Origin IGS: caggcgttctttttgtatatttgcgcacgaatcggaggaggctggtccgttcggggtagctttccgtacccctgatttatcgatcaaagtatcaacaatactatcttttcgcgct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcgcgaaaagatagtattgttgatactttgatcgataaatcaggggtacggaaagctaccccgaacggaccagcctcctccgattcgtgcgcaaatatacaaaaagaacgcctg Mask Tandem Repeat Region ================================================ caggcgttctttttgtatatttgcgcacgaatcggaggaggctggtccgttcggggtagctttccgtacccctgatttatcgatcaaagtatcaacaatactatcttttcgcgct Find is-nt database================================================ Query_seq: PG0524:PG0525|PG0524:PG0525:hypothetical protein:CTP synthetase:->->:569024..569138 115 caggcgttctttttgtatatttgcgcacgaatcggaggaggctggtccgttcggggtagctttccgtacccctgatttatcgatcaaagtatcaacaatactatcttttcgcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0524:PG0525|PG0524:PG0525:hypothetical protein:CTP synthetase:->->:569024..569138 115 caggcgttctttttgtatatttgcgcacgaatcggaggaggctggtccgttcggggtagctttccgtacccctgatttatcgatcaaagtatcaacaatactatcttttcgcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0524:PG0525|PG0524:PG0525:hypothetical protein:CTP synthetase:->->:569024..569138 115 caggcgttctttttgtatatttgcgcacgaatcggaggaggctggtccgttcggggtagctttccgtacccctgatttatcgatcaaagtatcaacaatactatcttttcgcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caggcgttctttttgtatatttgcgcacgaatcggaggaggctggtccgttcggggtagctttccgtacccctgatttatcgatcaaagtatcaacaatactatcttttcgcgct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 17 End: 115 ................ M F A H E S E E A G P F G V A F R T P D L S I K V S T I L S F R A Protein_Len: 33 Strand: - Start: 1 End: 99 L R E K Q I N A C S D S S A P G N P T A K R V G S K D I L T D V M ................ caggcgttctttttgtatatttgcgcacgaatcggaggaggctggtccgttcggggtagctttccgtacccctgatttatcgatcaaagtatcaacaatactatcttttcgcgct 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================================================ caggcgttctttttgtatatttgcgcacgaatcggaggaggctggtccgttcggggtagctttccgtacccctgatttatcgatcaaagtatcaacaatactatcttttcgcgct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 53 HP_score: -2.2 Tail_Score: -3.92075 Start: 51 End: 75 Full_Region: AGGAGGCTGGTCCGT TCGGGGTA GCTTTCCG TACCCCTGA TTTATCGATCAAAGT ..................................................TCGGGGTAGCTTTCCGTACCCCTGA........................................ Find igs database================================================ Query_seq: PG0524:PG0525|PG0524:PG0525:hypothetical protein:CTP synthetase:->->:569024..569138 115 caggcgttctttttgtatatttgcgcacgaatcggaggaggctggtccgttcggggtagctttccgtacccctgatttatcgatcaaagtatcaacaatactatcttttcgcgct Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_002950_PG0524_PG0525|hypothetical protein:CTP synthetase|POSITIVE:POSITIVE|[569024,569138]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 caggcgttctttttgtatatttgcgcacgaatcggaggaggctggtccgttcggggtagctttccgtacccctgatttatcgatcaaagtatcaacaatactatcttttcgcgct caggcgttctttttgtatatttgcgcacgaatcggaggaggctggtccgttcggggtagctttccgtacccctgatttatcgatcaaagtatcaacaatactatcttttcgcgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGGCGUUCUUUUUGUAUAUUUGCGCACGAAUCGGAGGAGGCUGGUCCGUUCGGGGUAGCUUUCCGUACCCCUGAUUUAUCGAUCAAAGUAUCAACAAUACUAUCUUUUCGCGCU ......................((((..(((((((.((((((((.(((....))).)))).))))......)))))))...(((...(((((.....)))))))).....)))). (-28.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGCGAAAAGAUAGUAUUGUUGAUACUUUGAUCGAUAAAUCAGGGGUACGGAAAGCUACCCCGAACGGACCAGCCUCCUCCGAUUCGUGCGCAAAUAUACAAAAAGAACGCCUG .(((((((.........((((((((......))))))))....(((((((.....).))))))...((((.........)))).)))))))........................ (-29.