Origin IGS: cagctttcagttatacttgttatacgaagatgttgtaggagaaagatccgttttttgcccatagagcaagctctgcaaagataagcaaaacgcattttacgtctgacgtttacttgcggagcggttgcatcagtgtctttcggtctgctcaaaaaagtgagaagcgaaagaacagctcgcgttttttttcgaaccgaacatggcaagattgcggttccaagaatttgagaatgcggcgcgagatctttttcgttttggttcgagaaagaaaaaatttacgaaccaaaatcaaaataaactcagaccacatttttccgaactgtaaaagttaatttattatgtccacaagacattctatagctacctctcgaaaacgattaaaggcaaatagtcaaagcttacattatggctattgtataaaatcatatacctttgtatctgtttgaatcatttttgctaaactgcgaaagagttgatcgattcattgtctagagaaattatccaaaagttgtttctgataaatttttaactgcat .........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.........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 atgcagttaaaaatttatcagaaacaacttttggataatttctctagacaatgaatcgatcaactctttcgcagtttagcaaaaatgattcaaacagatacaaaggtatatgattttatacaatagccataatgtaagctttgactatttgcctttaatcgttttcgagaggtagctatagaatgtcttgtggacataataaattaacttttacagttcggaaaaatgtggtctgagtttattttgattttggttcgtaaattttttctttctcgaaccaaaacgaaaaagatctcgcgccgcattctcaaattcttggaaccgcaatcttgccatgttcggttcgaaaaaaaacgcgagctgttctttcgcttctcacttttttgagcagaccgaaagacactgatgcaaccgctccgcaagtaaacgtcagacgtaaaatgcgttttgcttatctttgcagagcttgctctatgggcaaaaaacggatctttctcctacaacatcttcgtataacaagtataactgaaagctg Mask Tandem Repeat Region ================================================ cagctttcagttatacttgttatacgaagatgttgtaggagaaagatccgttttttgcccatagagcaagctctgcaaagataagcaaaacgcattttacgtctgacgtttacttgcggagcggttgcatcagtgtctttcggtctgctcaaaaaagtgagaagcgaaagaacagctcgcgttttttttcgaaccgaacatggcaagattgcggttccaagaatttgagaatgcggcgcgagatctttttcgttttggttcgagaaagaaaaaatttacgaaccaaaatcaaaataaactcagaccacatttttccgaactgtaaaagttaatttattatgtccacaagacattctatagctacctctcgaaaacgattaaaggcaaatagtcaaagcttacattatggctattgtataaaatcatatacctttgtatctgtttgaatcatttttgctaaactgcgaaagagttgatcgattcattgtctagagaaattatccaaaagttgtttctgataaatttttaactgcat Find is-nt database================================================ Query_seq: PG0381:PG0382|PG0381:PG0382:cell volume regulation protein CvrA:hypothetical protein:<-->:412796..413330 535 cagctttcagttatacttgttatacgaagatgttgtaggagaaagatccgttttttgcccatagagcaagctctgcaaagataagcaaaacgcattttacgtctgacgtttacttgcggagcggttgcatcagtgtctttcggtctgctcaaaaaagtgagaagcgaaagaacagctcgcgttttttttcgaaccgaacatggcaagattgcggttccaagaatttgagaatgcggcgcgagatctttttcgttttggttcgagaaagaaaaaatttacgaaccaaaatcaaaataaactcagaccacatttttccgaactgtaaaagttaatttattatgtccacaagacattctatagctacctctcgaaaacgattaaaggcaaatagtcaaagcttacattatggctattgtataaaatcatatacctttgtatctgtttgaatcatttttgctaaactgcgaaagagttgatcgattcattgtctagagaaattatccaaaagttgtttctgataaatttttaactgcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0381:PG0382|PG0381:PG0382:cell volume regulation protein CvrA:hypothetical protein:<-->:412796..413330 535 cagctttcagttatacttgttatacgaagatgttgtaggagaaagatccgttttttgcccatagagcaagctctgcaaagataagcaaaacgcattttacgtctgacgtttacttgcggagcggttgcatcagtgtctttcggtctgctcaaaaaagtgagaagcgaaagaacagctcgcgttttttttcgaaccgaacatggcaagattgcggttccaagaatttgagaatgcggcgcgagatctttttcgttttggttcgagaaagaaaaaatttacgaaccaaaatcaaaataaactcagaccacatttttccgaactgtaaaagttaatttattatgtccacaagacattctatagctacctctcgaaaacgattaaaggcaaatagtcaaagcttacattatggctattgtataaaatcatatacctttgtatctgtttgaatcatttttgctaaactgcgaaagagttgatcgattcattgtctagagaaattatccaaaagttgtttctgataaatttttaactgcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0381:PG0382|PG0381:PG0382:cell