Origin IGS: aaatacatacagctacttgctatcctataatgtttcaagagctccaaaatgttctttcaacattataggacatcgcagtagtttcatttaaaaatatctaatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgattagatatttttaaatgaaactactgcgatgtcctataatgttgaaagaacattttggagctcttgaaacattataggatagcaagtagctgtatgtattt Mask Tandem Repeat Region ================================================ aaatacatacagctacttgctatcctataatgtttcaagagctccaaaatgttctttcaacattataggacatcgcagtagtttcatttaaaaatatctaatca Find is-nt database================================================ Query_seq: FN0828:FN0829|FN0828:FN0829:ABC transporter permease protein:hypothetical protein:-><-:1489566..1489669 104 aaatacatacagctacttgctatcctataatgtttcaagagctccaaaatgttctttcaacattataggacatcgcagtagtttcatttaaaaatatctaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0828:FN0829|FN0828:FN0829:ABC transporter permease protein:hypothetical protein:-><-:1489566..1489669 104 aaatacatacagctacttgctatcctataatgtttcaagagctccaaaatgttctttcaacattataggacatcgcagtagtttcatttaaaaatatctaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0828:FN0829|FN0828:FN0829:ABC transporter permease protein:hypothetical protein:-><-:1489566..1489669 104 aaatacatacagctacttgctatcctataatgtttcaagagctccaaaatgttctttcaacattataggacatcgcagtagtttcatttaaaaatatctaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatacatacagctacttgctatcctataatgtttcaagagctccaaaatgttctttcaacattataggacatcgcagtagtttcatttaaaaatatctaatca Predict ORF larger than 30AA ================================================ aaatacatacagctacttgctatcctataatgtttcaagagctccaaaatgttctttcaacattataggacatcgcagtagtttcatttaaaaatatctaatca 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================================================ aaatacatacagctacttgctatcctataatgtttcaagagctccaaaatgttctttcaacattataggacatcgcagtagtttcatttaaaaatatctaatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0828:FN0829|FN0828:FN0829:ABC transporter permease protein:hypothetical protein:-><-:1489566..1489669 104 aaatacatacagctacttgctatcctataatgtttcaagagctccaaaatgttctttcaacattataggacatcgcagtagtttcatttaaaaatatctaatca Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_003454_FN0828_FN0829|ABC transporter permease protein:hypothetical protein|POSITIVE:NEGATIVE|[1489566,1489669]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 aaatacatacagctacttgctatcctataatgtttcaagagctccaaaatgttctttcaacattataggacatcgcagtagtttcatttaaaaatatctaatca aaatacatacagctacttgctatcctataatgtttcaagagctccaaaatgttctttcaacattataggacatcgcagtagtttcatttaaaaatatctaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUACAUACAGCUACUUGCUAUCCUAUAAUGUUUCAAGAGCUCCAAAAUGUUCUUUCAACAUUAUAGGACAUCGCAGUAGUUUCAUUUAAAAAUAUCUAAUCA ..........(((((((.((..((((((((((((..((((((........))))))..))))))))))))....)))))))))..................... (-29.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUAGAUAUUUUUAAAUGAAACUACUGCGAUGUCCUAUAAUGUUGAAAGAACAUUUUGGAGCUCUUGAAACAUUAUAGGAUAGCAAGUAGCUGUAUGUAUUU ...(((((....)))))......(((((((..((((((((((((((..((((.(........).))))..)))))))))))))))).)))))............ (-27.