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 419 69 25 76 27 NC_002950:PG2162|5end_lipid_A_disaccharide_synthase_2268764..2268994_NEGATIVE 417 70 21 167 105 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 413 66 23 192 147 NC_002950:PG1482|5end_conjugative_transposon_protein_TraF_1558779..1559009_NEGATIVE 406 68 31 171 133 NC_002950:PG1305|5end_glycine_dehydrogenase_1386538..1386768_NEGATIVE 397 70 21 94 39 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 393 73 32 187 138 NC_002950:PG1080|5end_3-hydroxyacyl-CoA_dehydrogenase_family_protein_1147366..1147596_POSITIVE 385 75 31 50 2 NC_002950:PG1783|5end_glycosyl_transferase,_group_2_family_protein_1871868..1872098_POSITIVE 384 66 22 98 51 NC_002950:PG2028|5end_ebsC_protein_2126027..2126257_POSITIVE 382 70 25 202 153 NC_002950:PG1999|5end_hypothetical_protein_2088821..2089051_NEGATIVE 381 70 22 71 22 NC_002950:PG0803|5end_glucosamine-6-phosphate_deaminase_860518..860748_NEGATIVE 377 74 32 164 107 NC_002950:PG1827|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1920014..1920244_POSITIVE 375 70 23 113 50 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 372 70 24 89 44 NC_002950:PG0147|5end_hypothetical_protein_169667..169897_NEGATIVE 370 70 25 118 60 NC_002950:PG0124|5end_hypothetical_protein_146234..146464_NEGATIVE 367 73 34 231 177 NC_002950:PG1577|5end_nicotinate-nucleotide_pyrophosphorylase_1654619..1654849_POSITIVE 367 67 25 188 145 NC_002950:PG1524|5end_2-succinyl-6-hydroxy-2,_4-cyclohexadiene-1-carboxylic_acid_synthase/2-oxoglutarate_decarboxylase_1602746..1602976_NEGATIVE 367 86 43 125 84 NC_002950:PG0851|5end_hypothetical_protein_912732..912962_NEGATIVE 366 66 22 73 23 NC_002950:PG1706|5end_hypothetical_protein_1794211..1794441_NEGATIVE 366 70 21 214 161 NC_002950:PG1477|5end_hypothetical_protein_1553496..1553726_NEGATIVE 365 60 15 172 118 NC_002950:PG0294|5end_glycosyl_transferase,_group_2_family_protein_330161..330391_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 464 75 31 139 90 NC_002950:PG1472|3end_hypothetical_protein_1549760..1549910_POSITIVE 453 62 23 60 7 NC_002950:PG0775|3end_acyl-CoA_dehydrogenase_family_protein_827432..827582_NEGATIVE 435 70 21 72 4 NC_002950:PG1055|3end_thiol_protease_1121202..1121352_NEGATIVE 397 70 21 110 55 NC_002950:PG0157|3end_regulatory_protein_RecX_180271..180421_POSITIVE 393 73 32 140 91 NC_002950:PG1079|3end_enoyl-CoA_hydratase/isomerase_family_protein_1147399..1147549_POSITIVE 385 75 31 63 15 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 385 75 36 70 18 NC_002950:PG1150|3end_hypothetical_protein_1233249..1233399_POSITIVE 384 66 22 89 42 NC_002950:PG2027|3end_hypothetical_protein_2126098..2126248_POSITIVE 378 60 11 103 44 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 375 70 23 132 69 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 374 70 23 69 16 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 372 70 24 102 57 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 370 70 25 114 56 NC_002950:PG0125|3end_hypothetical_protein_146238..146388_NEGATIVE 368 70 27 118 65 NC_002950:PG1021|3end_hypothetical_protein_1083395..1083545_NEGATIVE 366 66 22 52 2 NC_002950:PG1707|3end_hypothetical_protein_1794232..1794382_NEGATIVE 365 73 33 148 94 NC_002950:PG1966|3end_hypothetical_protein_2056118..2056268_NEGATIVE 364 75 32 49 4 NC_002950:PG0660|3end_nitroreductase_family_protein_709141..709291_NEGATIVE 360 71 31 89 36 NC_002950:PG1602|3end_hypothetical_protein_1681764..1681914_NEGATIVE 359 69 23 116 62 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE 356 67 28 142 98 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE