Origin IGS: taatgaaaaatagagttatatgaagcgcgtttttttaaaatattcctgtgaaaaaacgtaggatttatccgcattttttttcaaggaaaaaagagaaataaagaaatcactcttggatttcctcatgctattgag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctcaatagcatgaggaaatccaagagtgatttctttatttctcttttttccttgaaaaaaaatgcggataaatcctacgttttttcacaggaatattttaaaaaaacgcgcttcatataactctatttttcatta Mask Tandem Repeat Region ================================================ taatgaaaaatagagttatatgaagcgcgtttttttaaaatattcctgtgaaaaaacgtaggatttatccgcattttttttcaaggaaaaaagagaaataaagaaatcactcttggatttcctcatgctattgag Find is-nt database================================================ Query_seq: TF1225:TF1227|TF1225:TF1227:conserved hypothetical protein:hypothetical protein:->->:1313752..1313886 135 taatgaaaaatagagttatatgaagcgcgtttttttaaaatattcctgtgaaaaaacgtaggatttatccgcattttttttcaaggaaaaaagagaaataaagaaatcactcttggatttcctcatgctattgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1225:TF1227|TF1225:TF1227:conserved hypothetical protein:hypothetical protein:->->:1313752..1313886 135 taatgaaaaatagagttatatgaagcgcgtttttttaaaatattcctgtgaaaaaacgtaggatttatccgcattttttttcaaggaaaaaagagaaataaagaaatcactcttggatttcctcatgctattgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1225:TF1227|TF1225:TF1227:conserved hypothetical protein:hypothetical protein:->->:1313752..1313886 135 taatgaaaaatagagttatatgaagcgcgtttttttaaaatattcctgtgaaaaaacgtaggatttatccgcattttttttcaaggaaaaaagagaaataaagaaatcactcttggatttcctcatgctattgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatgaaaaatagagttatatgaagcgcgtttttttaaaatattcctgtgaaaaaacgtaggatttatccgcattttttttcaaggaaaaaagagaaataaagaaatcactcttggatttcctcatgctattgag Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 19 End: 126 .................. I F R T K K F Y E Q S F V Y S K D A N K K L S F L S I F F D S K S K R M ......... taatgaaaaatagagttatatgaagcgcgtttttttaaaatattcctgtgaaaaaacgtaggatttatccgcattttttttcaaggaaaaaagagaaataaagaaatcactcttggatttcctcatgctattgag 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================================================ taatgaaaaatagagttatatgaagcgcgtttttttaaaatattcctgtgaaaaaacgtaggatttatccgcattttttttcaaggaaaaaagagaaataaagaaatcactcttggatttcctcatgctattgag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1225:TF1227|TF1225:TF1227:conserved hypothetical protein:hypothetical protein:->->:1313752..1313886 135 taatgaaaaatagagttatatgaagcgcgtttttttaaaatattcctgtgaaaaaacgtaggatttatccgcattttttttcaaggaaaaaagagaaataaagaaatcactcttggatttcctcatgctattgag Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: tfor_TF1225_TF1227|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1313752,1313886]|135 HSP 1 e-value: 3.0E-44 bit: 178.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 taatgaaaaatagagttatatgaagcgcgnnnnnnnaaaatattcctgtgaaaaaacgtaggatttatccgcannnnnnnncaaggaaaaaagagaaataaagaaatcactcttggatttcctcatgctattgag taatgaaaaatagagttatatgaagcgcgtttttttaaaatattcctgtgaaaaaacgtaggatttatccgcattttttttcaaggaaaaaagagaaataaagaaatcactcttggatttcctcatgctattgag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGAAAAAUAGAGUUAUAUGAAGCGCGUUUUUUUAAAAUAUUCCUGUGAAAAAACGUAGGAUUUAUCCGCAUUUUUUUUCAAGGAAAAAAGAGAAAUAAAGAAAUCACUCUUGGAUUUCCUCAUGCUAUUGAG ...(((((((....(((......)))....))))))).....(((((.((((((((.((.(((....)))..)).)))))))))))))....(((((((.((((......))))..)))).)))........... (-24.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAAUAGCAUGAGGAAAUCCAAGAGUGAUUUCUUUAUUUCUCUUUUUUCCUUGAAAAAAAAUGCGGAUAAAUCCUACGUUUUUUCACAGGAAUAUUUUAAAAAAACGCGCUUCAUAUAACUCUAUUUUUCAUUA .......((.(((((((((((....).))))))))))..........(((((((((((((..((.(((....)))))..)))))))).)))))..............)).......................... (-24.