Origin IGS: ctaatcacctcactccattatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacacttttctcagaaaatttttctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagaaaaattttctgagaaaagtgtattttctatagctatatctaaaatggcagaaatgaatattaaattttagaaataagtttataaaaggaggtatgtgcctcctttttgttgtataatggagtgaggtgattag Mask Tandem Repeat Region ================================================ ctaatcacctcactccattatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacacttttctcagaaaatttttctc Find is-nt database================================================ Query_seq: SMT_1513:SMT_1514|SMT_1513:SMT_1514:hypothetical protein:methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase:<-<-:1495673..1495809 137 ctaatcacctcactccattatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacacttttctcagaaaatttttctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1513:SMT_1514|SMT_1513:SMT_1514:hypothetical protein:methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase:<-<-:1495673..1495809 137 ctaatcacctcactccattatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacacttttctcagaaaatttttctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1513:SMT_1514|SMT_1513:SMT_1514:hypothetical protein:methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase:<-<-:1495673..1495809 137 ctaatcacctcactccattatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacacttttctcagaaaatttttctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctaatcacctcactccattatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacacttttctcagaaaatttttctc Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 4 End: 135 ... M T S L H Y T T K R R H I P P F I N L F L K F N I H F C H F R Y S Y R K Y T F L R K F F .. ctaatcacctcactccattatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacacttttctcagaaaatttttctc 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================================================ ctaatcacctcactccattatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacacttttctcagaaaatttttctc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 88 HP_score: -6.8 Tail_Score: -5.25699 Start: 32 End: 47 Full_Region: aataagtttataaaa ggaggt atgt gcctcc tttttgttgtataat ...............................ggaggtatgtgcctcc.......................................................................................... Find igs database================================================ Query_seq: SMT_1513:SMT_1514|SMT_1513:SMT_1514:hypothetical protein:methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase:<-<-:1495673..1495809 137 ctaatcacctcactccattatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacacttttctcagaaaatttttctc Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: smit_SMT_1513_SMT_1514|hypothetical protein:methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase|NEGATIVE:NEGATIVE|[1495673,1495809]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 ctaatcacctcactccattatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacacttttctcagaaaatttttctc ctaatcacctcactccattatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacacttttctcagaaaatttttctc Inter-species Hit: Count: 3 Min: 1 Max: 134 Len: 134 Subject: NC_003028_SP_0825_SP_0826|methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase:hypothetical protein|POSITIVE:POSITIVE|[775619,775755]|137 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 134 Query Start:1 Query End:134 Subject Strand: NEGATIVE Subject Start: 4 Subject End: 137 ctaatcacctcactccattatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacacttttctcagaaaattttt... ctaatcacctcactccattatacaacaaaaaggaggcgcaaacctccttttataaacttatttctaaaatttaatattcatttctatcattttagatatagctatagaaaatacactttcctcagaaaattttt... Subject: NC_008533_SPD_0721_SPD_0722|methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase:YjeF-like protein|POSITIVE:POSITIVE|[736813,736953]|141 HSP 1 e-value: 4.0E-34 bit: 145.0 Len: 101 Query Start:17 Query End:117 Subject Strand: NEGATIVE Subject Start: 21 Subject End: 121 ................attatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacact.................... ................attatacaataaaaaggagacgcagacctccttttgtaatcttatatctaaaatttaatattcatttctgccattttagatatagctatagaaaatacact.................... Subject: NC_003098_spr0729_spr0730|Fold bifunctional protein; includes: methylenetetrahydrofolate dehydrogenase, methenyltetrahydrofolate cyclohydrolase.:hypothetical protein|POSITIVE:POSITIVE|[729282,729422]|141 HSP 1 e-value: 4.0E-34 bit: 145.0 Len: 101 Query Start:17 Query End:117 Subject Strand: NEGATIVE Subject Start: 21 Subject End: 121 ................attatacaacaaaaaggaggcacatacctccttttataaacttatttctaaaatttaatattcatttctgccattttagatatagctatagaaaatacact.................... ................attatacaataaaaaggagacgcagacctccttttgtaatcttatatctaaaatttaatattcatttctgccattttagatatagctatagaaaatacact.................