Origin IGS: cattataataggtagtatcgtttctgttttgtcgggttcatttcccaagcaatagcacacaaaacgcctgaggagaaacaaattccgacaaatccgtatggagctattggcacacaaaggtagggaagccgaatcaaaatctcctattatgaacggaggttttgtctcttttccggtttgcaaactgcaaacaaaggcctgacggcaaaggggcaggagtcctgtttcggctcctgccccttcgagaccggacggatcggttgtactacgatacggccgtttcgtagctgctatatataataaggtatagggagaacgtgggggaatggatcccatctacct .........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 aggtagatgggatccattcccccacgttctccctataccttattatatatagcagctacgaaacggccgtatcgtagtacaaccgatccgtccggtctcgaaggggcaggagccgaaacaggactcctgcccctttgccgtcaggcctttgtttgcagtttgcaaaccggaaaagagacaaaacctccgttcataataggagattttgattcggcttccctacctttgtgtgccaatagctccatacggatttgtcggaatttgtttctcctcaggcgttttgtgtgctattgcttgggaaatgaacccgacaaaacagaaacgatactacctattataatg Mask Tandem Repeat Region ================================================ cattataataggtagtatcgtttctgttttgtcgggttcatttcccaagcaatagcacacaaaacgcctgaggagaaacaaattccgacaaatccgtatggagctattggcacacaaaggtagggaagccgaatcaaaatctcctattatgaacggaggttttgtctcttttccggtttgcaaactgcaaacaaaggcctgacggcaaaggggcaggagtcctgtttcggctcctgccccttcgagaccggacggatcggttgtactacgatacggccgtttcgtagctgctatatataataaggtatagggagaacgtgggggaatggatcccatctacct Find is-nt database================================================ Query_seq: PG0279:PG0280|PG0279:PG0280:NADP-dependent malic enzyme:ABC transporter, permease protein, putative:<-<-:313045..313386 342 cattataataggtagtatcgtttctgttttgtcgggttcatttcccaagcaatagcacacaaaacgcctgaggagaaacaaattccgacaaatccgtatggagctattggcacacaaaggtagggaagccgaatcaaaatctcctattatgaacggaggttttgtctcttttccggtttgcaaactgcaaacaaaggcctgacggcaaaggggcaggagtcctgtttcggctcctgccccttcgagaccggacggatcggttgtactacgatacggccgtttcgtagctgctatatataataaggtatagggagaacgtgggggaatggatcccatctacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0279:PG0280|PG0279:PG0280:NADP-dependent malic enzyme:ABC transporter, permease protein, putative:<-<-:313045..313386 342 cattataataggtagtatcgtttctgttttgtcgggttcatttcccaagcaatagcacacaaaacgcctgaggagaaacaaattccgacaaatccgtatggagctattggcacacaaaggtagggaagccgaatcaaaatctcctattatgaacggaggttttgtctcttttccggtttgcaaactgcaaacaaaggcctgacggcaaaggggcaggagtcctgtttcggctcctgccccttcgagaccggacggatcggttgtactacgatacggccgtttcgtagctgctatatataataaggtatagggagaacgtgggggaatggatcccatctacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0279:PG0280|PG0279:PG0280:NADP-dependent malic enzyme:ABC transporter, permease protein, putative:<-<-:313045..313386 342 cattataataggtagtatcgtttctgttttgtcgggttcatttcccaagcaatagcacacaaaacgcctgaggagaaacaaattccgacaaatccgtatggagctattggcacacaaaggtagggaagccgaatcaaaatctcctattatgaacggaggttttgtctcttttccggtttgcaaactgcaaacaaaggcctgacggcaaaggggcaggagtcctgtttcggctcctgccccttcgagaccggacggatcggttgtactacgatacggccgtttcgtagctgctatatataataaggtatagggagaacgtgggggaatggatcccatctacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cattataataggtagtatcgtttctgttttgtcgggttcatttcccaagcaatagcacacaaaacgcctgaggagaaacaaattccgacaaatccgtatggagctattggcacacaaaggtagggaagccgaatcaaaatctcctattatgaacggaggttttgtctcttttccggtttgcaaactgcaaacaaaggcctgacggcaaaggggcaggagtcctgtttcggctcctgccccttcgagaccggacggatcggttgtactacgatacggccgtttcgtagctgctatatataataaggtatagggagaacgtgggggaatggatcccatctacct Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 68 End: 199 ................................................................... M R R N K F R Q I R M E L L A H K G R E A E S K S P I M N G G F V S F P V C K L Q T K A ............................................................................................................................................... Protein_Len: 