Origin IGS: ctattttctcctttgtcttactaaaaaaacttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaatcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga .........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 tcaatttacctcgtttttcattatatcataaagttagctaataagaaatgaagggcagtaagtcaagtaatcactttgaagtttcaaagtttgattttaagctttctttaagaaaactatattattctgaagaactctaaaatttcacagctatttattggtaatgactacagaattcctagtcattactagaaatggactagtttctttgaataatggaactgcataatcctcctattctagaacgggacgactagtatttcttttatgataggactagattgtggtataatagagagaataagtttttttagtaagacaaaggagaaaatag Mask Tandem Repeat Region ================================================ ctattttctcctttgtcttactaaaaaaacttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaatcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga Find is-nt database================================================ Query_seq: SMT_683:SMT_684|SMT_683:SMT_684:similar to CDP-ribitol pyrophosphorylase:polysaccharide biosynthesis protein, putative:<-->:592663..592996 334 ctattttctcctttgtcttactaaaaaaacttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaatcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_683:SMT_684|SMT_683:SMT_684:similar to CDP-ribitol pyrophosphorylase:polysaccharide biosynthesis protein, putative:<-->:592663..592996 334 ctattttctcctttgtcttactaaaaaaacttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaatcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_683:SMT_684|SMT_683:SMT_684:similar to CDP-ribitol pyrophosphorylase:polysaccharide biosynthesis protein, putative:<-->:592663..592996 334 ctattttctcctttgtcttactaaaaaaacttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaatcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctattttctcctttgtcttactaaaaaaacttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaatcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 3 End: 92 .. M F S F V L L K K L I L S I I P Q S S P I I K E I L V V P F .................................................................................................................................................................................................................................................. Protein_Len: 30 Strand: - Start: 198 End: 287 ..................................................................................................................................................................................................... L E E S Y Y L K R L S L K F D F K S V E F H N S S K S G K M ............................................... ctattttctcctttgtcttactaaaaaaacttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaatcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 42 End: 71 .........................................TTTTATGATAGGACTAGATTGTGGTATAAT....................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 286 End: 315 .............................................................................................................................................................................................................................................................................................ATTTCTTATTAGCTAACTTTATGATATAAT................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 17 End: 46 ................CTTACTAAAAAAACTTATTCTCTCTATTAT................................................................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctattttctcctttgtcttactaaaaaaacttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaatcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 56 HP_score: -2.3 Tail_Score: -4.47183 Start: 132 End: 156 Full_Region: atgactacagaattc ctagtcatt actaga aatggactag tttctttgaataatg ...................................................................................................................................ctagtcattactagaaatggactag.................................................................................................................................................................................. TransTerm Strand: - Conf: 72 HP_score: -6.2 Tail_Score: -4.21408 Start: 246 End: 261 Full_Region: taagtcaagtaatca ctttga agtt tcaaag tttgattttaagctt .....................................................................................................................................................................................................................................................ctttgaagtttcaaag......................................................................... Find