Origin IGS: taaaaacccgacttgccgtgtaatctctccgaaaatcggctgaagaaaaagaacgtcatcattccgataaaacagtgcatttttgttcttccttaattccgcaactttattataatccttgatatagtaaagcactaattaaatttcatagtattttatcaatttccttgtatgataaatcgctcatttatttgcagacgccatagcttccccttaccccaccaagcgtttaaggggagggctgcgcatgatattcccacaaaaactgaaggctta .........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 taagccttcagtttttgtgggaatatcatgcgcagccctccccttaaacgcttggtggggtaaggggaagctatggcgtctgcaaataaatgagcgatttatcatacaaggaaattgataaaatactatgaaatttaattagtgctttactatatcaaggattataataaagttgcggaattaaggaagaacaaaaatgcactgttttatcggaatgatgacgttctttttcttcagccgattttcggagagattacacggcaagtcgggttttta Mask Tandem Repeat Region ================================================ taaaaacccgacttgccgtgtaatctctccgaaaatcggctgaagaaaaagaacgtcatcattccgataaaacagtgcatttttgttcttccttaattccgcaactttattataatccttgatatagtaaagcactaattaaatttcatagtattttatcaatttccttgtatgataaatcgctcatttatttgcagacgccatagcttccccttaccccaccaagcgtttaaggggagggctgcgcatgatattcccacaaaaactgaaggctta Find is-nt database================================================ Query_seq: TF1904:TF1905|TF1904:TF1905:two-component system response regulator:conserved hypothetical protein:->->:2059796..2060071 276 taaaaacccgacttgccgtgtaatctctccgaaaatcggctgaagaaaaagaacgtcatcattccgataaaacagtgcatttttgttcttccttaattccgcaactttattataatccttgatatagtaaagcactaattaaatttcatagtattttatcaatttccttgtatgataaatcgctcatttatttgcagacgccatagcttccccttaccccaccaagcgtttaaggggagggctgcgcatgatattcccacaaaaactgaaggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1904:TF1905|TF1904:TF1905:two-component system response regulator:conserved hypothetical protein:->->:2059796..2060071 276 taaaaacccgacttgccgtgtaatctctccgaaaatcggctgaagaaaaagaacgtcatcattccgataaaacagtgcatttttgttcttccttaattccgcaactttattataatccttgatatagtaaagcactaattaaatttcatagtattttatcaatttccttgtatgataaatcgctcatttatttgcagacgccatagcttccccttaccccaccaagcgtttaaggggagggctgcgcatgatattcccacaaaaactgaaggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1904:TF1905|TF1904:TF1905:two-component system response regulator:conserved hypothetical protein:->->:2059796..2060071 276 taaaaacccgacttgccgtgtaatctctccgaaaatcggctgaagaaaaagaacgtcatcattccgataaaacagtgcatttttgttcttccttaattccgcaactttattataatccttgatatagtaaagcactaattaaatttcatagtattttatcaatttccttgtatgataaatcgctcatttatttgcagacgccatagcttccccttaccccaccaagcgtttaaggggagggctgcgcatgatattcccacaaaaactgaaggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaacccgacttgccgtgtaatctctccgaaaatcggctgaagaaaaagaacgtcatcattccgataaaacagtgcatttttgttcttccttaattccgcaactttattataatccttgatatagtaaagcactaattaaatttcatagtattttatcaatttccttgtatgataaatcgctcatttatttgcagacgccatagcttccccttaccccaccaagcgtttaaggggagggctgcgcatgatattcccacaaaaactgaaggctta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 179 End: 274 .................................................................................................................................................................................. M A H L F A D A I A S P Y P T K R L R G G L R M I F P Q K L K A .. Protein_Len: 43 Strand: + Start: 148 End: 276 ................................................................................................................................................... M V F Y Q F P C M I N R S F I C R R H S F P L P H Q A F K G R A A H D I P T K T E G L Protein_Len: 33 Strand: - Start: 162 End: 260 ................................................................................................................................................................. N G Q I I F R E N I Q L R W L K G K G W W A N L P L A A C S I G M ................ Protein_Len: 45 Strand: - Start: 1 End: 135 L F G V Q R T I E G F I P Q L F L V D D N R Y F L A N K N K R L E A V K N Y D K I Y Y L M ............................................................................................................................................. taaaaacccgacttgccgtgtaatctctccgaaaatcggctgaagaaaaagaacgtcatcattccgataaaacagtgcatttttgttcttccttaattccgcaactttattataatccttgatatagtaaagcactaattaaatttcatagtattttatcaatttccttgtatgataaatcgctcatttatttgcagacgccatagcttccccttaccccaccaagcgtttaaggggagggctgcgcatgatattcccacaaaaactgaaggctta 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================================================ taaaaacccgacttgccgtgtaatctctccgaaaatcggctgaagaaaaagaacgtcatcattccgataaaacagtgcatttttgttcttccttaattccgcaactttattataatccttgatatagtaaagcactaattaaatttcatagtattttatcaatttccttgtatgataaatcgctcatttatttgcagacgccatagcttccccttaccccaccaagcgtttaaggggagggctgcgcatgatattcccacaaaaactgaaggctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -3.1 Tail_Score: -5.06414 Start: 51 End: 64 Full_Region: tgcactgttttatcg gaatg atga cgttc tttttcttcagccga ..................................................gaatgatgacgttc.................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TF1904:TF1905|TF1904:TF1905:two-component system response regulator:conserved hypothetical protein:->->:2059796..2060071 276 taaaaacccgacttgccgtgtaatctctccgaaaatcggctgaagaaaaagaacgtcatcattccgataaaacagtgcatttttgttcttccttaattccgcaactttattataatccttgatatagtaaagcactaattaaatttcatagtattttatcaatttccttgtatgataaatcgctcatttatttgcagacgccatagcttccccttaccccaccaagcgtttaaggggagggctgcgcatgatattcccacaaaaactgaaggctta Intra-Species Hit: Count: 2 Min: 1 Max: 276 Len: 276 Subject: tfor_TF1904_TF1905|two-component system response regulator:conserved hypothetical protein|POSITIVE:POSITIVE|[2059796,2060071]|276 HSP 1 e-value: 1.0E-155 bit: 547.0 Len: 276 Query Start:1 Query End:276 Subject Strand: POSITIVE Subject Start: 1 Subject End: 276 taaaaacccgacttgccgtgtaatctctccgaaaatcggctgaagaaaaagaacgtcatcattccgataaaacagtgcatttttgttcttccttaattccgcaactttattataatccttgatatagtaaagcactaattaaatttcatagtattttatcaatttccttgtatgataaatcgctcatttatttgcagacgccatagcttccccttaccccaccaagcgtttaaggggagggctgcgcatgatattcccacaaaaactgaaggctta taaaaacccgacttgccgtgtaatctctccgaaaatcggctgaagaaaaagaacgtcatcattccgataaaacagtgcatttttgttcttccttaattccgcaactttattataatccttgatatagtaaagcactaattaaatttcatagtattttatcaatttccttgtatgataaatcgctcatttatttgcagacgccatagcttccccttaccccaccaagcgtttaaggggagggctgcgcatgatattcccacaaaaactgaaggctta Subject: tfor_TF1982_TF1983|1,4-alpha-glucan branching enzyme:conserved hypothetical protein|POSITIVE:POSITIVE|[2134191,2134823]|633 HSP 1 e-value: 2.0E-99 bit: 363.0 Len: 187 Query Start:90 Query End:276 Subject Strand: POSITIVE Subject Start: 447 Subject End: 633 .........................................................................................tccttaattccgcaactttattataatccttgatatagtaaagcactaattaaatttcatagtattttatcaatttccttgtatgataaatcgctcatttatttgcagacgccatagcttccccttaccccaccaagcgtttaaggggagggctgcgcatgatattcccacaaaaactgaaggctta .........................................................................................tccttaattccgcaactttattataatccttgatatagtaaagcactaattaaatttcatagtattttatcaatttccttgtatgataaatcgctcatttatttgcagacgccatagcttccccttaccccaccaagcgtttagggggagggctgcgcatgatattcccacaaaaactgaaggctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAACCCGACUUGCCGUGUAAUCUCUCCGAAAAUCGGCUGAAGAAAAAGAACGUCAUCAUUCCGAUAAAACAGUGCAUUUUUGUUCUUCCUUAAUUCCGCAACUUUAUUAUAAUCCUUGAUAUAGUAAAGCACUAAUUAAAUUUCAUAGUAUUUUAUCAAUUUCCUUGUAUGAUAAAUCGCUCAUUUAUUUGCAGACGCCAUAGCUUCCCCUUACCCCACCAAGCGUUUAAGGGGAGGGCUGCGCAUGAUAUUCCCACAAAAACUGAAGGCUUA ..............(((.................(((((.(((.((.........)).)))..)))))....((((....((((((..............((((((((((((((........)))))))))).................(((..(((((((((......)).)))))))..))).......))))....((..(((((((((((((..((.....).)..)))))))).))))).))...........))))))))))..)))... (-51.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCCUUCAGUUUUUGUGGGAAUAUCAUGCGCAGCCCUCCCCUUAAACGCUUGGUGGGGUAAGGGGAAGCUAUGGCGUCUGCAAAUAAAUGAGCGAUUUAUCAUACAAGGAAAUUGAUAAAAUACUAUGAAAUUUAAUUAGUGCUUUACUAUAUCAAGGAUUAUAAUAAAGUUGCGGAAUUAAGGAAGAACAAAAAUGCACUGUUUUAUCGGAAUGAUGACGUUCUUUUUCUUCAGCCGAUUUUCGGAGAGAUUACACGGCAAGUCGGGUUUUUA ...