Origin IGS: cgtgaaaaaagttgattggataagaaaaaaggcaagcgaagtgcattgtcccccgagagtctgacggggctatgtcaaaattcattcttggcacagcccccttttaggtacgtaagaatgcctaaagtacaaggtgctgaggctgattaaagtatgtgactgaagccgaatgtcgcaagcaacccggcaatttgcgcattatgacacaccgccatctcagcgtcaaagtactccgcttagagaggttacgggtaagaagagaagaggatagagggaatagggcttgagtgga .........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 tccactcaagccctattccctctatcctcttctcttcttacccgtaacctctctaagcggagtactttgacgctgagatggcggtgtgtcataatgcgcaaattgccgggttgcttgcgacattcggcttcagtcacatactttaatcagcctcagcaccttgtactttaggcattcttacgtacctaaaagggggctgtgccaagaatgaattttgacatagccccgtcagactctcgggggacaatgcacttcgcttgccttttttcttatccaatcaacttttttcacg Mask Tandem Repeat Region ================================================ cgtgaaaaaagttgattggataagaaaaaaggcaagcgaagtgcattgtcccccgagagtctgacggggctatgtcaaaattcattcttggcacagcccccttttaggtacgtaagaatgcctaaagtacaaggtgctgaggctgattaaagtatgtgactgaagccgaatgtcgcaagcaacccggcaatttgcgcattatgacacaccgccatctcagcgtcaaagtactccgcttagagaggttacgggtaagaagagaagaggatagagggaatagggcttgagtgga Find is-nt database================================================ Query_seq: PG0095:PG0097|PG0095:PG0097:DNA mismatch repair protein:hypothetical protein:<-<-:114854..115145 292 cgtgaaaaaagttgattggataagaaaaaaggcaagcgaagtgcattgtcccccgagagtctgacggggctatgtcaaaattcattcttggcacagcccccttttaggtacgtaagaatgcctaaagtacaaggtgctgaggctgattaaagtatgtgactgaagccgaatgtcgcaagcaacccggcaatttgcgcattatgacacaccgccatctcagcgtcaaagtactccgcttagagaggttacgggtaagaagagaagaggatagagggaatagggcttgagtgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0095:PG0097|PG0095:PG0097:DNA mismatch repair protein:hypothetical protein:<-<-:114854..115145 292 cgtgaaaaaagttgattggataagaaaaaaggcaagcgaagtgcattgtcccccgagagtctgacggggctatgtcaaaattcattcttggcacagcccccttttaggtacgtaagaatgcctaaagtacaaggtgctgaggctgattaaagtatgtgactgaagccgaatgtcgcaagcaacccggcaatttgcgcattatgacacaccgccatctcagcgtcaaagtactccgcttagagaggttacgggtaagaagagaagaggatagagggaatagggcttgagtgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0095:PG0097|PG0095:PG0097:DNA mismatch repair protein:hypothetical protein:<-<-:114854..115145 292 cgtgaaaaaagttgattggataagaaaaaaggcaagcgaagtgcattgtcccccgagagtctgacggggctatgtcaaaattcattcttggcacagcccccttttaggtacgtaagaatgcctaaagtacaaggtgctgaggctgattaaagtatgtgactgaagccgaatgtcgcaagcaacccggcaatttgcgcattatgacacaccgccatctcagcgtcaaagtactccgcttagagaggttacgggtaagaagagaagaggatagagggaatagggcttgagtgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtgaaaaaagttgattggataagaaaaaaggcaagcgaagtgcattgtcccccgagagtctgacggggctatgtcaaaattcattcttggcacagcccccttttaggtacgtaagaatgcctaaagtacaaggtgctgaggctgattaaagtatgtgactgaagccgaatgtcgcaagcaacccggcaatttgcgcattatgacacaccgccatctcagcgtcaaagtactccgcttagagaggttacgggtaagaagagaagaggatagagggaatagggcttgagtgga Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 16 End: 147 ............... M D K K K G K R S A L S P E S L T G L C Q N S F L A Q P P F R Y V R M P K V Q G A E A D ................................................................................................................................................. Protein_Len: 33 Strand: + Start: 170 End: 268 ......................................................................................................................................................................... M S Q A T R Q F A H Y D T P P S Q R Q S T P L R E V T G K K R R G ........................ Protein_Len: 43 Strand: + Start: 156 End: 284 ........................................................................................................................................................... M T E A E C R K Q P G N L R I M T H R H L S V K V L R L E R L R V R R E E D R G N R A ........ Protein_Len: 34 Strand: - Start: 125 End: 226 ............................................................................................................................ L V L H Q P Q N F Y T V S A S H R L C G P L K R M I V C R W R L T M .................................................................. Protein_Len: 31 Strand: - Start: 2 End: 94 . H F F N I P Y S F L C A F H M T G R S D S P A I D F N M R P M ...................................................................................................................................................................................................... cgtgaaaaaagttgattggataagaaaaaaggcaagcgaagtgcattgtcccccgagagtctgacggggctatgtcaaaattcattcttggcacagcccccttttaggtacgtaagaatgcctaaagtacaaggtgctgaggctgattaaagtatgtgactgaagccgaatgtcgcaagcaacccggcaatttgcgcattatgacacaccgccatctcagcgtcaaagtactccgcttagagaggttacgggtaagaagagaagaggatagagggaatagggcttgagtgga 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: 198 End: 227 .....................................................................................................................................................................................................TTTGACGCTGAGATGGCGGTGTGTCATAAT................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgtgaaaaaagttgattggataagaaaaaaggcaagcgaagtgcattgtcccccgagagtctgacggggctatgtcaaaattcattcttggcacagcccccttttaggtacgtaagaatgcctaaagtacaaggtgctgaggctgattaaagtatgtgactgaagccgaatgtcgcaagcaacccggcaatttgcgcattatgacacaccgccatctcagcgtcaaagtactccgcttagagaggttacgggtaagaagagaagaggatagagggaatagggcttgagtgga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 69 HP_score: -5.8 Tail_Score: -4.19817 Start: 65 End: 101 Full_Region: CCCCCGAGAGTCTGA CGGGGCTATGTCAAAA TTCAT TCTTGGCACAGCCCCC TTTTAGGTACGTAAG ................................................................CGGGGCTATGTCAAAATTCATTCTTGGCACAGCCCCC............................................................................................................................................................................................... TransTerm Strand: + Conf: 67 HP_score: -9.3 Tail_Score: -3.11569 Start: 66 End: 100 Full_Region: CCCCGAGAGTCTGAC GGGGCTATGTCAAAA TTCAT TCTTGGCACAGCCCC CTTTTAGGTACGTAA .................................................................GGGGCTATGTCAAAATTCATTCTTGGCACAGCCCC................................................................................................................................................................................................ Find igs database================================================ Query_seq: PG0095:PG0097|PG0095:PG0097:DNA mismatch repair protein:hypothetical protein:<-<-:114854..115145 292 cgtgaaaaaagttgattggataagaaaaaaggcaagcgaagtgcattgtcccccgagagtctgacggggctatgtcaaaattcattcttggcacagcccccttttaggtacgtaagaatgcctaaagtacaaggtgctgaggctgattaaagtatgtgactgaagccgaatgtcgcaagcaacccggcaatttgcgcattatgacacaccgccatctcagcgtcaaagtactccgcttagagaggttacgggtaagaagagaagaggatagagggaatagggcttgagtgga Intra-Species Hit: Count: 1 Min: 1 Max: 292 Len: 292 Subject: NC_002950_PG0095_PG0097|DNA mismatch repair protein:hypothetical protein|NEGATIVE:NEGATIVE|[114854,115145]|292 HSP 1 e-value: 1.0E-164 bit: 579.0 Len: 292 Query Start:1 Query End:292 Subject Strand: POSITIVE Subject Start: 1 Subject End: 292 cgtgaaaaaagttgattggataagaaaaaaggcaagcgaagtgcattgtcccccgagagtctgacggggctatgtcaaaattcattcttggcacagcccccttttaggtacgtaagaatgcctaaagtacaaggtgctgaggctgattaaagtatgtgactgaagccgaatgtcgcaagcaacccggcaatttgcgcattatgacacaccgccatctcagcgtcaaagtactccgcttagagaggttacgggtaagaagagaagaggatagagggaatagggcttgagtgga cgtgaaaaaagttgattggataagaaaaaaggcaagcgaagtgcattgtcccccgagagtctgacggggctatgtcaaaattcattcttggcacagcccccttttaggtacgtaagaatgcctaaagtacaaggtgctgaggctgattaaagtatgtgactgaagccgaatgtcgcaagcaacccggcaatttgcgcattatgacacaccgccatctcagcgtcaaagtactccgcttagagaggttacgggtaagaagagaagaggatagagggaatagggcttgagtgga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUGAAAAAAGUUGAUUGGAUAAGAAAAAAGGCAAGCGAAGUGCAUUGUCCCCCGAGAGUCUGACGGGGCUAUGUCAAAAUUCAUUCUUGGCACAGCCCCCUUUUAGGUACGUAAGAAUGCCUAAAGUACAAGGUGCUGAGGCUGAUUAAAGUAUGUGACUGAAGCCGAAUGUCGCAAGCAACCCGGCAAUUUGCGCAUUAUGACACACCGCCAUCUCAGCGUCAAAGUACUCCGCUUAGAGAGGUUACGGGUAAGAAGAGAAGAGGAUAGAGGGAAUAGGGCUUGAGUGGA ................................(((((....(.(.((((((((((...(((....((((((.((((((.........)))))).))))))..(((((((((....)..))))))))(..((((.(((((.((((......(((.....)))..))))...((.(....)))...))))).))))..).....))).....(((.((((((((...........))))..)))))))..)))).............)))))).).)......)))))...... (-73.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCACUCAAGCCCUAUUCCCUCUAUCCUCUUCUCUUCUUACCCGUAACCUCUCUAAGCGGAGUACUUUGACGCUGAGAUGGCGGUGUGUCAUAAUGCGCAAAUUGCCGGGUUGCUUGCGACAUUCGGCUUCAGUCACAUACUUUAAUCAGCCUCAGCACCUUGUACUUUAGGCAUUCUUACGUACCUAAAAGGGGGCUGUGCCAAGAAUGAAUUUUGACAUAGCCCCGUCAGACUCUCGGGGGACAAUGCACUUCGCUUGCCUUUUUUCUUAUCCAAUCAACUUUUUUCACG .....................................................((((((((((.(.(((..(((((...(((.((((((....)))))).....((((.((((....))))...)))).....................)))))))).(((((...((((((.((......)).))))))..(((((((((.(((((.....))))).)))))))))..........)))))..))).).))))))))))................................ (-70.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1056 80 31 171 122 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 687 209 162 183 137 NC_002950:PG1117|5end_MATE_efflux_family_protein_1190010..1190240_POSITIVE 493 110 62 68 16 NC_002950:PG1234|5end_hypothetical_protein_1310112..1310342_POSITIVE 391 70 22 134 68 NC_002950:PG1029|5end_hypothetical_protein_1091080..1091310_POSITIVE 391 99 51 225 173 NC_002950:PG0749|5end_hypothetical_protein_795654..795884_NEGATIVE 388 70 24 127 72 NC_002950:PG0499|5end_hypothetical_protein_538709..538939_POSITIVE 374 122 81 89 46 NC_002950:PG1366|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1447380..1447610_NEGATIVE 374 145 101 211 152 NC_002950:PG0804|5end_flavodoxin_861765..861995_NEGATIVE 369 98 51 211 145 NC_002950:PG1069|5end_alcohol_dehydrogenase,_zinc-containing,_putative_1135499..1135729_POSITIVE 359 76 31 61 17 NC_002950:PG0462|5end_transporter,_putative_506279..506509_NEGATIVE 351 68 28 205 165 NC_002950:PG2027|5end_hypothetical_protein_2125494..2125724_POSITIVE 351 190 141 218 160 NC_002950:PG1959|5end_ribosomal_protein_L33_2048405..2048635_NEGATIVE 351 103 66 77 40 NC_002950:PG1268|5end_hypothetical_protein_1347371..1347601_POSITIVE 351 217 175 216 168 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 349 70 28 53 8 NC_002950:PG1701|5end_glutamine_amidotransferase,_class_II/dipeptidase_1787953..1788183_NEGATIVE 347 79 35 52 1 NC_002950:PG1611|5end_hypothetical_protein_1691487..1691717_NEGATIVE 347 76 31 227 163 NC_002950:PG0192|5end_cationic_outer_membrane_protein_OmpH_229590..229820_POSITIVE 346 79 34 58 7 NC_002950:PG0593|5end_htrA_protein_650362..650592_POSITIVE 342 208 164 74 26 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 336 77 31 69 2 NC_002950:PG1434|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_1519022..1519252_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 434 100 52 49 1 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 409 102 61 46 8 NC_002950:PG1809|3end_2-oxoglutarate_oxidoreductase,_gamma_subunit_1905491..1905641_NEGATIVE 402 287 241 90 29 NC_002950:PG0309|3end_thiamine_biosynthesis_lipoprotein_ApbE_344010..344160_NEGATIVE 391 70 22 70 4 NC_002950:PG1028|3end_TPR_domain_protein_1091096..1091246_POSITIVE 386 108 66 53 9 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE 375 98 51 80 17 NC_002950:PG0343|3end_methionine_gamma-lyase_377181..377331_NEGATIVE 374 122 81 58 15 NC_002950:PG1367|3end_hypothetical_protein_1447411..1447561_NEGATIVE 358 106 66 44 7 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 354 99 53 67 20 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 349 275 236 116 74 NC_002950:PG2077|3end_hypothetical_protein_2177005..2177155_NEGATIVE 349 70 28 60 15 NC_002950:PG1702|3end_DNA_gyrase,_B_subunit_1787946..1788096_NEGATIVE 344 70 29 55 20 NC_002950:PG0775|3end_acyl-CoA_dehydrogenase_family_protein_827432..827582_NEGATIVE 339 275 237 133 91 NC_002950:PG0013|3end_hypothetical_protein_16441..16591_POSITIVE 338 260 211 147 106 NC_002950:PG1625|3end_hypothetical_protein_1708718..1708868_POSITIVE 338 108 63 71 26 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 336 285 244 92 59 NC_002950:PG2161|3end_transcriptional_regulator,_AraC_family_2266717..2266867_NEGATIVE 336 100 55 65 22 NC_002950:PG1729|3end_thiol_peroxidase_1818342..1818492_NEGATIVE 336 77 31 93 26 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 336 230 184 100 51 NC_002950:PG0171|3end_5'-nucleotidase_family_protein_193576..193726_POSITIVE 334 130 88 87 43 NC_002950:PG2029|3end_hypothetical_protein_2129202..2129352_POSITIVE