igs database================================================ Query_seq: SMT_683:SMT_684|SMT_683:SMT_684:similar to CDP-ribitol pyrophosphorylase:polysaccharide biosynthesis protein, putative:<-->:592663..592996 334 ctattttctcctttgtcttactaaaaaaacttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaatcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga Intra-Species Hit: Count: 1 Min: 1 Max: 334 Len: 334 Subject: smit_SMT_683_SMT_684|similar to CDP-ribitol pyrophosphorylase:polysaccharide biosynthesis protein, putative|NEGATIVE:POSITIVE|[592663,592996]|334 HSP 1 e-value: 1.0E-177 bit: 620.0 Len: 334 Query Start:1 Query End:334 Subject Strand: POSITIVE Subject Start: 1 Subject End: 334 ctattttctcctttgtcttactnnnnnnncttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaatcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga ctattttctcctttgtcttactaaaaaaacttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaatcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga Inter-species Hit: Count: 3 Min: 1 Max: 334 Len: 334 Subject: NC_008533_SPD_1127_SPD_1128|2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase:polysaccharide biosynthesis protein, putative|NEGATIVE:POSITIVE|[1158559,1158893]|335 HSP 1 e-value: 1.0E-132 bit: 472.0 Len: 334 Query Start:1 Query End:334 Subject Strand: POSITIVE Subject Start: 1 Subject End: 335 ctattttctcctttgtcttactnnnnnnncttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaa-tcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga ctattttctcctttgtcttactaaaaaaacttattctctctattataccacaatctagtcctatcataaaagaaatactggtcctccccttctagaataggagaattatgcagttctattattcaaagaaactagtccatttctagtaatgactaggaattctgtagcaattactaataaatggctgcgaaattttagagtccttcagaataatatactttccttaaagaaaacttaaaacttaagatttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga Subject: NC_003098_spr1149_spr1150|2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase:hypothetical protein|NEGATIVE:POSITIVE|[1151028,1151362]|335 HSP 1 e-value: 1.0E-132 bit: 472.0 Len: 334 Query Start:1 Query End:334 Subject Strand: POSITIVE Subject Start: 1 Subject End: 335 ctattttctcctttgtcttactnnnnnnncttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaa-tcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga ctattttctcctttgtcttactaaaaaaacttattctctctattataccacaatctagtcctatcataaaagaaatactggtcctccccttctagaataggagaattatgcagttctattattcaaagaaactagtccatttctagtaatgactaggaattctgtagcaattactaataaatggctgcgaaattttagagtccttcagaataatatactttccttaaagaaaacttaaaacttaagatttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga Subject: NC_003028_SP_1271_SP_1272|2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase:polysaccharide biosynthesis protein, putative|NEGATIVE:POSITIVE|[1204418,1204752]|335 HSP 1 e-value: 1.0E-132 bit: 472.0 Len: 334 Query Start:1 Query End:334 Subject Strand: POSITIVE Subject Start: 1 Subject End: 335 ctattttctcctttgtcttactnnnnnnncttattctctctattataccacaatctagtcctatcataaaagaaatactagtcgtcccgttctagaataggaggattatgcagttccattattcaaagaaactagtccatttctagtaatgactaggaattctgtagtcattaccaataaatagctgtgaaattttagagttcttcagaataatatagttttcttaaagaaagcttaaaa-tcaaactttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga ctattttctcctttgtcttactaaaaaaacttattctctctattataccacaatctagtcctatcataaaagaaatactggtcctccccttctagaataggagaattatgcagttctattattcaaagaaactagtccatttctagtaatgactaggaattctgtagcaattactaataaatggctgcgaaattttagagtccttcagaataatatactttccttaaagaaaacttaaaacttaagatttgaaacttcaaagtgattacttgacttactgcccttcatttcttattagctaactttatgatataatgaaaaacgaggtaaattga Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUUUUCUCCUUUGUCUUACUAAAAAAACUUAUUCUCUCUAUUAUACCACAAUCUAGUCCUAUCAUAAAAGAAAUACUAGUCGUCCCGUUCUAGAAUAGGAGGAUUAUGCAGUUCCAUUAUUCAAAGAAACUAGUCCAUUUCUAGUAAUGACUAGGAAUUCUGUAGUCAUUACCAAUAAAUAGCUGUGAAAUUUUAGAGUUCUUCAGAAUAAUAUAGUUUUCUUAAAGAAAGCUUAAAAUCAAACUUUGAAACUUCAAAGUGAUUACUUGACUUACUGCCCUUCAUUUCUUAUUAGCUAACUUUAUGAUAUAAUGAAAAACGAGGUAAAUUGA (.((((((((....(((.............((((((((((((..((..((((..(((.............((((((((((((.......((((.((((((..(((((....)))))..))))))..))))))))))..)))))).((((((((((((....)).)))))))))).......))).))))..))..)))))......)))))))...(((((((.....)))))))...((((..(((((((....)))))))))))....))).........((((((...(((((..........))))).))))))....)))).)))).). (-62.