volume regulation protein CvrA:hypothetical protein:<-->:412796..413330 535 cagctttcagttatacttgttatacgaagatgttgtaggagaaagatccgttttttgcccatagagcaagctctgcaaagataagcaaaacgcattttacgtctgacgtttacttgcggagcggttgcatcagtgtctttcggtctgctcaaaaaagtgagaagcgaaagaacagctcgcgttttttttcgaaccgaacatggcaagattgcggttccaagaatttgagaatgcggcgcgagatctttttcgttttggttcgagaaagaaaaaatttacgaaccaaaatcaaaataaactcagaccacatttttccgaactgtaaaagttaatttattatgtccacaagacattctatagctacctctcgaaaacgattaaaggcaaatagtcaaagcttacattatggctattgtataaaatcatatacctttgtatctgtttgaatcatttttgctaaactgcgaaagagttgatcgattcattgtctagagaaattatccaaaagttgtttctgataaatttttaactgcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagctttcagttatacttgttatacgaagatgttgtaggagaaagatccgttttttgcccatagagcaagctctgcaaagataagcaaaacgcattttacgtctgacgtttacttgcggagcggttgcatcagtgtctttcggtctgctcaaaaaagtgagaagcgaaagaacagctcgcgttttttttcgaaccgaacatggcaagattgcggttccaagaatttgagaatgcggcgcgagatctttttcgttttggttcgagaaagaaaaaatttacgaaccaaaatcaaaataaactcagaccacatttttccgaactgtaaaagttaatttattatgtccacaagacattctatagctacctctcgaaaacgattaaaggcaaatagtcaaagcttacattatggctattgtataaaatcatatacctttgtatctgtttgaatcatttttgctaaactgcgaaagagttgatcgattcattgtctagagaaattatccaaaagttgtttctgataaatttttaactgcat Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 94 End: 225 ............................................................................................. M L R L T F T C G A V A S V S F G L L K K V R S E R T A R V F F R T E H G K I A V P R I ...................................................................................................................................................................................................................................................................................................................... Protein_Len: 41 Strand: + Start: 200 End: 322 ....................................................................................................................................................................................................... M A R L R F Q E F E N A A R D L F R F G S R K K K F T N Q N Q N K L R P H F S E L ..................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 81 End: 329 ................................................................................ M S K T H F T S D V Y L R S G C I S V F R S A Q K S E K R K N S S R F F S N R T W Q D C G S K N L R M R R E I F F V L V .............................................................................................................................................................................................................. Protein_Len: 36 Strand: + Start: 336 End: 443 ............................................................................................................................................................................................................................................................................................................................................... M M S T R H S I A T S R K R L K A N S Q S L H Y G Y C I K S Y T F V S V ............................................................................................ Protein_Len: 53 Strand: - Start: 152 End: 310 ....................................................................................................................................................... F L S F R F F L E R K K E F R V H C S Q P E L F K L I R R S I K K T K T R S L F F K R V L I L I F E S W M ................................................................................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 3 End: 275 .. K R R V N V Q P A T A D T D K P R S L F T L L S L V A R T K K R V S C P L I A T G L I Q S H P A L D K E N Q N S F S F M .................................................................................................................................................................................................................................................................... cagctttcagttatacttgttatacgaagatgttgtaggagaaagatccgttttttgcccatagagcaagctctgcaaagataagcaaaacgcattttacgtctgacgtttacttgcggagcggttgcatcagtgtctttcggtctgctcaaaaaagtgagaagcgaaagaacagctcgcgttttttttcgaaccgaacatggcaagattgcggttccaagaatttgagaatgcggcgcgagatctttttcgttttggttcgagaaagaaaaaatttacgaaccaaaatcaaaataaactcagaccacatttttccgaactgtaaaagttaatttattatgtccacaagacattctatagctacctctcgaaaacgattaaaggcaaatagtcaaagcttacattatggctattgtataaaatcatatacctttgtatctgtttgaatcatttttgctaaactgcgaaagagttgatcgattcattgtctagagaaattatccaaaagttgtttctgataaatttttaactgcat 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================================================ cagctttcagttatacttgttatacgaagatgttgtaggagaaagatccgttttttgcccatagagcaagctctgcaaagataagcaaaacgcattttacgtctgacgtttacttgcggagcggttgcatcagtgtctttcggtctgctcaaaaaagtgagaagcgaaagaacagctcgcgttttttttcgaaccgaacatggcaagattgcggttccaagaatttgagaatgcggcgcgagatctttttcgttttggttcgagaaagaaaaaatttacgaaccaaaatcaaaataaactcagaccacatttttccgaactgtaaaagttaatttattatgtccacaagacattctatagctacctctcgaaaacgattaaaggcaaatagtcaaagcttacattatggctattgtataaaatcatatacctttgtatctgtttgaatcatttttgctaaactgcgaaagagttgatcgattcattgtctagagaaattatccaaaagttgtttctgataaatttttaactgcat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0381:PG0382|PG0381:PG0382:cell volume regulation protein CvrA:hypothetical protein:<-->:412796..413330 535 cagctttcagttatacttgttatacgaagatgttgtaggagaaagatccgttttttgcccatagagcaagctctgcaaagataagcaaaacgcattttacgtctgacgtttacttgcggagcggttgcatcagtgtctttcggtctgctcaaaaaagtgagaagcgaaagaacagctcgcgttttttttcgaaccgaacatggcaagattgcggttccaagaatttgagaatgcggcgcgagatctttttcgttttggttcgagaaagaaaaaatttacgaaccaaaatcaaaataaactcagaccacatttttccgaactgtaaaagttaatttattatgtccacaagacattctatagctacctctcgaaaacgattaaaggcaaatagtcaaagcttacattatggctattgtataaaatcatatacctttgtatctgtttgaatcatttttgctaaactgcgaaagagttgatcgattcattgtctagagaaattatccaaaagttgtttctgataaatttttaactgcat Intra-Species Hit: Count: 1 Min: 1 Max: 535 Len: 535 Subject: NC_002950_PG0381_PG0382|cell volume regulation protein CvrA:hypothetical protein|NEGATIVE:POSITIVE|[412796,413330]|535 HSP 1 e-value: 0.0 bit: 1013.0 Len: 535 Query Start:1 Query End:535 Subject Strand: POSITIVE Subject Start: 1 Subject End: 535 cagctttcagttatacttgttatacgaagatgttgtaggagaaagatccgttttttgcccatagagcaagctctgcaaagataagcaaaacgcattttacgtctgacgtttacttgcggagcggttgcatcagtgtctttcggtctgctcaaaaaagtgagaagcgaaagaacagctcgcgnnnnnnnncgaaccgaacatggcaagattgcggttccaagaatttgagaatgcggcgcgagatctttttcgttttggttcgagaaagaaaaaatttacgaaccaaaatcaaaataaactcagaccacatttttccgaactgtaaaagttaatttattatgtccacaagacattctatagctacctctcgaaaacgattaaaggcaaatagtcaaagcttacattatggctattgtataaaatcatatacctttgtatctgtttgaatcatttttgctaaactgcgaaagagttgatcgattcattgtctagagaaattatccaaaagttgtttctgataaatttttaactgcat