Origin IGS: agatacttacattccttagcttaaaagtcgaaaaagagatccgccgaagctcccccaaaagaggaatcccgtaaaaaccgaaaatctgtaatatactgtatgaaaagtctaacaaaatccctatcggcactcccgataaagaaaacacgagcggcaagacacaaaaaaacggaactgaaaaatccgaaatagtcgttcggtgatcaaaaaattctcgctcgtctttttttcgcttttggttcgagatttggaaaaaagacgaaccgtaaatccgaaatcatggcgcgagtttttcccgatttttcgttcgctttttgtctgttgcgactgctctatcagtagccgataacagattttatcacaaatgggtattcggagttttgtatcgaacgaaggggctgatcttctttcgctgttcctc .........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 gaggaacagcgaaagaagatcagccccttcgttcgatacaaaactccgaatacccatttgtgataaaatctgttatcggctactgatagagcagtcgcaacagacaaaaagcgaacgaaaaatcgggaaaaactcgcgccatgatttcggatttacggttcgtcttttttccaaatctcgaaccaaaagcgaaaaaaagacgagcgagaattttttgatcaccgaacgactatttcggatttttcagttccgtttttttgtgtcttgccgctcgtgttttctttatcgggagtgccgatagggattttgttagacttttcatacagtatattacagattttcggtttttacgggattcctcttttgggggagcttcggcggatctctttttcgacttttaagctaaggaatgtaagtatct Mask Tandem Repeat Region ================================================ agatacttacattccttagcttaaaagtcgaaaaagagatccgccgaagctcccccaaaagaggaatcccgtaaaaaccgaaaatctgtaatatactgtatgaaaagtctaacaaaatccctatcggcactcccgataaagaaaacacgagcggcaagacacaaaaaaacggaactgaaaaatccgaaatagtcgttcggtgatcaaaaaattctcgctcgtctttttttcgcttttggttcgagatttggaaaaaagacgaaccgtaaatccgaaatcatggcgcgagtttttcccgatttttcgttcgctttttgtctgttgcgactgctctatcagtagccgataacagattttatcacaaatgggtattcggagttttgtatcgaacgaaggggctgatcttctttcgctgttcctc Find is-nt database================================================ Query_seq: PG2094:PG2095|PG2094:PG2095:hypothetical protein:lipoprotein, putative:<-<-:2197959..2198379 421 agatacttacattccttagcttaaaagtcgaaaaagagatccgccgaagctcccccaaaagaggaatcccgtaaaaaccgaaaatctgtaatatactgtatgaaaagtctaacaaaatccctatcggcactcccgataaagaaaacacgagcggcaagacacaaaaaaacggaactgaaaaatccgaaatagtcgttcggtgatcaaaaaattctcgctcgtctttttttcgcttttggttcgagatttggaaaaaagacgaaccgtaaatccgaaatcatggcgcgagtttttcccgatttttcgttcgctttttgtctgttgcgactgctctatcagtagccgataacagattttatcacaaatgggtattcggagttttgtatcgaacgaaggggctgatcttctttcgctgttcctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2094:PG2095|PG2094:PG2095:hypothetical protein:lipoprotein, putative:<-<-:2197959..2198379 421 agatacttacattccttagcttaaaagtcgaaaaagagatccgccgaagctcccccaaaagaggaatcccgtaaaaaccgaaaatctgtaatatactgtatgaaaagtctaacaaaatccctatcggcactcccgataaagaaaacacgagcggcaagacacaaaaaaacggaactgaaaaatccgaaatagtcgttcggtgatcaaaaaattctcgctcgtctttttttcgcttttggttcgagatttggaaaaaagacgaaccgtaaatccgaaatcatggcgcgagtttttcccgatttttcgttcgctttttgtctgttgcgactgctctatcagtagccgataacagattttatcacaaatgggtattcggagttttgtatcgaacgaaggggctgatcttctttcgctgttcctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2094:PG2095|PG2094:PG2095:hypothetical protein:lipoprotein, putative:<-<-:2197959..2198379 421 agatacttacattccttagcttaaaagtcgaaaaagagatccgccgaagctcccccaaaagaggaatcccgtaaaaaccgaaaatctgtaatatactgtatgaaaagtctaacaaaatccctatcggcactcccgataaagaaaacacgagcggcaagacacaaaaaaacggaactgaaaaatccgaaatagtcgttcggtgatcaaaaaattctcgctcgtctttttttcgcttttggttcgagatttggaaaaaagacgaaccgtaaatccgaaatcatggcgcgagtttttcccgatttttcgttcgctttttgtctgttgcgactgctctatcagtagccgataacagattttatcacaaatgggtattcggagttttgtatcgaacgaaggggctgatcttctttcgctgttcctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agatacttacattccttagcttaaaagtcgaaaaagagatccgccgaagctcccccaaaagaggaatcccgtaaaaaccgaaaatctgtaatatactgtatgaaaagtctaacaaaatccctatcggcactcccgataaagaaaacacgagcggcaagacacaaaaaaacggaactgaaaaatccgaaatagtcgttcggtgatcaaaaaattctcgctcgtctttttttcgcttttggttcgagatttggaaaaaagacgaaccgtaaatccgaaatcatggcgcgagtttttcccgatttttcgttcgctttttgtctgttgcgactgctctatcagtagccgataacagattttatcacaaatgggtattcggagttttgtatcgaacgaaggggctgatcttctttcgctgttcctc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 91 End: 189 .......................................................................................... M Y C M K S L T K S L S A L P I K K T R A A R H K K T E L K N P K ........................................................................................................................................................................................................................................ Protein_Len: 39 Strand: + Start: 84 End: 200 ................................................................................... M C N I L Y E K S N K I P I G T P D K E N T S G K T Q K N G T E K S E I V V R ............................................................................................................................................................................................................................. Protein_Len: 43 Strand: + Start: 211 End: 339 .................................................................................................................................................................................................................. M L A R L F F A F G S R F G K K T N R K S E I M A R V F P D F S F A F C L L R L L Y Q .................................................................................. Protein_Len: 55 Strand: + Start: 182 End: 346 ..................................................................................................................................................................................... M R N S R S V I K K F S L V F F S L L V R D L E K R R T V N P K S W R E F F P I F R S L F V C C D C S I S S R ........................................................................... Protein_Len: 50 Strand: + Start: 270 End: 419 ............................................................................................................................................................................................................................................................................. M R N H G A S F S R F F V R F L S V A T A L S V A D N R F Y H K W V F G V L Y R T K G L I F F R C S .. Protein_Len: 60 Strand: - Start: 124 End: 372 ........................................................................................................................... R E T I L F N E S T K K E S K T R S K S F L R V T F G F D H R S N K G I K R E S K T Q Q S Q E I L L R Y C I K D C I P M ................................................. Protein_Len: 47 Strand: - Start: 24 End: 164 ....................... F D F F L D A S A G G F S S D R L F R F D T I Y Q I F L R V F D R D A S G I F F V R A A L C M ................................................................................................................