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAUUUACCUCGUUUUUCAUUAUAUCAUAAAGUUAGCUAAUAAGAAAUGAAGGGCAGUAAGUCAAGUAAUCACUUUGAAGUUUCAAAGUUUGAUUUUAAGCUUUCUUUAAGAAAACUAUAUUAUUCUGAAGAACUCUAAAAUUUCACAGCUAUUUAUUGGUAAUGACUACAGAAUUCCUAGUCAUUACUAGAAAUGGACUAGUUUCUUUGAAUAAUGGAACUGCAUAAUCCUCCUAUUCUAGAACGGGACGACUAGUAUUUCUUUUAUGAUAGGACUAGAUUGUGGUAUAAUAGAGAGAAUAAGUUUUUUUAGUAAGACAAAGGAGAAAAUAG .........(((.(((.((..........((((((.(((....(....)....)))...(((((((......(((((((....))))))))))))))..))))))..(((((((((((....((((((......(((((.....(((((.((((((.(((((((((((((.........))))))))))))))))))).((((((.((....((((.((((.(((.((.((.(((..((....))..))).)).))))).)))).))))...))))))))..))))).....))))))))))))))))))))))...)).))).)))....... (-75.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 889 120 71 211 162 smit:SMT_683|5end_similar_to_CDP-ribitol_pyrophosphorylase_592572..592802_NEGATIVE 295 176 133 161 112 smit:SMT_945|5end_cytidylate_kinase_895908..896138_NEGATIVE 277 142 102 157 99 smit:SMT_876|5end_hypothetical_protein_predicted_by_Glimmer/Critica_823502..823732_NEGATIVE 248 188 141 107 68 smit:SMT_1901|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1850537..1850767_POSITIVE 247 90 49 144 106 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 247 50 6 106 57 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 247 50 6 106 57 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 244 169 133 133 94 smit:SMT_982|5end_D-tyrosyl-tRNA(Tyr)_deacylase_929654..929884_NEGATIVE 244 115 77 53 11 smit:SMT_553|5end_hypothetical_protein_471128..471358_POSITIVE 243 107 77 230 195 smit:SMT_2166|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2039569..2039799_POSITIVE 243 176 131 213 161 smit:SMT_2106|5end_unknown,_predicted_membrane_protein_(TMS5)_1997163..1997393_POSITIVE 242 52 16 134 96 smit:SMT_953|5end_hypothetical_protein_901576..901806_NEGATIVE 240 116 74 215 176 smit:SMT_1470|5end_K06188_aquaporin_Z_1452560..1452790_POSITIVE 240 148 107 51 6 smit:SMT_802|5end_aldo/keto_reductase_family_712328..712558_NEGATIVE 239 170 139 211 178 smit:SMT_1613|5end_ribosomal_large_subunit_pseudouridine_synthase_B_1600608..1600838_POSITIVE 239 120 76 131 80 smit:SMT_922|5end_RNA-binding_protein_876566..876796_NEGATIVE 237 290 255 107 59 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 237 130 87 146 101 smit:SMT_399|5end_cytochrome_c-type_biogenesis_protein_CcdA_328366..328596_POSITIVE 236 165 123 60 27 smit:SMT_1652|5end_Cof_family_protein_1640534..1640764_POSITIVE 233 111 71 230 192 smit:SMT_1884|5end_hypothetical_protein_1838964..1839194_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 176 133 151 102 smit:SMT_946|3end_hypothetical_protein_895918..896068_NEGATIVE 277 142 102 101 43 smit:SMT_877|3end_hypothetical_protein_823558..823708_NEGATIVE 255 299 263 136 89 smit:SMT_369|3end_hypothetical_cytosolic_protein_304487..304637_POSITIVE 248 188 141 110 71 smit:SMT_1900|3end_K03710_GntR_family_transcriptional_regulator_1850620..1850770_POSITIVE 247 90 49 132 94 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 244 169 133 103 64 smit:SMT_983|3end_GTP_pyrophosphokinase_929684..929834_NEGATIVE 239 120 76 138 87 smit:SMT_923|3end_methionyl-tRNA_formyltransferase_876559..876709_NEGATIVE 237 290 255 105 57 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 236 165 123 63 30 smit:SMT_1651|3end_chromosome_segregation_SMC_protein_1640617..1640767_POSITIVE 233 86 48 54 13 smit:SMT_1636|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1623187..1623337_POSITIVE 231 170 125 71 27 smit:SMT_1327|3end_K03402_transcriptional_regulator_of_arginine_metabolism_1304296..1304446_POSITIVE 230 119 74 136 93 smit:SMT_134|3end_LysM_domain_protein_86157..86307_POSITIVE 227 176 131 146 93 smit:SMT_938|3end_hypothetical_protein_890813..890963_NEGATIVE 226 122 81 94 50 smit:SMT_1310|3end_D-alanine-activating_enzyme_1275867..1276017_POSITIVE 225 117 72 61 14 smit:SMT_1997|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_1921123..1921273_NEGATIVE 224 187 143 56 4 smit:SMT_2061|3end_K02011_iron(III)_transport_system_permease_protein_1970802..1970952_POSITIVE 224 178 132 144 104 smit:SMT_808|3end_hypothetical_protein_predicted_by_Glimmer/Critica_717897..718047_NEGATIVE 224 187 143 56 4 smit:SMT_202|3end_K02011_iron(III)_transport_system_permease_protein_132173..132323_NEGATIVE 223 42 1 45 5 smit:SMT_1167|3end_aminopeptidase_N_1112593..1112743_NEGATIVE 222 105 80 151 121 smit:SMT_1557|3end_hypothetical_protein_1543650..1543800_POSITIVE