Origin IGS: accctccttcccttatttgccaacgaccttatcgaagaggcccgtcatcaatatcggttcgtccggtatgatgatcggcctcttttcttattgacagtgtgtcatcatgcgcaaattgctgcgttgcttgcggcattcgtttcttagcgccttgtactttacgcattcttacccacctaaaatggggt .........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 accccattttaggtgggtaagaatgcgtaaagtacaaggcgctaagaaacgaatgccgcaagcaacgcagcaatttgcgcatgatgacacactgtcaataagaaaagaggccgatcatcataccggacgaaccgatattgatgacgggcctcttcgataaggtcgttggcaaataagggaaggagggt Mask Tandem Repeat Region ================================================ accctccttcccttatttgccaacgaccttatcgaagaggcccgtcatcaatatcggttcgtccggtatgatgatcggcctcttttcttattgacagtgtgtcatcatgcgcaaattgctgcgttgcttgcggcattcgtttcttagcgccttgtactttacgcattcttacccacctaaaatggggt Find is-nt database================================================ Query_seq: PG1116:PG1117|PG1116:PG1117:methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase:MATE efflux family protein:->->:1189962..1190149 188 accctccttcccttatttgccaacgaccttatcgaagaggcccgtcatcaatatcggttcgtccggtatgatgatcggcctcttttcttattgacagtgtgtcatcatgcgcaaattgctgcgttgcttgcggcattcgtttcttagcgccttgtactttacgcattcttacccacctaaaatggggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1116:PG1117|PG1116:PG1117:methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase:MATE efflux family protein:->->:1189962..1190149 188 accctccttcccttatttgccaacgaccttatcgaagaggcccgtcatcaatatcggttcgtccggtatgatgatcggcctcttttcttattgacagtgtgtcatcatgcgcaaattgctgcgttgcttgcggcattcgtttcttagcgccttgtactttacgcattcttacccacctaaaatggggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1116:PG1117|PG1116:PG1117:methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase:MATE efflux family protein:->->:1189962..1190149 188 accctccttcccttatttgccaacgaccttatcgaagaggcccgtcatcaatatcggttcgtccggtatgatgatcggcctcttttcttattgacagtgtgtcatcatgcgcaaattgctgcgttgcttgcggcattcgtttcttagcgccttgtactttacgcattcttacccacctaaaatggggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accctccttcccttatttgccaacgaccttatcgaagaggcccgtcatcaatatcggttcgtccggtatgatgatcggcctcttttcttattgacagtgtgtcatcatgcgcaaattgctgcgttgcttgcggcattcgtttcttagcgccttgtactttacgcattcttacccacctaaaatggggt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 31 End: 144 .............................. M E E A R H Q Y R F V R Y D D R P L F L L T V C H H A Q I A A L L A A F V S ............................................ Protein_Len: 33 Strand: + Start: 90 End: 188 ......................................................................................... M D S V S S C A N C C V A C G I R F L A P C T L R I L T H L K W G Protein_Len: 45 Strand: - Start: 32 End: 166 ............................... R L P G D D I D T R G T H H D A E K R I S L T D D H A F Q Q T A Q P M R K K A G Q V K R M ...................... accctccttcccttatttgccaacgaccttatcgaagaggcccgtcatcaatatcggttcgtccggtatgatgatcggcctcttttcttattgacagtgtgtcatcatgcgcaaattgctgcgttgcttgcggcattcgtttcttagcgccttgtactttacgcattcttacccacctaaaatggggt 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================================================ accctccttcccttatttgccaacgaccttatcgaagaggcccgtcatcaatatcggttcgtccggtatgatgatcggcctcttttcttattgacagtgtgtcatcatgcgcaaattgctgcgttgcttgcggcattcgtttcttagcgccttgtactttacgcattcttacccacctaaaatggggt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.2 Tail_Score: -4.89477 Start: 37 End: 82 Full_Region: AACGACCTTATCGAA GAGGCCCGTCATCAATATCGG TTCGT CCGGTATGATGATCGGCCTC TTTTCTTATTGACAG ....................................GAGGCCCGTCATCAATATCGGTTCGTCCGGTATGATGATCGGCCTC.......................................................................................................... TransTerm Strand: - Conf: 69 HP_score: -9.8 Tail_Score: -3.07291 Start: 37 End: 82 Full_Region: ctgtcaataagaaaa gaggccgatcatcataccgg acgaa ccgatattgatgacgggcctc ttcgataaggtcgtt ....................................gaggccgatcatcataccggacgaaccgatattgatgacgggcctc.......................................................................................................... TransTerm Strand: - Conf: 55 HP_score: -6.6 Tail_Score: -3.09327 Start: 39 End: 80 Full_Region: gtcaataagaaaaga ggccgatcatcataccgg acgaa ccgatattgatgacgggcc tcttcgataaggtcg ......................................ggccgatcatcataccggacgaaccgatattgatgacgggcc............................................................................................................ Find igs database================================================ Query_seq: PG1116:PG1117|PG1116:PG1117:methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase:MATE efflux family protein:->->:1189962..1190149 188 accctccttcccttatttgccaacgaccttatcgaagaggcccgtcatcaatatcggttcgtccggtatgatgatcggcctcttttcttattgacagtgtgtcatcatgcgcaaattgctgcgttgcttgcggcattcgtttcttagcgccttgtactttacgcattcttacccacctaaaatggggt Intra-Species Hit: Count: 1 Min: 1 Max: 188 Len: 188 Subject: NC_002950_PG1116_PG1117|methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase:MATE efflux family protein|POSITIVE:POSITIVE|[1189962,1190149]|188 HSP 1 e-value: 1.0E-102 bit: 373.0 Len: 188 Query Start:1 Query End:188 Subject Strand: POSITIVE Subject Start: 1 Subject End: 188 accctccttcccttatttgccaacgaccttatcgaagaggcccgtcatcaatatcggttcgtccggtatgatgatcggcctcttttcttattgacagtgtgtcatcatgcgcaaattgctgcgttgcttgcggcattcgtttcttagcgccttgtactttacgcattcttacccacctaaaatggggt accctccttcccttatttgccaacgaccttatcgaagaggcccgtcatcaatatcggttcgtccggtatgatgatcggcctcttttcttattgacagtgtgtcatcatgcgcaaattgctgcgttgcttgcggcattcgtttcttagcgccttgtactttacgcattcttacccacctaaaatggggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCCUCCUUCCCUUAUUUGCCAACGACCUUAUCGAAGAGGCCCGUCAUCAAUAUCGGUUCGUCCGGUAUGAUGAUCGGCCUCUUUUCUUAUUGACAGUGUGUCAUCAUGCGCAAAUUGCUGCGUUGCUUGCGGCAUUCGUUUCUUAGCGCCUUGUACUUUACGCAUUCUUACCCACCUAAAAUGGGGU ..........((((((((...............(((((((((.(((((((.((((((.....))))))))))))).)))))))))......(((.(((((((...((.(((((((((((((((.....)))))))...))))....))))..))......))))))).)))........)))))))). (-59.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCCCAUUUUAGGUGGGUAAGAAUGCGUAAAGUACAAGGCGCUAAGAAACGAAUGCCGCAAGCAACGCAGCAAUUUGCGCAUGAUGACACACUGUCAAUAAGAAAAGAGGCCGAUCAUCAUACCGGACGAACCGAUAUUGAUGACGGGCCUCUUCGAUAAGGUCGUUGGCAAAUAAGGGAAGGAGGGU ((((..((((.((((.((....(((((((((......((((............))))....((......))..)))))))))....)).))))(((((......((((((((..((((((((.(((.....))).)).))))))..))))))))((((...)))))))))........))))..)))) (-56.