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAAUCACCUCACUCCAUUAUACAACAAAAAGGAGGCACAUACCUCCUUUUAUAAACUUAUUUCUAAAAUUUAAUAUUCAUUUCUGCCAUUUUAGAUAUAGCUAUAGAAAAUACACUUUUCUCAGAAAAUUUUU ...........................(((((((((......)))))))))......((((.((((((((..................)))))))).))))....((((((.....))))))............ (-17.97) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUUUUCUGAGAAAAGUGUAUUUUCUAUAGCUAUAUCUAAAAUGGCAGAAAUGAAUAUUAAAUUUUAGAAAUAAGUUUAUAAAAGGAGGUAUGUGCCUCCUUUUUGUUGUAUAAUGGAGUGAGGUGAUUAG ......(((((((((..(((((..(((((...(((((.......))))))))))...)))))...))))))))).........((((((((((....))))))))))........................... (-26.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 875 50 1 141 92 smit:SMT_1513|5end_hypothetical_protein_1495582..1495812_NEGATIVE 327 50 7 61 6 smit:SMT_814|5end_UDP-N-acetyl_muramate-alanine_ligase_723666..723896_NEGATIVE 291 65 30 201 167 smit:SMT_731|5end_hypothetical_protein_predicted_by_Glimmer/Critica_638857..639087_NEGATIVE 273 50 1 144 82 smit:SMT_236|5end_ribosomal_small_subunit_pseudouridine_synthase_A_174625..174855_POSITIVE 245 50 1 168 113 smit:SMT_954|5end_cation-transporting_ATPase,_E1-E2_family_904025..904255_NEGATIVE 229 51 21 176 149 smit:SMT_1217|5end_hypothetical_protein_1176603..1176833_NEGATIVE 225 102 61 186 135 smit:SMT_1590|5end_DNA-entry_nuclease_1578565..1578795_POSITIVE 220 124 83 90 42 smit:SMT_966|5end_transcriptional_regulator,_TetR_family_912191..912421_NEGATIVE 216 126 81 160 106 smit:SMT_716|5end_50S_ribosomal_protein_L31_622410..622640_POSITIVE 214 50 8 224 176 smit:SMT_910|5end_type_I_restriction_enzyme_R_protein_861889..862119_NEGATIVE 210 38 5 105 78 smit:SMT_2026|5end_K03466_DNA_segregation_ATPase_FtsK/SpoIIIE,_S-DNA-T_family_1942432..1942662_NEGATIVE 210 47 27 209 190 smit:SMT_1728|5end_exodeoxyribonuclease_VII_large_subunit_1713248..1713478_POSITIVE 204 72 33 175 136 smit:SMT_1655|5end_glucose-6-phosphate_1-dehydrogenase_1645021..1645251_NEGATIVE 204 90 42 173 125 smit:SMT_1481|5end_endopeptidase_O_1462229..1462459_POSITIVE 204 125 81 88 46 smit:SMT_617|5end_hypothetical_protein_526415..526645_POSITIVE 204 87 43 94 52 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 204 87 43 94 52 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 203 39 1 148 105 smit:SMT_168|5end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_113670..113900_POSITIVE 202 50 6 203 162 smit:SMT_534|5end_hypothetical_protein_predicted_by_Glimmer/Critica_453571..453801_POSITIVE 202 50 6 203 162 smit:SMT_531|5end_hypothetical_protein_predicted_by_Glimmer/Critica_452672..452902_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 50 13 50 3 smit:SMT_815|3end_hypothetical_protein_723677..723827_NEGATIVE 291 65 30 98 64 smit:SMT_732|3end_K07467_phage_replication_initiation_protein_638960..639110_NEGATIVE 252 51 12 134 97 smit:SMT_1998|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1922640..1922790_POSITIVE 245 50 8 90 54 smit:SMT_364|3end_ribosome-binding_factor_A_301353..301503_POSITIVE 238 58 12 88 23 smit:SMT_1220|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1180509..1180659_NEGATIVE 229 51 21 91 64 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 227 65 27 98 65 smit:SMT_1848|3end_K03458_nucleobase:cation_symporter-2,_NCS2_family_1812694..1812844_NEGATIVE 225 102 61 147 96 smit:SMT_1589|3end_hypothetical_protein_1578606..1578756_POSITIVE 220 124 83 66 18 smit:SMT_967|3end_K01992_ABC-2_type_transport_system_permease_protein_912215..912365_NEGATIVE 220 51 16 56 13 smit:SMT_405|3end_zinc_metalloprotease_ZmpB,_truncated_339938..340088_POSITIVE 216 65 29 106 67 smit:SMT_1380|3end_pyrroline-5-carboxylate_reductase_1357667..1357817_NEGATIVE 216 126 81 64 10 smit:SMT_715|3end_DHH_subfamily_1_protein_622394..622544_POSITIVE 212 50 11 77 35 smit:SMT_1097|3end_alcohol_dehydrogenase_/_acetaldehyde_dehydrogenase_1038697..1038847_NEGATIVE 210 47 27 82 63 smit:SMT_1727|3end_uridine_kinase_1713201..1713351_POSITIVE 204 90 42 130 82 smit:SMT_1480|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1462266..1462416_POSITIVE 204 125 81 61 19 smit:SMT_616|3end_hypothetical_protein_526468..526618_POSITIVE 202 50 6 89 48 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 202 50 6 89 48 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 202 50 6 89 48 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE 202 50 6 89 48 smit:SMT_510|3end_hypothetical_protein_439357..439507_POSITIVE