Origin IGS: aacggcattatttgttcttctgttatgactttggtgataaatccctcggggataattttttgcaaaggaacagattatttgcggattgccggtttgatagagagacttttagtggtactttagccttggcttatcgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacgataagccaaggctaaagtaccactaaaagtctctctatcaaaccggcaatccgcaaataatctgttcctttgcaaaaaattatccccgagggatttatcaccaaagtcataacagaagaacaaataatgccgtt Mask Tandem Repeat Region ================================================ aacggcattatttgttcttctgttatgactttggtgataaatccctcggggataattttttgcaaaggaacagattatttgcggattgccggtttgatagagagacttttagtggtactttagccttggcttatcgtt Find is-nt database================================================ Query_seq: PG0477:PG0479|PG0477:PG0479:pantoate--beta-alanine ligase:hypothetical protein:<-->:519688..519825 138 aacggcattatttgttcttctgttatgactttggtgataaatccctcggggataattttttgcaaaggaacagattatttgcggattgccggtttgatagagagacttttagtggtactttagccttggcttatcgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0477:PG0479|PG0477:PG0479:pantoate--beta-alanine ligase:hypothetical protein:<-->:519688..519825 138 aacggcattatttgttcttctgttatgactttggtgataaatccctcggggataattttttgcaaaggaacagattatttgcggattgccggtttgatagagagacttttagtggtactttagccttggcttatcgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0477:PG0479|PG0477:PG0479:pantoate--beta-alanine ligase:hypothetical protein:<-->:519688..519825 138 aacggcattatttgttcttctgttatgactttggtgataaatccctcggggataattttttgcaaaggaacagattatttgcggattgccggtttgatagagagacttttagtggtactttagccttggcttatcgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacggcattatttgttcttctgttatgactttggtgataaatccctcggggataattttttgcaaaggaacagattatttgcggattgccggtttgatagagagacttttagtggtactttagccttggcttatcgtt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 7 End: 120 ...... M I C S S V M T L V I N P S G I I F C K G T D Y L R I A G L I E R L L V V L .................. Protein_Len: 42 Strand: + Start: 12 End: 137 ........... M F F C Y D F G D K S L G D N F L Q R N R L F A D C R F D R E T F S G T L A L A Y R . aacggcattatttgttcttctgttatgactttggtgataaatccctcggggataattttttgcaaaggaacagattatttgcggattgccggtttgatagagagacttttagtggtactttagccttggcttatcgtt 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================================================ aacggcattatttgttcttctgttatgactttggtgataaatccctcggggataattttttgcaaaggaacagattatttgcggattgccggtttgatagagagacttttagtggtactttagccttggcttatcgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0477:PG0479|PG0477:PG0479:pantoate--beta-alanine ligase:hypothetical protein:<-->:519688..519825 138 aacggcattatttgttcttctgttatgactttggtgataaatccctcggggataattttttgcaaaggaacagattatttgcggattgccggtttgatagagagacttttagtggtactttagccttggcttatcgtt Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: NC_002950_PG0477_PG0479|pantoate--beta-alanine ligase:hypothetical protein|NEGATIVE:POSITIVE|[519688,519825]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 aacggcattatttgttcttctgttatgactttggtgataaatccctcggggataattttttgcaaaggaacagattatttgcggattgccggtttgatagagagacttttagtggtactttagccttggcttatcgtt aacggcattatttgttcttctgttatgactttggtgataaatccctcggggataattttttgcaaaggaacagattatttgcggattgccggtttgatagagagacttttagtggtactttagccttggcttatcgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGGCAUUAUUUGUUCUUCUGUUAUGACUUUGGUGAUAAAUCCCUCGGGGAUAAUUUUUUGCAAAGGAACAGAUUAUUUGCGGAUUGCCGGUUUGAUAGAGAGACUUUUAGUGGUACUUUAGCCUUGGCUUAUCGUU ((((.(((((...((..((((((((.((((..((..((..(((((...)))))........(((((...........)))))..))..))))))))))))))..))...))))).......(((....)))...)))) (-33.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGAUAAGCCAAGGCUAAAGUACCACUAAAAGUCUCUCUAUCAAACCGGCAAUCCGCAAAUAAUCUGUUCCUUUGCAAAAAAUUAUCCCCGAGGGAUUUAUCACCAAAGUCAUAACAGAAGAACAAAUAAUGCCGUU ...((((((...(((((..((.....))...))))))).))))....(((((............((((((.(((((.........(((((...))))).......)))))....))))))