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 678 139 91 179 131 NC_002950:PG1408|5end_heavy_metal_efflux_pump,_CzcD_family_1491861..1492091_POSITIVE 529 140 93 201 143 NC_002950:PG1808|5end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase_1905243..1905473_NEGATIVE 395 44 3 151 102 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 395 80 32 168 109 NC_002950:PG0746|5end_sensor_histidine_kinase_793903..794133_NEGATIVE 392 79 40 229 179 NC_002950:PG2032|5end_primosomal_protein_N'_2133381..2133611_NEGATIVE 389 80 31 188 140 NC_002950:PG2029|5end_hypothetical_protein_2126543..2126773_POSITIVE 373 139 91 183 139 NC_002950:PG0212|5end_precorrin-6Y_C5,15-methyltransferase,_decarboxylating_249065..249295_NEGATIVE 366 79 31 217 158 NC_002950:PG2189|5end_aspartate_kinase_2297151..2297381_NEGATIVE 361 79 33 49 1 NC_002950:PG0704|5end_phosphoglycerate_mutase_family_protein_758928..759158_POSITIVE 358 177 131 205 163 NC_002950:PG0468|5end_mannose-6-phosphate_isomerase,_class_I_511384..511614_NEGATIVE 357 150 103 60 16 NC_002950:PG0004|5end_NAD-dependent_deacetylase_2968..3198_POSITIVE 354 140 91 61 8 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 353 68 22 195 139 NC_002950:PG0744|5end_RNA_methyltransferase,_TrmH_family_791897..792127_NEGATIVE 349 158 118 172 126 NC_002950:PG0348|5end_ATP-dependent_DNA_helicase_RecG_382345..382575_POSITIVE 348 87 42 67 15 NC_002950:PG0776|5end_electron_transfer_flavoprotein,_alpha_subunit_830184..830414_NEGATIVE 347 87 43 207 143 NC_002950:PG1635|5end_hypothetical_protein_1715861..1716091_NEGATIVE 344 70 25 55 4 NC_002950:PG1075|5end_coenzyme_A_transferase,_beta_subunit_1142778..1143008_POSITIVE 342 88 43 122 82 NC_002950:PG0896|5end_beta-galactosidase_957249..957479_POSITIVE 340 94 55 54 6 NC_002950:PG1297|5end_ribosomal_protein_S1_1375831..1376061_POSITIVE 339 78 33 75 11 NC_002950:PG1675|5end_hypothetical_protein_1760182..1760412_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 468 80 34 52 4 NC_002950:PG1116|3end_methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase_1189901..1190051_POSITIVE 389 42 3 148 105 NC_002950:PG1963|3end_Sua5/YciO/YrdC/YwlC_family_protein_2052993..2053143_POSITIVE 372 80 32 72 25 NC_002950:PG0731|3end_hypothetical_protein_782020..782170_NEGATIVE 354 79 32 76 9 NC_002950:PG0636|3end_MATE_efflux_family_protein_687707..687857_NEGATIVE 354 140 91 57 4 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 353 68 22 110 54 NC_002950:PG0745|3end_lactoylglutathione_lyase,_putative_791982..792132_NEGATIVE 351 79 31 123 61 NC_002950:PG0213|3end_precorrin-3_methylase/precorrin-8X_methylmutase_249058..249208_NEGATIVE 350 150 102 149 111 NC_002950:PG2021|3end_hypothetical_protein_2112921..2113071_NEGATIVE 349 158 118 129 83 NC_002950:PG0347|3end_UDP-glucose_4-epimerase_382382..382532_POSITIVE 348 87 42 58 6 NC_002950:PG0777|3end_electron_transfer_flavoprotein,_beta_subunit_830193..830343_NEGATIVE 342 153 117 78 31 NC_002950:PG1004|3end_prolyl_oligopeptidase_family_protein_1060433..1060583_NEGATIVE 339 79 37 47 4 NC_002950:PG0703|3end_cobalamin_(5'-phosphate)_synthase,_putative_759006..759156_POSITIVE 337 79 31 150 93 NC_002950:PG0042|3end_serine_hydroxymethyltransferase_50989..51139_POSITIVE 336 110 63 83 40 NC_002950:PG1226|3end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1304048..1304198_POSITIVE 333 47 1 93 36 NC_002950:PG0922|3end_hypothetical_protein_981228..981378_NEGATIVE 332 89 43 70 13 NC_002950:PG1323|3end_PhoH_family_protein_1402844..1402994_POSITIVE 330 74 33 122 71 NC_002950:PG1324|3end_Holliday_junction_resolvase_1402862..1403012_NEGATIVE 329 80 31 110 47 NC_002950:PG0768|3end_hypothetical_protein_821275..821425_NEGATIVE 328 79 34 84 24 NC_002950:PG0508|3end_HAD-superfamily_subfamily_IB_hydrolase,_TIGR01490_548136..548286_NEGATIVE 326 140 92 66 14 NC_002950:PG0632|3end_biopolymer_transport_protein_ExbD,_putative_685376..685526_POSITIVE