Origin IGS: aactatttttttcgtctgtaagggattattatttattgtgccctcaaatataaggaattaggcattagttgccaagcaggaacagccggacagaggcaaaagcactccttacaggattgccgtacgcagtccttttcaagattgtacttgcaggtgtgggcacaatcccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggggattgtgcccacacctgcaagtacaatcttgaaaaggactgcgtacggcaatcctgtaaggagtgcttttgcctctgtccggctgttcctgcttggcaactaatgcctaattccttatatttgagggcacaataaataataatcccttacagacgaaaaaaatagtt Mask Tandem Repeat Region ================================================ aactatttttttcgtctgtaagggattattatttattgtgccctcaaatataaggaattaggcattagttgccaagcaggaacagccggacagaggcaaaagcactccttacaggattgccgtacgcagtccttttcaagattgtacttgcaggtgtgggcacaatcccc Find is-nt database================================================ Query_seq: PG2207:PG2208|PG2207:PG2208:hypothetical protein:hypothetical protein:<-<-:2320252..2320421 170 aactatttttttcgtctgtaagggattattatttattgtgccctcaaatataaggaattaggcattagttgccaagcaggaacagccggacagaggcaaaagcactccttacaggattgccgtacgcagtccttttcaagattgtacttgcaggtgtgggcacaatcccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2207:PG2208|PG2207:PG2208:hypothetical protein:hypothetical protein:<-<-:2320252..2320421 170 aactatttttttcgtctgtaagggattattatttattgtgccctcaaatataaggaattaggcattagttgccaagcaggaacagccggacagaggcaaaagcactccttacaggattgccgtacgcagtccttttcaagattgtacttgcaggtgtgggcacaatcccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2207:PG2208|PG2207:PG2208:hypothetical protein:hypothetical protein:<-<-:2320252..2320421 170 aactatttttttcgtctgtaagggattattatttattgtgccctcaaatataaggaattaggcattagttgccaagcaggaacagccggacagaggcaaaagcactccttacaggattgccgtacgcagtccttttcaagattgtacttgcaggtgtgggcacaatcccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aactatttttttcgtctgtaagggattattatttattgtgccctcaaatataaggaattaggcattagttgccaagcaggaacagccggacagaggcaaaagcactccttacaggattgccgtacgcagtccttttcaagattgtacttgcaggtgtgggcacaatcccc Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 25 End: 168 ........................ M I I Y C A L K Y K E L G I S C Q A G T A G Q R Q K H S L Q D C R T Q S F S R L Y L Q V W A Q S .. Protein_Len: 34 Strand: + Start: 69 End: 170 .................................................................... M P S R N S R T E A K A L L T G L P Y A V L F K I V L A G V G T I P Protein_Len: 33 Strand: - Start: 68 End: 166 ................................................................... N G L L F L R V S A F A S R V P N G Y A T R K L I T S A P T P V M .... aactatttttttcgtctgtaagggattattatttattgtgccctcaaatataaggaattaggcattagttgccaagcaggaacagccggacagaggcaaaagcactccttacaggattgccgtacgcagtccttttcaagattgtacttgcaggtgtgggcacaatcccc 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: 84 Start: 47 End: 76 ..............................................CTTGGCAACTAATGCCTAATTCCTTATATT.............................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aactatttttttcgtctgtaagggattattatttattgtgccctcaaatataaggaattaggcattagttgccaagcaggaacagccggacagaggcaaaagcactccttacaggattgccgtacgcagtccttttcaagattgtacttgcaggtgtgggcacaatcccc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 76 HP_score: -7.4 Tail_Score: -4.26188 Start: 102 End: 120 Full_Region: aaaggactgcgtacg gcaatcct gta aggagtgc ttttgcctctgtccg .....................................................................................................gcaatcctgtaaggagtgc.................................................. TransTerm Strand: + Conf: 73 HP_score: -6.7 Tail_Score: -4.1585 Start: 114 End: 132 Full_Region: AAAGCACTCCTTACA GGATTGC CGTAC GCAGTCC TTTTCAAGATTGTAC .................................................................................................................GGATTGCCGTACGCAGTCC...................................... Find igs database================================================ Query_seq: PG2207:PG2208|PG2207:PG2208:hypothetical protein:hypothetical protein:<-<-:2320252..2320421 170 aactatttttttcgtctgtaagggattattatttattgtgccctcaaatataaggaattaggcattagttgccaagcaggaacagccggacagaggcaaaagcactccttacaggattgccgtacgcagtccttttcaagattgtacttgcaggtgtgggcacaatcccc Intra-Species Hit: Count: 1 Min: 13 Max: 170 Len: 158 Subject: NC_002950_PG2207_PG2208|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2320252,2320421]|170 HSP 1 e-value: 1.0E-84 bit: 313.0 Len: 158 Query Start:13 Query End:170 Subject Strand: POSITIVE Subject Start: 13 Subject End: 170 ............cgtctgtaagggattattatttattgtgccctcaaatataaggaattaggcattagttgccaagcaggaacagccggacagaggcaaaagcactccttacaggattgccgtacgcagtccttttcaagattgtacttgcaggtgtgggcacaatcccc ............cgtctgtaagggattattatttattgtgccctcaaatataaggaattaggcattagttgccaagcaggaacagccggacagaggcaaaagcactccttacaggattgccgtacgcagtccttttcaagattgtacttgcaggtgtgggcacaatcccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUCUGUAAGGGAUUAUUAUUUAUUGUGCCCUCAAAUAUAAGGAAUUAGGCAUUAGUUGCCAAGCAGGAACAGCCGGACAGAGGCAAAAGCACUCCUUACAGGAUUGCCGUACGCAGUCCUUUUCAAGAUUGUACUUGCAGGUGUGGGCACAAUCCCC .........