Origin IGS: aaggtttctcccttttttatgtttaatattatagcataaagtctcgaaattgacaaaggcttaagtgtaaagtacgcatgacaattcgaccttaggtatctgaatcttccctattgaattctttgtctttatcctgtacaatcatccggattattaaactttaggagaattgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcaattctcctaaagtttaataatccggatgattgtacaggataaagacaaagaattcaatagggaagattcagatacctaaggtcgaattgtcatgcgtactttacacttaagcctttgtcaatttcgagactttatgctataatattaaacataaaaaagggagaaacctt Mask Tandem Repeat Region ================================================ aaggtttctcccttttttatgtttaatattatagcataaagtctcgaaattgacaaaggcttaagtgtaaagtacgcatgacaattcgaccttaggtatctgaatcttccctattgaattctttgtctttatcctgtacaatcatccggattattaaactttaggagaattgc Find is-nt database================================================ Query_seq: TDE0450:TDE0451|TDE0450:TDE0451:hypothetical protein:arginine deiminase:<-->:508620..508792 173 aaggtttctcccttttttatgtttaatattatagcataaagtctcgaaattgacaaaggcttaagtgtaaagtacgcatgacaattcgaccttaggtatctgaatcttccctattgaattctttgtctttatcctgtacaatcatccggattattaaactttaggagaattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0450:TDE0451|TDE0450:TDE0451:hypothetical protein:arginine deiminase:<-->:508620..508792 173 aaggtttctcccttttttatgtttaatattatagcataaagtctcgaaattgacaaaggcttaagtgtaaagtacgcatgacaattcgaccttaggtatctgaatcttccctattgaattctttgtctttatcctgtacaatcatccggattattaaactttaggagaattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0450:TDE0451|TDE0450:TDE0451:hypothetical protein:arginine deiminase:<-->:508620..508792 173 aaggtttctcccttttttatgtttaatattatagcataaagtctcgaaattgacaaaggcttaagtgtaaagtacgcatgacaattcgaccttaggtatctgaatcttccctattgaattctttgtctttatcctgtacaatcatccggattattaaactttaggagaattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaggtttctcccttttttatgtttaatattatagcataaagtctcgaaattgacaaaggcttaagtgtaaagtacgcatgacaattcgaccttaggtatctgaatcttccctattgaattctttgtctttatcctgtacaatcatccggattattaaactttaggagaattgc Predict ORF larger than 30AA ================================================ aaggtttctcccttttttatgtttaatattatagcataaagtctcgaaattgacaaaggcttaagtgtaaagtacgcatgacaattcgaccttaggtatctgaatcttccctattgaattctttgtctttatcctgtacaatcatccggattattaaactttaggagaattgc 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: 93 Start: 28 End: 57 ...........................TTTGTCAATTTCGAGACTTTATGCTATAAT.................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 113 End: 142 ................................................................................................................ATTGAATTCTTTGTCTTTATCCTGTACAAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaggtttctcccttttttatgtttaatattatagcataaagtctcgaaattgacaaaggcttaagtgtaaagtacgcatgacaattcgaccttaggtatctgaatcttccctattgaattctttgtctttatcctgtacaatcatccggattattaaactttaggagaattgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0450:TDE0451|TDE0450:TDE0451:hypothetical protein:arginine deiminase:<-->:508620..508792 173 aaggtttctcccttttttatgtttaatattatagcataaagtctcgaaattgacaaaggcttaagtgtaaagtacgcatgacaattcgaccttaggtatctgaatcttccctattgaattctttgtctttatcctgtacaatcatccggattattaaactttaggagaattgc Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: NC_002967_TDE0450_TDE0451|hypothetical protein:arginine deiminase|NEGATIVE:POSITIVE|[508620,508792]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 aaggtttctcccttttttatgtttaatattatagcataaagtctcgaaattgacaaaggcttaagtgtaaagtacgcatgacaattcgaccttaggtatctgaatcttccctattgaattctttgtctttatcctgtacaatcatccggattattaaactttaggagaattgc aaggtttctcccttttttatgtttaatattatagcataaagtctcgaaattgacaaaggcttaagtgtaaagtacgcatgacaattcgaccttaggtatctgaatcttccctattgaattctttgtctttatcctgtacaatcatccggattattaaactttaggagaattgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGUUUCUCCCUUUUUUAUGUUUAAUAUUAUAGCAUAAAGUCUCGAAAUUGACAAAGGCUUAAGUGUAAAGUACGCAUGACAAUUCGACCUUAGGUAUCUGAAUCUUCCCUAUUGAAUUCUUUGUCUUUAUCCUGUACAAUCAUCCGGAUUAUUAAACUUUAGGAGAAUUGC .....((((((...(((((((((.........)))))))))..........(((((((......(((((...))))).....(((((((...((((.............))))))))))))))))))...((((.(.........).))))............)))))).... (-29.