Origin IGS: tgctctaaattctttattatcattagttgtgtataacaaagaacctatatgaatctgaaaagaatctgaaatgacaaaagattttgaaaaaattttttccgaccggctgatcgagcactttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaagtgctcgatcagccggtcggaaaaaattttttcaaaatcttttgtcatttcagattcttttcagattcatataggttctttgttatacacaactaatgataataaagaatttagagca Mask Tandem Repeat Region ================================================ tgctctaaattctttattatcattagttgtgtataacaaagaacctatatgaatctgaaaagaatctgaaatgacaaaagattttgaaaaaattttttccgaccggctgatcgagcactttc Find is-nt database================================================ Query_seq: PG0718:PG0719|PG0718:PG0719:hypothetical protein:sensor histidine kinase:<-<-:771664..771785 122 tgctctaaattctttattatcattagttgtgtataacaaagaacctatatgaatctgaaaagaatctgaaatgacaaaagattttgaaaaaattttttccgaccggctgatcgagcactttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0718:PG0719|PG0718:PG0719:hypothetical protein:sensor histidine kinase:<-<-:771664..771785 122 tgctctaaattctttattatcattagttgtgtataacaaagaacctatatgaatctgaaaagaatctgaaatgacaaaagattttgaaaaaattttttccgaccggctgatcgagcactttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0718:PG0719|PG0718:PG0719:hypothetical protein:sensor histidine kinase:<-<-:771664..771785 122 tgctctaaattctttattatcattagttgtgtataacaaagaacctatatgaatctgaaaagaatctgaaatgacaaaagattttgaaaaaattttttccgaccggctgatcgagcactttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgctctaaattctttattatcattagttgtgtataacaaagaacctatatgaatctgaaaagaatctgaaatgacaaaagattttgaaaaaattttttccgaccggctgatcgagcactttc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 26 End: 118 ......................... N H I V F F R Y S D S F F R F H C F I K F F N K G V P Q D L M .... Protein_Len: 37 Strand: - Start: 1 End: 111 A R F E K N D N T T Y L L S G I H I Q F S D S I V F S K S F I K E S R S M ........... tgctctaaattctttattatcattagttgtgtataacaaagaacctatatgaatctgaaaagaatctgaaatgacaaaagattttgaaaaaattttttccgaccggctgatcgagcactttc 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================================================ tgctctaaattctttattatcattagttgtgtataacaaagaacctatatgaatctgaaaagaatctgaaatgacaaaagattttgaaaaaattttttccgaccggctgatcgagcactttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0718:PG0719|PG0718:PG0719:hypothetical protein:sensor histidine kinase:<-<-:771664..771785 122 tgctctaaattctttattatcattagttgtgtataacaaagaacctatatgaatctgaaaagaatctgaaatgacaaaagattttgaaaaaattttttccgaccggctgatcgagcactttc Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: NC_002950_PG0718_PG0719|hypothetical protein:sensor histidine kinase|NEGATIVE:NEGATIVE|[771664,771785]|122 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 tgctctaaattctttattatcattagttgtgtataacaaagaacctatatgaatctgaaaagaatctgaaatgacaaaagattttgaaaaaattttttccgaccggctgatcgagcactttc tgctctaaattctttattatcattagttgtgtataacaaagaacctatatgaatctgaaaagaatctgaaatgacaaaagattttgaaaaaattttttccgaccggctgatcgagcactttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUCUAAAUUCUUUAUUAUCAUUAGUUGUGUAUAACAAAGAACCUAUAUGAAUCUGAAAAGAAUCUGAAAUGACAAAAGAUUUUGAAAAAAUUUUUUCCGACCGGCUGAUCGAGCACUUUC (((((....((((((.(((((((.....))).)))).))))))((.....((.(((....))).)).........(((((((((.....)))))))))......))......)))))..... (-19.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAGUGCUCGAUCAGCCGGUCGGAAAAAAUUUUUUCAAAAUCUUUUGUCAUUUCAGAUUCUUUUCAGAUUCAUAUAGGUUCUUUGUUAUACACAACUAAUGAUAAUAAAGAAUUUAGAGCA .....(((((((.(((..(((..(((((....)))))...)))..)))))......((.(((....))).))...(((((((((((((((.((.......)))))))))))))))))))))) (-22.