Origin IGS: agatagagtaattttttttaatgctccccgtggcgttatatgttatataacattttttttgtggagagtgatgtatgcatgaagaggttgcatgtcgaaactaataggagagtgcaaagaggaagcagaagagtacattcagacagaggtgggtgtcatattgcccatatgagacacctttgccaagaaaccgaatgcaaaaccccacccccacgtgcggtagtgtgagagcccggaaaatgaaaataggaggaaaatgaaaaaggttttcctcctacttgatttttagaattgtttttta .........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 taaaaaacaattctaaaaatcaagtaggaggaaaacctttttcattttcctcctattttcattttccgggctctcacactaccgcacgtgggggtggggttttgcattcggtttcttggcaaaggtgtctcatatgggcaatatgacacccacctctgtctgaatgtactcttctgcttcctctttgcactctcctattagtttcgacatgcaacctcttcatgcatacatcactctccacaaaaaaaatgttatataacatataacgccacggggagcattaaaaaaaattactctatct Mask Tandem Repeat Region ================================================ agatagagtaattttttttaatgctccccgtggcgttatatgttatataacattttttttgtggagagtgatgtatgcatgaagaggttgcatgtcgaaactaataggagagtgcaaagaggaagcagaagagtacattcagacagaggtgggtgtcatattgcccatatgagacacctttgccaagaaaccgaatgcaaaaccccacccccacgtgcggtagtgtgagagcccggaaaatgaaaataggaggaaaatgaaaaaggttttcctcctacttgatttttagaattgtttttta Find is-nt database================================================ Query_seq: TF2196:TF2197|TF2196:TF2197:hypothetical protein:conserved hypothetical protein:->->:2372241..2372541 301 agatagagtaattttttttaatgctccccgtggcgttatatgttatataacattttttttgtggagagtgatgtatgcatgaagaggttgcatgtcgaaactaataggagagtgcaaagaggaagcagaagagtacattcagacagaggtgggtgtcatattgcccatatgagacacctttgccaagaaaccgaatgcaaaaccccacccccacgtgcggtagtgtgagagcccggaaaatgaaaataggaggaaaatgaaaaaggttttcctcctacttgatttttagaattgtttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2196:TF2197|TF2196:TF2197:hypothetical protein:conserved hypothetical protein:->->:2372241..2372541 301 agatagagtaattttttttaatgctccccgtggcgttatatgttatataacattttttttgtggagagtgatgtatgcatgaagaggttgcatgtcgaaactaataggagagtgcaaagaggaagcagaagagtacattcagacagaggtgggtgtcatattgcccatatgagacacctttgccaagaaaccgaatgcaaaaccccacccccacgtgcggtagtgtgagagcccggaaaatgaaaataggaggaaaatgaaaaaggttttcctcctacttgatttttagaattgtttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2196:TF2197|TF2196:TF2197:hypothetical protein:conserved hypothetical protein:->->:2372241..2372541 301 agatagagtaattttttttaatgctccccgtggcgttatatgttatataacattttttttgtggagagtgatgtatgcatgaagaggttgcatgtcgaaactaataggagagtgcaaagaggaagcagaagagtacattcagacagaggtgggtgtcatattgcccatatgagacacctttgccaagaaaccgaatgcaaaaccccacccccacgtgcggtagtgtgagagcccggaaaatgaaaataggaggaaaatgaaaaaggttttcctcctacttgatttttagaattgtttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agatagagtaattttttttaatgctccccgtggcgttatatgttatataacattttttttgtggagagtgatgtatgcatgaagaggttgcatgtcgaaactaataggagagtgcaaagaggaagcagaagagtacattcagacagaggtgggtgtcatattgcccatatgagacacctttgccaagaaaccgaatgcaaaaccccacccccacgtgcggtagtgtgagagcccggaaaatgaaaataggaggaaaatgaaaaaggttttcctcctacttgatttttagaattgtttttta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 40 End: 225 ....................................... M L Y N I F F V E S D V C M K R L H V E T N R R V Q R G S R R V H S D R G G C H I A H M R H L C Q E T E C K T P P P R A ............................................................................ Protein_Len: 35 Strand: + Start: 153 End: 257 ........................................................................................................................................................ M S Y C P Y E T P L P R N R M Q N P T P T C G S V R A R K M K I G G K ............................................ Protein_Len: 39 Strand: - Start: 142 End: 258 ............................................................................................................................................. V S T P T M N G M H S V K A L F G F A F G W G W T R Y H S L G S F S F L L F M ........................................... Protein_Len: 48 Strand: - Start: 104 End: 247 ....................................................................................................... Y S L A F L F C F L V N L C L H T D Y Q G Y S V G K G L F R I C F G V G V H P L T L A R F I F M ...................................................... Protein_Len: 31 Strand: - Start: 46 End: 138 ............................................. I V N K K H L T I Y A H L P Q M D F S I P S H L S S A S S Y M ................................................................................................................................................................... Protein_Len: 36 Strand: - Start: 39 End: 146 ...................................... I N Y L M K K T S L S T H M F L N C T S V L L L T C L P L L L T C E S M ........................................................................................................................................................... agatagagtaattttttttaatgctccccgtggcgttatatgttatataacattttttttgtggagagtgatgtatgcatgaagaggttgcatgtcgaaactaataggagagtgcaaagaggaagcagaagagtacattcagacagaggtgggtgtcatattgcccatatgagacacctttgccaagaaaccgaatgcaaaaccccacccccacgtgcggtagtgtgagagcccggaaaatgaaaataggaggaaaatgaaaaaggttttcctcctacttgatttttagaattgtttttta 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================================================ agatagagtaattttttttaatgctccccgtggcgttatatgttatataacattttttttgtggagagtgatgtatgcatgaagaggttgcatgtcgaaactaataggagagtgcaaagaggaagcagaagagtacattcagacagaggtgggtgtcatattgcccatatgagacacctttgccaagaaaccgaatgcaaaaccccacccccacgtgcggtagtgtgagagcccggaaaatgaaaataggaggaaaatgaaaaaggttttcctcctacttgatttttagaattgtttttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 40 HP_score: -2.3 Tail_Score: -2.71712 Start: 151 End: 177 Full_Region: CATTCAGACAGAGGT GGGTGTCATAT TGCCC ATATGAGACAC CTTTGCCAAGAAACC ......................................................................................................................................................GGGTGTCATATTGCCCATATGAGACAC............................................................................................................................ TransTerm Strand: + Conf: 63 HP_score: -5.7 Tail_Score: -3.82528 Start: 246 End: 278 Full_Region: GCCCGGAAAATGAAA ATAGGAGGAAAAT GAAAAAG GTTTTCCTCCTAC TTGATTTTTAGAATT .....................................................................................................................................................................................................................................................ATAGGAGGAAAATGAAAAAGGTTTTCCTCCTAC....................... TransTerm Strand: + Conf: 70 HP_score: -9.2 Tail_Score: -2.88433 Start: 247 End: 277 Full_Region: CCCGGAAAATGAAAA TAGGAGGAAAAT GAAAAAG GTTTTCCTCCTA CTTGATTTTTAGAAT ......................................................................................................................................................................................................................................................TAGGAGGAAAATGAAAAAGGTTTTCCTCCTA........................ TransTerm Strand: + Conf: 61 HP_score: -7.4 Tail_Score: -2.9838 Start: 249 End: 275 Full_Region: CGGAAAATGAAAATA GGAGGAAAAT GAAAAAG GTTTTCCTCC TACTTGATTTTTAGA ........................................................................................................................................................................................................................................................GGAGGAAAATGAAAAAGGTTTTCCTCC.......................... Find igs database================================================ Query_seq: TF2196:TF2197|TF2196:TF2197:hypothetical protein:conserved hypothetical protein:->->:2372241..2372541 301 agatagagtaattttttttaatgctccccgtggcgttatatgttatataacattttttttgtggagagtgatgtatgcatgaagaggttgcatgtcgaaactaataggagagtgcaaagaggaagcagaagagtacattcagacagaggtgggtgtcatattgcccatatgagacacctttgccaagaaaccgaatgcaaaaccccacccccacgtgcggtagtgtgagagcccggaaaatgaaaataggaggaaaatgaaaaaggttttcctcctacttgatttttagaattgtttttta Intra-Species Hit: Count: 1 Min: 20 Max: 301 Len: 282 Subject: tfor_TF2196_TF2197|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2372241,2372541]|301 HSP 1 e-value: 1.0E-144 bit: 511.0 Len: 282 Query Start:20 Query End:301 Subject Strand: POSITIVE Subject Start: 20 Subject End: 301 ...................aatgctccccgtggcgttatatgttatataacannnnnnnngtggagagtgatgtatgcatgaagaggttgcatgtcgaaactaataggagagtgcaaagaggaagcagaagagtacattcagacagaggtgggtgtcatattgcccatatgagacacctttgccaagaaaccgaatgcaaaaccccacccccacgtgcggtagtgtgagagcccggaaaatgaaaataggaggaaaatgaaaaaggttttcctcctacttgatttttagaattgtttttta ...................aatgctccccgtggcgttatatgttatataacattttttttgtggagagtgatgtatgcatgaagaggttgcatgtcgaaactaataggagagtgcaaagaggaagcagaagagtacattcagacagaggtgggtgtcatattgcccatatgagacacctttgccaagaaaccgaatgcaaaaccccacccccacgtgcggtagtgtgagagcccggaaaatgaaaataggaggaaaatgaaaaaggttttcctcctacttgatttttagaattgtttttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGCUCCCCGUGGCGUUAUAUGUUAUAUAACAUUUUUUUUGUGGAGAGUGAUGUAUGCAUGAAGAGGUUGCAUGUCGAAACUAAUAGGAGAGUGCAAAGAGGAAGCAGAAGAGUACAUUCAGACAGAGGUGGGUGUCAUAUUGCCCAUAUGAGACACCUUUGCCAAGAAACCGAAUGCAAAACCCCACCCCCACGUGCGGUAGUGUGAGAGCCCGGAAAAUGAAAAUAGGAGGAAAAUGAAAAAGGUUUUCCUCCUACUUGAUUUUUAGAAUUGUUUUUUA .(((((((((((((.....(((((.(((((.((((((((....)))))))).))))))))))..(.((((((((.(((..........(((.((((.................)))).))).(.((((((((....((((((.....))))))..)))))))).).......))))))))..))).)....))))).).)).)))))((((((...((((((.((..((((((((((((.......)))))))))))).)).))))))......)))))).. (-73.43) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAACAAUUCUAAAAAUCAAGUAGGAGGAAAACCUUUUUCAUUUUCCUCCUAUUUUCAUUUUCCGGGCUCUCACACUACCGCACGUGGGGGUGGGGUUUUGCAUUCGGUUUCUUGGCAAAGGUGUCUCAUAUGGGCAAUAUGACACCCACCUCUGUCUGAAUGUACUCUUCUGCUUCCUCUUUGCACUCUCCUAUUAGUUUCGACAUGCAACCUCUUCAUGCAUACAUCACUCUCCACAAAAAAAAUGUUAUAUAACAUAUAACGCCACGGGGAGCAUU .....................((((((((((((((.........))))))))))))))...((..((((((................(((((((.(((((..(((((((((.(((..((((.(((((..((((((.....))))))....))))).)))).)))..........(((.........)))..............)))).))))))))))...(((....)))...))))))).......(((((....))))).....))).)))..)).... (-71.