cagctttcagttatacttgttatacgaagatgttgtaggagaaagatccgttttttgcccatagagcaagctctgcaaagataagcaaaacgcattttacgtctgacgtttacttgcggagcggttgcatcagtgtctttcggtctgctcaaaaaagtgagaagcgaaagaacagctcgcgttttttttcgaaccgaacatggcaagattgcggttccaagaatttgagaatgcggcgcgagatctttttcgttttggttcgagaaagaaaaaatttacgaaccaaaatcaaaataaactcagaccacatttttccgaactgtaaaagttaatttattatgtccacaagacattctatagctacctctcgaaaacgattaaaggcaaatagtcaaagcttacattatggctattgtataaaatcatatacctttgtatctgtttgaatcatttttgctaaactgcgaaagagttgatcgattcattgtctagagaaattatccaaaagttgtttctgataaatttttaactgcat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGCUUUCAGUUAUACUUGUUAUACGAAGAUGUUGUAGGAGAAAGAUCCGUUUUUUGCCCAUAGAGCAAGCUCUGCAAAGAUAAGCAAAACGCAUUUUACGUCUGACGUUUACUUGCGGAGCGGUUGCAUCAGUGUCUUUCGGUCUGCUCAAAAAAGUGAGAAGCGAAAGAACAGCUCGCGUUUUUUUUCGAACCGAACAUGGCAAGAUUGCGGUUCCAAGAAUUUGAGAAUGCGGCGCGAGAUCUUUUUCGUUUUGGUUCGAGAAAGAAAAAAUUUACGAACCAAAAUCAAAAUAAACUCAGACCACAUUUUUCCGAACUGUAAAAGUUAAUUUAUUAUGUCCACAAGACAUUCUAUAGCUACCUCUCGAAAACGAUUAAAGGCAAAUAGUCAAAGCUUACAUUAUGGCUAUUGUAUAAAAUCAUAUACCUUUGUAUCUGUUUGAAUCAUUUUUGCUAAACUGCGAAAGAGUUGAUCGAUUCAUUGUCUAGAGAAAUUAUCCAAAAGUUGUUUCUGAUAAAUUUUUAACUGCAU .......((((((.....((((((.(((..(.((((.(((.(..((.((((.((((((((((.(((((.(((((((((.(.(((((.(.(((.......))).)...)))))))))))))))...))).)).)))...((((((.((...(((((((((((...(....).....))))).))))))..)).))))))...)))))))..)))).)).........(((((((.(((..(((.(..((((.(((((((((((.(((........))).))))))))))).))))..).))).).)).)))))))...((((.....)))).........).))))))).)..)))))))))........(((..(((((((...(((((((.(((((((........))))...(((((......)))))..)))...))))))).....(((((((......)))))))..))))))).))).(((((.(((((((((.......)))).)))))))))).....))))))... (-130.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGCAGUUAAAAAUUUAUCAGAAACAACUUUUGGAUAAUUUCUCUAGACAAUGAAUCGAUCAACUCUUUCGCAGUUUAGCAAAAAUGAUUCAAACAGAUACAAAGGUAUAUGAUUUUAUACAAUAGCCAUAAUGUAAGCUUUGACUAUUUGCCUUUAAUCGUUUUCGAGAGGUAGCUAUAGAAUGUCUUGUGGACAUAAUAAAUUAACUUUUACAGUUCGGAAAAAUGUGGUCUGAGUUUAUUUUGAUUUUGGUUCGUAAAUUUUUUCUUUCUCGAACCAAAACGAAAAAGAUCUCGCGCCGCAUUCUCAAAUUCUUGGAACCGCAAUCUUGCCAUGUUCGGUUCGAAAAAAAACGCGAGCUGUUCUUUCGCUUCUCACUUUUUUGAGCAGACCGAAAGACACUGAUGCAACCGCUCCGCAAGUAAACGUCAGACGUAAAAUGCGUUUUGCUUAUCUUUGCAGAGCUUGCUCUAUGGGCAAAAAACGGAUCUUUCUCCUACAACAUCUUCGUAUAACAAGUAUAACUGAAAGCUG ...((((((.......((((.........(((((((.((((..((((((..((((..((.....)).))))..))))))...)))).)))))))...((((....)))).)))).((((((.....(((((..((((((((((.(((((((((((...(((....))))))))))..)))).....((((((((........((((......((((((((....((((((((.(((((((.(((((.((((((((((..((........))..))))))))))))))).))).)))).)))))))).........((.((((((.(((........))))))))).))........))))))))(((((((((.((((......)))).))..)))))))...))))........)))))))).....((.((((((.....)))))).)).........))))))))))..))))).........(((......)))............))))))......))))))....... (-134.29) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 961 140 91 231 182 NC_002950:PG0381|5end_cell_volume_regulation_protein_CvrA_412705..412935_NEGATIVE 540 280 231 156 107 NC_002950:PG2063|5end_hypothetical_protein_2160596..2160826_NEGATIVE 540 280 231 143 94 NC_002950:PG0132|5end_hypothetical_protein_152879..153109_POSITIVE 448 266 227 49 11 NC_002950:PG1799|5end_hypothetical_protein_1894499..1894729_POSITIVE 445 266 227 71 33 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 407 150 107 231 182 NC_002950:PG0738|5end_cytidine/deoxycytidylate_deaminase_family_protein_786463..786693_POSITIVE 395 240 193 231 184 NC_002950:PG2127|5end_hypothetical_protein_2233552..2233782_NEGATIVE 392 260 212 87 44 NC_002950:PG0007|5end_hypothetical_protein_6913..7143_NEGATIVE 391 74 31 197 155 NC_002950:PG2066|5end_lipoprotein,_putative_2162116..2162346_POSITIVE 374 237 191 217 169 NC_002950:PG0068|5end_hypothetical_protein_81748..81978_POSITIVE 373 263 228 66 30 NC_002950:PG1617|5end_hypothetical_protein_1697755..1697985_NEGATIVE 371 178 136 183 133 NC_002950:PG0707|5end_TonB-dependent_receptor,_putative_763632..763862_NEGATIVE 359 148 101 55 3 NC_002950:PG0159|5end_endopeptidase_PepO_183164..183394_NEGATIVE 358 130 84 115 65 NC_002950:PG1640|5end_DNA-damage-inducible_protein_F_1721245..1721475_NEGATIVE 358 150 101 218 149 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 357 148 101 154 107 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 356 148 103 110 70 NC_002950:PG0788|5end_hypothetical_protein_840676..840906_NEGATIVE 354 280 236 46 2 NC_002950:PG0080|5end_hypothetical_protein_93832..94062_NEGATIVE 352 148 101 86 39 NC_002950:PG1218|5end_hypothetical_protein_1295937..1296167_POSITIVE 352 63 25 44 10 NC_002950:PG0335|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_370706..370936_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 391 74 31 106 64 NC_002950:PG2065|3end_conserved_hypothetical_protein_TIGR00048_2162105..2162255_POSITIVE 364 150 101 124 81 NC_002950:PG1738|3end_hypothetical_protein_1824097..1824247_NEGATIVE 362 320 273 68 21 NC_002950:PG1626|3end_hypothetical_protein_1710486..1710636_POSITIVE 358 130 84 100 50 NC_002950:PG1641|3end_phosphotyrosine_protein_phosphatase_1721260..1721410_NEGATIVE 358 150 101 129 60 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 356 148 103 84 44 NC_002950:PG0789|3end_hypothetical_protein_840702..840852_NEGATIVE 352 148 101 56 9 NC_002950:PG1217|3end_hypothetical_protein_1295987..1296137_POSITIVE 349 148 105 132 85 NC_002950:PG1235|3end_epimerase/reductase,_putative_1310300..1310450_NEGATIVE 348 262 227 113 79 NC_002950:PG1718|3end_hypothetical_protein_1806532..1806682_NEGATIVE 347 150 111 75 39 NC_002950:PG1613|3end_glyoxalase_family_protein_1693164..1693314_NEGATIVE 343 131 91 150 105 NC_002950:PG1208|3end_molecular_chaperone_DnaK_1284993..1285143_NEGATIVE 334 160 111 108 45 NC_002950:PG1411|3end_potassium_uptake_protein_TrkA,_putative_1493481..1493631_NEGATIVE 333 151 112 118 76 NC_002950:PG1648|3end_RelA/SpoT_family_protein_1730082..1730232_POSITIVE 330 150 103 76 34 NC_002950:PG0235|3end_carboxyl-terminal_protease_273232..273382_POSITIVE 326 238 194 62 14 NC_002950:PG2161|3end_transcriptional_regulator,_AraC_family_2266717..2266867_NEGATIVE 326 150 101 57 9 NC_002950:PG2158|3end_hypothetical_protein_2264473..2264623_POSITIVE 326 144 102 147 97 NC_002950:PG0517|3end_hypothetical_protein_559215..559365_NEGATIVE 325 150 103 53 2 NC_002950:PG0733|3end_riboflavin_synthase_subunit_alpha_783856..784006_POSITIVE 322 148 101 143 85 NC_002950:PG1859|3end_glycerate_kinase_family_protein_1957174..1957324_NEGATIVE 322 150 101 107 56 NC_002950:PG0629|3end_inorganic_polyphosphate/ATP-NAD_kinase_682498..682648_NEGATIVE