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 629 80 31 216 167 NC_003454:FN2091|5end_hypothetical_protein_602481..602711_NEGATIVE 446 80 31 183 133 NC_003454:FN0695|5end_ABC_transporter_ATP-binding_protein_1352886..1353116_POSITIVE 301 69 21 186 141 NC_003454:FN1862|5end_L-beta-lysine_5,6-aminomutase_beta_subunit_353122..353352_NEGATIVE 267 69 23 188 141 NC_003454:FN0053|5end_Branched-chain_amino_acid_transport_system_carrier_protein_689340..689570_POSITIVE 245 86 42 166 100 NC_003454:FN1533|5end_Electron_transfer_flavoprotein_alpha-subunit_46321..46551_NEGATIVE 243 42 11 224 191 NC_003454:FN1731|5end_Anthranilate_synthase_component_II_231037..231267_NEGATIVE 236 68 38 45 18 NC_003454:FN0772|5end_Flavodoxin_1428694..1428924_POSITIVE 227 59 11 90 44 NC_003454:FN1019|5end_3-hydroxybutyryl-CoA_dehydrogenase_1673784..1674014_NEGATIVE 227 85 54 212 184 NC_003454:FN1741|5end_ATP_synthase_subunit_I_240477..240707_NEGATIVE 222 47 16 73 34 NC_003454:FN0579|5end_Hypothetical_cytosolic_protein_1229803..1230033_POSITIVE 218 97 57 221 180 NC_003454:FN1150|5end_hypothetical_protein_1805151..1805381_NEGATIVE 216 58 13 43 1 NC_003454:FN1621|5end_elongation_factor_Ts_128673..128903_POSITIVE 213 67 22 59 14 NC_003454:FN0187|5end_Thiol:disulfide_interchange_protein_tlpA_811590..811820_POSITIVE 210 49 11 38 2 NC_003454:FN0421|5end_carbamoyl-phosphate_synthase_small_subunit_1061936..1062166_POSITIVE 209 45 1 164 123 NC_003454:FN1799|5end_Spermidine/putrescine_transport_system_permease_protein_potC_280776..281006_POSITIVE 204 84 48 203 158 NC_003454:FN0751|5end_L-asparaginase_I_1410731..1410961_NEGATIVE 203 89 41 44 3 NC_003454:FN1808|5end_hypothetical_protein_289905..290135_NEGATIVE 202 61 37 107 81 NC_003454:FN1317|5end_RNA_polymerase_sigma_factor_1971085..1971315_NEGATIVE 202 59 11 214 169 NC_003454:FN0639|5end_hypothetical_protein_1297427..1297657_NEGATIVE 201 65 28 59 17 NC_003454:FN0490|5end_Integral_membrane_protein_1136234..1136464_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 629 80 31 83 34 NC_003454:FN2092|3end_Integral_membrane_protein_602614..602764_NEGATIVE 450 90 41 58 8 NC_003454:FN1260|3end_Sensory_Transduction_Protein_Kinase_1915863..1916013_NEGATIVE 446 80 31 81 31 NC_003454:FN0694|3end_S-layer_protein_1352864..1353014_POSITIVE 430 80 31 68 19 NC_003454:FN1076|3end_hypothetical_protein_1723677..1723827_POSITIVE 297 70 23 68 21 NC_003454:FN0828|3end_ABC_transporter_permease_protein_1489505..1489655_POSITIVE 267 69 23 59 12 NC_003454:FN0052|3end_Arsenate_reductase_689291..689441_POSITIVE 236 68 38 48 21 NC_003454:FN0771|3end_Oxygen-independent_coproporphyrinogen_III_oxidase_1428777..1428927_POSITIVE 227 59 11 74 28 NC_003454:FN1020|3end_3-hydroxybutyryl-CoA_dehydratase_1673800..1673950_NEGATIVE 222 47 16 55 16 NC_003454:FN0578|3end_ATP-dependent_DNA_helicase_recQ_1229865..1230015_POSITIVE 209 76 32 147 116 NC_003454:FN1253|3end_hypothetical_protein_1910229..1910379_NEGATIVE 202 61 37 91 65 NC_003454:FN1318|3end_RNA_polymerase_sigma_factor_rpoD_1971101..1971251_NEGATIVE 201 65 28 54 12 NC_003454:FN0491|3end_Alanine_racemase_1136239..1136389_NEGATIVE 199 46 13 44 10 NC_003454:FN0718|3end_hypothetical_protein_1376004..1376154_POSITIVE 198 66 23 131 85 NC_003454:FN1454|3end_D-alanine--D-alanine_ligase_2134796..2134946_NEGATIVE 198 39 3 131 88 NC_003454:FN1088|3end_NADH_oxidase_1733095..1733245_POSITIVE 197 45 13 77 36 NC_003454:FN1163|3end_Thioredoxin_reductase_1821810..1821960_POSITIVE 197 70 25 77 22 NC_003454:FN1997|3end_Transcriptional_regulator_500158..500308_POSITIVE 196 59 13 83 29 NC_003454:FN1098|3end_hypothetical_protein_1743898..1744048_POSITIVE 196 83 42 151 88 NC_003454:FN1534|3end_Electron_transfer_flavoprotein_beta-subunit_46333..46483_NEGATIVE 195 50 4 119 61 NC_003454:FN0269|3end_Transposase_896846..896996_POSITIVE