Origin IGS: ttcgtacttgtttgataaccgagtgtagcaatcgttagttaggtttataagtgtgttgacagttcaaatgcgattgccctgtgagttgccctgaaatatctgtcccacagtctcaaaaagcagtaaatttgcgcggt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 accgcgcaaatttactgctttttgagactgtgggacagatatttcagggcaactcacagggcaatcgcatttgaactgtcaacacacttataaacctaactaacgattgctacactcggttatcaaacaagtacgaa Mask Tandem Repeat Region ================================================ ttcgtacttgtttgataaccgagtgtagcaatcgttagttaggtttataagtgtgttgacagttcaaatgcgattgccctgtgagttgccctgaaatatctgtcccacagtctcaaaaagcagtaaatttgcgcggt Find is-nt database================================================ Query_seq: PG2220:PG2221|PG2220:PG2221:hypothetical protein:MiaB-like tRNA modifying enzyme:->->:2335429..2335565 137 ttcgtacttgtttgataaccgagtgtagcaatcgttagttaggtttataagtgtgttgacagttcaaatgcgattgccctgtgagttgccctgaaatatctgtcccacagtctcaaaaagcagtaaatttgcgcggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2220:PG2221|PG2220:PG2221:hypothetical protein:MiaB-like tRNA modifying enzyme:->->:2335429..2335565 137 ttcgtacttgtttgataaccgagtgtagcaatcgttagttaggtttataagtgtgttgacagttcaaatgcgattgccctgtgagttgccctgaaatatctgtcccacagtctcaaaaagcagtaaatttgcgcggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2220:PG2221|PG2220:PG2221:hypothetical protein:MiaB-like tRNA modifying enzyme:->->:2335429..2335565 137 ttcgtacttgtttgataaccgagtgtagcaatcgttagttaggtttataagtgtgttgacagttcaaatgcgattgccctgtgagttgccctgaaatatctgtcccacagtctcaaaaagcagtaaatttgcgcggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcgtacttgtttgataaccgagtgtagcaatcgttagttaggtttataagtgtgttgacagttcaaatgcgattgccctgtgagttgccctgaaatatctgtcccacagtctcaaaaagcagtaaatttgcgcggt Predict ORF larger than 30AA ================================================ ttcgtacttgtttgataaccgagtgtagcaatcgttagttaggtttataagtgtgttgacagttcaaatgcgattgccctgtgagttgccctgaaatatctgtcccacagtctcaaaaagcagtaaatttgcgcggt 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================================================ ttcgtacttgtttgataaccgagtgtagcaatcgttagttaggtttataagtgtgttgacagttcaaatgcgattgccctgtgagttgccctgaaatatctgtcccacagtctcaaaaagcagtaaatttgcgcggt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2220:PG2221|PG2220:PG2221:hypothetical protein:MiaB-like tRNA modifying enzyme:->->:2335429..2335565 137 ttcgtacttgtttgataaccgagtgtagcaatcgttagttaggtttataagtgtgttgacagttcaaatgcgattgccctgtgagttgccctgaaatatctgtcccacagtctcaaaaagcagtaaatttgcgcggt Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: NC_002950_PG2220_PG2221|hypothetical protein:MiaB-like tRNA modifying enzyme|POSITIVE:POSITIVE|[2335429,2335565]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 ttcgtacttgtttgataaccgagtgtagcaatcgttagttaggtttataagtgtgttgacagttcaaatgcgattgccctgtgagttgccctgaaatatctgtcccacagtctcaaaaagcagtaaatttgcgcggt ttcgtacttgtttgataaccgagtgtagcaatcgttagttaggtttataagtgtgttgacagttcaaatgcgattgccctgtgagttgccctgaaatatctgtcccacagtctcaaaaagcagtaaatttgcgcggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGUACUUGUUUGAUAACCGAGUGUAGCAAUCGUUAGUUAGGUUUAUAAGUGUGUUGACAGUUCAAAUGCGAUUGCCCUGUGAGUUGCCCUGAAAUAUCUGUCCCACAGUCUCAAAAAGCAGUAAAUUUGCGCGGU .(((((.(((.(((.((((((..((((..((((........))))))))..)).)))).)))..))).)))))..(((.((..((((...(((......(((.....)))..........)))..))))..)).))) (-26.69) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCGCGCAAAUUUACUGCUUUUUGAGACUGUGGGACAGAUAUUUCAGGGCAACUCACAGGGCAAUCGCAUUUGAACUGUCAACACACUUAUAAACCUAACUAACGAUUGCUACACUCGGUUAUCAAACAAGUACGAA ...............((((((.((((.((.((..(......)..)).))...)))).)))))).(((.(((((...(((....)))..................(((.(((......))).)))...))))).))). (-22.