...........))))).. (-24.09) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 961 130 81 221 172 NC_002950:PG0477|5end_pantoate--beta-alanine_ligase_519597..519827_NEGATIVE 356 130 82 224 156 NC_002950:PG1977|5end_hypothetical_protein_2066693..2066923_NEGATIVE 347 130 82 183 136 NC_002950:PG0307|5end_NADH-ubiquinone_oxidoreductase_342560..342790_POSITIVE 314 129 81 61 5 NC_002950:PG0771|5end_hypothetical_protein_824524..824754_POSITIVE 307 90 41 231 178 NC_002950:PG1767|5end_lipoprotein,_putative_1853995..1854225_POSITIVE 307 127 82 58 20 NC_002950:PG0332|5end_transcription_termination_factor_Rho_365619..365849_POSITIVE 303 89 43 111 67 NC_002950:PG0997|5end_transcriptional_regulator,_putative_1056666..1056896_POSITIVE 297 89 42 202 142 NC_002950:PG1417|5end_fumarate_hydratase_class_I,_anaerobic_1501295..1501525_POSITIVE 290 129 81 166 116 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 290 130 86 230 195 NC_002950:PG1133|5end_hypothetical_protein_1213571..1213801_POSITIVE 290 130 81 199 155 NC_002950:PG0851|5end_hypothetical_protein_912732..912962_NEGATIVE 288 104 67 54 18 NC_002950:PG1835|5end_lipoprotein,_putative_1927073..1927303_POSITIVE 286 104 63 226 182 NC_002950:PG0189|5end_hypothetical_protein_225291..225521_POSITIVE 285 110 62 166 119 NC_002950:PG0450|5end_hypothetical_protein_490812..491042_POSITIVE 285 104 62 159 112 NC_002950:PG0085|5end_alpha-galactosidase_99172..99402_POSITIVE 284 130 81 217 169 NC_002950:PG1480|5end_conjugative_transposon_protein_TraI_1555895..1556125_NEGATIVE 282 130 81 128 76 NC_002950:PG1102|5end_hypothetical_protein_1173637..1173867_NEGATIVE 281 90 41 62 20 NC_002950:PG0709|5end_peptidyl-prolyl_cis-trans_isomerase_FkpA,_FKBP-type_765417..765647_NEGATIVE 276 126 81 180 140 NC_002950:PG1418|5end_DNA_polymerase_III,_gamma_and_tau_subunits_1503064..1503294_POSITIVE 274 50 3 123 86 NC_002950:PG0917|5end_GtrA_family_protein_978097..978327_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 130 82 150 105 NC_002950:PG0957|3end_riboflavin_biosynthesis_protein_RibF_1018131..1018281_POSITIVE 285 110 62 141 94 NC_002950:PG0449|3end_TPR_domain_protein_490867..491017_POSITIVE 278 94 55 70 37 NC_002950:PG1340|3end_L-lactate_permease_1420298..1420448_NEGATIVE 278 127 83 60 18 NC_002950:PG0352|3end_sialidase,_putative_388847..388997_POSITIVE 276 126 81 57 17 NC_002950:PG1417|3end_fumarate_hydratase_class_I,_anaerobic_1503021..1503171_POSITIVE 276 98 56 58 6 NC_002950:PG0710|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_765447..765597_NEGATIVE 274 47 4 54 15 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE 273 49 18 140 109 NC_002950:PG1242|3end_replicative_DNA_helicase_1319101..1319251_POSITIVE 270 108 61 57 3 NC_002950:PG0160|3end_hypothetical_protein_183183..183333_NEGATIVE 269 130 81 120 69 NC_002950:PG0091|3end_transporter,_putative_106183..106333_NEGATIVE 268 105 65 127 70 NC_002950:PG0480|3end_precorrin-2_C20-methyltransferase,_putative_520606..520756_NEGATIVE 264 107 62 49 6 NC_002950:PG1461|3end_hypothetical_protein_1540927..1541077_POSITIVE 262 120 80 96 48 NC_002950:PG1537|3end_hypothetical_protein_1617603..1617753_POSITIVE 262 90 41 109 63 NC_002950:PG0856|3end_hypothetical_protein_917175..917325_POSITIVE 262 117 78 136 103 NC_002950:PG0070|3end_UDP-N-acetylglucosamine_acyltransferase_83940..84090_NEGATIVE 259 126 82 145 87 NC_002950:PG1241|3end_GTP-binding_protein_LepA_1317480..1317630_POSITIVE 259 49 3 45 1 NC_002950:PG0977|3end_ubiquinone/menaquinone_biosynthesis_methyltransferase_1040116..1040266_POSITIVE 259 77 31 149 95 NC_002950:PG0369|3end_phosphopantetheine_adenylyltransferase_403751..403901_POSITIVE 259 116 71 56 23 NC_002950:PG0325|3end_hypothetical_protein_359085..359235_NEGATIVE 258 130 82 117 77 NC_002950:PG1777|3end_hypothetical_protein_1867105..1867255_POSITIVE