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 819 120 71 211 162 NC_002950:PG0718|5end_hypothetical_protein_771573..771803_NEGATIVE 265 119 101 26 3 NC_002950:PG0213|5end_precorrin-3_methylase/precorrin-8X_methylmutase_250464..250694_NEGATIVE 256 119 84 47 6 NC_002950:PG0255|5end_translation_initiation_factor_IF-2_286542..286772_POSITIVE 255 116 89 56 24 NC_002950:PG1996|5end_deoxyribose-phosphate_aldolase_2085921..2086151_POSITIVE 251 116 73 156 101 NC_002950:PG1978|5end_hypothetical_protein_2067337..2067567_NEGATIVE 246 116 72 190 149 NC_002950:PG0360|5end_lemA_protein_393482..393712_POSITIVE 239 117 94 54 25 NC_002950:PG1917|5end_methionine_aminopeptidase,_type_I_2014490..2014720_NEGATIVE 237 120 100 152 136 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 236 119 103 157 140 NC_002950:PG1994|5end_D-tyrosyl-tRNA_deacylase_2085127..2085357_POSITIVE 235 118 98 31 10 NC_002950:PG0499|5end_hypothetical_protein_538709..538939_POSITIVE 234 117 99 21 2 NC_002950:PG1392|5end_rod_shape-determining_protein_RodA,_putative_1474416..1474646_NEGATIVE 233 116 98 213 190 NC_002950:PG2099|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2207932..2208162_NEGATIVE 230 116 86 85 61 NC_002950:PG0722|5end_hypothetical_protein_774891..775121_NEGATIVE 229 116 83 65 35 NC_002950:PG0918|5end_hypothetical_protein_978818..979048_NEGATIVE 228 117 103 218 201 NC_002950:PG1102|5end_hypothetical_protein_1173637..1173867_NEGATIVE 227 116 93 153 122 NC_002950:PG2121|5end_L-asparaginase_2229624..2229854_NEGATIVE 225 120 99 228 198 NC_002950:PG0159|5end_endopeptidase_PepO_183164..183394_NEGATIVE 224 102 62 192 154 NC_002950:PG1791|5end_hypothetical_protein_1881166..1881396_NEGATIVE 224 120 90 45 15 NC_002950:PG1457|5end_hypothetical_protein_1538650..1538880_POSITIVE 222 117 93 228 197 NC_002950:PG1476|5end_conjugative_transposon_protein_TraM_1553219..1553449_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 120 100 33 7 NC_002950:PG0554|3end_hypothetical_protein_611661..611811_POSITIVE 274 108 64 124 79 NC_002950:PG0652|3end_hypothetical_protein_703899..704049_NEGATIVE 255 116 89 69 37 NC_002950:PG1995|3end_hypothetical_protein_2086014..2086164_POSITIVE 246 116 71 149 85 NC_002950:PG1223|3end_hypothetical_protein_1299744..1299894_POSITIVE 246 116 72 146 105 NC_002950:PG0359|3end_flavin_reductase_domain_protein_393518..393668_POSITIVE 241 114 82 39 10 NC_002950:PG0424|3end_hypothetical_protein_463213..463363_POSITIVE 239 117 94 54 25 NC_002950:PG1918|3end_preprotein_translocase_SecY_2014490..2014640_NEGATIVE 237 119 92 55 25 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 236 119 103 150 133 NC_002950:PG1993|3end_excinuclease_ABC,_C_subunit_2085200..2085350_POSITIVE 234 117 99 31 12 NC_002950:PG1393|3end_penicillin-binding_protein_2,_putative_1474406..1474556_NEGATIVE 227 117 100 82 61 NC_002950:PG2140|3end_ribosomal_protein_L32_2246399..2246549_POSITIVE 221 117 99 98 78 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 220 117 92 34 1 NC_002950:PG1943|3end_hypothetical_protein_2028974..2029124_NEGATIVE 220 120 99 137 117 NC_002950:PG1632|3end_aldose_1-epimerase_1713415..1713565_POSITIVE 218 117 98 122 97 NC_002950:PG0979|3end_hypothetical_protein_1040990..1041140_POSITIVE 212 116 94 131 110 NC_002950:PG2107|3end_thiamine_biosynthesis_protein_ThiH_2215546..2215696_NEGATIVE 212 120 80 149 106 NC_002950:PG1487|3end_hypothetical_protein_1561799..1561949_POSITIVE 210 116 91 145 115 NC_002950:PG0170|3end_methionyl-tRNA_synthetase_191774..191924_POSITIVE 209 113 80 35 9 NC_002950:PG1706|3end_hypothetical_protein_1793849..1793999_NEGATIVE 208 112 72 70 33 NC_002950:PG0484|3end_hypothetical_protein_523851..524001_NEGATIVE