Origin IGS: ttttgatatgaaaaaatggtagtttaaatagggctgttgcaaatcaatagttatatttgcaataagccctttattttttaacagtagaatgaaaggttttaaataat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attatttaaaacctttcattctactgttaaaaaataaagggcttattgcaaatataactattgatttgcaacagccctatttaaactaccattttttcatatcaaaa Mask Tandem Repeat Region ================================================ ttttgatatgaaaaaatggtagtttaaatagggctgttgcaaatcaatagttatatttgcaataagccctttattttttaacagtagaatgaaaggttttaaataat Find is-nt database================================================ Query_seq: FN2103:FN2104|FN2103:FN2104:RecA protein:hypothetical protein:->->:614270..614376 107 ttttgatatgaaaaaatggtagtttaaatagggctgttgcaaatcaatagttatatttgcaataagccctttattttttaacagtagaatgaaaggttttaaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2103:FN2104|FN2103:FN2104:RecA protein:hypothetical protein:->->:614270..614376 107 ttttgatatgaaaaaatggtagtttaaatagggctgttgcaaatcaatagttatatttgcaataagccctttattttttaacagtagaatgaaaggttttaaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2103:FN2104|FN2103:FN2104:RecA protein:hypothetical protein:->->:614270..614376 107 ttttgatatgaaaaaatggtagtttaaatagggctgttgcaaatcaatagttatatttgcaataagccctttattttttaacagtagaatgaaaggttttaaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttgatatgaaaaaatggtagtttaaatagggctgttgcaaatcaatagttatatttgcaataagccctttattttttaacagtagaatgaaaggttttaaataat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 1 End: 90 K S I F F H Y N L Y P Q Q L D I T I N A I L G K N K L L L M ................. ttttgatatgaaaaaatggtagtttaaatagggctgttgcaaatcaatagttatatttgcaataagccctttattttttaacagtagaatgaaaggttttaaataat 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================================================ ttttgatatgaaaaaatggtagtttaaatagggctgttgcaaatcaatagttatatttgcaataagccctttattttttaacagtagaatgaaaggttttaaataat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -4.8 Tail_Score: -5.04249 Start: 31 End: 69 Full_Region: ATGGTAGTTTAAATA GGGCTGTTGCAAAT CAATAGTTAT ATTTGCAATAAGCCC TTTATTTTTTAACAG ..............................GGGCTGTTGCAAATCAATAGTTATATTTGCAATAAGCCC...................................... Find igs database================================================ Query_seq: FN2103:FN2104|FN2103:FN2104:RecA protein:hypothetical protein:->->:614270..614376 107 ttttgatatgaaaaaatggtagtttaaatagggctgttgcaaatcaatagttatatttgcaataagccctttattttttaacagtagaatgaaaggttttaaataat Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_003454_FN2103_FN2104|RecA protein:hypothetical protein|POSITIVE:POSITIVE|[614270,614376]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ttttgatatgaaaaaatggtagtttaaatagggctgttgcaaatcaatagttatatttgcaataagccctttattttttaacagtagaatgaaaggttttaaataat ttttgatatgaaaaaatggtagtttaaatagggctgttgcaaatcaatagttatatttgcaataagccctttattttttaacagtagaatgaaaggttttaaataat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGAUAUGAAAAAAUGGUAGUUUAAAUAGGGCUGUUGCAAAUCAAUAGUUAUAUUUGCAAUAAGCCCUUUAUUUUUUAACAGUAGAAUGAAAGGUUUUAAAUAAU .....................(((((((.(((((((((((((((..........))))))))).))))))(((((((........))))))).....)))))))... (-21.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUUAAAACCUUUCAUUCUACUGUUAAAAAAUAAAGGGCUUAUUGCAAAUAUAACUAUUGAUUUGCAACAGCCCUAUUUAAACUACCAUUUUUUCAUAUCAAAA .....................................((((((..((((((((..........)))))))).))))))............................. (-16.