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAUUCUCCUAAAGUUUAAUAAUCCGGAUGAUUGUACAGGAUAAAGACAAAGAAUUCAAUAGGGAAGAUUCAGAUACCUAAGGUCGAAUUGUCAUGCGUACUUUACACUUAAGCCUUUGUCAAUUUCGAGACUUUAUGCUAUAAUAUUAAACAUAAAAAAGGGAGAAACCUU ....(((((((........((((((.....))))))..((.((((((.............((((.............))))...((((((((.((.((...............))...)).))).)))))..)))))).))....................)))))))..... (-29.68) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 872 100 51 191 142 NC_002967:TDE0450|5end_hypothetical_protein_508529..508759_NEGATIVE 275 139 100 171 132 NC_002967:TDE1297|5end_LysM_domain/M23/M37_peptidase_domain_protein_1334782..1335012_NEGATIVE 264 116 75 52 7 NC_002967:TDE0435|5end_ATP-dependent_DNA_helicase,_RecQ_family_491261..491491_NEGATIVE 259 138 94 201 153 NC_002967:TDE0774|5end_50S_ribosomal_protein_L16_810165..810395_POSITIVE 258 130 81 228 179 NC_002967:TDE0771|5end_ribosomal_protein_S19_808795..809025_POSITIVE 253 139 95 91 52 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 251 117 72 191 140 NC_002967:TDE2596|5end_hypothetical_protein_2632039..2632269_NEGATIVE 250 60 17 168 120 NC_002967:TDE2540|5end_lipoprotein,_putative_2567981..2568211_NEGATIVE 248 167 131 162 128 NC_002967:TDE0444|5end_glutamine_amidotransferase_class-I_domain_protein_498966..499196_POSITIVE 246 150 118 123 90 NC_002967:TDE0702|5end_ABC_transporter,_ATP-binding_protein_737969..738199_NEGATIVE 246 44 2 138 92 NC_002967:TDE0659|5end_hypothetical_protein_696202..696432_NEGATIVE 245 150 101 103 39 NC_002967:TDE0797|5end_acylphosphatase_820859..821089_POSITIVE 240 139 94 183 122 NC_002967:TDE1147|5end_hypothetical_protein_1185960..1186190_NEGATIVE 236 136 97 50 2 NC_002967:TDE2355|5end_carbon_storage_regulator_2390838..2391068_POSITIVE 235 150 114 225 193 NC_002967:TDE1106|5end_translation_initiation_factor_IF-2_1140882..1141112_NEGATIVE 234 128 85 74 35 NC_002967:TDE1645|5end_polypeptide_deformylase_1696052..1696282_NEGATIVE 231 153 121 193 153 NC_002967:TDE1076|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1106936..1107166_POSITIVE 230 128 85 209 174 NC_002967:TDE1928|5end_hypothetical_protein_1945748..1945978_POSITIVE 229 90 41 52 7 NC_002967:TDE1693|5end_hypothetical_protein_1749226..1749456_NEGATIVE 229 166 128 40 2 NC_002967:TDE0963|5end_DNA_polymerase_IV_985895..986125_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 68 26 64 22 NC_002967:TDE2103|3end_glycosyl_transferase,_group_2_family_protein_2127527..2127677_NEGATIVE 255 118 72 100 56 NC_002967:TDE0903|3end_ATP-dependent_DNA_helicase_PcrA_922296..922446_POSITIVE 250 99 51 91 43 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE 248 167 131 108 74 NC_002967:TDE0443|3end_hypothetical_protein_498992..499142_POSITIVE 246 150 118 126 93 NC_002967:TDE0703|3end_transcriptional_regulator,_AbrB_family_737966..738116_NEGATIVE 246 44 2 61 15 NC_002967:TDE0660|3end_transcriptional_regulator,_putative_696279..696429_NEGATIVE 245 150 101 110 46 NC_002967:TDE0796|3end_histidinol_phosphate_phosphatase_HisJ_family_protein_820946..821096_POSITIVE 242 90 42 56 17 NC_002967:TDE1964|3end_Na/Pi_cotransporter_family_protein_1977131..1977281_NEGATIVE 236 136 97 50 2 NC_002967:TDE2354|3end_hypothetical_protein_2390918..2391068_POSITIVE 234 128 85 77 38 NC_002967:TDE1646|3end_hypothetical_protein_1696049..1696199_NEGATIVE 232 130 84 151 109 NC_002967:TDE0354|3end_general_stress_protein_14_399001..399151_POSITIVE 229 90 41 55 10 NC_002967:TDE1694|3end_hypothetical_protein_1749223..1749373_NEGATIVE 225 78 34 50 9 NC_002967:TDE1500|3end_hypothetical_protein_1546763..1546913_NEGATIVE 225 138 92 136 91 NC_002967:TDE0705|3end_SPFH_domain/Band_7_family_protein_739339..739489_NEGATIVE 222 135 94 128 85 NC_002967:TDE1286|3end_TPR_domain_protein_1322817..1322967_POSITIVE 221 129 87 31 1 NC_002967:TDE2098|3end_hypothetical_protein_2124951..2125101_NEGATIVE 220 166 129 38 1 NC_002967:TDE0962|3end_hypothetical_protein_985973..986123_POSITIVE 219 152 121 40 16 NC_002967:TDE2362|3end_hypothetical_protein_2396963..2397113_NEGATIVE 218 127 86 82 47 NC_002967:TDE2737|3end_hypothetical_protein_2792690..2792840_POSITIVE 218 111 72 85 53 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE