Origin IGS: agatactgattttcccgagcctacaaaacggataggccgagaaacaacgcgatattttttgcgttttagcgatttcgtatgaacgaaaatgggcgcatgaaggttttaaaagcgtatgaaaataaatacgcttatacatacaagattcattgagatatgtcgtatatttggacattattccggcgttattacctgatagttgttctcgataatgaaacaagctgttaaacagtgtattaaatgttattgatcatttagcatgcgtaacagcgtgaggaaacaaatggtaccggtacttaccctatagcagggaaaccggcgaataaaatatcata .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatgatattttattcgccggtttccctgctatagggtaagtaccggtaccatttgtttcctcacgctgttacgcatgctaaatgatcaataacatttaatacactgtttaacagcttgtttcattatcgagaacaactatcaggtaataacgccggaataatgtccaaatatacgacatatctcaatgaatcttgtatgtataagcgtatttattttcatacgcttttaaaaccttcatgcgcccattttcgttcatacgaaatcgctaaaacgcaaaaaatatcgcgttgtttctcggcctatccgttttgtaggctcgggaaaatcagtatct Mask Tandem Repeat Region ================================================ agatactgattttcccgagcctacaaaacggataggccgagaaacaacgcgatattttttgcgttttagcgatttcgtatgaacgaaaatgggcgcatgaaggttttaaaagcgtatgaaaataaatacgcttatacatacaagattcattgagatatgtcgtatatttggacattattccggcgttattacctgatagttgttctcgataatgaaacaagctgttaaacagtgtattaaatgttattgatcatttagcatgcgtaacagcgtgaggaaacaaatggtaccggtacttaccctatagcagggaaaccggcgaataaaatatcata Find is-nt database================================================ Query_seq: TF3008:TF3009|TF3008:TF3009:zinc protease:RNA polymerase ECF-type sigma factor:->->:3228898..3229232 335 agatactgattttcccgagcctacaaaacggataggccgagaaacaacgcgatattttttgcgttttagcgatttcgtatgaacgaaaatgggcgcatgaaggttttaaaagcgtatgaaaataaatacgcttatacatacaagattcattgagatatgtcgtatatttggacattattccggcgttattacctgatagttgttctcgataatgaaacaagctgttaaacagtgtattaaatgttattgatcatttagcatgcgtaacagcgtgaggaaacaaatggtaccggtacttaccctatagcagggaaaccggcgaataaaatatcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3008:TF3009|TF3008:TF3009:zinc protease:RNA polymerase ECF-type sigma factor:->->:3228898..3229232 335 agatactgattttcccgagcctacaaaacggataggccgagaaacaacgcgatattttttgcgttttagcgatttcgtatgaacgaaaatgggcgcatgaaggttttaaaagcgtatgaaaataaatacgcttatacatacaagattcattgagatatgtcgtatatttggacattattccggcgttattacctgatagttgttctcgataatgaaacaagctgttaaacagtgtattaaatgttattgatcatttagcatgcgtaacagcgtgaggaaacaaatggtaccggtacttaccctatagcagggaaaccggcgaataaaatatcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3008:TF3009|TF3008:TF3009:zinc protease:RNA polymerase ECF-type sigma factor:->->:3228898..3229232 335 agatactgattttcccgagcctacaaaacggataggccgagaaacaacgcgatattttttgcgttttagcgatttcgtatgaacgaaaatgggcgcatgaaggttttaaaagcgtatgaaaataaatacgcttatacatacaagattcattgagatatgtcgtatatttggacattattccggcgttattacctgatagttgttctcgataatgaaacaagctgttaaacagtgtattaaatgttattgatcatttagcatgcgtaacagcgtgaggaaacaaatggtaccggtacttaccctatagcagggaaaccggcgaataaaatatcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agatactgattttcccgagcctacaaaacggataggccgagaaacaacgcgatattttttgcgttttagcgatttcgtatgaacgaaaatgggcgcatgaaggttttaaaagcgtatgaaaataaatacgcttatacatacaagattcattgagatatgtcgtatatttggacattattccggcgttattacctgatagttgttctcgataatgaaacaagctgttaaacagtgtattaaatgttattgatcatttagcatgcgtaacagcgtgaggaaacaaatggtaccggtacttaccctatagcagggaaaccggcgaataaaatatcata Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: - Start: 2 End: 247 . A I E Y S R F H A C S P K L L T H F Y I R K Y M C S E N L Y T T Y K S M I G A N N G S L Q E R Y H F L S N F L T N F T M ........................................................................................ Protein_Len: 30 Strand: - Start: 1 End: 90 S V S K G S G V F R I P R S V V R Y K K R K L S K T H V F M ..................................................................................................................................................................................................................................................... agatactgattttcccgagcctacaaaacggataggccgagaaacaacgcgatattttttgcgttttagcgatttcgtatgaacgaaaatgggcgcatgaaggttttaaaagcgtatgaaaataaatacgcttatacatacaagattcattgagatatgtcgtatatttggacattattccggcgttattacctgatagttgttctcgataatgaaacaagctgttaaacagtgtattaaatgttattgatcatttagcatgcgtaacagcgtgaggaaacaaatggtaccggtacttaccctatagcagggaaaccggcgaataaaatatcata 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: 82 Start: 149 End: 178 ....................................................................................................................................................ATTGAGATATGTCGTATATTTGGACATTAT............................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agatactgattttcccgagcctacaaaacggataggccgagaaacaacgcgatattttttgcgttttagcgatttcgtatgaacgaaaatgggcgcatgaaggttttaaaagcgtatgaaaataaatacgcttatacatacaagattcattgagatatgtcgtatatttggacattattccggcgttattacctgatagttgttctcgataatgaaacaagctgttaaacagtgtattaaatgttattgatcatttagcatgcgtaacagcgtgaggaaacaaatggtaccggtacttaccctatagcagggaaaccggcgaataaaatatcata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 55 HP_score: -2.5 Tail_Score: -4.17491 Start: 48 End: 63 Full_Region: TAGGCCGAGAAACAA CGCGA TATTTT TTGCG TTTTAGCGATTTCGT ...............................................CGCGATATTTTTTGCG................................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: TF3008:TF3009|TF3008:TF3009:zinc protease:RNA polymerase ECF-type sigma factor:->->:3228898..3229232 335 agatactgattttcccgagcctacaaaacggataggccgagaaacaacgcgatattttttgcgttttagcgatttcgtatgaacgaaaatgggcgcatgaaggttttaaaagcgtatgaaaataaatacgcttatacatacaagattcattgagatatgtcgtatatttggacattattccggcgttattacctgatagttgttctcgataatgaaacaagctgttaaacagtgtattaaatgttattgatcatttagcatgcgtaacagcgtgaggaaacaaatggtaccggtacttaccctatagcagggaaaccggcgaataaaatatcata Intra-Species Hit: Count: 1 Min: 1 Max: 335 Len: 335 Subject: tfor_TF3008_TF3009|zinc protease:RNA polymerase ECF-type sigma factor|POSITIVE:POSITIVE|[3228898,3229232]|335 HSP 1 e-value: 0.0 bit: 664.0 Len: 335 Query Start:1 Query End:335 Subject Strand: POSITIVE Subject Start: 1 Subject End: 335 agatactgattttcccgagcctacaaaacggataggccgagaaacaacgcgatattttttgcgttttagcgatttcgtatgaacgaaaatgggcgcatgaaggttttaaaagcgtatgaaaataaatacgcttatacatacaagattcattgagatatgtcgtatatttggacattattccggcgttattacctgatagttgttctcgataatgaaacaagctgttaaacagtgtattaaatgttattgatcatttagcatgcgtaacagcgtgaggaaacaaatggtaccggtacttaccctatagcagggaaaccggcgaataaaatatcata agatactgattttcccgagcctacaaaacggataggccgagaaacaacgcgatattttttgcgttttagcgatttcgtatgaacgaaaatgggcgcatgaaggttttaaaagcgtatgaaaataaatacgcttatacatacaagattcattgagatatgtcgtatatttggacattattccggcgttattacctgatagttgttctcgataatgaaacaagctgttaaacagtgtattaaatgttattgatcatttagcatgcgtaacagcgtgaggaaacaaatggtaccggtacttaccctatagcagggaaaccggcgaataaaatatcata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUACUGAUUUUCCCGAGCCUACAAAACGGAUAGGCCGAGAAACAACGCGAUAUUUUUUGCGUUUUAGCGAUUUCGUAUGAACGAAAAUGGGCGCAUGAAGGUUUUAAAAGCGUAUGAAAAUAAAUACGCUUAUACAUACAAGAUUCAUUGAGAUAUGUCGUAUAUUUGGACAUUAUUCCGGCGUUAUUACCUGAUAGUUGUUCUCGAUAAUGAAACAAGCUGUUAAACAGUGUAUUAAAUGUUAUUGAUCAUUUAGCAUGCGUAACAGCGUGAGGAAACAAAUGGUACCGGUACUUACCCUAUAGCAGGGAAACCGGCGAAUAAAAUAUCAUA .((((.....((((.((.((((((......).))))))).))))....(((((((.(((((((((....((.((((((....)))))).))))))).((((.((..((.((((((((........)))))))).))...))....))))..)))).))))))).((((((..((((.((((.(((((.((((.((((((((.(((........)))...))))))))....((((..((((((........))))))))))..)))).)))))..))))...))))...(((((..((.((((.....)))))))))))))))))...))))... (-82.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGAUAUUUUAUUCGCCGGUUUCCCUGCUAUAGGGUAAGUACCGGUACCAUUUGUUUCCUCACGCUGUUACGCAUGCUAAAUGAUCAAUAACAUUUAAUACACUGUUUAACAGCUUGUUUCAUUAUCGAGAACAACUAUCAGGUAAUAACGCCGGAAUAAUGUCCAAAUAUACGACAUAUCUCAAUGAAUCUUGUAUGUAUAAGCGUAUUUAUUUUCAUACGCUUUUAAAACCUUCAUGCGCCCAUUUUCGUUCAUACGAAAUCGCUAAAACGCAAAAAAUAUCGCGUUGUUUCUCGGCCUAUCCGUUUUGUAGGCUCGGGAAAAUCAGUAUCU ...((((((......((((((..(((((...))))).....))))))........((((((...(((((((.(((((.((((((........))))))...)).))).)))))))