Origin IGS: agtatttttttgtattgctaatgactttgatttataagtaacattcgtagacgaggaggctaattggattgagattgtataccgtttagaggatcatagtagaagtatgtaatgtccaaaggtgtcggaatgtgttctttgaagatgttcaactgaaacgcgacaaagatatgtaaaaatattgctgcatagatgaaattaaccaatagacctcaggggacaaccgcctcaaaatgctcccgtttaagtttgattgtagtgatgtgtttttgatatgcgaggggaatagtcttttgagagagagcaaatacttgttgattcgttcgatctcatggaaatgtcgttcctgtcatcactcattgtcgttcagtcttcgtgactatacagtgtaggaagtttggtaaggtttgccgagaggaggtgtgtcggttt .........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 aaaccgacacacctcctctcggcaaaccttaccaaacttcctacactgtatagtcacgaagactgaacgacaatgagtgatgacaggaacgacatttccatgagatcgaacgaatcaacaagtatttgctctctctcaaaagactattcccctcgcatatcaaaaacacatcactacaatcaaacttaaacgggagcattttgaggcggttgtcccctgaggtctattggttaatttcatctatgcagcaatatttttacatatctttgtcgcgtttcagttgaacatcttcaaagaacacattccgacacctttggacattacatacttctactatgatcctctaaacggtatacaatctcaatccaattagcctcctcgtctacgaatgttacttataaatcaaagtcattagcaatacaaaaaaatact Mask Tandem Repeat Region ================================================ agtatttttttgtattgctaatgactttgatttataagtaacattcgtagacgaggaggctaattggattgagattgtataccgtttagaggatcatagtagaagtatgtaatgtccaaaggtgtcggaatgtgttctttgaagatgttcaactgaaacgcgacaaagatatgtaaaaatattgctgcatagatgaaattaaccaatagacctcaggggacaaccgcctcaaaatgctcccgtttaagtttgattgtagtgatgtgtttttgatatgcgaggggaatagtcttttgagagagagcaaatacttgttgattcgttcgatctcatggaaatgtcgttcctgtcatcactcattgtcgttcagtcttcgtgactatacagtgtaggaagtttggtaaggtttgccgagaggaggtgtgtcggttt Find is-nt database================================================ Query_seq: PG1039:PG1040|PG1039:PG1040:integral membrane protein:transcriptional regulator, putative:<-<-:1107143..1107574 432 agtatttttttgtattgctaatgactttgatttataagtaacattcgtagacgaggaggctaattggattgagattgtataccgtttagaggatcatagtagaagtatgtaatgtccaaaggtgtcggaatgtgttctttgaagatgttcaactgaaacgcgacaaagatatgtaaaaatattgctgcatagatgaaattaaccaatagacctcaggggacaaccgcctcaaaatgctcccgtttaagtttgattgtagtgatgtgtttttgatatgcgaggggaatagtcttttgagagagagcaaatacttgttgattcgttcgatctcatggaaatgtcgttcctgtcatcactcattgtcgttcagtcttcgtgactatacagtgtaggaagtttggtaaggtttgccgagaggaggtgtgtcggttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1039:PG1040|PG1039:PG1040:integral membrane protein:transcriptional regulator, putative:<-<-:1107143..1107574 432 agtatttttttgtattgctaatgactttgatttataagtaacattcgtagacgaggaggctaattggattgagattgtataccgtttagaggatcatagtagaagtatgtaatgtccaaaggtgtcggaatgtgttctttgaagatgttcaactgaaacgcgacaaagatatgtaaaaatattgctgcatagatgaaattaaccaatagacctcaggggacaaccgcctcaaaatgctcccgtttaagtttgattgtagtgatgtgtttttgatatgcgaggggaatagtcttttgagagagagcaaatacttgttgattcgttcgatctcatggaaatgtcgttcctgtcatcactcattgtcgttcagtcttcgtgactatacagtgtaggaagtttggtaaggtttgccgagaggaggtgtgtcggttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1039:PG1040|PG1039:PG1040:integral membrane protein:transcriptional regulator, putative:<-<-:1107143..1107574 432 agtatttttttgtattgctaatgactttgatttataagtaacattcgtagacgaggaggctaattggattgagattgtataccgtttagaggatcatagtagaagtatgtaatgtccaaaggtgtcggaatgtgttctttgaagatgttcaactgaaacgcgacaaagatatgtaaaaatattgctgcatagatgaaattaaccaatagacctcaggggacaaccgcctcaaaatgctcccgtttaagtttgattgtagtgatgtgtttttgatatgcgaggggaatagtcttttgagagagagcaaatacttgttgattcgttcgatctcatggaaatgtcgttcctgtcatcactcattgtcgttcagtcttcgtgactatacagtgtaggaagtttggtaaggtttgccgagaggaggtgtgtcggttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtatttttttgtattgctaatgactttgatttataagtaacattcgtagacgaggaggctaattggattgagattgtataccgtttagaggatcatagtagaagtatgtaatgtccaaaggtgtcggaatgtgttctttgaagatgttcaactgaaacgcgacaaagatatgtaaaaatattgctgcatagatgaaattaaccaatagacctcaggggacaaccgcctcaaaatgctcccgtttaagtttgattgtagtgatgtgtttttgatatgcgaggggaatagtcttttgagagagagcaaatacttgttgattcgttcgatctcatggaaatgtcgttcctgtcatcactcattgtcgttcagtcttcgtgactatacagtgtaggaagtttggtaaggtttgccgagaggaggtgtgtcggttt Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 