Origin IGS: tacagtatttctcagttgcttgatggggcgagtggcgaagggggtttttgttcacttgctccgttcgacagtggtctctaatagctctttgttgaaaaaact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agttttttcaacaaagagctattagagaccactgtcgaacggagcaagtgaacaaaaacccccttcgccactcgccccatcaagcaactgagaaatactgta Mask Tandem Repeat Region ================================================ tacagtatttctcagttgcttgatggggcgagtggcgaagggggtttttgttcacttgctccgttcgacagtggtctctaatagctctttgttgaaaaaact Find is-nt database================================================ Query_seq: PG0503:PG0504|PG0503:PG0504:dipeptidyl aminopeptidase IV:lipoyl synthase:->->:544272..544373 102 tacagtatttctcagttgcttgatggggcgagtggcgaagggggtttttgttcacttgctccgttcgacagtggtctctaatagctctttgttgaaaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0503:PG0504|PG0503:PG0504:dipeptidyl aminopeptidase IV:lipoyl synthase:->->:544272..544373 102 tacagtatttctcagttgcttgatggggcgagtggcgaagggggtttttgttcacttgctccgttcgacagtggtctctaatagctctttgttgaaaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0503:PG0504|PG0503:PG0504:dipeptidyl aminopeptidase IV:lipoyl synthase:->->:544272..544373 102 tacagtatttctcagttgcttgatggggcgagtggcgaagggggtttttgttcacttgctccgttcgacagtggtctctaatagctctttgttgaaaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacagtatttctcagttgcttgatggggcgagtggcgaagggggtttttgttcacttgctccgttcgacagtggtctctaatagctctttgttgaaaaaact Predict ORF larger than 30AA ================================================ tacagtatttctcagttgcttgatggggcgagtggcgaagggggtttttgttcacttgctccgttcgacagtggtctctaatagctctttgttgaaaaaact 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================================================ tacagtatttctcagttgcttgatggggcgagtggcgaagggggtttttgttcacttgctccgttcgacagtggtctctaatagctctttgttgaaaaaact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0503:PG0504|PG0503:PG0504:dipeptidyl aminopeptidase IV:lipoyl synthase:->->:544272..544373 102 tacagtatttctcagttgcttgatggggcgagtggcgaagggggtttttgttcacttgctccgttcgacagtggtctctaatagctctttgttgaaaaaact Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: NC_002950_PG0503_PG0504|dipeptidyl aminopeptidase IV:lipoyl synthase|POSITIVE:POSITIVE|[544272,544373]|102 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 tacagtatttctcagttgcttgatggggcgagtggcgaagggggtttttgttcacttgctccgttcgacagtggtctctaatagctctttgttgaaaaaact tacagtatttctcagttgcttgatggggcgagtggcgaagggggtttttgttcacttgctccgttcgacagtggtctctaatagctctttgttgaaaaaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAGUAUUUCUCAGUUGCUUGAUGGGGCGAGUGGCGAAGGGGGUUUUUGUUCACUUGCUCCGUUCGACAGUGGUCUCUAAUAGCUCUUUGUUGAAAAAACU .......((((.(((..(((....(((((.(.((.((((.(((((............))))).)))).)).).)))))....)))...)))..))))..... (-29.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUUUUCAACAAAGAGCUAUUAGAGACCACUGUCGAACGGAGCAAGUGAACAAAAACCCCCUUCGCCACUCGCCCCAUCAAGCAACUGAGAAAUACUGUA ((((((((((.......(((......(((....)))....((.((.((((..................)))).)).))....)))...))))))).)))