41 Strand: + Start: 162 End: 284 ................................................................................................................................................................. M S L F R F A N C K Q R P D G K G A G V L F R L L P L R D R T D R L Y Y D T A V S .......................................................... Protein_Len: 55 Strand: + Start: 133 End: 297 .................................................................................................................................... M K I S Y Y E R R F C L F S G L Q T A N K G L T A K G Q E S C F G S C P F E T G R I G C T T I R P F R S C Y I ............................................. Protein_Len: 41 Strand: - Start: 150 End: 272 ..................................................................................................................................................... S R L N Q R K E P K C V A F L P R V A F P C S D Q K P E Q G K S V P R I P Q V V M ...................................................................... Protein_Len: 46 Strand: - Start: 6 End: 140 ..... * L L Y Y R K Q K T P N M E W A I A C L V G S S F C I G V F G Y P A I P V C L Y P L R I L M .......................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 1 End: 336 P K T E K G T Q L S C V F A Q R C L P L L G T E A G A G E L G S P D T T S R Y P R K T A A I Y L L T Y P S R P P I S G M ...... cattataataggtagtatcgtttctgttttgtcgggttcatttcccaagcaatagcacacaaaacgcctgaggagaaacaaattccgacaaatccgtatggagctattggcacacaaaggtagggaagccgaatcaaaatctcctattatgaacggaggttttgtctcttttccggtttgcaaactgcaaacaaaggcctgacggcaaaggggcaggagtcctgtttcggctcctgccccttcgagaccggacggatcggttgtactacgatacggccgtttcgtagctgctatatataataaggtatagggagaacgtgggggaatggatcccatctacct 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================================================ cattataataggtagtatcgtttctgttttgtcgggttcatttcccaagcaatagcacacaaaacgcctgaggagaaacaaattccgacaaatccgtatggagctattggcacacaaaggtagggaagccgaatcaaaatctcctattatgaacggaggttttgtctcttttccggtttgcaaactgcaaacaaaggcctgacggcaaaggggcaggagtcctgtttcggctcctgccccttcgagaccggacggatcggttgtactacgatacggccgtttcgtagctgctatatataataaggtatagggagaacgtgggggaatggatcccatctacct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 51 HP_score: -4.4 Tail_Score: -3.43039 Start: 135 End: 164 Full_Region: GTAGGGAAGCCGAAT CAAAATCTCC TATTATGAAC GGAGGTTTTG TCTCTTTTCCGGTTT ......................................................................................................................................CAAAATCTCCTATTATGAACGGAGGTTTTG.................................................................................................................................................................................. TransTerm Strand: - Conf: 86 HP_score: -9.1 Tail_Score: -4.4784 Start: 196 End: 253 Full_Region: tagtacaaccgatcc gtccggtctcgaaggggcaggagcc gaaaca ggactcctgcccctttgccgtcaggcc tttgtttgcagtttg ...................................................................................................................................................................................................gtccggtctcgaaggggcaggagccgaaacaggactcctgcccctttgccgtcaggcc......................................................................................... TransTerm Strand: - Conf: 95 HP_score: -14.8 Tail_Score: -3.60098 Start: 210 End: 240 Full_Region: ccgtccggtctcgaa ggggcaggagcc gaaaca ggactcctgcccc tttgccgtcaggcct .................................................................................................................................................................................................................ggggcaggagccgaaacaggactcctgcccc...................................................................................................... Find igs database================================================ Query_seq: PG0279:PG0280|PG0279:PG0280:NADP-dependent malic enzyme:ABC transporter, permease protein, putative:<-<-:313045..313386 342 cattataataggtagtatcgtttctgttttgtcgggttcatttcccaagcaatagcacacaaaacgcctgaggagaaacaaattccgacaaatccgtatggagctattggcacacaaaggtagggaagccgaatcaaaatctcctattatgaacggaggttttgtctcttttccggtttgcaaactgcaaacaaaggcctgacggcaaaggggcaggagtcctgtttcggctcctgccccttcgagaccggacggatcggttgtactacgatacggccgtttcgtagctgctatatataataaggtatagggagaacgtgggggaatggatcccatctacct Intra-Species Hit: Count: 1 Min: 1 Max: 342 Len: 342 Subject: NC_002950_PG0279_PG0280|NADP-dependent malic enzyme:ABC transporter, permease protein, putative|NEGATIVE:NEGATIVE|[313045,313386]|342 HSP 1 e-value: 0.0 bit: 678.0 Len: 342 Query Start:1 Query End:342 Subject Strand: POSITIVE Subject Start: 1 Subject End: 342 cattataataggtagtatcgtttctgttttgtcgggttcatttcccaagcaatagcacacaaaacgcctgaggagaaacaaattccgacaaatccgtatggagctattggcacacaaaggtagggaagccgaatcaaaatctcctattatgaacggaggttttgtctcttttccggtttgcaaactgcaaacaaaggcctgacggcaaaggggcaggagtcctgtttcggctcctgccccttcgagaccggacggatcggttgtactacgatacggccgtttcgtagctgctatatataataaggtatagggagaacgtgggggaatggatcccatctacct cattataataggtagtatcgtttctgttttgtcgggttcatttcccaagcaatagcacacaaaacgcctgaggagaaacaaattccgacaaatccgtatggagctattggcacacaaaggtagggaagccgaatcaaaatctcctattatgaacggaggttttgtctcttttccggtttgcaaactgcaaacaaaggcctgacggcaaaggggcaggagtcctgtttcggctcctgccccttcgagaccggacggatcggttgtactacgatacggccgtttcgtagctgctatatataataaggtatagggagaacgtgggggaatggatcccatctacct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUAUAAUAGGUAGUAUCGUUUCUGUUUUGUCGGGUUCAUUUCCCAAGCAAUAGCACACAAAACGCCUGAGGAGAAACAAAUUCCGACAAAUCCGUAUGGAGCUAUUGGCACACAAAGGUAGGGAAGCCGAAUCAAAAUCUCCUAUUAUGAACGGAGGUUUUGUCUCUUUUCCGGUUUGCAAACUGCAAACAAAGGCCUGACGGCAAAGGGGCAGGAGUCCUGUUUCGGCUCCUGCCCCUUCGAGACCGGACGGAUCGGUUGUACUACGAUACGGCCGUUUCGUAGCUGCUAUAUAUAAUAAGGUAUAGGGAGAACGUGGGGGAAUGGAUCCCAUCUACCU .........((((((.((.(..((((((((.(((.((((...((((..((....)).........((((.((.((..........((((..((((((.(((.((..(((((...........((((((..((..((((((((((..........))))))))))..)))))))).((((((.....))))))....))).))..)).((((((((((((((.......)))))))))))))).....))).))))))..))))..((((((.((....)).)))))))).))..........))))...)))))))).))).))))))))..).)))))))) (-122.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUAGAUGGGAUCCAUUCCCCCACGUUCUCCCUAUACCUUAUUAUAUAUAGCAGCUACGAAACGGCCGUAUCGUAGUACAACCGAUCCGUCCGGUCUCGAAGGGGCAGGAGCCGAAACAGGACUCCUGCCCCUUUGCCGUCAGGCCUUUGUUUGCAGUUUGCAAACCGGAAAAGAGACAAAACCUCCGUUCAUAAUAGGAGAUUUUGAUUCGGCUUCCCUACCUUUGUGUGCCAAUAGCUCCAUACGGAUUUGUCGGAAUUUGUUUCUCCUCAGGCGUUUUGUGUGCUAUUGCUUGGGAAAUGAACCCGACAAAACAGAAACGAUACUACCUAUUAUAAUG ((((((..((((.....))))...((((((........................(((((((.((....)).)))))))......(((((((.((((...(((((((((((((((......)).)))))))))))))))))...(((....((((((.....)))))).((((..(((.(((((.((((..........)))).))))).)))...))))............)))...........)))))))((((((..((..(((((...((((((....(....)...)))))))))))..)).))))))....)).))))...))))))......... (-114.