(((...(((((((.((..(((.........(((..((((((((..(((...)))...)))))))).)))..(((.((((((..(((((.((...(((((((...........)))))))...)).....)))))......((((((.((((........)))).))))))))))))......((((((.((.((((((..((((.....))))..)).)))).)).)))))).))).)))..)).)))))))....))).............. (-64.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 412 246 206 56 6 tfor:TF2746|5end_hypothetical_protein_2927996..2928226_POSITIVE 374 258 211 225 182 tfor:TF2931|5end_3-deoxy-D-manno-2-octulosonic_acid_(Kdo_transferase)_3134275..3134505_POSITIVE 361 230 194 58 24 tfor:TF2724|5end_anti-sigma_factor_2898193..2898423_POSITIVE 360 254 211 75 30 tfor:TF1606|5end_outer_membrane_protein_1722352..1722582_POSITIVE 347 247 201 151 87 tfor:TF1763|5end_K+-dependent_Na+/Ca+_exchanger_related-protein_1900406..1900636_POSITIVE 345 250 205 160 105 tfor:TF2171|5end_hypothetical_protein_2345485..2345715_POSITIVE 345 250 205 160 105 tfor:TF2166|5end_hypothetical_protein_2342115..2342345_POSITIVE 343 210 162 219 175 tfor:TF2772|5end_tRNA_pseudouridine_synthase_B_2957383..2957613_POSITIVE 340 43 7 89 38 tfor:TF0994|5end_maltose_O-acetyltransferase_1049127..1049357_POSITIVE 334 248 201 172 120 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 333 240 195 141 90 tfor:TF0340|5end_hypothetical_protein_363893..364123_POSITIVE 331 42 8 71 33 tfor:TF0216|5end_50S_ribosomal_protein_L20_242476..242706_POSITIVE 330 246 207 179 134 tfor:TF1363|5end_conserved_hypothetical_protein_1444083..1444313_POSITIVE 330 246 205 149 105 tfor:TF0346|5end_hypothetical_protein_367048..367278_POSITIVE 329 246 202 169 118 tfor:TF1983|5end_conserved_hypothetical_protein_2134684..2134914_POSITIVE 329 240 194 230 176 tfor:TF1979|5end_conserved_hypothetical_protein_2127957..2128187_POSITIVE 329 239 197 216 174 tfor:TF0643|5end_probable_tRNA_methyltransferase_684195..684425_POSITIVE 328 251 211 57 5 tfor:TF1259|5end_hypothetical_protein_1338549..1338779_POSITIVE 323 35 8 57 31 tfor:TF3108|5end_glutamine-hydrolyzing_carbamoyl-phosphate_synthase,_large_subunit_3338732..3338962_POSITIVE 322 246 201 39 1 tfor:TF2640|5end_hypothetical_protein_2809106..2809336_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 254 211 57 12 tfor:TF1605|3end_outer_membrane_protein,_TonB_dependent_receptor_1722414..1722564_POSITIVE 358 246 205 85 40 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 350 244 201 64 23 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 344 245 202 140 78 tfor:TF2607|3end_conserved_hypothetical_protein_2784645..2784795_POSITIVE 341 245 205 51 16 tfor:TF1592|3end_hypothetical_protein_1708557..1708707_POSITIVE 334 244 201 105 68 tfor:TF0370|3end_hypothetical_protein_386317..386467_POSITIVE 330 246 207 75 30 tfor:TF1362|3end_hypothetical_protein_1444059..1444209_POSITIVE 320 258 215 70 36 tfor:TF0419|3end_conserved_hypothetical_protein_435794..435944_POSITIVE 320 250 201 108 54 tfor:TF0351|3end_hypothetical_protein_371226..371376_POSITIVE 318 228 192 46 8 tfor:TF2275|3end_conserved_hypothetical_protein_2438300..2438450_POSITIVE 317 248 205 30 1 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 314 57 24 51 5 tfor:TF2759|3end_xylose_repressor,_ROK_family_2944853..2945003_POSITIVE 313 246 205 45 1 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 312 58 15 146 88 tfor:TF0940|3end_transposase_982040..982190_POSITIVE 307 259 213 54 8 tfor:TF2264|3end_transfer_region-related_protein,_TraO_2433542..2433692_POSITIVE 305 228 181 151 93 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 305 55 13 97 52 tfor:TF1434|3end_transketolase_1519595..1519745_POSITIVE 302 255 211 63 12 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 301 240 191 150 94 tfor:TF1168|3end_hypothetical_protein_1249092..1249242_POSITIVE 297 249 218 130 96 tfor:TF2025|3end_hypothetical_protein_2182180..2182330_POSITIVE