Origin IGS: tagagtgatgaggtgatggtatatgatttaaggtgaaaagatagggtttcttgtgacagaaatataaaccgccagattgcaaagaatatgccaagtgcgcaatagattaaagataaaagaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgtcttttatctttaatctattgcgcacttggcatattctttgcaatctggcggtttatatttctgtcacaagaaaccctatcttttcaccttaaatcatataccatcacctcatcactcta Mask Tandem Repeat Region ================================================ tagagtgatgaggtgatggtatatgatttaaggtgaaaagatagggtttcttgtgacagaaatataaaccgccagattgcaaagaatatgccaagtgcgcaatagattaaagataaaagaca Find is-nt database================================================ Query_seq: TF2617:TF2618|TF2617:TF2618:conserved hypothetical protein:integral membrane protein, possible zinc transporter:->->:2795233..2795354 122 tagagtgatgaggtgatggtatatgatttaaggtgaaaagatagggtttcttgtgacagaaatataaaccgccagattgcaaagaatatgccaagtgcgcaatagattaaagataaaagaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2617:TF2618|TF2617:TF2618:conserved hypothetical protein:integral membrane protein, possible zinc transporter:->->:2795233..2795354 122 tagagtgatgaggtgatggtatatgatttaaggtgaaaagatagggtttcttgtgacagaaatataaaccgccagattgcaaagaatatgccaagtgcgcaatagattaaagataaaagaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2617:TF2618|TF2617:TF2618:conserved hypothetical protein:integral membrane protein, possible zinc transporter:->->:2795233..2795354 122 tagagtgatgaggtgatggtatatgatttaaggtgaaaagatagggtttcttgtgacagaaatataaaccgccagattgcaaagaatatgccaagtgcgcaatagattaaagataaaagaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagagtgatgaggtgatggtatatgatttaaggtgaaaagatagggtttcttgtgacagaaatataaaccgccagattgcaaagaatatgccaagtgcgcaatagattaaagataaaagaca Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 3 End: 107 .. L S S T I T Y S K L H F S L T E Q S L F I F R W I A F F I G L A C Y M ............... Protein_Len: 34 Strand: - Start: 2 End: 103 . S H H P S P I H N L T F L Y P K K H C F Y L G G S Q L S Y A L H A M ................... tagagtgatgaggtgatggtatatgatttaaggtgaaaagatagggtttcttgtgacagaaatataaaccgccagattgcaaagaatatgccaagtgcgcaatagattaaagataaaagaca 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================================================ PromScan Matrix: RpoN Strand: - Score: 85 Start: 78 End: 94 .............................................................................TTGGCATATTCTTTGCA............................ tagagtgatgaggtgatggtatatgatttaaggtgaaaagatagggtttcttgtgacagaaatataaaccgccagattgcaaagaatatgccaagtgcgcaatagattaaagataaaagaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2617:TF2618|TF2617:TF2618:conserved hypothetical protein:integral membrane protein, possible zinc transporter:->->:2795233..2795354 122 tagagtgatgaggtgatggtatatgatttaaggtgaaaagatagggtttcttgtgacagaaatataaaccgccagattgcaaagaatatgccaagtgcgcaatagattaaagataaaagaca Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: tfor_TF2617_TF2618|conserved hypothetical protein:integral membrane protein, possible zinc transporter|POSITIVE:POSITIVE|[2795233,2795354]|122 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 tagagtgatgaggtgatggtatatgatttaaggtgaaaagatagggtttcttgtgacagaaatataaaccgccagattgcaaagaatatgccaagtgcgcaatagattaaagataaaagaca tagagtgatgaggtgatggtatatgatttaaggtgaaaagatagggtttcttgtgacagaaatataaaccgccagattgcaaagaatatgccaagtgcgcaatagattaaagataaaagaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAGUGAUGAGGUGAUGGUAUAUGAUUUAAGGUGAAAAGAUAGGGUUUCUUGUGACAGAAAUAUAAACCGCCAGAUUGCAAAGAAUAUGCCAAGUGCGCAAUAGAUUAAAGAUAAAAGACA ....(..((..(((...(((.((((.(((...((.(.((((.......)))).).))..))))))).))))))..))..)........((((....).)))..................... (-16.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCUUUUAUCUUUAAUCUAUUGCGCACUUGGCAUAUUCUUUGCAAUCUGGCGGUUUAUAUUUCUGUCACAAGAAACCCUAUCUUUUCACCUUAAAUCAUAUACCAUCACCUCAUCACUCUA .......................(((.....(((.......)))......))).......