Origin IGS: ctcatcgcttagacgcacatttgtcgattcggttacagtcccgggtgagatctttcgtcaaacttacacgaaaacattcattttgagacctcattctcccctatctattagatgaactccgtgtgctcggctccttcctttttctccacatcccgatgactattatcatatattggttacacggacataccacctgcgagaaaaatttttcagccttagtcttgcagatttcaaaactaaggtatactt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagtataccttagttttgaaatctgcaagactaaggctgaaaaatttttctcgcaggtggtatgtccgtgtaaccaatatatgataatagtcatcgggatgtggagaaaaaggaaggagccgagcacacggagttcatctaatagataggggagaatgaggtctcaaaatgaatgttttcgtgtaagtttgacgaaagatctcacccgggactgtaaccgaatcgacaaatgtgcgtctaagcgatgag Mask Tandem Repeat Region ================================================ ctcatcgcttagacgcacatttgtcgattcggttacagtcccgggtgagatctttcgtcaaacttacacgaaaacattcattttgagacctcattctcccctatctattagatgaactccgtgtgctcggctccttcctttttctccacatcccgatgactattatcatatattggttacacggacataccacctgcgagaaaaatttttcagccttagtcttgcagatttcaaaactaaggtatactt Find is-nt database================================================ Query_seq: PG1660:PG1661|PG1660:PG1661:RNA polymerase sigma-70 factor, ECF subfamily:hypothetical protein:<-->:1744359..1744607 249 ctcatcgcttagacgcacatttgtcgattcggttacagtcccgggtgagatctttcgtcaaacttacacgaaaacattcattttgagacctcattctcccctatctattagatgaactccgtgtgctcggctccttcctttttctccacatcccgatgactattatcatatattggttacacggacataccacctgcgagaaaaatttttcagccttagtcttgcagatttcaaaactaaggtatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1660:PG1661|PG1660:PG1661:RNA polymerase sigma-70 factor, ECF subfamily:hypothetical protein:<-->:1744359..1744607 249 ctcatcgcttagacgcacatttgtcgattcggttacagtcccgggtgagatctttcgtcaaacttacacgaaaacattcattttgagacctcattctcccctatctattagatgaactccgtgtgctcggctccttcctttttctccacatcccgatgactattatcatatattggttacacggacataccacctgcgagaaaaatttttcagccttagtcttgcagatttcaaaactaaggtatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1660:PG1661|PG1660:PG1661:RNA polymerase sigma-70 factor, ECF subfamily:hypothetical protein:<-->:1744359..1744607 249 ctcatcgcttagacgcacatttgtcgattcggttacagtcccgggtgagatctttcgtcaaacttacacgaaaacattcattttgagacctcattctcccctatctattagatgaactccgtgtgctcggctccttcctttttctccacatcccgatgactattatcatatattggttacacggacataccacctgcgagaaaaatttttcagccttagtcttgcagatttcaaaactaaggtatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcatcgcttagacgcacatttgtcgattcggttacagtcccgggtgagatctttcgtcaaacttacacgaaaacattcattttgagacctcattctcccctatctattagatgaactccgtgtgctcggctccttcctttttctccacatcccgatgactattatcatatattggttacacggacataccacctgcgagaaaaatttttcagccttagtcttgcagatttcaaaactaaggtatactt Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 93 End: 248 ............................................................................................ M L P Y L L D E L R V L G S F L F L H I P M T I I I Y W L H G H T T C E K N F S A L V L Q I S K L R Y T . Protein_Len: 42 Strand: - Start: 104 End: 229 ....................................................................................................... R N S S S R T S P E K R K R W M G I V I I M Y Q N C P C V V Q S F F K E A K T K C M .................... Protein_Len: 31 Strand: - Start: 5 End: 94 .... * R K S A C K D I R N C D R T L D K T L S V R F C E N Q S R M ........................................................................................................................................................... ctcatcgcttagacgcacatttgtcgattcggttacagtcccgggtgagatctttcgtcaaacttacacgaaaacattcattttgagacctcattctcccctatctattagatgaactccgtgtgctcggctccttcctttttctccacatcccgatgactattatcatatattggttacacggacataccacctgcgagaaaaatttttcagccttagtcttgcagatttcaaaactaaggtatactt 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================================================ ctcatcgcttagacgcacatttgtcgattcggttacagtcccgggtgagatctttcgtcaaacttacacgaaaacattcattttgagacctcattctcccctatctattagatgaactccgtgtgctcggctccttcctttttctccacatcccgatgactattatcatatattggttacacggacataccacctgcgagaaaaatttttcagccttagtcttgcagatttcaaaactaaggtatactt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1660:PG1661|PG1660:PG1661:RNA polymerase sigma-70 factor, ECF subfamily:hypothetical protein:<-->:1744359..1744607 249 ctcatcgcttagacgcacatttgtcgattcggttacagtcccgggtgagatctttcgtcaaacttacacgaaaacattcattttgagacctcattctcccctatctattagatgaactccgtgtgctcggctccttcctttttctccacatcccgatgactattatcatatattggttacacggacataccacctgcgagaaaaatttttcagccttagtcttgcagatttcaaaactaaggtatactt Intra-Species Hit: Count: 1 Min: 1 Max: 249 Len: 249 Subject: NC_002950_PG1660_PG1661|RNA polymerase sigma-70 factor, ECF subfamily:hypothetical protein|NEGATIVE:POSITIVE|[1744359,1744607]|249 HSP 1 e-value: 1.0E-139 bit: 494.0 Len: 249 Query Start:1 Query End:249 Subject Strand: POSITIVE Subject Start: 1 Subject End: 249 ctcatcgcttagacgcacatttgtcgattcggttacagtcccgggtgagatctttcgtcaaacttacacgaaaacattcattttgagacctcattctcccctatctattagatgaactccgtgtgctcggctccttcctttttctccacatcccgatgactattatcatatattggttacacggacataccacctgcgagaaaaatttttcagccttagtcttgcagatttcaaaactaaggtatactt ctcatcgcttagacgcacatttgtcgattcggttacagtcccgggtgagatctttcgtcaaacttacacgaaaacattcattttgagacctcattctcccctatctattagatgaactccgtgtgctcggctccttcctttttctccacatcccgatgactattatcatatattggttacacggacataccacctgcgagaaaaatttttcagccttagtcttgcagatttcaaaactaaggtatactt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAUCGCUUAGACGCACAUUUGUCGAUUCGGUUACAGUCCCGGGUGAGAUCUUUCGUCAAACUUACACGAAAACAUUCAUUUUGAGACCUCAUUCUCCCCUAUCUAUUAGAUGAACUCCGUGUGCUCGGCUCCUUCCUUUUUCUCCACAUCCCGAUGACUAUUAUCAUAUAUUGGUUACACGGACAUACCACCUGCGAGAAAAAUUUUUCAGCCUUAGUCUUGCAGAUUUCAAAACUAAGGUAUACUU .((.((((...((((......)))).....(((....((((((((.((((...((((((..........(((....))).....((((......))))............))))))..(((......)))............)))).....)))).((((((.(((...))).))))))...))))..)))....))))))...........((((((((.(((.......))).))))))))...... (-50.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAUACCUUAGUUUUGAAAUCUGCAAGACUAAGGCUGAAAAAUUUUUCUCGCAGGUGGUAUGUCCGUGUAACCAAUAUAUGAUAAUAGUCAUCGGGAUGUGGAGAAAAAGGAAGGAGCCGAGCACACGGAGUUCAUCUAAUAGAUAGGGGAGAAUGAGGUCUCAAAAUGAAUGUUUUCGUGUAAGUUUGACGAAAGAUCUCACCCGGGACUGUAACCGAAUCGACAAAUGUGCGUCUAAGCGAUGAG .......(((((((((((.......)))))))))))............((((((...((((.....((((((.....))))))...((((((.(((((.....((((.............(((((((((((((((((((((.....)))..((((......))))...))))))...)))))))..))))).(....).)))).))))))))))).))))....(((........)))...)))).)). (-63.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1010 50 1 141 92 NC_002950:PG1660|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1744268..1744498_NEGATIVE 403 154 111 194 151 NC_002950:PG1327|5end_aminotransferase,_putative_1406580..1406810_NEGATIVE 373 149 110 200 145 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 367 138 92 71 24 NC_002950:PG1213|5end_ribonuclease_H_1292433..1292663_POSITIVE 364 139 96 134 87 NC_002950:PG0216|5end_hypothetical_protein_251956..252186_POSITIVE 352 155 111 225 182 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 352 146 111 192 148 NC_002950:PG0165|5end_heat_shock_protein_15_187807..188037_NEGATIVE 351 59 11 203 152 NC_002950:PG1902|5end_uridylate_kinase_2002147..2002377_NEGATIVE 348 47 1 221 176 NC_002950:PG1254|5end_acetyltransferase,_GNAT_family_1332121..1332351_NEGATIVE 346 156 111 221 158 NC_002950:PG1588|5end_hypothetical_protein_1666532..1666762_NEGATIVE 343 166 121 208 164 NC_002950:PG1089|5end_DNA-binding_response_regulator_RprY_1156260..1156490_NEGATIVE 342 46 1 231 175 NC_002950:PG2104|5end_hypothetical_protein_2213619..2213849_NEGATIVE 340 70 28 44 2 NC_002950:PG1718|5end_hypothetical_protein_1806807..1807037_NEGATIVE 334 48 5 69 27 NC_002950:PG1217|5end_hypothetical_protein_1295575..1295805_POSITIVE 328 50 1 107 44 NC_002950:PG2225|5end_hypothetical_protein_2339440..2339670_POSITIVE 327 60 14 142 92 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 326 156 118 53 18 NC_002950:PG1693|5end_HesA/MoeB/ThiF_family_protein_1777919..1778149_NEGATIVE 326 44 1 122 74 NC_002950:PG0753|5end_protease_798301..798531_POSITIVE 323 158 118 95 41 NC_002950:PG1109|5end_mobilization_protein_1182792..1183022_NEGATIVE 317 59 11 69 19 NC_002950:PG0930|5end_hypothetical_protein_987542..987772_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 403 154 111 151 108 NC_002950:PG1328|3end_CoA_ligase_family_protein_1406623..1406773_NEGATIVE 364 139 96 126 79 NC_002950:PG0215|3end_hypothetical_protein_252028..252178_POSITIVE 351 59 11 120 69 NC_002950:PG1903|3end_hypothetical_protein_2002230..2002380_NEGATIVE 347 153 114 105 59 NC_002950:PG1964|3end_bacterial_sugar_transferase_2054396..2054546_POSITIVE 335 137 93 102 59 NC_002950:PG2125|3end_transcriptional_regulator,_AraC_family_2231376..2231526_NEGATIVE 334 48 5 79 37 NC_002950:PG1216|3end_hypothetical_protein_1295665..1295815_POSITIVE 328 50 1 87 24 NC_002950:PG2224|3end_hypothetical_protein_2339500..2339650_POSITIVE 326 156 118 56 21 NC_002950:PG1694|3end_hypothetical_protein_1777916..1778066_NEGATIVE 326 44 1 138 90 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 319 59 11 138 80 NC_002950:PG1570|3end_rhodanese-like_domain_protein_1648582..1648732_NEGATIVE 318 138 97 43 2 NC_002950:PG1212|3end_TPR_domain_protein_1292485..1292635_POSITIVE 314 177 131 63 10 NC_002950:PG0577|3end_phospho-N-acetylmuramoyl-pentapeptide-_transferase_634536..634686_POSITIVE 306 56 14 151 111 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 306 59 15 144 90 NC_002950:PG0068|3end_hypothetical_protein_82079..82229_POSITIVE 305 154 113 136 84 NC_002950:PG0472|3end_iron-sulfur_cluster_binding_protein,_putative_514414..514564_POSITIVE 305 46 5 150 106 NC_002950:PG0020|3end_transcriptional_regulator,_MarR_family_24166..24316_POSITIVE 302 167 121 129 82 NC_002950:PG1276|3end_DNA-binding_protein,_histone-like_family_1353531..1353681_POSITIVE 302 163 123 147 113 NC_002950:PG0633|3end_hypothetical_protein_686208..686358_POSITIVE 302 167 121 129 82 NC_002950:PG0566|3end_DNA-binding_protein,_histone-like_family_622935..623085_NEGATIVE 300 161 130 65 31 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE