Origin IGS: tagcccgcaattcgctgaaaatggctatctttgcatgacatattagaaggtaacggcgactggcagagccttttgccgcctatatataacataagaccgcaaggcgtttcgagcgaaaatctggtaaattgacactacggagacgattgcgtgatgcttatgctatgcctacgcatagcgtgcattcacgtactctccgtaaaaggctttaccagagccgtcgcttgaaagtagtgtgatttgcacgctacttttttgcccttgcccaacgaaaggaaacgata .........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 tatcgtttcctttcgttgggcaagggcaaaaaagtagcgtgcaaatcacactactttcaagcgacggctctggtaaagccttttacggagagtacgtgaatgcacgctatgcgtaggcatagcataagcatcacgcaatcgtctccgtagtgtcaatttaccagattttcgctcgaaacgccttgcggtcttatgttatatataggcggcaaaaggctctgccagtcgccgttaccttctaatatgtcatgcaaagatagccattttcagcgaattgcgggcta Mask Tandem Repeat Region ================================================ tagcccgcaattcgctgaaaatggctatctttgcatgacatattagaaggtaacggcgactggcagagccttttgccgcctatatataacataagaccgcaaggcgtttcgagcgaaaatctggtaaattgacactacggagacgattgcgtgatgcttatgctatgcctacgcatagcgtgcattcacgtactctccgtaaaaggctttaccagagccgtcgcttgaaagtagtgtgatttgcacgctacttttttgcccttgcccaacgaaaggaaacgata Find is-nt database================================================ Query_seq: TF2237:TF2238|TF2237:TF2238:two-component system response regulator involved in CTn:conserved hypothetical protein:->->:2413954..2414237 284 tagcccgcaattcgctgaaaatggctatctttgcatgacatattagaaggtaacggcgactggcagagccttttgccgcctatatataacataagaccgcaaggcgtttcgagcgaaaatctggtaaattgacactacggagacgattgcgtgatgcttatgctatgcctacgcatagcgtgcattcacgtactctccgtaaaaggctttaccagagccgtcgcttgaaagtagtgtgatttgcacgctacttttttgcccttgcccaacgaaaggaaacgata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2237:TF2238|TF2237:TF2238:two-component system response regulator involved in CTn:conserved hypothetical protein:->->:2413954..2414237 284 tagcccgcaattcgctgaaaatggctatctttgcatgacatattagaaggtaacggcgactggcagagccttttgccgcctatatataacataagaccgcaaggcgtttcgagcgaaaatctggtaaattgacactacggagacgattgcgtgatgcttatgctatgcctacgcatagcgtgcattcacgtactctccgtaaaaggctttaccagagccgtcgcttgaaagtagtgtgatttgcacgctacttttttgcccttgcccaacgaaaggaaacgata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2237:TF2238|TF2237:TF2238:two-component system response regulator involved in CTn:conserved hypothetical protein:->->:2413954..2414237 284 tagcccgcaattcgctgaaaatggctatctttgcatgacatattagaaggtaacggcgactggcagagccttttgccgcctatatataacataagaccgcaaggcgtttcgagcgaaaatctggtaaattgacactacggagacgattgcgtgatgcttatgctatgcctacgcatagcgtgcattcacgtactctccgtaaaaggctttaccagagccgtcgcttgaaagtagtgtgatttgcacgctacttttttgcccttgcccaacgaaaggaaacgata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagcccgcaattcgctgaaaatggctatctttgcatgacatattagaaggtaacggcgactggcagagccttttgccgcctatatataacataagaccgcaaggcgtttcgagcgaaaatctggtaaattgacactacggagacgattgcgtgatgcttatgctatgcctacgcatagcgtgcattcacgtactctccgtaaaaggctttaccagagccgtcgcttgaaagtagtgtgatttgcacgctacttttttgcccttgcccaacgaaaggaaacgata Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 31 End: 129 .............................. M H D I L E G N G D W Q S L L P P I Y N I R P Q G V S S E N L V N ........................................................................................................................................................... Protein_Len: 36 Strand: + Start: 129 End: 236 ................................................................................................................................ M T L R R R L R D A Y A M P T H S V H S R T L R K R L Y Q S R R L K V V ................................................ Protein_Len: 34 Strand: - Start: 46 End: 147 ............................................. F T V A V P L A K Q R R Y I V Y S R L A N R A F I Q Y I S V V S V M ......................................................................................................................................... Protein_Len: 30 Strand: - Start: 3 End: 92 .. G A I R Q F H S D K C S M N S P L P S Q C L R K G G I Y L M ................................................................................................................................................................................................ tagcccgcaattcgctgaaaatggctatctttgcatgacatattagaaggtaacggcgactggcagagccttttgccgcctatatataacataagaccgcaaggcgtttcgagcgaaaatctggtaaattgacactacggagacgattgcgtgatgcttatgctatgcctacgcatagcgtgcattcacgtactctccgtaaaaggctttaccagagccgtcgcttgaaagtagtgtgatttgcacgctacttttttgcccttgcccaacgaaaggaaacgata 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================================================ tagcccgcaattcgctgaaaatggctatctttgcatgacatattagaaggtaacggcgactggcagagccttttgccgcctatatataacataagaccgcaaggcgtttcgagcgaaaatctggtaaattgacactacggagacgattgcgtgatgcttatgctatgcctacgcatagcgtgcattcacgtactctccgtaaaaggctttaccagagccgtcgcttgaaagtagtgtgatttgcacgctacttttttgcccttgcccaacgaaaggaaacgata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 91 HP_score: -7.6 Tail_Score: -5.09426 Start: 231 End: 251 Full_Region: AGCCGTCGCTTGAAA GTAGTGTG ATTTG CACGCTAC TTTTTTGCCCTTGCC ......................................................................................................................................................................................................................................GTAGTGTGATTTGCACGCTAC................................. Find igs database================================================ Query_seq: TF2237:TF2238|TF2237:TF2238:two-component system response regulator involved in CTn:conserved hypothetical protein:->->:2413954..2414237 284 tagcccgcaattcgctgaaaatggctatctttgcatgacatattagaaggtaacggcgactggcagagccttttgccgcctatatataacataagaccgcaaggcgtttcgagcgaaaatctggtaaattgacactacggagacgattgcgtgatgcttatgctatgcctacgcatagcgtgcattcacgtactctccgtaaaaggctttaccagagccgtcgcttgaaagtagtgtgatttgcacgctacttttttgcccttgcccaacgaaaggaaacgata Intra-Species Hit: Count: 1 Min: 1 Max: 284 Len: 284 Subject: tfor_TF2237_TF2238|two-component system response regulator involved in CTn:conserved hypothetical protein|POSITIVE:POSITIVE|[2413954,2414237]|284 HSP 1 e-value: 1.0E-159 bit: 563.0 Len: 284 Query Start:1 Query End:284 Subject Strand: POSITIVE Subject Start: 1 Subject End: 284 tagcccgcaattcgctgaaaatggctatctttgcatgacatattagaaggtaacggcgactggcagagccttttgccgcctatatataacataagaccgcaaggcgtttcgagcgaaaatctggtaaattgacactacggagacgattgcgtgatgcttatgctatgcctacgcatagcgtgcattcacgtactctccgtaaaaggctttaccagagccgtcgcttgaaagtagtgtgatttgcacgctacttttttgcccttgcccaacgaaaggaaacgata