(((((..........(((((((.((..............((((.....))))..(((((.(((((..((..(((((....)).))).....((((((((.....))))))))..))..).)))).)))))...)).)))))))))))). (-51.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGGAUUGUGCCCACACCUGCAAGUACAAUCUUGAAAAGGACUGCGUACGGCAAUCCUGUAAGGAGUGCUUUUGCCUCUGUCCGGCUGUUCCUGCUUGGCAACUAAUGCCUAAUUCCUUAUAUUUGAGGGCACAAUAAAUAAUAAUCCCUUACAGACG (((((((((((((.((..(((..((((..((((....))))....)))).)))....((((((((((......(((.......)))...........((((.....))))..))))))))))..)).)))))))..........))))))........ (-46.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1078 120 71 223 174 NC_002950:PG2207|5end_hypothetical_protein_2320161..2320391_NEGATIVE 386 120 73 54 4 NC_002950:PG0083|5end_hypothetical_protein_96952..97182_POSITIVE 366 110 63 209 162 NC_002950:PG0876|5end_tRNA_modification_GTPase_940806..941036_NEGATIVE 357 110 64 55 8 NC_002950:PG0740|5end_NLP/P60_family_protein_787836..788066_POSITIVE 350 98 56 88 42 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 349 86 43 187 124 NC_002950:PG1058|5end_OmpA_family_protein_1124034..1124264_POSITIVE 349 97 51 102 53 NC_002950:PG1029|5end_hypothetical_protein_1091080..1091310_POSITIVE 345 86 42 161 116 NC_002950:PG1713|5end_lipoprotein,_putative_1801811..1802041_NEGATIVE 343 92 51 87 35 NC_002950:PG0306|5end_electron_transport_complex,_RnfABCDGE_type,_G_subunit_341916..342146_POSITIVE 342 148 101 82 22 NC_002950:PG0002|5end_hexapeptide_transferase_family_protein_1295..1525_POSITIVE 336 150 105 90 27 NC_002950:PG0800|5end_hypothetical_protein_856278..856508_NEGATIVE 332 120 72 191 143 NC_002950:PG2027|5end_hypothetical_protein_2125494..2125724_POSITIVE 331 119 75 229 182 NC_002950:PG0172|5end_exonuclease_193493..193723_POSITIVE 329 74 40 67 33 NC_002950:PG1385|5end_TPR_domain_protein_1466335..1466565_NEGATIVE 329 110 63 74 30 NC_002950:PG0758|5end_peptidyl-dipeptidase_Dcp_808554..808784_NEGATIVE 328 116 75 45 4 NC_002950:PG0179|5end_hypothetical_protein_201783..202013_POSITIVE 327 108 62 200 158 NC_002950:PG1487|5end_hypothetical_protein_1561468..1561698_POSITIVE 324 149 101 188 136 NC_002950:PG0736|5end_ribonuclease_HII_785608..785838_POSITIVE 321 120 75 49 1 NC_002950:PG1434|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_1519022..1519252_POSITIVE 321 149 104 62 1 NC_002950:PG0334|5end_glycosyl_transferase,_group_2_family_protein_369751..369981_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 120 72 73 21 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 358 120 73 52 9 NC_002950:PG0086|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_100545..100695_NEGATIVE 357 110 64 80 33 NC_002950:PG0739|3end_ribonuclease_Z_787941..788091_POSITIVE 350 98 56 58 12 NC_002950:PG0170|3end_methionyl-tRNA_synthetase_191774..191924_POSITIVE 348 120 75 112 66 NC_002950:PG1484|3end_hypothetical_protein_1559275..1559425_NEGATIVE 345 86 42 124 79 NC_002950:PG1714|3end_pyridoxamine-phosphate_oxidase_1801848..1801998_NEGATIVE 343 92 51 60 8 NC_002950:PG0305|3end_electron_transport_complex,_RnfABCDGE_type,_D_subunit_341969..342119_POSITIVE 342 148 101 69 9 NC_002950:PG0001|3end_chromosomal_replication_initiation_protein_1362..1512_POSITIVE 336 150 105 105 42 NC_002950:PG0801|3end_polyA_polymerase_family_protein_856263..856413_NEGATIVE 319 110 61 88 27 NC_002950:PG1411|3end_potassium_uptake_protein_TrkA,_putative_1493481..1493631_NEGATIVE 318 86 41 52 11 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 316 118 72 145 106 NC_002950:PG1987|3end_CRISPR-associated_TM1811_family_protein_2075786..2075936_NEGATIVE 310 136 93 111 65 NC_002950:PG2125|3end_transcriptional_regulator,_AraC_family_2231376..2231526_NEGATIVE 310 139 91 51 8 NC_002950:PG1805|3end_V-type_ATP_synthase_subunit_D_1900283..1900433_POSITIVE 309 91 56 151 114 NC_002950:PG2171|3end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_2278013..2278163_NEGATIVE 308 120 73 150 106 NC_002950:PG0289|3end_hypothetical_protein_323980..324130_POSITIVE 307 147 107 32 2 NC_002950:PG1663|3end_ABC_transporter,_ATP-binding_protein_1745868..1746018_POSITIVE 306 75 36 148 98 NC_002950:PG1057|3end_hypothetical_protein_1124092..1124242_POSITIVE 306 119 72 131 70 NC_002950:PG0814|3end_hypothetical_protein_875904..876054_NEGATIVE 306 110 67 84 38 NC_002950:PG0572|3end_hypothetical_protein_627434..627584_NEGATIVE