Origin IGS: gtcgtttttctcacttatcggacttatccgaaaataattgagggtgagccaagtggatcctaaaagctggacacaaaacttttaggattcacttggctcaccctttacttattgggtttatgactctagaaacgaactgttatgccgtttcggtgtcagatcggtcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagaccgatctgacaccgaaacggcataacagttcgtttctagagtcataaacccaataagtaaagggtgagccaagtgaatcctaaaagttttgtgtccagcttttaggatccacttggctcaccctcaattattttcggataagtccgataagtgagaaaaacgac Mask Tandem Repeat Region ================================================ gtcgtttttctcacttatcggacttatccgaaaataattgagggtgagccaagtggatcctaaaagctggacacaaaacttttaggattcacttggctcaccctttacttattgggtttatgactctagaaacgaactgttatgccgtttcggtgtcagatcggtcttt Find is-nt database================================================ Query_seq: PG1080:PG1081|PG1080:PG1081:3-hydroxyacyl-CoA dehydrogenase family protein:acetate kinase:-><-:1148352..1148520 169 gtcgtttttctcacttatcggacttatccgaaaataattgagggtgagccaagtggatcctaaaagctggacacaaaacttttaggattcacttggctcaccctttacttattgggtttatgactctagaaacgaactgttatgccgtttcggtgtcagatcggtcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1080:PG1081|PG1080:PG1081:3-hydroxyacyl-CoA dehydrogenase family protein:acetate kinase:-><-:1148352..1148520 169 gtcgtttttctcacttatcggacttatccgaaaataattgagggtgagccaagtggatcctaaaagctggacacaaaacttttaggattcacttggctcaccctttacttattgggtttatgactctagaaacgaactgttatgccgtttcggtgtcagatcggtcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1080:PG1081|PG1080:PG1081:3-hydroxyacyl-CoA dehydrogenase family protein:acetate kinase:-><-:1148352..1148520 169 gtcgtttttctcacttatcggacttatccgaaaataattgagggtgagccaagtggatcctaaaagctggacacaaaacttttaggattcacttggctcaccctttacttattgggtttatgactctagaaacgaactgttatgccgtttcggtgtcagatcggtcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtcgtttttctcacttatcggacttatccgaaaataattgagggtgagccaagtggatcctaaaagctggacacaaaacttttaggattcacttggctcaccctttacttattgggtttatgactctagaaacgaactgttatgccgtttcggtgtcagatcggtcttt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 57 End: 167 ........................................................ M L K A G H K T F R I H L A H P L L I G F M T L E T N C Y A V S V S D R S .. gtcgtttttctcacttatcggacttatccgaaaataattgagggtgagccaagtggatcctaaaagctggacacaaaacttttaggattcacttggctcaccctttacttattgggtttatgactctagaaacgaactgttatgccgtttcggtgtcagatcggtcttt 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================================================ gtcgtttttctcacttatcggacttatccgaaaataattgagggtgagccaagtggatcctaaaagctggacacaaaacttttaggattcacttggctcaccctttacttattgggtttatgactctagaaacgaactgttatgccgtttcggtgtcagatcggtcttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -17.9 Tail_Score: -3.0449 Start: 44 End: 102 Full_Region: CGAAAATAATTGAGG GTGAGCCAAGTGGATCCTAAAAGCT GGACACAA AACTTTTAGGATTCACTTGGCTCACC CTTTACTTATTGGGT ...........................................GTGAGCCAAGTGGATCCTAAAAGCTGGACACAAAACTTTTAGGATTCACTTGGCTCACC................................................................... TransTerm Strand: + Conf: 56 HP_score: -3.6 Tail_Score: -4.09292 Start: 45 End: 103 Full_Region: GAAAATAATTGAGGG TGAGCCAAGTGGATCCTAAAAGCT GGACACAA AACTTTTAGGATTCACTTGGCTCACCC TTTACTTATTGGGTT ............................................TGAGCCAAGTGGATCCTAAAAGCTGGACACAAAACTTTTAGGATTCACTTGGCTCACCC.................................................................. TransTerm Strand: + Conf: 67 HP_score: -8.8 Tail_Score: -3.07307 Start: 53 End: 92 Full_Region: TTGAGGGTGAGCCAA GTGGATCCTAAAAGCT GGACACAA AACTTTTAGGATTCAC TTGGCTCACCCTTTA ....................................................GTGGATCCTAAAAGCTGGACACAAAACTTTTAGGATTCAC............................................................................. TransTerm Strand: - Conf: 67 HP_score: -8.8 Tail_Score: -3.06183 Start: 53 End: 92 Full_Region: taaagggtgagccaa gtgaatcctaaaagtt ttgtgtcc agcttttaggatccac ttggctcaccctcaa ....................................................gtgaatcctaaaagttttgtgtccagcttttaggatccac............................................................................. TransTerm Strand: + Conf: 48 HP_score: -3.7 Tail_Score: -3.19192 Start: 58 End: 87 Full_Region: GGTGAGCCAAGTGGA TCCTAAAAGCT GGACACAA AACTTTTAGGA TTCACTTGGCTCACC .........................................................TCCTAAAAGCTGGACACAAAACTTTTAGGA.................................................................................. Find igs database================================================ Query_seq: PG1080:PG1081|PG1080:PG1081:3-hydroxyacyl-CoA dehydrogenase family protein:acetate kinase:-><-:1148352..1148520 169 gtcgtttttctcacttatcggacttatccgaaaataattgagggtgagccaagtggatcctaaaagctggacacaaaacttttaggattcacttggctcaccctttacttattgggtttatgactctagaaacgaactgttatgccgtttcggtgtcagatcggtcttt Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: NC_002950_PG1080_PG1081|3-hydroxyacyl-CoA dehydrogenase family protein:acetate kinase|POSITIVE:NEGATIVE|[1148352,1148520]|169 HSP 1 e-value: 3.0E-91 bit: 335.0 Len: 169 Query Start:1 Query End:169 Subject Strand: POSITIVE Subject Start: 1 Subject End: 169 gtcgtttttctcacttatcggacttatccgaaaataattgagggtgagccaagtggatcctaaaagctggacacaaaacttttaggattcacttggctcaccctttacttattgggtttatgactctagaaacgaactgttatgccgtttcggtgtcagatcggtcttt gtcgtttttctcacttatcggacttatccgaaaataattgagggtgagccaagtggatcctaaaagctggacacaaaacttttaggattcacttggctcaccctttacttattgggtttatgactctagaaacgaactgttatgccgtttcggtgtcagatcggtcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCGUUUUUCUCACUUAUCGGACUUAUCCGAAAAUAAUUGAGGGUGAGCCAAGUGGAUCCUAAAAGCUGGACACAAAACUUUUAGGAUUCACUUGGCUCACCCUUUACUUAUUGGGUUUAUGACUCUAGAAACGAACUGUUAUGCCGUUUCGGUGUCAGAUCGGUCUUU (((((....(((.....(((((....))))).(((((..(((((((((((((((((((((((((((.((....))...)))))))))))))))))))))))))))...))))))))...)))))........(((.(((..((((((...))))))))).)))...... (-71.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGACCGAUCUGACACCGAAACGGCAUAACAGUUCGUUUCUAGAGUCAUAAACCCAAUAAGUAAAGGGUGAGCCAAGUGAAUCCUAAAAGUUUUGUGUCCAGCUUUUAGGAUCCACUUGGCUCACCCUCAAUUAUUUUCGGAUAAGUCCGAUAAGUGAGAAAAACGAC .........(((.((...((((((((......).)))))))...............(((((....(((((((((((((((.((((((((((((........)))))))))))).)))))))))))))))...))))).(((((....)))))...)).)))........ (-63.