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 2 End: 271 . I S Y S F D L L I G I P V G S L S F V L P L V C F F P V S F D S I T T R H D F F E R E D K K R K Q N S I Q F F S S G Y M ...................................................................................................................................................... agatacttacattccttagcttaaaagtcgaaaaagagatccgccgaagctcccccaaaagaggaatcccgtaaaaaccgaaaatctgtaatatactgtatgaaaagtctaacaaaatccctatcggcactcccgataaagaaaacacgagcggcaagacacaaaaaaacggaactgaaaaatccgaaatagtcgttcggtgatcaaaaaattctcgctcgtctttttttcgcttttggttcgagatttggaaaaaagacgaaccgtaaatccgaaatcatggcgcgagtttttcccgatttttcgttcgctttttgtctgttgcgactgctctatcagtagccgataacagattttatcacaaatgggtattcggagttttgtatcgaacgaaggggctgatcttctttcgctgttcctc 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================================================ agatacttacattccttagcttaaaagtcgaaaaagagatccgccgaagctcccccaaaagaggaatcccgtaaaaaccgaaaatctgtaatatactgtatgaaaagtctaacaaaatccctatcggcactcccgataaagaaaacacgagcggcaagacacaaaaaaacggaactgaaaaatccgaaatagtcgttcggtgatcaaaaaattctcgctcgtctttttttcgcttttggttcgagatttggaaaaaagacgaaccgtaaatccgaaatcatggcgcgagtttttcccgatttttcgttcgctttttgtctgttgcgactgctctatcagtagccgataacagattttatcacaaatgggtattcggagttttgtatcgaacgaaggggctgatcttctttcgctgttcctc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 83 HP_score: -7.2 Tail_Score: -4.70613 Start: 118 End: 142 Full_Region: ttgccgctcgtgttt tctttatcgg gagtg ccgataggga ttttgttagactttt .....................................................................................................................tctttatcgggagtgccgataggga....................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 85 HP_score: -2.9 Tail_Score: -5.80248 Start: 170 End: 186 Full_Region: accgaacgactattt cggattt ttc agttccg tttttttgtgtcttg .........................................................................................................................................................................cggatttttcagttccg........................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 52 HP_score: -3.7 Tail_Score: -3.44381 Start: 184 End: 200 Full_Region: agaattttttgatca ccgaa cgactat ttcgg atttttcagttccgt .......................................................................................................................................................................................ccgaacgactatttcgg............................................................................................................................................................................................................................. TransTerm Strand: + Conf: 64 HP_score: -4.1 Tail_Score: -4.37886 Start: 318 End: 353 Full_Region: TTCGTTCGCTTTTTG TCTGTTGCGACTGCT CTATC AGTAGCCGATAACAGA TTTTATCACAAATGG .............................................................................................................................................................................................................................................................................................................................TCTGTTGCGACTGCTCTATCAGTAGCCGATAACAGA.................................................................... Find igs database================================================ Query_seq: PG2094:PG2095|PG2094:PG2095:hypothetical protein:lipoprotein, putative:<-<-:2197959..2198379 421 agatacttacattccttagcttaaaagtcgaaaaagagatccgccgaagctcccccaaaagaggaatcccgtaaaaaccgaaaatctgtaatatactgtatgaaaagtctaacaaaatccctatcggcactcccgataaagaaaacacgagcggcaagacacaaaaaaacggaactgaaaaatccgaaatagtcgttcggtgatcaaaaaattctcgctcgtctttttttcgcttttggttcgagatttggaaaaaagacgaaccgtaaatccgaaatcatggcgcgagtttttcccgatttttcgttcgctttttgtctgttgcgactgctctatcagtagccgataacagattttatcacaaatgggtattcggagttttgtatcgaacgaaggggctgatcttctttcgctgttcctc