(((((......))))).............................................. ( -9.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 47 1 143 87 tfor:TF1480|5end_ABC_transporter,_permease_component_1573512..1573742_POSITIVE 275 100 51 214 172 tfor:TF1298|5end_possible_membrane_protein_1380107..1380337_POSITIVE 272 60 12 62 10 tfor:TF1478|5end_membrane_fusion_efflux_protein_1571101..1571331_POSITIVE 271 80 31 106 58 tfor:TF0310|5end_conserved_hypothetical_protein_334685..334915_POSITIVE 265 90 43 151 100 tfor:TF0875|5end_outer_membrane_receptor,_TonB-linked_926829..927059_POSITIVE 264 103 69 34 4 tfor:TF2396|5end_dimethyladenosine_transferase_2567725..2567955_POSITIVE 261 100 54 168 125 tfor:TF2721|5end_conserved_hypothetical_protein_2895590..2895820_POSITIVE 261 80 31 68 16 tfor:TF2596|5end_conserved_hypothetical_protein;_possible_lipoprotein_2766667..2766897_POSITIVE 261 81 41 69 22 tfor:TF2340|5end_hypothetical_protein_2500665..2500895_POSITIVE 260 100 51 53 10 tfor:TF2509|5end_ATP-dependent_clp_protease,_proteolytic_subunit_2687562..2687792_POSITIVE 259 50 2 154 105 tfor:TF2055|5end_UDP-N-acetyl-D-mannosaminuronic_acid_dehydrogenase_2219463..2219693_POSITIVE 258 49 2 148 94 tfor:TF2706|5end_possible_aminopeptidase_2877291..2877521_POSITIVE 255 113 71 73 43 tfor:TF0338|5end_alkaline_phosphatase_361788..362018_POSITIVE 254 47 2 113 64 tfor:TF1589|5end_surface_antigen_BspA_1703189..1703419_POSITIVE 253 49 4 227 181 tfor:TF2245|5end_conserved_hypothetical_protein_2420654..2420884_POSITIVE 253 101 69 159 134 tfor:TF1947|5end_conserved_hypothetical_protein_2095521..2095751_POSITIVE 251 99 51 195 146 tfor:TF2133|5end_aspartate-semialdehyde_dehydrogenase_2310275..2310505_POSITIVE 250 61 24 225 188 tfor:TF2347|5end_outer_membrane_protein,_TonB_dependent_receptor_2510155..2510385_POSITIVE 248 80 32 60 7 tfor:TF1759|5end_membrane-bound_lytic_murein_transglycosylase_D_precursor_1895472..1895702_POSITIVE 248 80 41 102 58 tfor:TF0232|5end_conserved_hypothetical_protein_258347..258577_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 47 1 143 87 tfor:TF1479|3end_ABC_transporter,_permease_component_1573592..1573742_POSITIVE 286 46 4 95 56 tfor:TF1504|3end_conserved_hypothetical_protein_1610665..1610815_POSITIVE 283 100 70 53 22 tfor:TF0181|3end_ATP-dependent_DNA_helicase_194863..195013_POSITIVE 278 100 51 71 16 tfor:TF0362|3end_hypothetical_protein_380199..380349_POSITIVE 272 60 12 84 32 tfor:TF1476|3end_outer_membrane_protein_P49_1571203..1571353_POSITIVE 271 80 31 116 68 tfor:TF0309|3end_conserved_hypothetical_protein_334775..334925_POSITIVE 259 45 2 63 19 tfor:TF3141|3end_NADH:_ubiquinone_oxidoreductase,_subunit_A_3376267..3376417_POSITIVE 259 50 2 146 97 tfor:TF2054|3end_UDP-N-acetylglucosamine_2-epimerase_2219535..2219685_POSITIVE 258 49 2 141 87 tfor:TF2705|3end_conserved_hypothetical_protein;_possible_SufE_Fe/S-cluster-related_protein_2877364..2877514_POSITIVE 255 113 71 73 43 tfor:TF0336|3end_Xaa-Pro_aminopeptidase_361868..362018_POSITIVE 252 49 3 85 32 tfor:TF1484|3end_penicillin_binding_protein_1582065..1582215_POSITIVE 247 56 11 143 102 tfor:TF1929|3end_conserved_hypothetical_protein_2076614..2076764_POSITIVE 245 100 51 71 16 tfor:TF2166|3end_hypothetical_protein_2342362..2342512_POSITIVE 245 100 51 71 16 tfor:TF0366|3end_hypothetical_protein_383811..383961_POSITIVE 244 98 51 129 80 tfor:TF0479|3end_transcriptional_regulator_498405..498555_POSITIVE 242 80 45 52 14 tfor:TF1758|3end_conserved_hypothetical_protein_1895544..1895694_POSITIVE 242 98 52 79 14 tfor:TF0451|3end_rhomboid_family_membrane_protein_471046..471196_POSITIVE 240 106 69 151 110 tfor:TF2172|3end_hypothetical_protein_2346135..2346285_POSITIVE 240 106 69 79 38 tfor:TF2173|3end_hypothetical_protein_2346063..2346213_POSITIVE 239 101 69 151 117 tfor:TF2472|3end_GAF_domain-containing_protein_2650468..2650618_POSITIVE