234 End: 389 ......................................................................................................................................................................................................................................... M L P F K F D C S D V F L I C E G N S L L R E S K Y L L I R S I S W K C R S C H H S L S F S L R D Y T V ........................................... Protein_Len: 38 Strand: - Start: 247 End: 360 ...................................................................................................................................................................................................................................................... T Q N Y H H T K S I R P S Y D K S L S C I S T S E N S R M S I D N R D D S M ........................................................................ Protein_Len: 59 Strand: - Start: 152 End: 328 ....................................................................................................................................................... S F R S L S I Y F Y Q Q M S S I L W Y V E P S L R R L I S G N L N S Q L S T N K I H S P F L R K L S L L Y K N I R E M ........................................................................................................ Protein_Len: 48 Strand: - Start: 63 End: 206 .............................................................. N S Q S Q I G N L P D Y Y F Y T I D L P T P I H E K F I N L Q F A V F I H L F I A A Y I F N V M .................................................................................................................................................................................................................................. agtatttttttgtattgctaatgactttgatttataagtaacattcgtagacgaggaggctaattggattgagattgtataccgtttagaggatcatagtagaagtatgtaatgtccaaaggtgtcggaatgtgttctttgaagatgttcaactgaaacgcgacaaagatatgtaaaaatattgctgcatagatgaaattaaccaatagacctcaggggacaaccgcctcaaaatgctcccgtttaagtttgattgtagtgatgtgtttttgatatgcgaggggaatagtcttttgagagagagcaaatacttgttgattcgttcgatctcatggaaatgtcgttcctgtcatcactcattgtcgttcagtcttcgtgactatacagtgtaggaagtttggtaaggtttgccgagaggaggtgtgtcggttt 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: 81 Start: 68 End: 97 ...................................................................ATTGAGATTGTATACCGTTTAGAGGATCAT............................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtatttttttgtattgctaatgactttgatttataagtaacattcgtagacgaggaggctaattggattgagattgtataccgtttagaggatcatagtagaagtatgtaatgtccaaaggtgtcggaatgtgttctttgaagatgttcaactgaaacgcgacaaagatatgtaaaaatattgctgcatagatgaaattaaccaatagacctcaggggacaaccgcctcaaaatgctcccgtttaagtttgattgtagtgatgtgtttttgatatgcgaggggaatagtcttttgagagagagcaaatacttgttgattcgttcgatctcatggaaatgtcgttcctgtcatcactcattgtcgttcagtcttcgtgactatacagtgtaggaagtttggtaaggtttgccgagaggaggtgtgtcggttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 41 HP_score: -2.4 Tail_Score: -2.8194 Start: 334 End: 347 Full_Region: TTCGTTCGATCTCAT GGAA ATGTCG TTCC TGTCATCACTCATTG .............................................................................................................................................................................................................................................................................................................................................GGAAATGTCGTTCC..................................................................................... Find igs database================================================ Query_seq: PG1039:PG1040|PG1039:PG1040:integral membrane protein:transcriptional regulator, putative:<-<-:1107143..1107574 432 agtatttttttgtattgctaatgactttgatttataagtaacattcgtagacgaggaggctaattggattgagattgtataccgtttagaggatcatagtagaagtatgtaatgtccaaaggtgtcggaatgtgttctttgaagatgttcaactgaaacgcgacaaagatatgtaaaaatattgctgcatagatgaaattaaccaatagacctcaggggacaaccgcctcaaaatgctcccgtttaagtttgattgtagtgatgtgtttttgatatgcgaggggaatagtcttttgagagagagcaaatacttgttgattcgttcgatctcatggaaatgtcgttcctgtcatcactcattgtcgttcagtcttcgtgactatacagtgtaggaagtttggtaaggtttgccgagaggaggtgtgtcggttt Intra-Species Hit: Count: 1 Min: 12 Max: 432 Len: 421 Subject: NC_002950_PG1039_PG1040|integral membrane protein:transcriptional regulator, putative|NEGATIVE:NEGATIVE|[1107143,1107574]|432 HSP 1 e-value: 0.0 bit: 835.0 Len: 421 Query Start:12 Query End:432 Subject Strand: POSITIVE Subject Start: 12 Subject End: 432 ...........gtattgctaatgactttgatttataagtaacattcgtagacgaggaggctaattggattgagattgtataccgtttagaggatcatagtagaagtatgtaatgtccaaaggtgtcggaatgtgttctttgaagatgttcaactgaaacgcgacaaagatatgtaaaaatattgctgcatagatgaaattaaccaatagacctcaggggacaaccgcctcaaaatgctcccgtttaagtttgattgtagtgatgtgtttttgatatgcgaggggaatagtcttttgagagagagcaaatacttgttgattcgttcgatctcatggaaatgtcgttcctgtcatcactcattgtcgttcagtcttcgtgactatacagtgtaggaagtttggtaaggtttgccgagaggaggtgtgtcggttt ...........gtattgctaatgactttgatttataagtaacattcgtagacgaggaggctaattggattgagattgtataccgtttagaggatcatagtagaagtatgtaatgtccaaaggtgtcggaatgtgttctttgaagatgttcaactgaaacgcgacaaagatatgtaaaaatattgctgcatagatgaaattaaccaatagacctcaggggacaaccgcctcaaaatgctcccgtttaagtttgattgtagtgatgtgtttttgatatgcgaggggaatagtcttttgagagagagcaaatacttgttgattcgttcgatctcatggaaatgtcgttcctgtcatcactcattgtcgttcagtcttcgtgactatacagtgtaggaagtttggtaaggtttgccgagaggaggtgtgtcggttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUUGCUAAUGACUUUGAUUUAUAAGUAACAUUCGUAGACGAGGAGGCUAAUUGGAUUGAGAUUGUAUACCGUUUAGAGGAUCAUAGUAGAAGUAUGUAAUGUCCAAAGGUGUCGGAAUGUGUUCUUUGAAGAUGUUCAACUGAAACGCGACAAAGAUAUGUAAAAAUAUUGCUGCAUAGAUGAAAUUAACCAAUAGACCUCAGGGGACAACCGCCUCAAAAUGCUCCCGUUUAAGUUUGAUUGUAGUGAUGUGUUUUUGAUAUGCGAGGGGAAUAGUCUUUUGAGAGAGAGCAAAUACUUGUUGAUUCGUUCGAUCUCAUGGAAAUGUCGUUCCUGUCAUCACUCAUUGUCGUUCAGUCUUCGUGACUAUACAGUGUAGGAAGUUUGGUAAGGUUUGCCGAGAGGAGGUGUGUCGGUUU ((.((((.((((((((........))))..)))).))))))...(((((((.((((.((((.........((.......)).((((.((((.(((((...(((((......(((((...(((.(((.(((((....)))))..)))))))))))..)))))......))))).))))....))))..))))))))))).))))....(((((((.((((.....(((.((...............((((((.(((....(((((.(.(((.((.....(((..(((((..((((.(((........))).))))..))))).)))....)).))))))))).)))))))))..((..((((.....))))..))......)).)))((((((.....)))))))))).))).))))..... (-96.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACCGACACACCUCCUCUCGGCAAACCUUACCAAACUUCCUACACUGUAUAGUCACGAAGACUGAACGACAAUGAGUGAUGACAGGAACGACAUUUCCAUGAGAUCGAACGAAUCAACAAGUAUUUGCUCUCUCUCAAAAGACUAUUCCCCUCGCAUAUCAAAAACACAUCACUACAAUCAAACUUAAACGGGAGCAUUUUGAGGCGGUUGUCCCCUGAGGUCUAUUGGUUAAUUUCAUCUAUGCAGCAAUAUUUUUACAUAUCUUUGUCGCGUUUCAGUUGAACAUCUUCAAAGAACACAUUCCGACACCUUUGGACAUUACAUACUUCUACUAUGAUCCUCUAAACGGUAUACAAUCUCAAUCCAAUUAGCCUCCUCGUCUACGAAUGUUACUUAUAAAUCAAAGUCAUUAGCAAUAC .....((((.(((.((((..((....))........(((((.....(((.(((((.....))))).)))....(((((((((...((((......)))).(((((..((.((((((.....).))))).))..)))))..............................))))))).)).............)))))......)))).)))))))....(((((..(((((.....((((.((((((.((((...............)))).))))...)).))))........................(((((((((.....((((.......))))....)))))).))).............)))))..))))).(((....))).((((((((........))))....)))).... (-78.