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 966 130 81 221 172 NC_002950:PG0279|5end_NADP-dependent_malic_enzyme_312954..313184_NEGATIVE 497 256 211 140 100 NC_002950:PG0984|5end_hypothetical_protein_1046919..1047149_NEGATIVE 495 260 213 200 156 NC_002950:PG0678|5end_pyrazinamidase/nicotinamidase,_putative_728879..729109_POSITIVE 494 269 221 76 31 NC_002950:PG1783|5end_glycosyl_transferase,_group_2_family_protein_1871868..1872098_POSITIVE 460 229 185 61 11 NC_002950:PG1712|5end_alpha-1,2-mannosidase_family_protein_1801325..1801555_NEGATIVE 454 260 211 184 126 NC_002950:PG0164|5end_hypothetical_protein_187395..187625_NEGATIVE 451 236 193 132 65 NC_002950:PG1710|5end_ISPg5,_transposase_Orf2_1795357..1795587_POSITIVE 451 236 193 132 65 NC_002950:PG1644|5end_ISPg5,_transposase_Orf2_1725619..1725849_NEGATIVE 451 236 193 132 65 NC_002950:PG0591|5end_ISPg5,_transposase_Orf2_648484..648714_POSITIVE 451 236 193 132 65 NC_002950:PG0041|5end_ISPg5_transposase_Orf2_48377..48607_POSITIVE 445 250 201 158 98 NC_002950:PG1494|5end_hypothetical_protein_1569841..1570071_POSITIVE 439 235 195 68 11 NC_002950:PG2159|5end_protoporphyrinogen_oxidase_2264397..2264627_POSITIVE 435 260 218 71 14 NC_002950:PG1175|5end_ABC_transporter,_ATP-binding_protein,_putative_1255876..1256106_NEGATIVE 434 290 247 47 3 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 425 239 196 191 135 NC_002950:PG0961|5end_hypothetical_protein_1022272..1022502_NEGATIVE 421 259 213 79 27 NC_002950:PG0213|5end_precorrin-3_methylase/precorrin-8X_methylmutase_250464..250694_NEGATIVE 415 129 82 61 20 NC_002950:PG1283|5end_hypothetical_protein_1360553..1360783_POSITIVE 415 256 211 45 9 NC_002950:PG0468|5end_mannose-6-phosphate_isomerase,_class_I_511384..511614_NEGATIVE 406 247 201 62 7 NC_002950:PG0578|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_634480..634710_POSITIVE 405 260 213 67 16 NC_002950:PG1875|5end_hemolysin_1970621..1970851_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 494 269 221 89 44 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 473 260 211 146 83 NC_002950:PG0198|3end_hypothetical_protein_237501..237651_POSITIVE 451 236 193 78 11 NC_002950:PG1709|3end_ISPg5,_transposase_Orf1_1795383..1795533_POSITIVE 451 236 193 78 11 NC_002950:PG1645|3end_ISPg5,_transposase_Orf1_1725673..1725823_NEGATIVE 451 236 193 78 11 NC_002950:PG0590|3end_ISPg5,_transposase_Orf1_648510..648660_POSITIVE 451 236 193 78 11 NC_002950:PG0040|3end_ISPg5_transposase_Orf1_48403..48553_POSITIVE 439 235 195 64 7 NC_002950:PG2158|3end_hypothetical_protein_2264473..2264623_POSITIVE 426 259 213 145 103 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 425 239 196 136 80 NC_002950:PG0962|3end_prolyl-tRNA_synthetase_1022327..1022477_NEGATIVE 423 260 211 146 79 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 412 260 214 79 30 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 405 260 213 55 4 NC_002950:PG1876|3end_hypothetical_protein_1970633..1970783_NEGATIVE 403 290 246 39 2 NC_002950:PG0735|3end_aminotransferase,_class_V_785677..785827_POSITIVE 400 260 211 66 24 NC_002950:PG2147|3end_xanthine_phosphoribosyltransferase_2254819..2254969_NEGATIVE 399 260 215 149 95 NC_002950:PG1884|3end_alpha-L-fucosidase_precursor,_putative_1978968..1979118_NEGATIVE 397 241 201 60 23 NC_002950:PG1872|3end_urocanate_hydratase_1966932..1967082_NEGATIVE 396 250 201 127 76 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 394 259 211 149 102 NC_002950:PG0335|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_369804..369954_NEGATIVE 389 225 182 110 71 NC_002950:PG0381|3end_cell_volume_regulation_protein_CvrA_411185..411335_NEGATIVE 387 240 193 68 26 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE