Origin IGS: ttttaatggtcaatggttaaaacggctttctttagttatatttaactataaaaattagttttgaaactaaattatctcgttatttgtagtcgtaatttgaacaggaggatagacgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acgtctatcctcctgttcaaattacgactacaaataacgagataatttagtttcaaaactaatttttatagttaaatataactaaagaaagccgttttaaccattgaccattaaaa Mask Tandem Repeat Region ================================================ ttttaatggtcaatggttaaaacggctttctttagttatatttaactataaaaattagttttgaaactaaattatctcgttatttgtagtcgtaatttgaacaggaggatagacgt Find is-nt database================================================ Query_seq: TF1253:TF1254|TF1253:TF1254:hypothetical protein:conserved hypothetical protein; possible transcriptional regulator:->->:1336272..1336387 116 ttttaatggtcaatggttaaaacggctttctttagttatatttaactataaaaattagttttgaaactaaattatctcgttatttgtagtcgtaatttgaacaggaggatagacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1253:TF1254|TF1253:TF1254:hypothetical protein:conserved hypothetical protein; possible transcriptional regulator:->->:1336272..1336387 116 ttttaatggtcaatggttaaaacggctttctttagttatatttaactataaaaattagttttgaaactaaattatctcgttatttgtagtcgtaatttgaacaggaggatagacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1253:TF1254|TF1253:TF1254:hypothetical protein:conserved hypothetical protein; possible transcriptional regulator:->->:1336272..1336387 116 ttttaatggtcaatggttaaaacggctttctttagttatatttaactataaaaattagttttgaaactaaattatctcgttatttgtagtcgtaatttgaacaggaggatagacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttaatggtcaatggttaaaacggctttctttagttatatttaactataaaaattagttttgaaactaaattatctcgttatttgtagtcgtaatttgaacaggaggatagacgt Predict ORF larger than 30AA ================================================ ttttaatggtcaatggttaaaacggctttctttagttatatttaactataaaaattagttttgaaactaaattatctcgttatttgtagtcgtaatttgaacaggaggatagacgt 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================================================ ttttaatggtcaatggttaaaacggctttctttagttatatttaactataaaaattagttttgaaactaaattatctcgttatttgtagtcgtaatttgaacaggaggatagacgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -4.8 Tail_Score: -4.98857 Start: 55 End: 70 Full_Region: aaataacgagataat ttagtt tcaa aactaa tttttatagttaaat ......................................................ttagtttcaaaactaa.............................................. Find igs database================================================ Query_seq: TF1253:TF1254|TF1253:TF1254:hypothetical protein:conserved hypothetical protein; possible transcriptional regulator:->->:1336272..1336387 116 ttttaatggtcaatggttaaaacggctttctttagttatatttaactataaaaattagttttgaaactaaattatctcgttatttgtagtcgtaatttgaacaggaggatagacgt Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: tfor_TF1253_TF1254|hypothetical protein:conserved hypothetical protein; possible transcriptional regulator|POSITIVE:POSITIVE|[1336272,1336387]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 ttttaatggtcaatggttaaaacggctttctttagttatatttaactataaaaattagttttgaaactaaattatctcgttatttgtagtcgtaatttgaacaggaggatagacgt ttttaatggtcaatggttaaaacggctttctttagttatatttaactataaaaattagttttgaaactaaattatctcgttatttgtagtcgtaatttgaacaggaggatagacgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAAUGGUCAAUGGUUAAAACGGCUUUCUUUAGUUAUAUUUAACUAUAAAAAUUAGUUUUGAAACUAAAUUAUCUCGUUAUUUGUAGUCGUAAUUUGAACAGGAGGAUAGACGU ........(((..((.(((((((((((.....((((((....))))))......((((((....)))))).................))))))..))))).))....)))...... (-16.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGUCUAUCCUCCUGUUCAAAUUACGACUACAAAUAACGAGAUAAUUUAGUUUCAAAACUAAUUUUUAUAGUUAAAUAUAACUAAAGAAAGCCGUUUUAACCAUUGACCAUUAAAA .............((.((((..................(((((......))))).((((...(((((.((((((....)))))).)))))...))))......)))).))...... (-11.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 205 109 74 191 162 tfor:TF2975|5end_endonuclease_IV_3182394..3182624_POSITIVE 203 107 74 70 39 tfor:TF0244|5end_DNA_recombination_protein_274683..274913_POSITIVE 199 46 5 68 20 tfor:TF1040|5end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_1101253..1101483_POSITIVE 199 110 77 49 16 tfor:TF0558|5end_conserved_hypothetical_protein_590116..590346_POSITIVE 198 38 6 163 136 tfor:TF2723|5end_30S_ribosomal_protein_S20_2897689..2897919_POSITIVE 198 38 1 190 150 tfor:TF1873|5end_possible_hemolysin_secretion_protein_2026745..2026975_POSITIVE 198 38 1 190 150 tfor:TF1131|5end_membrane-fusion_protein;_possible_hemolysin_secretion_protein_1207611..1207841_POSITIVE 195 108 75 182 156 tfor:TF2440|5end_conserved_hypothetical_protein;_possible_DNA_mismatch_repair_protein_2616858..2617088_POSITIVE 194 108 72 223 186 tfor:TF0657|5end_conserved_hypothetical_protein_702893..703123_POSITIVE 192 108 74 155 122 tfor:TF2579|5end_30S_ribosomal_protein_S4_2747202..2747432_POSITIVE 192 109 78 157 126 tfor:TF0253|5end_conserved_hypothetical_protein_283707..283937_POSITIVE 192 110 73 142 109 tfor:TF0076|5end_probable_carbohydrate_kinase,_PfkB_family_83279..83509_POSITIVE 191 36 7 56 22 tfor:TF1487|5end_orotate_phosphoribosyltransferase_1587807..1588037_POSITIVE 190 110 71 164 119 tfor:TF0284|5end_alanine_racemase_311988..312218_POSITIVE 190 36 12 211 188 tfor:TF0203|5end_PhoH-like_protein_229255..229485_POSITIVE 189 92 57 231 191 tfor:TF1677|5end_ATP_synthase,_beta_subunit_1789321..1789551_POSITIVE 189 108 62 73 24 tfor:TF0052|5end_hypothetical_protein_57611..57841_POSITIVE 188 105 68 137 102 tfor:TF1902|5end_two-component_system_sensor_histidine_kinase_2057521..2057751_POSITIVE 187 109 76 174 144 tfor:TF3003|5end_hypothetical_protein_3220382..3220612_POSITIVE 185 108 61 190 141 tfor:TF2940|5end_50S_ribosomal_protein_L11_3141367..3141597_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 35 3 91 56 tfor:TF1660|3end_hypothetical_protein_1775600..1775750_POSITIVE 228 25 3 116 94 tfor:TF1762|3end_hypothetical_protein_1899648..1899798_POSITIVE 228 25 3 47 25 tfor:TF1761|3end_hypothetical_protein_1899579..1899729_POSITIVE 221 110 77 56 22 tfor:TF2155|3end_transposase_2331096..2331246_POSITIVE 211 37 7 146 120 tfor:TF0959|3end_periplasmic_protease_1008540..1008690_POSITIVE 203 107 74 65 34 tfor:TF0243|3end_conserved_hypothetical_protein_274758..274908_POSITIVE 199 110 66 150 106 tfor:TF3010|3end_possible_anti-sigma_factor_3230888..3231038_POSITIVE 199 110 77 39 6 tfor:TF0557|3end_conserved_hypothetical_protein_590186..590336_POSITIVE 196 20 3 84 67 tfor:TF0018|3end_hypothetical_protein_12091..12241_POSITIVE 194 33 8 127 103 tfor:TF2143|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2319704..2319854_POSITIVE 192 108 74 37 4 tfor:TF2578|3end_30S_ribosomal_protein_S11_2747164..2747314_POSITIVE 192 109 78 129 98 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 191 36 7 56 22 tfor:TF1486|3end_hypothetical_protein_1587887..1588037_POSITIVE 191 110 65 92 42 tfor:TF1195|3end_hypothetical_protein_1278845..1278995_POSITIVE 185 108 61 125 76 tfor:TF2939|3end_transcription_antiterminator_3141382..3141532_POSITIVE 182 32 2 131 100 tfor:TF1902|3end_two-component_system_sensor_histidine_kinase_2059055..2059205_POSITIVE 181 107 62 99 54 tfor:TF2309|3end_cysteinyl-tRNA_synthetase_2470522..2470672_POSITIVE 180 61 23 89 48 tfor:TF0709|3end_preprotein_translocase,_subunit_SecA_757241..757391_POSITIVE 179 99 78 51 30 tfor:TF1672|3end_ATP_synthase,_B_subunit_1787297..1787447_POSITIVE 179 32 7 59 31 tfor:TF1455|3end_conserved_hypothetical_protein_1541661..1541811_POSITIVE