end_hypothetical_protein_1576099..1576329_POSITIVE 395 270 221 221 153 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 392 79 31 61 17 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 390 269 223 186 147 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 373 310 264 141 86 NC_002950:PG1899|5end_TonB-dependent_receptor,_putative_1999724..1999954_NEGATIVE 367 89 42 164 117 NC_002950:PG0451|5end_CBS_domain_protein_491519..491749_POSITIVE 366 246 201 218 177 NC_002950:PG0403|5end_hypothetical_protein_439761..439991_NEGATIVE 365 80 33 69 9 NC_002950:PG1999|5end_hypothetical_protein_2088821..2089051_NEGATIVE 362 269 222 62 17 NC_002950:PG0927|5end_conserved_hypothetical_protein_TIGR00150_985050..985280_NEGATIVE 362 80 33 78 33 NC_002950:PG0433|5end_tetrapyrrole_methylase_family_protein_471396..471626_NEGATIVE 361 249 209 47 4 NC_002950:PG0230|5end_transaldolase_265372..265602_POSITIVE 354 280 235 208 156 NC_002950:PG1961|5end_hypothetical_protein_2051153..2051383_NEGATIVE 351 264 222 58 11 NC_002950:PG0236|5end_hypothetical_protein_273224..273454_POSITIVE 349 96 54 181 137 NC_002950:PG1481|5end_conjugative_transposon_protein_TraG_1558447..1558677_NEGATIVE 348 50 4 54 4 NC_002950:PG1963|5end_Sua5/YciO/YrdC/YwlC_family_protein_2052338..2052568_POSITIVE 347 250 203 113 53 NC_002950:PG0942|5end_ISPg5,_transposase_Orf1_1002063..1002293_POSITIVE 345 90 44 124 75 NC_002950:PG1887|5end_rhodanese-like_domain_protein_1984565..1984795_POSITIVE 345 99 52 192 144 NC_002950:PG1685|5end_hypothetical_protein_1772998..1773228_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 88 43 79 29 NC_002950:PG1499|3end_hypothetical_protein_1576101..1576251_POSITIVE 392 79 31 48 4 NC_002950:PG1862|3end_hypothetical_protein_1960070..1960220_NEGATIVE 376 186 145 65 25 NC_002950:PG0196|3end_peptidase,_M16_family_235808..235958_POSITIVE 373 310 264 66 11 NC_002950:PG1900|3end_ribosome-associated_GTPase_1999799..1999949_NEGATIVE 362 269 222 50 5 NC_002950:PG0928|3end_response_regulator_985062..985212_NEGATIVE 361 67 33 151 111 NC_002950:PG0125|3end_hypothetical_protein_146238..146388_NEGATIVE 360 240 193 47 1 NC_002950:PG0636|3end_MATE_efflux_family_protein_687707..687857_NEGATIVE 351 288 243 145 99 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 350 237 191 147 93 NC_002950:PG1977|3end_hypothetical_protein_2064687..2064837_NEGATIVE 345 85 41 104 65 NC_002950:PG0734|3end_nitroreductase_family_protein_784404..784554_POSITIVE 344 266 221 144 99 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 344 288 244 150 106 NC_002950:PG1797|3end_DNA-binding_response_regulator/sensor_histidine_kinase_1892978..1893128_POSITIVE 342 269 222 124 78 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 342 205 161 58 20 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 338 276 232 142 103 NC_002950:PG0926|3end_hypothetical_protein_984407..984557_NEGATIVE 337 227 181 132 81 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 337 87 46 112 78 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 336 98 55 64 15 NC_002950:PG2140|3end_ribosomal_protein_L32_2246399..2246549_POSITIVE 336 288 242 127 73 NC_002950:PG2026|3end_phosphoglycerate_mutase_family_protein_2125545..2125695_POSITIVE 336 88 43 56 8 NC_002950:PG0489|3end_polysaccharide_biosynthesis-related_protein_530808..530958_POSITIVE