Origin IGS: attttttaatcctcattcataaattaggtacaaagatatgaatactaaaatgttatttattgacgaaaaagtcatcgaaaatgttcattttggatatttccagtagctttctattccgaacagagcctttaagcaggctgcgtattggcgatgggcgtttttttagtactgaactttaatcaaggaatgaaagttgaattttgtacatccgttgatacgaaaccattcagctcgcctattgccagcacaatatta .........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 taatattgtgctggcaataggcgagctgaatggtttcgtatcaacggatgtacaaaattcaactttcattccttgattaaagttcagtactaaaaaaacgcccatcgccaatacgcagcctgcttaaaggctctgttcggaatagaaagctactggaaatatccaaaatgaacattttcgatgactttttcgtcaataaataacattttagtattcatatctttgtacctaatttatgaatgaggattaaaaaat Mask Tandem Repeat Region ================================================ attttttaatcctcattcataaattaggtacaaagatatgaatactaaaatgttatttattgacgaaaaagtcatcgaaaatgttcattttggatatttccagtagctttctattccgaacagagcctttaagcaggctgcgtattggcgatgggcgtttttttagtactgaactttaatcaaggaatgaaagttgaattttgtacatccgttgatacgaaaccattcagctcgcctattgccagcacaatatta Find is-nt database================================================ Query_seq: TF1677:TF1678|TF1677:TF1678:ATP synthase, beta subunit:periplasmic protease:->->:1790982..1791236 255 attttttaatcctcattcataaattaggtacaaagatatgaatactaaaatgttatttattgacgaaaaagtcatcgaaaatgttcattttggatatttccagtagctttctattccgaacagagcctttaagcaggctgcgtattggcgatgggcgtttttttagtactgaactttaatcaaggaatgaaagttgaattttgtacatccgttgatacgaaaccattcagctcgcctattgccagcacaatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1677:TF1678|TF1677:TF1678:ATP synthase, beta subunit:periplasmic protease:->->:1790982..1791236 255 attttttaatcctcattcataaattaggtacaaagatatgaatactaaaatgttatttattgacgaaaaagtcatcgaaaatgttcattttggatatttccagtagctttctattccgaacagagcctttaagcaggctgcgtattggcgatgggcgtttttttagtactgaactttaatcaaggaatgaaagttgaattttgtacatccgttgatacgaaaccattcagctcgcctattgccagcacaatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1677:TF1678|TF1677:TF1678:ATP synthase, beta subunit:periplasmic protease:->->:1790982..1791236 255 attttttaatcctcattcataaattaggtacaaagatatgaatactaaaatgttatttattgacgaaaaagtcatcgaaaatgttcattttggatatttccagtagctttctattccgaacagagcctttaagcaggctgcgtattggcgatgggcgtttttttagtactgaactttaatcaaggaatgaaagttgaattttgtacatccgttgatacgaaaccattcagctcgcctattgccagcacaatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttttaatcctcattcataaattaggtacaaagatatgaatactaaaatgttatttattgacgaaaaagtcatcgaaaatgttcattttggatatttccagtagctttctattccgaacagagcctttaagcaggctgcgtattggcgatgggcgtttttttagtactgaactttaatcaaggaatgaaagttgaattttgtacatccgttgatacgaaaccattcagctcgcctattgccagcacaatatta Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 42 End: 176 ......................................... M L K C Y L L T K K S S K M F I L D I S S S F L F R T E P L S R L R I G D G R F F S T E L ............................................................................... Protein_Len: 37 Strand: + Start: 145 End: 255 ................................................................................................................................................ M A M G V F L V L N F N Q G M K V E F C T S V D T K P F S S P I A S T I L Protein_Len: 30 Strand: - Start: 56 End: 145 ....................................................... K N V F F D D F I N M K S I E L L K R N R V S G K L L S R M .............................................................................................................. attttttaatcctcattcataaattaggtacaaagatatgaatactaaaatgttatttattgacgaaaaagtcatcgaaaatgttcattttggatatttccagtagctttctattccgaacagagcctttaagcaggctgcgtattggcgatgggcgtttttttagtactgaactttaatcaaggaatgaaagttgaattttgtacatccgttgatacgaaaccattcagctcgcctattgccagcacaatatta 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================================================ attttttaatcctcattcataaattaggtacaaagatatgaatactaaaatgttatttattgacgaaaaagtcatcgaaaatgttcattttggatatttccagtagctttctattccgaacagagcctttaagcaggctgcgtattggcgatgggcgtttttttagtactgaactttaatcaaggaatgaaagttgaattttgtacatccgttgatacgaaaccattcagctcgcctattgccagcacaatatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1677:TF1678|TF1677:TF1678:ATP synthase, beta subunit:periplasmic protease:->->:1790982..1791236 255 attttttaatcctcattcataaattaggtacaaagatatgaatactaaaatgttatttattgacgaaaaagtcatcgaaaatgttcattttggatatttccagtagctttctattccgaacagagcctttaagcaggctgcgtattggcgatgggcgtttttttagtactgaactttaatcaaggaatgaaagttgaattttgtacatccgttgatacgaaaccattcagctcgcctattgccagcacaatatta Intra-Species Hit: Count: 1 Min: 1 Max: 255 Len: 255 Subject: tfor_TF1677_TF1678|ATP synthase, beta subunit:periplasmic protease|POSITIVE:POSITIVE|[1790982,1791236]|255 HSP 1 e-value: 1.0E-130 bit: 464.0 Len: 255 Query Start:1 Query End:255 Subject Strand: POSITIVE Subject Start: 1 Subject End: 255 attttttaatcctcattcataaattaggtacaaagatatgaatactaaaatgttatttattgacgaaaaagtcatcgaaaatgttcattttggatatttccagtagctttctattccgaacagagcctttaagcaggctgcgtattggcgatgggcgnnnnnnnagtactgaactttaatcaaggaatgaaagttgaattttgtacatccgttgatacgaaaccattcagctcgcctattgccagcacaatatta attttttaatcctcattcataaattaggtacaaagatatgaatactaaaatgttatttattgacgaaaaagtcatcgaaaatgttcattttggatatttccagtagctttctattccgaacagagcctttaagcaggctgcgtattggcgatgggcgtttttttagtactgaactttaatcaaggaatgaaagttgaattttgtacatccgttgatacgaaaccattcagctcgcctattgccagcacaatatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUUAAUCCUCAUUCAUAAAUUAGGUACAAAGAUAUGAAUACUAAAAUGUUAUUUAUUGACGAAAAAGUCAUCGAAAAUGUUCAUUUUGGAUAUUUCCAGUAGCUUUCUAUUCCGAACAGAGCCUUUAAGCAGGCUGCGUAUUGGCGAUGGGCGUUUUUUUAGUACUGAACUUUAAUCAAGGAAUGAAAGUUGAAUUUUGUACAUCCGUUGAUACGAAACCAUUCAGCUCGCCUAUUGCCAGCACAAUAUUA ..........................((...((((.((((((((((((((((.(((((..((((......))))....)))))..)))))))).)))))...))).)))).....))......(((((......)))))..((.(((((((((((((................((((....))))......((((((((((((((((.....)).))))))...))))))))))))))))))))).))....... (-57.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUUGUGCUGGCAAUAGGCGAGCUGAAUGGUUUCGUAUCAACGGAUGUACAAAAUUCAACUUUCAUUCCUUGAUUAAAGUUCAGUACUAAAAAAACGCCCAUCGCCAAUACGCAGCCUGCUUAAAGGCUCUGUUCGGAAUAGAAAGCUACUGGAAAUAUCCAAAAUGAACAUUUUCGAUGACUUUUUCGUCAAUAAAUAACAUUUUAGUAUUCAUAUCUUUGUACCUAAUUUAUGAAUGAGGAUUAAAAAAU .......(((.((((.((.((((.(((((((..((....(((((.(((((................))))).))))).)).)))))))..........)))).)).)))).)))..(((((......))))).((((((...(((....))).((((....))))...)))))).....(((((.....)))))...........(((((((.(((((.((................))))))).)))))))... (-50.58) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 157 115 205 163 tfor:TF0886|5end_conjugative_transposon_protein_fragment_937914..938144_POSITIVE 417 157 115 45 3 tfor:TF0885|5end_conjugative_transposon_protein_fragment_937754..937984_POSITIVE 397 158 116 146 99 tfor:TF1451|5end_conserved_hypothetical_protein_1535876..1536106_POSITIVE 383 160 113 147 98 tfor:TF2914|5end_hypothetical_protein_3109345..3109575_POSITIVE 382 157 114 162 117 tfor:TF2231|5end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_2400307..2400537_POSITIVE 372 158 121 213 172 tfor:TF0911|5end_transposase_953720..953950_POSITIVE 369 138 91 141 80 tfor:TF0754|5end_GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-redu_ctase_(GDP-L-fucose_synthetase)_801631..801861_POSITIVE 356 160 112 57 4 tfor:TF0996|5end_ribonuclease_D_1050882..1051112_POSITIVE 354 249 203 56 12 tfor:TF2349|5end_conserved_hypothetical_protein_2513192..2513422_POSITIVE 353 248 202 193 145 tfor:TF2770|5end_conserved_hypothetical_protein_2956308..2956538_POSITIVE 352 168 125 45 2 tfor:TF0553|5end_Bacteroides_aerotolerance_protein,_BatD_584462..584692_POSITIVE 342 160 117 65 13 tfor:TF2080|5end_carboxyl-terminal_protease_2246880..2247110_POSITIVE 342 156 115 174 135 tfor:TF1070|5end_hydrolase_1139704..1139934_POSITIVE 339 160 116 219 167 tfor:TF2520|5end_conserved_hypothetical_protein_2698917..2699147_POSITIVE 339 159 111 188 148 tfor:TF2318|5end_conserved_hypothetical_protein_2475603..2475833_POSITIVE 338 157 136 225 207 tfor:TF1955|5end_amino_acid_exporter,_possible_threonine_efflux_protein_2106952..2107182_POSITIVE 337 150 106 134 100 tfor:TF2912|5end_hypothetical_protein_3106508..3106738_POSITIVE 336 157 115 55 15 tfor:TF3134|5end_HD_superfamily_hydrolase_3367990..3368220_POSITIVE 333 247 210 56 18 tfor:TF1071|5end_hypothetical_protein_1140969..1141199_POSITIVE 326 149 109 181 139 tfor:TF2908|5end_transcriptional_regulator,_AraC_family_3103696..3103926_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 157 115 61 19 tfor:TF0884|3end_hypothetical_protein_937850..938000_POSITIVE 369 138 91 143 82 tfor:TF0752|3end_nucleotide-binding_protein;_MAF-like_protein_801713..801863_POSITIVE 356 160 112 57 4 tfor:TF0995|3end_conserved_hypothetical_protein_1050962..1051112_POSITIVE 338 157 136 133 115 tfor:TF1954|3end_long-chain-fatty-acid--CoA_ligase_2106940..2107090_POSITIVE 326 149 109 86 44 tfor:TF2907|3end_CDP-diacylglycerol-serine-O-phosphatidyltransfera_se_3103681..3103831_POSITIVE 324 160 117 133 87 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 321 157 117 150 106 tfor:TF2035|3end_conserved_hypothetical_protein_2195851..2196001_POSITIVE 319 156 116 93 34 tfor:TF2746|3end_hypothetical_protein_2928246..2928396_POSITIVE 318 250 201 150 88 tfor:TF0174|3end_hypothetical_protein_185600..185750_POSITIVE 316 150 102 141 100 tfor:TF0061|3end_hypothetical_protein_65006..65156_POSITIVE 313 159 111 56 8 tfor:TF1474|3end_6-phosphogluconolactonase_1568123..1568273_POSITIVE 313 129 87 51 3 tfor:TF0337|3end_hypothetical_protein_360711..360861_POSITIVE 312 156 122 44 7 tfor:TF0417|3end_hypothetical_protein_434856..435006_POSITIVE 310 159 116 92 42 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 310 159 114 140 75 tfor:TF0637|3end_TPR-repeat-containing_protein_675410..675560_POSITIVE 309 155 125 150 116 tfor:TF1328|3end_possible_cytidylyltransferase_1408650..1408800_POSITIVE 306 160 116 131 83 tfor:TF1154|3end_RNA_pseudouridylate_synthetase_1236822..1236972_POSITIVE 305 173 135 54 12 tfor:TF3000|3end_hypothetical_protein_3216740..3216890_POSITIVE 305 160 117 103 48 tfor:TF2331|3end_conserved_hypothetical_protein_2491767..2491917_POSITIVE 305 154 121 44 14 tfor:TF0418|3end_possible_methyl-accepting_chemotaxis_protein_435326..435476_POSITIVE