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 464 216 171 221 172 tfor:TF2158|5end_conserved_hypothetical_protein_2333857..2334087_POSITIVE 404 218 172 229 176 tfor:TF2931|5end_3-deoxy-D-manno-2-octulosonic_acid_(Kdo_transferase)_3134275..3134505_POSITIVE 388 220 171 181 135 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 385 260 228 174 139 tfor:TF0200|5end_2-nitropropane_dioxygenase_225061..225291_POSITIVE 362 220 172 174 97 tfor:TF0340|5end_hypothetical_protein_363893..364123_POSITIVE 356 218 172 62 1 tfor:TF2091|5end_3-oxoacyl-acyl-carrier-protein_synthase_2259690..2259920_POSITIVE 355 135 91 230 182 tfor:TF1025|5end_hypothetical_protein_1082301..1082531_POSITIVE 351 136 93 226 182 tfor:TF2045|5end_aminoacyl-histidine_dipeptidase_2206114..2206344_POSITIVE 351 216 176 63 8 tfor:TF1664|5end_conserved_hypothetical_protein_1778761..1778991_POSITIVE 342 166 125 231 177 tfor:TF1694|5end_conserved_hypothetical_protein_1812493..1812723_POSITIVE 339 237 195 145 101 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 339 237 195 105 61 tfor:TF1917|5end_hypothetical_protein_2069997..2070227_POSITIVE 336 134 91 95 50 tfor:TF0972|5end_conserved_hypothetical_protein_1022798..1023028_POSITIVE 331 131 91 134 93 tfor:TF2977|5end_candidate_b-glycosyltransferase,_Glycosyltransferase_Family_2_protein_3185228..3185458_POSITIVE 331 235 192 86 40 tfor:TF1173|5end_ABC_transporter,_permease_component_1255444..1255674_POSITIVE 331 217 172 43 1 tfor:TF0038|5end_conserved_hypothetical_protein_39907..40137_POSITIVE 329 199 152 208 173 tfor:TF1857|5end_conserved_hypothetical_protein_2014366..2014596_POSITIVE 328 219 171 220 154 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 327 166 124 162 125 tfor:TF0023|5end_possible_response_element_in_two_component_regulation_19446..19676_POSITIVE 325 220 172 174 97 tfor:TF0346|5end_hypothetical_protein_367048..367278_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 216 173 82 26 tfor:TF1762|3end_hypothetical_protein_1899648..1899798_POSITIVE 343 279 231 43 1 tfor:TF2302|3end_conserved_hypothetical_protein;_possible_outer_membrane_protein_2458063..2458213_POSITIVE 339 237 195 133 89 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 336 134 91 67 22 tfor:TF0971|3end_conserved_hypothetical_protein_1022850..1023000_POSITIVE 332 221 184 41 2 tfor:TF2374|3end_UDP-3-O-(R-3-hydoxymyristoyl)-glucosamine-N-acylt_ransferase_2540892..2541042_POSITIVE 331 131 91 134 93 tfor:TF2976|3end_hypothetical_protein_3185308..3185458_POSITIVE 331 217 172 47 5 tfor:TF0037|3end_sialic_acid-specific_9-O-acetylesterase_39991..40141_POSITIVE 324 214 172 69 11 tfor:TF2900|3end_conserved_hypothetical_protein_3090029..3090179_POSITIVE 322 133 99 146 107 tfor:TF2735|3end_hypothetical_protein_2917928..2918078_POSITIVE 316 109 61 123 63 tfor:TF2760|3end_MarR__family_transcriptional_regulator_2945449..2945599_POSITIVE 316 78 37 147 110 tfor:TF0632|3end_hypothetical_protein_668151..668301_POSITIVE 311 90 49 54 15 tfor:TF2353|3end_conserved_hypothetical_protein_2518608..2518758_POSITIVE 310 217 172 57 13 tfor:TF1298|3end_possible_membrane_protein_1381197..1381347_POSITIVE 309 219 173 108 64 tfor:TF3159|3end_conserved_hypothetical_protein;_possible_transcriptional_regulator_3395611..3395761_POSITIVE 308 195 151 64 15 tfor:TF2321|3end_hypothetical_protein_2482657..2482807_POSITIVE 307 218 172 54 8 tfor:TF1818|3end_conserved_hypothetical_protein_1958754..1958904_POSITIVE 306 225 189 76 44 tfor:TF2922|3end_surface_antigen_BspA_3121538..3121688_POSITIVE 306 216 171 56 13 tfor:TF0776|3end_ABC_transporter,_permease_component_826173..826323_POSITIVE 304 225 191 72 36 tfor:TF0823|3end_conserved_hypothetical_protein_881633..881783_POSITIVE 301 200 158 86 50 tfor:TF2366|3end_conserved_hypothetical_protein_2531892..2532042_POSITIVE