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 436 100 51 224 166 NC_002950:PG1025|5end_hypothetical_protein_1087141..1087371_POSITIVE 383 94 51 107 64 NC_002950:PG0554|5end_hypothetical_protein_611465..611695_POSITIVE 313 74 34 48 11 NC_002950:PG0676|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_727275..727505_NEGATIVE 303 89 41 209 151 NC_002950:PG2207|5end_hypothetical_protein_2320161..2320391_NEGATIVE 302 57 18 198 159 NC_002950:PG0323|5end_hypothetical_protein_357388..357618_NEGATIVE 302 110 64 75 18 NC_002950:PG0090|5end_Dps_family_protein_105524..105754_POSITIVE 293 70 25 69 29 NC_002950:PG0965|5end_phosphatidylserine_decarboxylase_1025776..1026006_NEGATIVE 284 158 113 155 111 NC_002950:PG2200|5end_TPR_domain_protein_2308807..2309037_NEGATIVE 278 71 42 52 27 NC_002950:PG0350|5end_internalin-related_protein_386810..387040_NEGATIVE 277 83 42 87 51 NC_002950:PG0978|5end_shikimate_5-dehydrogenase_1040033..1040263_POSITIVE 276 50 1 149 109 NC_002950:PG1172|5end_iron-sulfur_cluster_binding_protein,_putative_1251173..1251403_POSITIVE 271 59 15 173 128 NC_002950:PG1387|5end_hypothetical_protein_1470058..1470288_NEGATIVE 268 153 111 227 178 NC_002950:PG0375|5end_50S_ribosomal_protein_L13_405934..406164_POSITIVE 265 75 40 164 124 NC_002950:PG0603|5end_cytidylate_kinase_659570..659800_POSITIVE 262 157 111 164 107 NC_002950:PG1998|5end_polyprenyl_synthetase_2088029..2088259_NEGATIVE 261 148 101 189 149 NC_002950:PG2142|5end_GTP-binding_protein_Era_2247585..2247815_POSITIVE 260 157 112 73 29 NC_002950:PG1080|5end_3-hydroxyacyl-CoA_dehydrogenase_family_protein_1147366..1147596_POSITIVE 260 71 38 142 112 NC_002950:PG0240|5end_hydrolase,_haloacid_dehalogenase-like_family_277093..277323_NEGATIVE 259 160 114 140 93 NC_002950:PG2002|5end_dihydrodipicolinate_reductase_2091587..2091817_NEGATIVE 259 77 39 63 17 NC_002950:PG0272|5end_CBS_domain_protein_304399..304629_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 482 94 51 50 7 NC_002950:PG2192|3end_peptidase,_M23/M37_family_2299334..2299484_POSITIVE 463 117 79 65 25 NC_002950:PG1080|3end_3-hydroxyacyl-CoA_dehydrogenase_family_protein_1148291..1148441_POSITIVE 333 75 32 58 13 NC_002950:PG0548|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_605759..605909_POSITIVE 306 50 1 132 81 NC_002950:PG0124|3end_hypothetical_protein_145614..145764_NEGATIVE 302 97 55 47 1 NC_002950:PG1385|3end_TPR_domain_protein_1465133..1465283_NEGATIVE 284 158 113 119 75 NC_002950:PG2201|3end_peptide_deformylase_2308843..2308993_NEGATIVE 281 60 14 139 90 NC_002950:PG0352|3end_sialidase,_putative_388847..388997_POSITIVE 277 83 42 90 54 NC_002950:PG0977|3end_ubiquinone/menaquinone_biosynthesis_methyltransferase_1040116..1040266_POSITIVE 276 50 1 71 31 NC_002950:PG1171|3end_oxidoreductase,_putative_1251175..1251325_POSITIVE 271 59 15 136 91 NC_002950:PG1388|3end_hypothetical_protein_1470095..1470245_NEGATIVE 265 75 40 134 94 NC_002950:PG0602|3end_hypothetical_protein_659620..659770_POSITIVE 261 148 101 110 70 NC_002950:PG2141|3end_3-oxoacyl-(acyl_carrier_protein)_synthase_2247586..2247736_POSITIVE 259 160 114 79 32 NC_002950:PG2003|3end_deoxyguanosinetriphosphate_triphosphohydrolase_2091648..2091798_NEGATIVE 256 50 2 72 23 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 256 148 106 150 103 NC_002950:PG0903|3end_hypothetical_protein_969098..969248_NEGATIVE 254 98 51 103 55 NC_002950:PG1925|3end_ribosomal_protein_S14_2018406..2018556_NEGATIVE 254 52 20 33 3 NC_002950:PG1414|3end_hypothetical_protein_1499704..1499854_POSITIVE 254 67 28 69 16 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 253 157 111 95 42 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 253 61 26 79 37 NC_002950:PG2038|3end_N-acetylmuramoyl-L-alanine_amidase,_putative_2137809..2137959_NEGATIVE