Origin IGS: taataaaatataaagggactgttgatatgctaaatattaaataaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaaacagagaaactcgctttgctcaaacacctctgattttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttatttttattaatataagttagggattttaacagtccccattatagttttagttatatagaggagtagaat .........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 attctactcctctatataactaaaactataatggggactgttaaaatccctaacttatattaataaaaataagtgagttacattccagattttaggataaaaattaaatagaatgagccgagcaaaatcagaggtgtttgagcaaagcgagtttctctgttttgcagcgaattcttaatttttatccgtttaaaaatctagctagtaacgaacttttttatttaatatttagcatatcaacagtccctttatattttatta Mask Tandem Repeat Region ================================================ taataaaatataaagggactgttgatatgctaaatattaaataaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaaacagagaaactcgctttgctcaaacacctctgattttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttatttttattaatataagttagggattttaacagtccccattatagttttagttatatagaggagtagaat Find is-nt database================================================ Query_seq: FN0116:FN0117|FN0116:FN0117:Chaperone protein dnaK:O6-methylguanine-DNA methyltransferase:->->:750217..750477 261 taataaaatataaagggactgttgatatgctaaatattaaataaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaaacagagaaactcgctttgctcaaacacctctgattttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttatttttattaatataagttagggattttaacagtccccattatagttttagttatatagaggagtagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0116:FN0117|FN0116:FN0117:Chaperone protein dnaK:O6-methylguanine-DNA methyltransferase:->->:750217..750477 261 taataaaatataaagggactgttgatatgctaaatattaaataaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaaacagagaaactcgctttgctcaaacacctctgattttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttatttttattaatataagttagggattttaacagtccccattatagttttagttatatagaggagtagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0116:FN0117|FN0116:FN0117:Chaperone protein dnaK:O6-methylguanine-DNA methyltransferase:->->:750217..750477 261 taataaaatataaagggactgttgatatgctaaatattaaataaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaaacagagaaactcgctttgctcaaacacctctgattttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttatttttattaatataagttagggattttaacagtccccattatagttttagttatatagaggagtagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taataaaatataaagggactgttgatatgctaaatattaaataaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaaacagagaaactcgctttgctcaaacacctctgattttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttatttttattaatataagttagggattttaacagtccccattatagttttagttatatagaggagtagaat Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 65 End: 181 ................................................................ M F K R I K I K N S L Q N R E T R F A Q T P L I L L G S F Y L I F I L K S G M ................................................................................ Protein_Len: 41 Strand: - Start: 2 End: 124 . I F Y L P V T S I S F I L Y F L E N S A L N K F P Y F N L I R Q L V S F S A K S M ......................................................................................................................................... taataaaatataaagggactgttgatatgctaaatattaaataaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaaacagagaaactcgctttgctcaaacacctctgattttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttatttttattaatataagttagggattttaacagtccccattatagttttagttatatagaggagtagaat 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================================================ taataaaatataaagggactgttgatatgctaaatattaaataaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaaacagagaaactcgctttgctcaaacacctctgattttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttatttttattaatataagttagggattttaacagtccccattatagttttagttatatagaggagtagaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0116:FN0117|FN0116:FN0117:Chaperone protein dnaK:O6-methylguanine-DNA methyltransferase:->->:750217..750477 261 taataaaatataaagggactgttgatatgctaaatattaaataaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaaacagagaaactcgctttgctcaaacacctctgattttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttatttttattaatataagttagggattttaacagtccccattatagttttagttatatagaggagtagaat Intra-Species Hit: Count: 9 Min: 1 Max: 261 Len: 261 Subject: NC_003454_FN0116_FN0117|Chaperone protein dnaK:O6-methylguanine-DNA methyltransferase|POSITIVE:POSITIVE|[750217,750477]|261 HSP 1 e-value: 1.0E-146 bit: 517.0 Len: 261 Query Start:1 Query End:261 Subject Strand: POSITIVE Subject Start: 1 Subject End: 261 taataaaatataaagggactgttgatatgctaaatattaaataaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaaacagagaaactcgctttgctcaaacacctctgattttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttatttttattaatataagttagggattttaacagtccccattatagttttagttatatagaggagtagaat taataaaatataaagggactgttgatatgctaaatattaaataaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaaacagagaaactcgctttgctcaaacacctctgattttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttatttttattaatataagttagggattttaacagtccccattatagttttagttatatagaggagtagaat