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 898 80 31 182 133 NC_002950:PG1039|5end_integral_membrane_protein_1107052..1107282_NEGATIVE 356 410 364 180 135 NC_002950:PG1780|5end_8-amino-7-oxononanoate_synthase_1868786..1869016_POSITIVE 356 368 322 53 13 NC_002950:PG0230|5end_transaldolase_265372..265602_POSITIVE 355 408 361 60 17 NC_002950:PG1999|5end_hypothetical_protein_2088821..2089051_NEGATIVE 330 379 331 157 101 NC_002950:PG0657|5end_Maf-like_protein_707782..708012_NEGATIVE 329 369 321 114 54 NC_002950:PG1762|5end_protein-export_membrane_protein_SecD/protein-export_membrane_protein_SecF_1847988..1848218_POSITIVE 325 180 132 180 131 NC_002950:PG0752|5end_uracil_phosphoribosyltransferase_797667..797897_POSITIVE 323 337 294 123 80 NC_002950:PG1459|5end_hypothetical_protein_1539769..1539999_NEGATIVE 321 232 196 169 136 NC_002950:PG2029|5end_hypothetical_protein_2126543..2126773_POSITIVE 321 380 333 166 118 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 319 418 389 140 104 NC_002950:PG0157|5end_regulatory_protein_RecX_179706..179936_POSITIVE 318 410 363 138 88 NC_002950:PG1862|5end_hypothetical_protein_1960363..1960593_NEGATIVE 317 419 381 176 131 NC_002950:PG1500|5end_hypothetical_protein_1576099..1576329_POSITIVE 314 248 201 157 104 NC_002950:PG0659|5end_hypothetical_protein_709148..709378_NEGATIVE 314 412 376 226 187 NC_002950:PG0374|5end_hypothetical_protein_405564..405794_NEGATIVE 313 215 172 47 1 NC_002950:PG1998|5end_polyprenyl_synthetase_2088029..2088259_NEGATIVE 310 118 71 64 6 NC_002950:PG1184|5end_alginate_O-acetyltransferase,_putative_1266870..1267100_NEGATIVE 310 360 312 189 137 NC_002950:PG0256|5end_CvpA_family_protein_289509..289739_POSITIVE 306 324 281 152 109 NC_002950:PG1178|5end_hypothetical_protein_1260337..1260567_NEGATIVE 306 420 375 229 169 NC_002950:PG0868|5end_mobilization_protein_931853..932083_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 391 420 380 136 87 NC_002950:PG1711|3end_alpha-1,2-mannosidase_family_protein_1796652..1796802_NEGATIVE 353 220 171 136 71 NC_002950:PG1789|3end_peptidyl-dipeptidase_Dcp_1877417..1877567_NEGATIVE 341 418 376 116 77 NC_002950:PG1300|3end_hypothetical_protein_1378530..1378680_NEGATIVE 332 419 376 143 97 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 330 379 331 141 85 NC_002950:PG0658|3end_phosphatase,_YrbI_family_707798..707948_NEGATIVE 320 235 192 137 96 NC_002950:PG0800|3end_hypothetical_protein_854719..854869_NEGATIVE 319 420 384 143 107 NC_002950:PG1434|3end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_1519770..1519920_POSITIVE 319 365 321 115 69 NC_002950:PG0963|3end_hypothetical_protein_1024087..1024237_NEGATIVE 319 418 389 143 107 NC_002950:PG0156|3end_modification_methylase,_HemK_family_179789..179939_POSITIVE 318 410 363 137 87 NC_002950:PG1863|3end_hypothetical_protein_1960364..1960514_NEGATIVE 318 420 371 131 74 NC_002950:PG0767|3end_4-alpha-glucanotransferase_818557..818707_NEGATIVE 317 419 381 98 53 NC_002950:PG1499|3end_hypothetical_protein_1576101..1576251_POSITIVE 308 418 375 51 4 NC_002950:PG2000|3end_signal_peptidase-related_protein_2088842..2088992_NEGATIVE 306 294 257 77 32 NC_002950:PG2046|3end_hypothetical_protein_2145793..2145943_POSITIVE 306 324 281 148 105 NC_002950:PG1179|3end_hypothetical_protein_1260341..1260491_NEGATIVE 304 410 361 126 81 NC_002950:PG2026|3end_phosphoglycerate_mutase_family_protein_2125545..2125695_POSITIVE 303 419 376 126 75 NC_002950:PG1599|3end_hypothetical_protein_1679955..1680105_POSITIVE 302 410 362 142 94 NC_002950:PG0646|3end_iron_compound_ABC_transporter,_ATP-binding_protein_698070..698220_NEGATIVE 302 417 375 63 20 NC_002950:PG0013|3end_hypothetical_protein_16441..16591_POSITIVE 301 419 381 61 18 NC_002950:PG0127|3end_ferrochelatase_149667..149817_POSITIVE