Origin IGS: aacaatcaacaaaacaaaagcaagccttaaagctcttttaccgcaataaaacattttcataggctcacataatgccataaattgaagatatatgcaagccggtattttttttgataaaacttcttacaatttataccggccgataaacaacctcatcagcccttacatttttctctaaaatttggtataataatagaatattggagttttatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataaaactccaatattctattattataccaaattttagagaaaaatgtaagggctgatgaggttgtttatcggccggtataaattgtaagaagttttatcaaaaaaaataccggcttgcatatatcttcaatttatggcattatgtgagcctatgaaaatgttttattgcggtaaaagagctttaaggcttgcttttgttttgttgattgtt Mask Tandem Repeat Region ================================================ aacaatcaacaaaacaaaagcaagccttaaagctcttttaccgcaataaaacattttcataggctcacataatgccataaattgaagatatatgcaagccggtattttttttgataaaacttcttacaatttataccggccgataaacaacctcatcagcccttacatttttctctaaaatttggtataataatagaatattggagttttatt Find is-nt database================================================ Query_seq: TDE2182:TDE2183|TDE2182:TDE2183:hypothetical protein:hypothetical protein:<-->:2215126..2215338 213 aacaatcaacaaaacaaaagcaagccttaaagctcttttaccgcaataaaacattttcataggctcacataatgccataaattgaagatatatgcaagccggtattttttttgataaaacttcttacaatttataccggccgataaacaacctcatcagcccttacatttttctctaaaatttggtataataatagaatattggagttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2182:TDE2183|TDE2182:TDE2183:hypothetical protein:hypothetical protein:<-->:2215126..2215338 213 aacaatcaacaaaacaaaagcaagccttaaagctcttttaccgcaataaaacattttcataggctcacataatgccataaattgaagatatatgcaagccggtattttttttgataaaacttcttacaatttataccggccgataaacaacctcatcagcccttacatttttctctaaaatttggtataataatagaatattggagttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2182:TDE2183|TDE2182:TDE2183:hypothetical protein:hypothetical protein:<-->:2215126..2215338 213 aacaatcaacaaaacaaaagcaagccttaaagctcttttaccgcaataaaacattttcataggctcacataatgccataaattgaagatatatgcaagccggtattttttttgataaaacttcttacaatttataccggccgataaacaacctcatcagcccttacatttttctctaaaatttggtataataatagaatattggagttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacaatcaacaaaacaaaagcaagccttaaagctcttttaccgcaataaaacattttcataggctcacataatgccataaattgaagatatatgcaagccggtattttttttgataaaacttcttacaatttataccggccgataaacaacctcatcagcccttacatttttctctaaaatttggtataataatagaatattggagttttatt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 1 End: 105 V I L L V F A L R L A R K G C Y F M K M P E C L A M F Q L Y I C A P M ............................................................................................................ aacaatcaacaaaacaaaagcaagccttaaagctcttttaccgcaataaaacattttcataggctcacataatgccataaattgaagatatatgcaagccggtattttttttgataaaacttcttacaatttataccggccgataaacaacctcatcagcccttacatttttctctaaaatttggtataataatagaatattggagttttatt 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: 83 Start: 162 End: 191 .................................................................................................................................................................CTTACATTTTTCTCTAAAATTTGGTATAAT...................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 69 End: 98 ....................................................................CTTGCATATATCTTCAATTTATGGCATTAT................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacaatcaacaaaacaaaagcaagccttaaagctcttttaccgcaataaaacattttcataggctcacataatgccataaattgaagatatatgcaagccggtattttttttgataaaacttcttacaatttataccggccgataaacaacctcatcagcccttacatttttctctaaaatttggtataataatagaatattggagttttatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2182:TDE2183|TDE2182:TDE2183:hypothetical protein:hypothetical protein:<-->:2215126..2215338 213 aacaatcaacaaaacaaaagcaagccttaaagctcttttaccgcaataaaacattttcataggctcacataatgccataaattgaagatatatgcaagccggtattttttttgataaaacttcttacaatttataccggccgataaacaacctcatcagcccttacatttttctctaaaatttggtataataatagaatattggagttttatt Intra-Species Hit: Count: 1 Min: 1 Max: 213 Len: 213 Subject: NC_002967_TDE2182_TDE2183|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2215126,2215338]|213 HSP 1 e-value: 1.0E-103 bit: 375.0 Len: 213 Query Start:1 Query End:213 Subject Strand: POSITIVE Subject Start: 1 Subject End: 213 aacaatcaacaaaacaaaagcaagccttaaagctcttttaccgcaataaaacattttcataggctcacataatgccataaattgaagatatatgcaagccggtannnnnnnngataaaacttcttacaatttataccggccgataaacaacctcatcagcccttacatttttctctaaaatttggtataataatagaatattggagttttatt aacaatcaacaaaacaaaagcaagccttaaagctcttttaccgcaataaaacattttcataggctcacataatgccataaattgaagatatatgcaagccggtattttttttgataaaacttcttacaatttataccggccgataaacaacctcatcagcccttacatttttctctaaaatttggtataataatagaatattggagttttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAUCAACAAAACAAAAGCAAGCCUUAAAGCUCUUUUACCGCAAUAAAACAUUUUCAUAGGCUCACAUAAUGCCAUAAAUUGAAGAUAUAUGCAAGCCGGUAUUUUUUUUGAUAAAACUUCUUACAAUUUAUACCGGCCGAUAAACAACCUCAUCAGCCCUUACAUUUUUCUCUAAAAUUUGGUAUAAUAAUAGAAUAUUGGAGUUUUAUU ...........................