Subject: NC_003454_FN0483_FN0484|Uracil phosphoribosyltransferase:Lipase|POSITIVE:POSITIVE|[1129 362,1129609]|248 HSP 1 e-value: 5.0E-26 bit: 119.0 Len: 147 Query Start:54 Query End:200 Subject Strand: POSITIVE Subject Start: 19 Subject End: 165 .....................................................ttactagctagatttttaaacggataaaaattaagaattcgctgcaaaacagagaaactcgctttgctcaaacacctctgat-tttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttatttttatt............................................................. .....................................................ttactagccagatttcctaacggataaaaattaagaattcgctgcaaattcgctaaactcacttcgttcaaacacag-tgagatttgctcggctcattctatttaatttttatcctaaaatttggaatgtaattcgcttatttttatt............................................................. Subject: NC_003454_FN0391_FN0392|Hydrolase (HAD superfamily):Oxygen-independent coproporphyrinogen III oxidase|POSITIVE:POSITIVE|[1029557,1029763]|207 HSP 1 e-value: 8.0E-25 bit: 115.0 Len: 62 Query Start:136 Query End:197 Subject Strand: POSITIVE Subject Start: 100 Subject End: 161 .......................................................................................................................................tttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttattttt................................................................ .......................................................................................................................................tttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactctcttattttt................................................................ HSP 2 e-value: 2.0E-10 bit: 67.9 Len: 54 Query Start:48 Query End:101 Subject Strand: POSITIVE Subject Start: 5 Subject End: 58 ...............................................agttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaa................................................................................................................................................................ ...............................................agttcgttactagccagatttcttaacgaataaaaattaagaatttgctgcaaa................................................................................................................................................................ Subject: NC_003454_FN0084_FN0085|Acetaldehyde dehydrogenase [acetylating]:Ethanolamine utilization cobalamin adenosyltransferase|POSITIVE:POSITIVE|[723155, 723409]|255 HSP 1 e-value: 3.0E-24 bit: 113.0 Len: 57 Query Start:141 Query End:197 Subject Strand: POSITIVE Subject Start: 155 Subject End: 211 ............................................................................................................................................tcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttattttt................................................................ ............................................................................................................................................tcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttattttt................................................................ HSP 2 e-value: 4.0E-11 bit: 69.9 Len: 55 Query Start:43 Query End:97 Subject Strand: POSITIVE Subject Start: 7 Subject End: 61 ..........................................aaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctg.................................................................................................................................................................... ..........................................aaaatagttcgttactagccaaatttcttaacggataaaaattaagaattcgctg.................................................................................................................................................................... Subject: NC_003454_FN1835_FN1836|hypothetical protein:Tetratricopeptide repeat family protein|NEGATIVE:NEGATIVE|[323771,323993]|223 HSP 1 e-value: 5.0E-23 bit: 109.0 Len: 63 Query Start:136 Query End:198 Subject Strand: NEGATIVE Subject Start: 51 Subject End: 113 .......................................................................................................................................tttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttattttta............................................................... .......................................................................................................................................tttgctcggctcattctatttaatttttatcctaaaatctggaatataactcacttgttttta............................................................... HSP 2 e-value: 3.0E-18 bit: 93.7 Len: 59 Query Start:43 Query End:101 Subject Strand: NEGATIVE Subject Start: 156 Subject End: 214 ..........................................aaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaa................................................................................................................................................................ ..........................................aaaaaagttcgttactagccagatttcttaacggataaaaattaagaattcgctgcaaa................................................................................................................................................................ Subject: NC_003454_FN2095_FN2096|General secretion pathway protein E:hypothetical protein|NEGATIVE:NEGATIVE|[606171,606356]|186 HSP 1 e-value: 7.0E-22 bit: 105.0 Len: 143 Query Start:56 Query End:198 Subject Strand: NEGATIVE Subject Start: 32 Subject End: 174 .......................................................actagctagatttttaaacggataaaaattaagaattcgctgcaaa-acagagaaactcgctttgctcaaacac-ctctgattttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttattttta............................................................... .......................................................actagccagatttcttaacagataaaaattaagaattcgctgcaaattcag-taaactcacttcgttcagacacactgagattt-gctcggctcattctatttaatttttattctagaatctggaatgtaattcacttattttta............................................................... Subject: NC_003454_FN1818_FN1819|Hemolysin activator protein precursor:Export ABC transporter|NEGATIVE:POSITIVE|[307046,307658]|613 HSP 1 e-value: 5.0E-20 bit: 99.6 Len: 62 Query Start:136 Query End:197 Subject Strand: POSITIVE Subject Start: 501 Subject End: 562 .......................................................................................................................................tttgctcggctcattctatttaatttttatcctaaaatctggaatgtaactcacttattttt................................................................ .......................................................................................................................................tttgctcggttcattctatttaatttttatcttaaaatctggaatgtaactcccttattttt................................................................ HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 59 Query Start:43 Query End:101 Subject Strand: POSITIVE Subject Start: 401 Subject End: 459 ..........................................aaaaaagttcgttactagctagatttttaaacggataaaaattaagaattcgctgcaaa................................................................................................................................................................ ..........................................aaaatagttcattactagccagatttcttaatagctaaaaattaagaattcgctgcaaa................................................................................................................................................................ Subject: NC_003454_FN1651_FN1652|Oligopeptide transport system permease protein oppB:Oligopeptide-binding protein oppA|NEGATIVE:NEGATIVE|[145890,146130]|241 HSP 1 e-value: 4.0E-17 bit: 89.7 Len: 136 Query Start:62 Query End:197 Subject Strand: POSITIVE Subject Start: 55 Subject End: 191 .............................................................tagatttttaaacggataaaaattaagaattcgctgcaaaacagagaaactcgctttgctcaaacacctctgattttgctcggctcattctatttaatttttatcctaaaatctggaat-gtaactcacttattttt................................................................ .............................................................tagatttcttaacggataaaaattaagaattcgctgtaaattctaccaactcgctatgctcagacacgtcgagatttactcggctcattctatttaattttcatcctaaaatctacattcgtaactcacttattttt................................................................ Subject: NC_003454_FN1486_FN1487|Integral membrane protein with CBS domains:hypothetical protein|NEGATIVE:NEGATIVE|[2169390,2169648]|259 HSP 1 e-value: 3.0E-12 bit: 73.8 Len: 49 Query Start:136 Query End:184 Subject Strand: NEGATIVE Subject Start: 64 Subject End: 112 .......................................................................................................................................tttgctcggctcattctatttaatttttatcctaaaatctggaatgtaa............................................................................. .......................................................................................................................................tttgctcggctcattctatttaatttttgttctaaaatctagaatgtaa............................................................................. HSP 2 e-value: 4.0E-8 bit: 60.0 Len: 42 Query Start:54 Query End:95 Subject Strand: NEGATIVE Subject Start: 200 Subject End: 241 .....................................................ttactagctagatttttaaacggataaaaattaagaattcgc...................................................................................................................................................................... .....................................................ttactagccagattttttaacgaataaaaattaagaattcgc...................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAAAAUAUAAAGGGACUGUUGAUAUGCUAAAUAUUAAAUAAAAAAGUUCGUUACUAGCUAGAUUUUUAAACGGAUAAAAAUUAAGAAUUCGCUGCAAAACAGAGAAACUCGCUUUGCUCAAACACCUCUGAUUUUGCUCGGCUCAUUCUAUUUAAUUUUUAUCCUAAAAUCUGGAAUGUAACUCACUUAUUUUUAUUAAUAUAAGUUAGGGAUUUUAACAGUCCCCAUUAUAGUUUUAGUUAUAUAGAGGAGUAGAAU ...((((((((((.(((((((((((..(.(((((((((((.(((((((((..(((((...(((((((((.....(((((((((((((((((..((((((((((((((.....................))))).))))))..)))..)))))...)))))))))))).)))))))))...)))))..)))..)))))))))))))...)))).)...)))))))))))..)))).)))))).................... (-70.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUACUCCUCUAUAUAACUAAAACUAUAAUGGGGACUGUUAAAAUCCCUAACUUAUAUUAAUAAAAAUAAGUGAGUUACAUUCCAGAUUUUAGGAUAAAAAUUAAAUAGAAUGAGCCGAGCAAAAUCAGAGGUGUUUGAGCAAAGCGAGUUUCUCUGUUUUGCAGCGAAUUCUUAAUUUUUAUCCGUUUAAAAAUCUAGCUAGUAACGAACUUUUUUAUUUAAUAUUUAGCAUAUCAACAGUCCCUUUAUAUUUUAUUA ....................(((((.(((((.((((((((((.......((((...(((((((((((((..(((..(((((...(.(((((((.((((((((((((...(((((..((...((((((.((((((..((((.......))))..)))))))))))).))..))))))))))))))))).....))))))).)...)))))..))))))))).)))))))))))......))))))))))))))))))))... (-69.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 748 190 141 132 83 NC_003454:FN1460|5end_Hypothetical_cytosolic_protein_2141429..2141659_POSITIVE 607 100 51 178 129 NC_003454:FN0714|5end_NADH_oxidase_1372062..1372292_POSITIVE 544 155 111 131 87 NC_003454:FN1507|5end_riboflavin_synthase_subunit_alpha_12073..12303_POSITIVE 486 97 53 181 137 NC_003454:FN1651|5end_Oligopeptide_transport_system_permease_protein_oppB_145799..146029_NEGATIVE 428 100 51 223 174 NC_003454:FN0798|5end_Fructose-1,6-bisphosphatase_1455835..1456065_POSITIVE 387 97 51 67 21 NC_003454:FN1604|5end_hypothetical_protein_113822..114052_NEGATIVE 387 97 51 228 182 NC_003454:FN1603|5end_2',3'-cyclic_nucleotide_3'-phosphodiesterase_113661..113891_NEGATIVE 374 77 33 141 90 NC_003454:FN1440|5end_1-phosphofructokinase_2107238..2107468_POSITIVE 366 190 147 222 182 NC_003454:FN1615|5end_Integral_membrane_protein_125125..125355_POSITIVE 360 197 157 193 153 NC_003454:FN0367|5end_Integral_membrane_protein_996901..997131_NEGATIVE 333 200 174 159 133 NC_003454:FN1898|5end_Sugar_transport_ATP-binding_protein_386569..386799_NEGATIVE 326 130 83 68 26 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 291 90 43 161 113 NC_003454:FN0081|5end_Ethanolamine_utilization_protein_eutL_720035..720265_POSITIVE 273 226 181 224 183 NC_003454:FN0551|5end_Bacterial_regulatory_proteins,_crp_family_1203276..1203506_POSITIVE 244 100 53 198 150 NC_003454:FN0392|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1029624..1029854_POSITIVE 236 97 53 191 148 NC_003454:FN0085|5end_Ethanolamine_utilization_cobalamin_adenosyltransferase_723270..723500_POSITIVE 236 148 102 129 90 NC_003454:FN1586|5end_O-succinylbenzoate-CoA_synthase_98542..98772_NEGATIVE 228 239 191 211 156 NC_003454:FN0775|5end_putative_aminopeptidase_2_1430568..1430798_POSITIVE 225 196 158 94 44 NC_003454:FN0424|5end_Dihydroorotate_dehydrogenase_1067119..1067349_POSITIVE 220 139 96 177 134 NC_003454:FN0330|5end_SSU_ribosomal_protein_S9P_964583..964813_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 661 190 143 69 22 NC_003454:FN0713|3end_Chromate_transport_protein_1371943..1372093_POSITIVE 478 170 121 53 4 NC_003454:FN1506|3end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_12060..12210_POSITIVE 411 190 142 50 1 NC_003454:FN0796|3end_pyruvate_phosphate_dikinase_1455643..1455793_POSITIVE 374 77 33 68 17 NC_003454:FN1439|3end_Transcriptional_regulator,_DeoR_family_2107245..2107395_POSITIVE 360 197 157 56 16 NC_003454:FN0368|3end_adenylosuccinate_lyase_997038..997188_NEGATIVE 334 197 159 40 1 NC_003454:FN1652|3end_Oligopeptide-binding_protein_oppA_146041..146191_NEGATIVE 291 90 43 54 6 NC_003454:FN0080|3end_ethanolamine_ammonia-lyase_small_subunit_720008..720158_POSITIVE 276 190 142 76 27 NC_003454:FN1836|3end_Tetratricopeptide_repeat_family_protein_323904..324054_NEGATIVE 240 177 136 65 25 NC_003454:FN0483|3end_Uracil_phosphoribosyltransferase_1129301..1129451_POSITIVE 235 177 131 73 28 NC_003454:FN2096|3end_hypothetical_protein_606267..606417_NEGATIVE 228 239 191 81 26 NC_003454:FN0774|3end_Hypothetical_cytosolic_protein_1430518..1430668_POSITIVE 228 165 126 144 98 NC_003454:FN0488|3end_NAD-specific_glutamate_dehydrogenase_1134456..1134606_POSITIVE 225 196 158 82 32 NC_003454:FN0423|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit_1067187..1067337_POSITIVE 217 226 181 65 21 NC_003454:FN1825|3end_hypothetical_protein_314511..314661_POSITIVE 216 228 181 76 34 NC_003454:FN0116|3end_Chaperone_protein_dnaK_750156..750306_POSITIVE 212 146 116 49 17 NC_003454:FN1658|3end_prolyl-tRNA_synthetase_153188..153338_NEGATIVE 211 142 109 102 73 NC_003454:FN0065|3end_Transcription_accessory_protein_(S1_RNA_binding_domain)_702184..702334_POSITIVE 211 226 185 72 36 NC_003454:FN1992|3end_Ribose-phosphate_pyrophosphokinase_496995..497145_POSITIVE 206 150 103 102 46 NC_003454:FN1782|3end_Phosphocarrier_protein_HPr_264221..264371_NEGATIVE 202 156 112 140 91 NC_003454:FN1334|3end_N-acetylmuramoyl-L-alanine_amidase_1987603..1987753_NEGATIVE