............((((((((((....((((.........(((......)))..((((((((.((.((.....)))).))))))))..((((((((........)))))))).....))))...((((.....((((((....)))))).........))))...........)))).))))))((((((.......))))))..))))))...)))))). (-81.24) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 320 271 70 27 tfor:TF3070|5end_conserved_hypothetical_protein_3294380..3294610_POSITIVE 354 208 161 128 82 tfor:TF2159|5end_conserved_hypothetical_protein_2334446..2334676_POSITIVE 350 300 251 195 146 tfor:TF0147|5end_patatin-like_phospholipase_156798..157028_POSITIVE 342 104 63 78 29 tfor:TF1857|5end_conserved_hypothetical_protein_2014366..2014596_POSITIVE 342 93 51 80 35 tfor:TF0626|5end_hypothetical_protein_661945..662175_POSITIVE 337 78 35 218 180 tfor:TF2652|5end_hypothetical_protein_2821803..2822033_POSITIVE 337 78 35 170 132 tfor:TF2651|5end_hypothetical_protein_2821755..2821985_POSITIVE 335 324 284 44 12 tfor:TF0712|5end_TPR-repeat-containing_protein_761348..761578_POSITIVE 330 326 282 80 34 tfor:TF3111|5end_hypothetical_protein_3346601..3346831_POSITIVE 326 119 76 54 1 tfor:TF2780|5end_hypothetical_protein_2966060..2966290_POSITIVE 326 163 126 65 27 tfor:TF0806|5end_conserved_hypothetical_protein_863575..863805_POSITIVE 325 292 261 35 8 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 325 52 15 45 4 tfor:TF0444|5end_Na+-translocating_NADH-quinone_oxidoreductase,_subunit_5_465869..466099_POSITIVE 324 59 14 55 8 tfor:TF3105|5end_hypothetical_protein_3338068..3338298_POSITIVE 323 59 15 202 153 tfor:TF2535|5end_histidyl-tRNA_synthetase_2717740..2717970_POSITIVE 319 70 28 165 126 tfor:TF0034|5end_outer_membrane_protein_32551..32781_POSITIVE 309 77 31 65 23 tfor:TF2643|5end_possible_O-antigen_transporter_2811744..2811974_POSITIVE 309 329 290 89 49 tfor:TF1908|5end_possible_phosphoglycerate_mutase_2062695..2062925_POSITIVE 309 46 1 214 173 tfor:TF0622|5end_hypothetical_protein_656650..656880_POSITIVE 306 52 15 161 126 tfor:TF0687|5end_hypothetical_protein_732226..732456_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 55 16 129 88 tfor:TF1938|3end_hypothetical_protein_2086270..2086420_POSITIVE 337 78 35 141 103 tfor:TF2650|3end_succinate_dehydrogenase,_iron-sulfur_subunit_2821806..2821956_POSITIVE 319 70 28 137 98 tfor:TF0033|3end_outer_membrane_protein_32603..32753_POSITIVE 317 299 253 140 97 tfor:TF1592|3end_hypothetical_protein_1708557..1708707_POSITIVE 309 77 31 68 26 tfor:TF2642|3end_acetylornithine_deacetylase_2811827..2811977_POSITIVE 305 316 271 68 22 tfor:TF0276|3end_hypothetical_protein_300982..301132_POSITIVE 303 99 58 139 103 tfor:TF3078|3end_ribonucleoside_diphosphate_reductase,_alpha_subunit_3309226..3309376_POSITIVE 302 70 30 129 81 tfor:TF1900|3end_conserved_hypothetical_protein_2056532..2056682_POSITIVE 302 163 128 37 1 tfor:TF0805|3end_possible_hydrolase,_HAD_superfamily_863627..863777_POSITIVE 295 322 286 135 104 tfor:TF1840|3end_transposase_1991416..1991566_POSITIVE 294 79 31 151 102 tfor:TF0082|3end_transcriptional_regulator,_TetR_family_89264..89414_POSITIVE 293 299 253 140 97 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 291 320 271 137 72 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 291 100 55 146 92 tfor:TF0718|3end_methylenetetrahydrofolate_dehydrogenase;_methenyltetrahydrofolate_cyclohydrolase_769980..770130_POSITIVE 288 209 162 144 102 tfor:TF3163|3end_conserved_hypothetical_protein_3403717..3403867_POSITIVE 286 186 158 110 81 tfor:TF1744|3end_phenylacetate-CoA_ligase_1879218..1879368_POSITIVE 284 320 273 56 10 tfor:TF0952|3end_conserved_hypothetical_protein_998009..998159_POSITIVE 282 51 15 84 27 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 279 104 62 48 1 tfor:TF1856|3end_conserved_hypothetical_protein_2014416..2014566_POSITIVE 278 289 249 124 86 tfor:TF2025|3end_hypothetical_protein_2182180..2182330_POSITIVE