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 575 40 1 226 187 NC_002950:PG2220|5end_hypothetical_protein_2334935..2335165_POSITIVE 574 80 33 181 135 NC_002950:PG1787|5end_hypothetical_protein_1875908..1876138_NEGATIVE 550 44 1 229 185 NC_002950:PG1363|5end_hypothetical_protein_1443804..1444034_POSITIVE 446 40 1 226 187 NC_002950:PG1059|5end_hypothetical_protein_1126495..1126725_NEGATIVE 357 40 1 227 187 NC_002950:PG0499|5end_hypothetical_protein_538709..538939_POSITIVE 329 107 62 69 23 NC_002950:PG0160|5end_hypothetical_protein_184085..184315_NEGATIVE 320 109 70 92 30 NC_002950:PG0980|5end_hypothetical_protein_1040897..1041127_POSITIVE 315 110 62 84 41 NC_002950:PG2085|5end_tryptophanyl-tRNA_synthetase_2185532..2185762_POSITIVE 307 109 69 166 130 NC_002950:PG1748|5end_transketolase_1834929..1835159_NEGATIVE 305 105 64 231 182 NC_002950:PG0702|5end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_757100..757330_POSITIVE 299 110 68 55 18 NC_002950:PG0718|5end_hypothetical_protein_771573..771803_NEGATIVE 295 59 17 46 1 NC_002950:PG0879|5end_hypothetical_protein_942536..942766_NEGATIVE 293 105 68 50 17 NC_002950:PG1522|5end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1600170..1600400_NEGATIVE 289 43 1 230 178 NC_002950:PG1225|5end_ABC_transporter,_ATP-binding_protein_1301385..1301615_POSITIVE 287 113 71 61 16 NC_002950:PG0976|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1038326..1038556_POSITIVE 283 104 70 228 198 NC_002950:PG2100|5end_immunoreactive_63_kDa_antigen_PG102_2210191..2210421_NEGATIVE 283 91 62 172 141 NC_002950:PG0701|5end_cobinamide_kinase/cobinamide_phosphate_guanylyltransferase_756511..756741_POSITIVE 279 89 44 170 123 NC_002950:PG2111|5end_thiS_protein_2221482..2221712_NEGATIVE 279 93 51 60 7 NC_002950:PG1935|5end_50S_ribosomal_protein_L2_2023192..2023422_NEGATIVE 276 123 81 58 4 NC_002950:PG0287|5end_hypothetical_protein_320457..320687_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 467 93 51 50 2 NC_002950:PG2094|3end_hypothetical_protein_2193321..2193471_NEGATIVE 341 92 51 88 43 NC_002950:PG0078|3end_hypothetical_protein_91566..91716_NEGATIVE 320 109 70 105 43 NC_002950:PG0979|3end_hypothetical_protein_1040990..1041140_POSITIVE 293 105 68 50 17 NC_002950:PG1523|3end_naphthoate_synthase_1600170..1600320_NEGATIVE 289 115 71 151 112 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE 278 104 61 148 101 NC_002950:PG0585|3end_YqeY_family_protein_643801..643951_POSITIVE 276 120 75 39 1 NC_002950:PG0959|3end_ATP-binding_protein,_Mrp/Nbp35_family_1020023..1020173_NEGATIVE 276 93 60 147 100 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 273 79 38 38 2 NC_002950:PG1595|3end_ribulose-phosphate_3-epimerase_1673594..1673744_NEGATIVE 273 113 71 48 2 NC_002950:PG0807|3end_NusB_family_protein_863630..863780_NEGATIVE 272 106 68 150 110 NC_002950:PG1467|3end_methlytransferase,_UbiE/COQ5_family_1543901..1544051_POSITIVE 269 103 70 79 44 NC_002950:PG1945|3end_hypothetical_protein_2032220..2032370_POSITIVE 262 112 71 96 45 NC_002950:PG1540|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_1620409..1620559_POSITIVE 262 110 61 147 99 NC_002950:PG1352|3end_hypothetical_protein_1432737..1432887_NEGATIVE 262 123 81 122 78 NC_002950:PG0056|3end_hypothetical_protein_69782..69932_POSITIVE 260 94 51 103 55 NC_002950:PG0134|3end_magnesium_transporter_155783..155933_NEGATIVE 259 102 61 47 1 NC_002950:PG0563|3end_hypothetical_protein_620935..621085_NEGATIVE 256 108 62 132 81 NC_002950:PG0021|3end_TIM-barrel_protein,_putative,_NifR3_family_24122..24272_NEGATIVE 254 93 75 84 62 NC_002950:PG2026|3end_phosphoglycerate_mutase_family_protein_2125545..2125695_POSITIVE 254 109 61 86 38 NC_002950:PG1483|3end_conjugative_transposon_protein_TraE_1558783..1558933_NEGATIVE