... (-15.77) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 404 67 21 177 137 NC_002950:PG1975|5end_hemagglutinin_protein_HagC_2063218..2063448_POSITIVE 379 66 21 166 117 NC_002950:PG0327|5end_hypothetical_protein_362061..362291_NEGATIVE 372 65 21 223 173 NC_002950:PG0349|5end_hydrolase,_haloacid_dehalogenase-like_family_384459..384689_POSITIVE 366 95 53 139 99 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 364 67 21 150 105 NC_002950:PG2157|5end_glutamine_cyclotransferase-related_protein_2262943..2263173_POSITIVE 363 57 16 84 40 NC_002950:PG1160|5end_L-threonine-O-3-phosphate_decarboxylase,_putative_1239988..1240218_NEGATIVE 358 80 31 128 59 NC_002950:PG1928|5end_50S_ribosomal_protein_L14_2019945..2020175_NEGATIVE 355 46 5 59 10 NC_002950:PG1584|5end_batC_protein_1661331..1661561_POSITIVE 355 76 32 55 6 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 354 67 22 101 61 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 353 59 11 166 118 NC_002950:PG1497|5end_DNA-binding_protein,_histone-like_family_1574085..1574315_POSITIVE 352 67 26 148 100 NC_002950:PG1173|5end_YkgG_family_protein_1252435..1252665_POSITIVE 351 60 14 231 175 NC_002950:PG1943|5end_hypothetical_protein_2030260..2030490_NEGATIVE 351 62 22 229 191 NC_002950:PG1639|5end_hypothetical_protein_1719919..1720149_NEGATIVE 349 64 23 102 43 NC_002950:PG0475|5end_oxygen-independent_coproporphyrinogen_III_oxidase,_putative_517218..517448_NEGATIVE 348 68 23 152 93 NC_002950:PG0273|5end_4'-phosphopantetheinyl_transferase_family_protein_305694..305924_POSITIVE 347 87 41 96 53 NC_002950:PG0133|5end_hypothetical_protein_155764..155994_NEGATIVE 344 68 22 206 152 NC_002950:PG2159|5end_protoporphyrinogen_oxidase_2264397..2264627_POSITIVE 344 63 22 84 33 NC_002950:PG0281|5end_ABC_transporter,_permease_protein,_putative_316023..316253_NEGATIVE 342 70 23 66 18 NC_002950:PG0734|5end_nitroreductase_family_protein_783773..784003_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 60 11 140 96 NC_002950:PG0767|3end_4-alpha-glucanotransferase_818557..818707_NEGATIVE 379 66 21 72 23 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 358 80 31 126 57 NC_002950:PG1929|3end_ribosomal_protein_S17_2019947..2020097_NEGATIVE 355 46 5 62 13 NC_002950:PG1583|3end_batB_protein_1661414..1661564_POSITIVE 354 67 22 87 47 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 349 64 23 105 46 NC_002950:PG0476|3end_yngK_protein_517215..517365_NEGATIVE 348 68 23 116 57 NC_002950:PG0272|3end_CBS_domain_protein_305738..305888_POSITIVE 347 87 41 77 34 NC_002950:PG0134|3end_magnesium_transporter_155783..155933_NEGATIVE 346 63 21 148 105 NC_002950:PG0401|3end_hypothetical_protein_437765..437915_NEGATIVE 343 44 13 32 6 NC_002950:PG1117|3end_MATE_efflux_family_protein_1191541..1191691_POSITIVE 342 70 23 69 21 NC_002950:PG0733|3end_riboflavin_synthase_subunit_alpha_783856..784006_POSITIVE 334 65 24 103 56 NC_002950:PG0021|3end_TIM-barrel_protein,_putative,_NifR3_family_24122..24272_NEGATIVE 332 67 22 106 54 NC_002950:PG1666|3end_efflux_transporter,_MFP_component,_RND_family_1749628..1749778_POSITIVE 331 63 25 109 73 NC_002950:PG1831|3end_ATP-dependent_DNA_helicase_RecQ_1923455..1923605_NEGATIVE 327 69 25 149 105 NC_002950:PG1967|3end_TPR_domain_protein_2058135..2058285_POSITIVE 327 44 12 123 91 NC_002950:PG1711|3end_alpha-1,2-mannosidase_family_protein_1796652..1796802_NEGATIVE 325 70 26 62 11 NC_002950:PG1723|3end_ribosomal_protein_S20_1813403..1813553_POSITIVE 319 64 22 64 25 NC_002950:PG0186|3end_lipoprotein_RagB_222997..223147_POSITIVE 317 75 32 131 71 NC_002950:PG1732|3end_integrase/recombinase_XerD_1821177..1821327_POSITIVE 317 59 13 72 27 NC_002950:PG1482|3end_conjugative_transposon_protein_TraF_1558444..1558594_NEGATIVE