Intra-Species Hit: Count: 1 Min: 1 Max: 421 Len: 421 Subject: NC_002950_PG2094_PG2095|hypothetical protein:lipoprotein, putative|NEGATIVE:NEGATIVE|[2197959,2198379]|421 HSP 1 e-value: 0.0 bit: 751.0 Len: 421 Query Start:1 Query End:421 Subject Strand: POSITIVE Subject Start: 1 Subject End: 421 agatacttacattccttagcttaaaagtcgaaaaagagatccgccgaagctcccccaaaagaggaatcccgtaaaaaccgaaaatctgtaatatactgtatgaaaagtctaacaaaatccctatcggcactcccgataaagaaaacacgagcggcaagacacnnnnnnncggaactgaaaaatccgaaatagtcgttcggtgatcaaaaaattctcgctcgtcnnnnnnncgcttttggttcgagatttggaaaaaagacgaaccgtaaatccgaaatcatggcgcgagtttttcccgatttttcgttcgctttttgtctgttgcgactgctctatcagtagccgataacagattttatcacaaatgggtattcggagttttgtatcgaacgaaggggctgatcttctttcgctgttcctc agatacttacattccttagcttaaaagtcgaaaaagagatccgccgaagctcccccaaaagaggaatcccgtaaaaaccgaaaatctgtaatatactgtatgaaaagtctaacaaaatccctatcggcactcccgataaagaaaacacgagcggcaagacacaaaaaaacggaactgaaaaatccgaaatagtcgttcggtgatcaaaaaattctcgctcgtctttttttcgcttttggttcgagatttggaaaaaagacgaaccgtaaatccgaaatcatggcgcgagtttttcccgatttttcgttcgctttttgtctgttgcgactgctctatcagtagccgataacagattttatcacaaatgggtattcggagttttgtatcgaacgaaggggctgatcttctttcgctgttcctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUACUUACAUUCCUUAGCUUAAAAGUCGAAAAAGAGAUCCGCCGAAGCUCCCCCAAAAGAGGAAUCCCGUAAAAACCGAAAAUCUGUAAUAUACUGUAUGAAAAGUCUAACAAAAUCCCUAUCGGCACUCCCGAUAAAGAAAACACGAGCGGCAAGACACAAAAAAACGGAACUGAAAAAUCCGAAAUAGUCGUUCGGUGAUCAAAAAAUUCUCGCUCGUCUUUUUUUCGCUUUUGGUUCGAGAUUUGGAAAAAAGACGAACCGUAAAUCCGAAAUCAUGGCGCGAGUUUUUCCCGAUUUUUCGUUCGCUUUUUGUCUGUUGCGACUGCUCUAUCAGUAGCCGAUAACAGAUUUUAUCACAAAUGGGUAUUCGGAGUUUUGUAUCGAACGAAGGGGCUGAUCUUCUUUCGCUGUUCCUC .........................((.(((((..((((((.(((...(((((..........(((((((((........(((((((((.((.(((((...((..((((........((..((((((.....))))))..))........((((((.((((...((((.((((...((((((((.((((.(.((((.(.(((((......(((..((.((((((((((((((..(((......)))..))))))))))))))..))..))).....))))).).)))).).))))..)))))))).)))).))))))))))))))))))..))...)))))....)).))))))))).......))))).)))))))))(((((.....)))))..))).)))))).)))))))....... (-111.96) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGAACAGCGAAAGAAGAUCAGCCCCUUCGUUCGAUACAAAACUCCGAAUACCCAUUUGUGAUAAAAUCUGUUAUCGGCUACUGAUAGAGCAGUCGCAACAGACAAAAAGCGAACGAAAAAUCGGGAAAAACUCGCGCCAUGAUUUCGGAUUUACGGUUCGUCUUUUUUCCAAAUCUCGAACCAAAAGCGAAAAAAAGACGAGCGAGAAUUUUUUGAUCACCGAACGACUAUUUCGGAUUUUUCAGUUCCGUUUUUUUGUGUCUUGCCGCUCGUGUUUUCUUUAUCGGGAGUGCCGAUAGGGAUUUUGUUAGACUUUUCAUACAGUAUAUUACAGAUUUUCGGUUUUUACGGGAUUCCUCUUUUGGGGGAGCUUCGGCGGAUCUCUUUUUCGACUUUUAAGCUAAGGAAUGUAAGUAUCU .(((.((..((((((((((((..(((((..((...((((.......(((((....)))))(((((((((((.((((((((..(((((((((((((.((((.(.(((((((((((((((((((((.((((....(((..(..(((((..((((((.((.((((((((((((.......(((.........))))))))))))))))).))))))...)))))..)..)))...)))).)))))))).))).)).)))))))).).)))).))).)......)))))))))....))))))))))))))))))).............))))...)).((.(..((.......))..).)).......))))).((....)).))))).))))))).((((......)))).......)).))) (-115.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 977 80 31 171 122 NC_002950:PG2094|5end_hypothetical_protein_2197868..2198098_NEGATIVE 395 326 282 55 13 NC_002950:PG0488|5end_Holliday_junction_DNA_helicase_RuvB_528169..528399_POSITIVE 388 87 41 60 16 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 378 250 206 199 154 NC_002950:PG0132|5end_hypothetical_protein_152879..153109_POSITIVE 363 346 301 206 154 NC_002950:PG1134|5end_thioredoxin_reductase_1214350..1214580_POSITIVE 353 158 117 220 178 NC_002950:PG1659|5end_hypothetical_protein_1743747..1743977_NEGATIVE 352 80 38 223 181 NC_002950:PG1343|5end_lipoate-protein_ligase_B_1423628..1423858_POSITIVE 350 329 283 227 181 NC_002950:PG1692|5end_ABC_transporter,_ATP-binding_protein_1777173..1777403_NEGATIVE 345 419 372 150 92 NC_002950:PG2142|5end_GTP-binding_protein_Era_2247585..2247815_POSITIVE 342 347 306 218 174 NC_002950:PG1940|5end_elongation_factor_EF-2_2027220..2027450_NEGATIVE 341 298 255 171 108 NC_002950:PG2002|5end_dihydrodipicolinate_reductase_2091587..2091817_NEGATIVE 335 417 375 126 76 NC_002950:PG1021|5end_hypothetical_protein_1083592..1083822_NEGATIVE 334 318 273 158 111 NC_002950:PG2055|5end_dihydroorotate_dehydrogenase_2153060..2153290_NEGATIVE 333 298 259 189 141 NC_002950:PG0978|5end_shikimate_5-dehydrogenase_1040033..1040263_POSITIVE 332 326 282 204 146 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 330 416 373 196 148 NC_002950:PG0192|5end_cationic_outer_membrane_protein_OmpH_229590..229820_POSITIVE 328 419 372 178 131 NC_002950:PG2164|5end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2270125..2270355_NEGATIVE 328 336 296 61 24 NC_002950:PG2156|5end_conserved_hypothetical_protein_TIGR00046_2262645..2262875_NEGATIVE 328 330 286 213 160 NC_002950:PG0259|5end_hypothetical_protein_292278..292508_POSITIVE 328 344 302 167 126 NC_002950:PG0125|5end_hypothetical_protein_146786..147016_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 383 340 297 131 75 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE 345 419 372 71 13 NC_002950:PG2141|3end_3-oxoacyl-(acyl_carrier_protein)_synthase_2247586..2247736_POSITIVE 341 298 255 110 47 NC_002950:PG2003|3end_deoxyguanosinetriphosphate_triphosphohydrolase_2091648..2091798_NEGATIVE 341 160 117 108 61 NC_002950:PG0441|3end_hypothetical_protein_481447..481597_POSITIVE 330 416 373 139 91 NC_002950:PG0191|3end_outer_membrane_protein,_putative_229613..229763_POSITIVE 328 80 41 148 116 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 326 333 297 43 1 NC_002950:PG1846|3end_hypothetical_protein_1946254..1946404_POSITIVE 319 420 373 50 1 NC_002950:PG0882|3end_hypothetical_protein_945204..945354_POSITIVE 319 300 256 102 60 NC_002950:PG0423|3end_hypothetical_protein_462573..462723_POSITIVE 312 330 281 83 14 NC_002950:PG2121|3end_L-asparaginase_2228545..2228695_NEGATIVE 311 418 375 75 20 NC_002950:PG0572|3end_hypothetical_protein_627434..627584_NEGATIVE 307 419 374 42 1 NC_002950:PG1285|3end_glucosamine-6-phosphate_deaminase_1364941..1365091_POSITIVE 306 420 374 104 60 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 304 330 281 114 72 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 304 240 191 133 86 NC_002950:PG1473|3end_conjugative_transposon_protein_TraQ_1549761..1549911_NEGATIVE 303 325 281 80 34 NC_002950:PG1919|3end_ribosomal_protein_L15_2015835..2015985_NEGATIVE 303 419 374 140 83 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 303 402 367 132 98 NC_002950:PG0957|3end_riboflavin_biosynthesis_protein_RibF_1018131..1018281_POSITIVE 302 314 271 67 27 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 301 253 217 85 34 NC_002950:PG2032|3end_primosomal_protein_N'_2130868..2131018_NEGATIVE