tagcccgcaattcgctgaaaatggctatctttgcatgacatattagaaggtaacggcgactggcagagccttttgccgcctatatataacataagaccgcaaggcgtttcgagcgaaaatctggtaaattgacactacggagacgattgcgtgatgcttatgctatgcctacgcatagcgtgcattcacgtactctccgtaaaaggctttaccagagccgtcgcttgaaagtagtgtgatttgcacgctacttttttgcccttgcccaacgaaaggaaacgata Inter-species Hit: Count: 1 Min: 4 Max: 283 Len: 280 Subject: NC_006347_BF0137_BF0138|hypothetical protein:rteB gene product|NEGATIVE:NEGATIVE|[143597,143875]|279 HSP 1 e-value: 2.0E-84 bit: 313.0 Len: 280 Query Start:4 Query End:283 Subject Strand: NEGATIVE Subject Start: 2 Subject End: 279 ...cccgcaattcgctgaaaatggctatctttgcatgacatattagaaggtaacggcgactggcag-agccttttgccgcctatatataacataagaccgcaaggcgtttcgagcgaaaatctggtaaattgacactacggagacgattgcgtgatgcttatgctatgcctacgcatagcgtgcattcacgtactctccgtaaaaggctttaccagagccgtcgcttgaaagtagtgtgatttgcacgctacttttttgcccttgcccaacgaaaggaaacgat. ...cccgtaattcactgaatttggctatctttgcataacatttgagaaa--aacggcgattggcaggagcttttcgccgccaacatataggataagaccgcaaggcgtttcaagcgaaaatctggtaaattggaactacggagacgattgcgtgatgcttatgctatgcttacgcatagcgtgcattcacgtactctccgt-aaaggctttaccagagccatcgcttgaaggtagtgtgaattgcacgctacttttttacccttgcctaacgaaaggaaacgat. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCGCAAUUCGCUGAAAAUGGCUAUCUUUGCAUGACAUAUUAGAAGGUAACGGCGACUGGCAGAGCCUUUUGCCGCCUAUAUAUAACAUAAGACCGCAAGGCGUUUCGAGCGAAAAUCUGGUAAAUUGACACUACGGAGACGAUUGCGUGAUGCUUAUGCUAUGCCUACGCAUAGCGUGCAUUCACGUACUCUCCGUAAAAGGCUUUACCAGAGCCGUCGCUUGAAAGUAGUGUGAUUUGCACGCUACUUUUUUGCCCUUGCCCAACGAAAGGAAACGAU ...((((...(((......))).....)))).............(((...((((((..(((...)))..))))))))).................((((((.(((((((((((...(((((((((.......((((((((....((((((((((..(((((((((....)))))))))))).))))))).))))))))......)))))))))....))))))))).((((((((.....))))))))......)))))))).........(....)... (-103.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGUUUCCUUUCGUUGGGCAAGGGCAAAAAAGUAGCGUGCAAAUCACACUACUUUCAAGCGACGGCUCUGGUAAAGCCUUUUACGGAGAGUACGUGAAUGCACGCUAUGCGUAGGCAUAGCAUAAGCAUCACGCAAUCGUCUCCGUAGUGUCAAUUUACCAGAUUUUCGCUCGAAACGCCUUGCGGUCUUAUGUUAUAUAUAGGCGGCAAAAGGCUCUGCCAGUCGCCGUUACCUUCUAAUAUGUCAUGCAAAGAUAGCCAUUUUCAGCGAAUUGCGGG .((((.....((((((((((..((((.....(((((.(((.....))).)))))(((.(((((..(.(((((((((.....((((((((((..(((((.(((..(((((((....)))))))....))))))))....).)))))))))......))))))))))..))))).)))..))))((((....(((((((......((((((.(..(((...)))..).))))))......)))))))...))))......))).....)))))))..)))). (-99.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 425 190 147 136 90 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 386 179 135 113 73 tfor:TF2158|5end_conserved_hypothetical_protein_2333857..2334087_POSITIVE 383 98 51 215 163 tfor:TF2770|5end_conserved_hypothetical_protein_2956308..2956538_POSITIVE 380 218 175 229 173 tfor:TF3033|5end_S1_RNA_binding_domain_protein,_S1_ribosomal_protein_3256786..3257016_POSITIVE 376 180 136 126 78 tfor:TF2695|5end_prephenate_dehydratase_2869618..2869848_POSITIVE 367 50 1 78 25 tfor:TF0165|5end_conserved_hypothetical_protein_174749..174979_POSITIVE 365 198 152 52 1 tfor:TF2257|5end_transfer_region-related_protein,_TraJ_2428541..2428771_POSITIVE 358 65 21 51 14 tfor:TF2382|5end_transposase_2546867..2547097_POSITIVE 356 97 51 190 158 tfor:TF2831|5end_ABC_transporter,_permease_component_3021317..3021547_POSITIVE 356 179 131 62 15 tfor:TF2663|5end_hypothetical_protein_2837152..2837382_POSITIVE 355 140 91 62 13 tfor:TF3024|5end_periplasmic_protease_3247204..3247434_POSITIVE 353 196 151 231 178 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 352 180 132 212 159 tfor:TF1179|5end_two-component_sensor_histidine_kinase_1266057..1266287_POSITIVE 350 196 151 195 144 tfor:TF2820|5end_argininosuccinate_synthetase_3009876..3010106_POSITIVE 350 187 141 104 58 tfor:TF0993|5end_hypothetical_protein_1048457..1048687_POSITIVE 344 223 181 47 2 tfor:TF3009|5end_RNA_polymerase_ECF-type_sigma_factor_3229093..3229323_POSITIVE 343 250 201 203 155 tfor:TF2130|5end_conserved_hypothetical_protein;_possible_permease_2306486..2306716_POSITIVE 342 219 171 104 50 tfor:TF1508|5end_anti-sigma_factor_1616345..1616575_POSITIVE 341 77 34 204 153 tfor:TF0554|5end_Bacteroides_aerotolerance_protein,_BatC_586303..586533_POSITIVE 340 77 34 190 151 tfor:TF2272|5end_conserved_hypothetical_protein_2436156..2436386_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 180 137 151 99 tfor:TF2877|3end_regulatory_protein_3067288..3067438_POSITIVE 386 179 135 100 60 tfor:TF2157|3end_conserved_hypothetical_protein_2333924..2334074_POSITIVE 376 180 136 148 100 tfor:TF2693|3end_possible_aminotransferase_2869720..2869870_POSITIVE 367 50 1 75 22 tfor:TF0164|3end_conserved_hypothetical_protein_174826..174976_POSITIVE 355 140 91 79 30 tfor:TF3022|3end_chorismate_synthase_3247301..3247451_POSITIVE 350 187 141 140 94 tfor:TF0992|3end_hypothetical_protein_1048573..1048723_POSITIVE 344 137 94 54 11 tfor:TF2911|3end_hypothetical_protein_3106640..3106790_POSITIVE 340 77 34 141 102 tfor:TF2271|3end_conserved_hypothetical_protein_2436187..2436337_POSITIVE 335 189 141 54 14 tfor:TF1717|3end_DNA_mismatch_repair_protein_1840494..1840644_POSITIVE 332 87 42 53 9 tfor:TF1160|3end_MutT/nudix_family_protein_1241008..1241158_POSITIVE 332 108 61 115 60 tfor:TF0673|3end_conserved_hypothetical_protein_717355..717505_POSITIVE 332 230 190 53 11 tfor:TF0433|3end_60_kDa_inner_membrane_protein_455386..455536_POSITIVE 331 245 201 86 36 tfor:TF2668|3end_hypothetical_protein_2842733..2842883_POSITIVE 331 245 201 58 8 tfor:TF2667|3end_hypothetical_protein_2842705..2842855_POSITIVE 331 245 201 58 8 tfor:TF2664|3end_hypothetical_protein_2841730..2841880_POSITIVE 331 244 202 130 84 tfor:TF0991|3end_probable_NAD(FAD)-dependent_dehydrogenase_1048334..1048484_POSITIVE 331 98 51 109 55 tfor:TF0242|3end_conserved_hypothetical_protein_274069..274219_POSITIVE 330 77 43 90 56 tfor:TF2749|3end_possible_hemolysin_2934518..2934668_POSITIVE 330 138 91 46 2 tfor:TF0229|3end_beta-galactosidase_257003..257153_POSITIVE 329 68 22 42 7 tfor:TF3043|3end_conserved_hypothetical_protein_3272409..3272559_POSITIVE