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 70 26 198 162 NC_003454:FN0374|5end_Single-stranded-DNA-specific_exonuclease_recJ_1002654..1002884_POSITIVE 288 76 31 143 106 NC_003454:FN1269|5end_Hypothetical_lipoprotein_1926242..1926472_NEGATIVE 286 69 22 43 1 NC_003454:FN0531|5end_hypothetical_protein_1186389..1186619_POSITIVE 279 80 31 160 116 NC_003454:FN1446|5end_Transposase_2116033..2116263_POSITIVE 271 69 31 211 183 NC_003454:FN1337|5end_hypothetical_protein_1991481..1991711_NEGATIVE 271 69 31 64 36 NC_003454:FN1509|5end_hypothetical_protein_14176..14406_NEGATIVE 262 52 17 40 5 NC_003454:FN0027|5end_hypothetical_protein_664891..665121_NEGATIVE 253 70 26 212 180 NC_003454:FN2010|5end_Transcriptional_regulator,_MarR_family_510302..510532_NEGATIVE 252 70 21 183 136 NC_003454:FN1257|5end_C4-dicarboxylate_transporter_small_subunit_1913664..1913894_NEGATIVE 248 40 3 150 112 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 248 40 3 46 8 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 243 59 17 87 50 NC_003454:FN2105|5end_Integral_membrane_protein_614701..614931_POSITIVE 238 64 30 64 26 NC_003454:FN2068|5end_dGTP_triphosphohydrolase_578986..579216_NEGATIVE 233 65 21 67 22 NC_003454:FN0699|5end_Protein_translocase_subunit_secD_1357051..1357281_POSITIVE 226 90 55 225 189 NC_003454:FN1103|5end_Excinuclease_ABC_subunit_A_1746559..1746789_POSITIVE 222 80 31 163 116 NC_003454:FN0740|5end_imidazolonepropionase_1398914..1399144_NEGATIVE 220 79 31 133 80 NC_003454:FN1512|5end_Phophatidylinositol-4-phosphate_5-kinase_15845..16075_POSITIVE 215 67 30 226 196 NC_003454:FN0165|5end_hypothetical_protein_793491..793721_POSITIVE 215 60 31 210 180 NC_003454:FN1638|5end_50S_ribosomal_protein_L16_137501..137731_NEGATIVE 215 40 16 188 166 NC_003454:FN1577|5end_Rod_shape-determining_protein_mreB_88405..88635_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 408 72 31 83 39 NC_003454:FN1907|3end_Thymidylate_synthase_400546..400696_POSITIVE 401 70 30 61 21 NC_003454:FN2103|3end_RecA_protein_614209..614359_POSITIVE 370 69 30 84 38 NC_003454:FN1340|3end_Glutamyl-tRNA_synthetase_1993353..1993503_NEGATIVE 370 69 30 65 19 NC_003454:FN0528|3end_Cold_shock_protein_1184746..1184896_POSITIVE 362 72 31 66 22 NC_003454:FN1908|3end_Glycerophosphoryl_diester_phosphodiesterase_400596..400746_NEGATIVE 355 80 31 93 46 NC_003454:FN0637|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1295636..1295786_NEGATIVE 343 70 30 63 15 NC_003454:FN0371|3end_hypothetical_protein_1000840..1000990_POSITIVE 338 70 30 80 42 NC_003454:FN0636|3end_hypothetical_protein_1295609..1295759_POSITIVE 326 90 44 105 58 NC_003454:FN0532|3end_Hypothetical_membrane-spanning_protein_1186524..1186674_NEGATIVE 304 77 32 92 44 NC_003454:FN1141|3end_Formate_transporter_1790493..1790643_NEGATIVE 289 88 49 98 53 NC_003454:FN1427|3end_Phenazine_biosynthesis_protein_phzF_2096763..2096913_POSITIVE 288 76 31 59 22 NC_003454:FN1270|3end_Hypothetical_cytosolic_protein_1926326..1926476_NEGATIVE 286 69 22 147 105 NC_003454:FN0531|3end_hypothetical_protein_1186573..1186723_POSITIVE 280 68 30 84 50 NC_003454:FN1266|3end_UTP--glucose-1-phosphate_uridylyltransferase_1922158..1922308_NEGATIVE 278 79 32 99 52 NC_003454:FN1140|3end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_1790473..1790623_POSITIVE 272 70 26 57 13 NC_003454:FN1944|3end_Sodium-dependent_tryptophan_transporter_448026..448176_POSITIVE 271 69 31 138 110 NC_003454:FN1338|3end_hypothetical_protein_1991554..1991704_NEGATIVE 271 80 31 93 48 NC_003454:FN1276|3end_hypothetical_protein_1935280..1935430_POSITIVE 271 78 31 82 42 NC_003454:FN1784|3end_hypothetical_protein_265735..265885_NEGATIVE 271 69 31 141 113 NC_003454:FN1509|3end_hypothetical_protein_14099..14249_NEGATIVE