Origin IGS: gatatgggcaccagatttaagagccttaatctgtttttcaatgattgatccgccatatactgagcnnnnnttaattaattaannnnnctgcggtggtttccacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagtggaaaccaccgcagnnnnnttaattaattaannnnngctcagtatatggcggatcaatcattgaaaaacagattaaggctcttaaatctggtgcccatatc Mask Tandem Repeat Region ================================================ gatatgggcaccagatttaagagccttaatctgtttttcaatgattgatccgccatatactgagcnnnnnttaattaattaannnnnctgcggtggtttccacta Find is-nt database================================================ Query_seq: SMT_930:SMT_931|SMT_930:SMT_931:ATP-dependent RNA helicase:cobyric acid synthase:<-->:884526..884630 105 gatatgggcaccagatttaagagccttaatctgtttttcaatgattgatccgccatatactgagcnnnnnttaattaattaannnnnctgcggtggtttccacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_930:SMT_931|SMT_930:SMT_931:ATP-dependent RNA helicase:cobyric acid synthase:<-->:884526..884630 105 gatatgggcaccagatttaagagccttaatctgtttttcaatgattgatccgccatatactgagcnnnnnttaattaattaannnnnctgcggtggtttccacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_930:SMT_931|SMT_930:SMT_931:ATP-dependent RNA helicase:cobyric acid synthase:<-->:884526..884630 105 gatatgggcaccagatttaagagccttaatctgtttttcaatgattgatccgccatatactgagcnnnnnttaattaattaannnnnctgcggtggtttccacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatatgggcaccagatttaagagccttaatctgtttttcaatgattgatccgccatatactgagcnnnnnttaattaattaannnnnctgcggtggtttccacta Predict ORF larger than 30AA ================================================ gatatgggcaccagatttaagagccttaatctgtttttcaatgattgatccgccatatactgagcnnnnnttaattaattaannnnnctgcggtggtttccacta 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================================================ gatatgggcaccagatttaagagccttaatctgtttttcaatgattgatccgccatatactgagcnnnnnttaattaattaannnnnctgcggtggtttccacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_930:SMT_931|SMT_930:SMT_931:ATP-dependent RNA helicase:cobyric acid synthase:<-->:884526..884630 105 gatatgggcaccagatttaagagccttaatctgtttttcaatgattgatccgccatatactgagcnnnnnttaattaattaannnnnctgcggtggtttccacta Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: smit_SMT_930_SMT_931|ATP-dependent RNA helicase:cobyric acid synthase|NEGATIVE:POSITIVE|[884526,884630]|105 HSP 1 e-value: 2.0E-35 bit: 149.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 gatatgggcaccagatttaagagccttaatctgtttttcaatgattgatccgccatatactgagcnnnnnttaattaattaannnnnctgcggtggtttccacta gatatgggcaccagatttaagagccttaatctgtttttcaatgattgatccgccatatactgagcnnnnnttaattaattaannnnnctgcggtggtttccacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAUGGGCACCAGAUUUAAGAGCCUUAAUCUGUUUUUCAAUGAUUGAUCCGCCAUAUACUGAGCNNNNNUUAAUUAAUUAANNNNNCUGCGGUGGUUUCCACUA .((((((.(..((((((.(((...)))))))))....(((.....)))...))))))).................................(((((...))))). (-14.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUGGAAACCACCGCAGNNNNNUUAAUUAAUUAANNNNNGCUCAGUAUAUGGCGGAUCAAUCAUUGAAAAACAGAUUAAGGCUCUUAAAUCUGGUGCCCAUAUC ..((((......))))...............................((((((((..(((.....)))....(((((((((...))).)))))).)).)))))). (-15.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 827 60 11 151 102 smit:SMT_930|5end_ATP-dependent_RNA_helicase_884435..884665_NEGATIVE 258 50 5 194 133 smit:SMT_1489|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1468892..1469122_POSITIVE 254 60 12 99 46 smit:SMT_1510|5end_ribose_5-phosphate_isomerase_1493488..1493718_NEGATIVE 241 56 13 183 138 smit:SMT_1509|5end_phosphopentomutase_1492781..1493011_NEGATIVE 240 65 21 70 4 smit:SMT_1194|5end_phosphoribosylformylglycinamidine_cyclo-ligase_1153171..1153401_NEGATIVE 235 64 22 144 97 smit:SMT_261|5end_ImpB/MucB/SamB_family_protein_200160..200390_POSITIVE 233 64 22 79 35 smit:SMT_1823|5end_GTP-binding_protein_1794982..1795212_POSITIVE 217 57 16 187 140 smit:SMT_1390|5end_hypothetical_protein_1367321..1367551_NEGATIVE 216 50 4 219 178 smit:SMT_1409|5end_hypothetical_protein_1388514..1388744_NEGATIVE 212 62 22 96 64 smit:SMT_1545|5end_choline-binding_protein_1530026..1530256_NEGATIVE 208 50 4 88 50 smit:SMT_1076|5end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_/_dihydroneopterin_aldolase_1014813..1015043_NEGATIVE 206 60 11 168 114 smit:SMT_158|5end_putative_Holliday_junction_resolvase_103795..104025_POSITIVE 203 56 19 60 15 smit:SMT_1870|5end_K07566_putative_translation_factor_1829819..1830049_NEGATIVE 203 56 11 173 129 smit:SMT_1481|5end_endopeptidase_O_1462229..1462459_POSITIVE 203 52 11 228 186 smit:SMT_1287|5end_50S_ribosomal_protein_L9_1250358..1250588_POSITIVE 203 53 11 41 1 smit:SMT_514|5end_tRNA_(guanine-N(1)-)-methyltransferase_441377..441607_POSITIVE 200 50 8 100 60 smit:SMT_191|5end_adenylate_kinase_125745..125975_POSITIVE 199 52 11 72 27 smit:SMT_1295|5end_transcriptional_regulator_CtsR_1256830..1257060_POSITIVE 199 37 1 130 77 smit:SMT_615|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_524884..525114_POSITIVE 198 49 4 116 59 smit:SMT_2049|5end_3-oxoacyl-_1959539..1959769_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 53 15 51 9 smit:SMT_513|3end_16S_rRNA_processing_protein_RimM_441467..441617_POSITIVE 235 64 22 140 93 smit:SMT_260|3end_phage_transcriptional_repressor_200236..200386_POSITIVE 233 64 22 76 32 smit:SMT_1822|3end_hypothetical_protein_1795059..1795209_POSITIVE 218 61 22 145 100 smit:SMT_2048|3end_competence-specific_global_transcription_modulator_1957961..1958111_NEGATIVE 212 65 22 132 81 smit:SMT_137|3end_hypothetical_protein_88137..88287_NEGATIVE 209 50 1 54 7 smit:SMT_1858|3end_K03497_chromosome_partitioning_protein,_ParB_family_1821687..1821837_NEGATIVE 208 50 4 45 7 smit:SMT_1077|3end_GTP_cyclohydrolase_I_1014856..1015006_NEGATIVE 208 38 5 145 115 smit:SMT_802|3end_aldo/keto_reductase_family_711486..711636_NEGATIVE 203 56 19 76 31 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 203 56 11 130 86 smit:SMT_1480|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1462266..1462416_POSITIVE 199 52 12 148 99 smit:SMT_1475|3end_K02004_1458661..1458811_POSITIVE 199 37 1 124 71 smit:SMT_614|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_524958..525108_POSITIVE 198 49 4 116 59 smit:SMT_2050|3end_K03712_MarR_family_transcriptional_regulator_1959539..1959689_NEGATIVE 195 47 1 72 20 smit:SMT_577|3end_transcriptional_regulator,_LysR_family_496144..496294_POSITIVE 194 59 26 54 16 smit:SMT_2169|3end_hypothetical_protein_2041383..2041533_NEGATIVE 194 59 26 54 16 smit:SMT_2151|3end_hypothetical_protein_2025026..2025176_NEGATIVE 194 59 26 54 16 smit:SMT_2148|3end_hypothetical_protein_2023141..2023291_NEGATIVE 194 59 26 54 16 smit:SMT_2147|3end_hypothetical_protein_2022401..2022551_NEGATIVE 194 59 26 54 16 smit:SMT_2144|3end_hypothetical_protein_2020647..2020797_NEGATIVE 194 59 26 54 16 smit:SMT_971|3end_hypothetical_protein_917916..918066_NEGATIVE