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 63 21 171 120 tfor:TF0604|5end_hypothetical_protein_635385..635615_POSITIVE 250 128 84 171 134 tfor:TF0282|5end_probable_tonB-linked_outer_membrane_receptor_309101..309331_POSITIVE 238 84 44 204 149 tfor:TF2686|5end_ABC_transporter,_ATP-binding_protein_2862741..2862971_POSITIVE 229 74 45 78 53 tfor:TF1734|5end_conserved_hypothetical_protein_1856556..1856786_POSITIVE 224 110 64 218 171 tfor:TF1772|5end_ISPg4-related_transposase_(IS5_family)_1908672..1908902_POSITIVE 222 86 46 169 135 tfor:TF2467|5end_3-dehydroquinate_dehydratase_II_2645827..2646057_POSITIVE 220 129 82 206 158 tfor:TF1912|5end_transcriptional_regulator,_TetR_family_2065970..2066200_POSITIVE 218 129 84 158 109 tfor:TF2420|5end_hypothetical_protein_2599235..2599465_POSITIVE 207 81 43 207 171 tfor:TF2582|5end_ABC_transporter,_ATP-binding_protein_2749433..2749663_POSITIVE 207 59 14 138 86 tfor:TF1215|5end_haloacid_dehalogenase-like_hydrolase_1302510..1302740_POSITIVE 206 86 57 53 19 tfor:TF2442|5end_heat_shock_protein_60_2618557..2618787_POSITIVE 206 50 1 151 114 tfor:TF0776|5end_ABC_transporter,_permease_component_824855..825085_POSITIVE 205 83 47 230 194 tfor:TF2012|5end_conserved_hypothetical_protein_2165380..2165610_POSITIVE 203 69 24 74 27 tfor:TF2358|5end_possible_small-conductance_mechanosensitive_channel_2523829..2524059_POSITIVE 202 88 50 143 96 tfor:TF0619|5end_ubiquinone_biosynthesis_methyltransferase_653943..654173_POSITIVE 201 90 45 33 3 tfor:TF1449|5end_RNA_polymerase_sigma_factor,_RpoD_1533124..1533354_POSITIVE 199 130 86 112 70 tfor:TF2230|5end_CTn_excision_protein_2399799..2400029_POSITIVE 199 70 21 54 18 tfor:TF1699|5end_mobilization_protein,_BmgA_1819695..1819925_POSITIVE 199 79 46 58 31 tfor:TF1409|5end_outer_membrane_protein_TolC_1485479..1485709_POSITIVE 198 72 45 73 43 tfor:TF2275|5end_conserved_hypothetical_protein_2436934..2437164_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 128 84 149 112 tfor:TF0281|3end_hypothetical_protein_309159..309309_POSITIVE 238 84 44 108 53 tfor:TF2685|3end_iron-regulated_ABC-type_transporter_membrane_component_2862725..2862875_POSITIVE 220 129 82 89 41 tfor:TF1911|3end_conserved_hypothetical_protein_2065933..2066083_POSITIVE 213 30 2 92 67 tfor:TF2583|3end_possible_ABC_transporter,__permease_component_2751026..2751176_POSITIVE 211 70 21 93 33 tfor:TF1350|3end_possible_transcriptional_regulator_1430636..1430786_POSITIVE 208 88 43 48 3 tfor:TF1225|3end_conserved_hypothetical_protein_1313691..1313841_POSITIVE 207 81 43 64 28 tfor:TF2581|3end_50S_ribosomal_protein_L17_2749370..2749520_POSITIVE 207 59 14 82 30 tfor:TF1214|3end_conserved_hypothetical_protein_1302534..1302684_POSITIVE 206 50 1 135 98 tfor:TF0775|3end_ABC_transporter,_permease_component_824919..825069_POSITIVE 205 83 47 80 44 tfor:TF2011|3end_transposase_2165310..2165460_POSITIVE 203 69 24 65 18 tfor:TF2357|3end_collagenase_2523900..2524050_POSITIVE 202 88 50 143 96 tfor:TF0618|3end_shikimate_5-dehydrogenase_654023..654173_POSITIVE 200 96 57 40 6 tfor:TF1740|3end_hypothetical_protein_1869192..1869342_POSITIVE 199 70 21 61 25 tfor:TF1698|3end_mobilization_protein_1819782..1819932_POSITIVE 199 79 46 45 18 tfor:TF1408|3end_cation_efflux_system_protein_1485546..1485696_POSITIVE 198 72 45 45 15 tfor:TF2274|3end_conserved_hypothetical_protein_2436986..2437136_POSITIVE 198 72 43 101 68 tfor:TF0010|3end_conserved_hypothetical_protein_4790..4940_POSITIVE 196 43 7 66 40 tfor:TF3101|3end_hypothetical_protein_3332659..3332809_POSITIVE 195 83 43 73 36 tfor:TF2284|3end_hypothetical_protein_2440846..2440996_POSITIVE 195 87 41 72 26 tfor:TF1608|3end_sulfate_transporter_1728463..1728613_POSITIVE