(((((((((..((............(((((((..(((.........)))......))))))).(((((..((((((((.....(((.(((......))))))...)))))))).(((..........)))...........................))))).........))..))))))))).. (-31.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAACUCCAAUAUUCUAUUAUUAUACCAAAUUUUAGAGAAAAAUGUAAGGGCUGAUGAGGUUGUUUAUCGGCCGGUAUAAAUUGUAAGAAGUUUUAUCAAAAAAAAUACCGGCUUGCAUAUAUCUUCAAUUUAUGGCAUUAUGUGAGCCUAUGAAAAUGUUUUAUUGCGGUAAAAGAGCUUUAAGGCUUGCUUUUGUUUUGUUGAUUGUU ((((((((....................(((.(..((..(((.(.(((((((((((((((((....))))))))))(((((...(((((((....)))).))).....)))))..))))))).).)))..))..).)))......(..(((((.((((..(.((((((....)))))).)..)))))))))..)....))))))))....... (-47.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 830 70 21 161 112 NC_002967:TDE2182|5end_hypothetical_protein_2215035..2215265_NEGATIVE 302 170 121 230 180 NC_002967:TDE2235|5end_methylaspartate_ammonia-lyase_2274588..2274818_NEGATIVE 281 162 121 157 110 NC_002967:TDE0502|5end_ankyrin_repeat_protein_556558..556788_NEGATIVE 274 75 34 204 147 NC_002967:TDE2105|5end_hypothetical_protein_2131484..2131714_NEGATIVE 265 65 24 131 87 NC_002967:TDE1380|5end_hypothetical_protein_1421284..1421514_NEGATIVE 259 65 24 191 147 NC_002967:TDE1172|5end_hypothetical_protein_1201006..1201236_POSITIVE 259 80 32 93 26 NC_002967:TDE0778|5end_ribosomal_protein_L24_811487..811717_POSITIVE 257 107 61 77 22 NC_002967:TDE2631|5end_peptide_ABC_transporter,_permease_protein,_putative_2671829..2672059_POSITIVE 257 69 21 67 10 NC_002967:TDE2243|5end_CutC_family_protein_2282954..2283184_NEGATIVE 257 119 73 143 86 NC_002967:TDE1598|5end_ABC_transporter,_ATP-binding_protein_1648910..1649140_NEGATIVE 257 129 85 67 26 NC_002967:TDE0650|5end_hypothetical_protein_684697..684927_POSITIVE 249 79 33 228 191 NC_002967:TDE0509|5end_hypothetical_protein_560373..560603_NEGATIVE 249 187 157 134 100 NC_002967:TDE0486|5end_hypothetical_protein_543612..543842_NEGATIVE 247 102 61 203 164 NC_002967:TDE2340|5end_FMN-binding_domain_protein_2377855..2378085_NEGATIVE 245 158 112 144 96 NC_002967:TDE1447|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_1492612..1492842_POSITIVE 238 70 23 108 57 NC_002967:TDE1321|5end_conserved_hypothetical_protein_TIGR00257_1359335..1359565_POSITIVE 237 164 137 45 15 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 236 58 14 231 175 NC_002967:TDE1214|5end_flagellar_basal_body_protein_1246307..1246537_POSITIVE 233 80 32 105 46 NC_002967:TDE2770|5end_flagellar_hook-length_control_protein_FliK_2824417..2824647_NEGATIVE 232 100 53 143 97 NC_002967:TDE2592|5end_DbpA_RNA_binding_domain_protein_2627026..2627256_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 162 121 135 88 NC_002967:TDE0503|3end_hypothetical_protein_556580..556730_NEGATIVE 274 161 121 151 108 NC_002967:TDE2236|3end_methylaspartate_mutase,_E_subunit_2274660..2274810_NEGATIVE 265 65 24 127 83 NC_002967:TDE1381|3end_V-type_ATP_synthase_subunit_E_1421288..1421438_NEGATIVE 259 162 136 130 106 NC_002967:TDE1665|3end_hypothetical_protein_1718908..1719058_NEGATIVE 259 176 133 65 27 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 259 80 32 83 16 NC_002967:TDE0777|3end_50S_ribosomal_protein_L14_811557..811707_POSITIVE 257 107 61 80 25 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE 257 119 73 133 76 NC_002967:TDE1599|3end_ABC_transporter,_ATP-binding/permease_protein_1648920..1649070_NEGATIVE 253 38 1 81 44 NC_002967:TDE0362|3end_bacterial_Ig-like_domain_protein_407501..407651_NEGATIVE 250 67 22 100 57 NC_002967:TDE0166|3end_hypothetical_protein_195050..195200_NEGATIVE 249 187 157 118 84 NC_002967:TDE0487|3end_ABC_transporter,_ATP-binding_protein_543628..543778_NEGATIVE 247 64 24 123 69 NC_002967:TDE1337|3end_hypothetical_protein_1373766..1373916_NEGATIVE 245 158 112 131 83 NC_002967:TDE1446|3end_hypothetical_protein_1492679..1492829_POSITIVE 244 173 131 137 91 NC_002967:TDE0923|3end_ABC_transporter,_ATP-binding/permease_protein_943920..944070_NEGATIVE 241 140 93 86 22 NC_002967:TDE0058|3end_hypothetical_protein_67398..67548_POSITIVE 238 70 23 111 60 NC_002967:TDE1320|3end_ComEC/Rec2-related_protein_1359418..1359568_POSITIVE 238 108 62 48 5 NC_002967:TDE0904|3end_hypothetical_protein_922278..922428_NEGATIVE 237 164 137 32 2 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 236 174 131 139 91 NC_002967:TDE0797|3end_acylphosphatase_821223..821373_POSITIVE 230 168 124 140 105 NC_002967:TDE0595|3end_hypothetical_protein_634838..634988_NEGATIVE