Origin IGS: tagggagacttcagtaataagatgaaggtaagataaactgtagaatgacagatcggtatggaaatacggtaaaaaagaatacgaatatttttattttattccttttctgtttacatttgcatggttttttcatgtattttacagttataattacaatatcaaacttaactaact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agttagttaagtttgatattgtaattataactgtaaaatacatgaaaaaaccatgcaaatgtaaacagaaaaggaataaaataaaaatattcgtattcttttttaccgtatttccataccgatctgtcattctacagtttatcttaccttcatcttattactgaagtctcccta Mask Tandem Repeat Region ================================================ tagggagacttcagtaataagatgaaggtaagataaactgtagaatgacagatcggtatggaaatacggtaaaaaagaatacgaatatttttattttattccttttctgtttacatttgcatggttttttcatgtattttacagttataattacaatatcaaacttaactaact Find is-nt database================================================ Query_seq: TF2802:TF2803|TF2802:TF2803:possible outer membrane protein:dehydrogenase, possible NADH-dependent dehydrogenase:->->:2991875..2992048 174 tagggagacttcagtaataagatgaaggtaagataaactgtagaatgacagatcggtatggaaatacggtaaaaaagaatacgaatatttttattttattccttttctgtttacatttgcatggttttttcatgtattttacagttataattacaatatcaaacttaactaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2802:TF2803|TF2802:TF2803:possible outer membrane protein:dehydrogenase, possible NADH-dependent dehydrogenase:->->:2991875..2992048 174 tagggagacttcagtaataagatgaaggtaagataaactgtagaatgacagatcggtatggaaatacggtaaaaaagaatacgaatatttttattttattccttttctgtttacatttgcatggttttttcatgtattttacagttataattacaatatcaaacttaactaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2802:TF2803|TF2802:TF2803:possible outer membrane protein:dehydrogenase, possible NADH-dependent dehydrogenase:->->:2991875..2992048 174 tagggagacttcagtaataagatgaaggtaagataaactgtagaatgacagatcggtatggaaatacggtaaaaaagaatacgaatatttttattttattccttttctgtttacatttgcatggttttttcatgtattttacagttataattacaatatcaaacttaactaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagggagacttcagtaataagatgaaggtaagataaactgtagaatgacagatcggtatggaaatacggtaaaaaagaatacgaatatttttattttattccttttctgtttacatttgcatggttttttcatgtattttacagttataattacaatatcaaacttaactaact Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 33 End: 173 ................................ M N C R M T D R Y G N T V K K N T N I F I L F L F C L H L H G F F M Y F T V I I T I S N L T N . Protein_Len: 48 Strand: - Start: 14 End: 157 ............. Y Y S S P L I F Q L I V S R Y P F V T F F F V F I K I K N R K Q K C K C P K K M Y K V T I I V M ................. tagggagacttcagtaataagatgaaggtaagataaactgtagaatgacagatcggtatggaaatacggtaaaaaagaatacgaatatttttattttattccttttctgtttacatttgcatggttttttcatgtattttacagttataattacaatatcaaacttaactaact Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 128 End: 157 ...............................................................................................................................TTTCATGTATTTTACAGTTATAATTACAAT................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagggagacttcagtaataagatgaaggtaagataaactgtagaatgacagatcggtatggaaatacggtaaaaaagaatacgaatatttttattttattccttttctgtttacatttgcatggttttttcatgtattttacagttataattacaatatcaaacttaactaact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -2.1 Tail_Score: -3.70689 Start: 120 End: 134 Full_Region: TTCTGTTTACATTTG CATGG TTTTT TCATG TATTTTACAGTTATA .......................................................................................................................CATGGTTTTTTCATG........................................ Find igs database================================================ Query_seq: TF2802:TF2803|TF2802:TF2803:possible outer membrane protein:dehydrogenase, possible NADH-dependent dehydrogenase:->->:2991875..2992048 174 tagggagacttcagtaataagatgaaggtaagataaactgtagaatgacagatcggtatggaaatacggtaaaaaagaatacgaatatttttattttattccttttctgtttacatttgcatggttttttcatgtattttacagttataattacaatatcaaacttaactaact Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: tfor_TF2802_TF2803|possible outer membrane protein:dehydrogenase, possible NADH-dependent dehydrogenase|POSITIVE:POSITIVE|[2991875,2992048]|174 HSP 1 e-value: 4.0E-41 bit: 168.0 Len: 85 Query Start:1 Query End:85 Subject Strand: POSITIVE Subject Start: 1 Subject End: 85 tagggagacttcagtaataagatgaaggtaagataaactgtagaatgacagatcggtatggaaatacggtaaaaaagaatacgaa......................................................................................... tagggagacttcagtaataagatgaaggtaagataaactgtagaatgacagatcggtatggaaatacggtaaaaaagaatacgaa......................................................................................... HSP 2 e-value: 4.0E-10 bit: 65.9 Len: 33 Query Start:142 Query End:174 Subject Strand: POSITIVE Subject Start: 142 Subject End: 174 .............................................................................................................................................cagttataattacaatatcaaacttaactaact .............................................................................................................................................cagttataattacaatatcaaacttaactaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGGAGACUUCAGUAAUAAGAUGAAGGUAAGAUAAACUGUAGAAUGACAGAUCGGUAUGGAAAUACGGUAAAAAAGAAUACGAAUAUUUUUAUUUUAUUCCUUUUCUGUUUACAUUUGCAUGGUUUUUUCAUGUAUUUUACAGUUAUAAUUACAAUAUCAAACUUAACUAACU .(((....))).........((((...((((....(((((((((..((((((.(.((((....)))).).......(((((.(((((....))))))))))....))))))......(((((((.....))))))).)))))))))....))))..)))).............. (-36.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUAGUUAAGUUUGAUAUUGUAAUUAUAACUGUAAAAUACAUGAAAAAACCAUGCAAAUGUAAACAGAAAAGGAAUAAAAUAAAAAUAUUCGUAUUCUUUUUUACCGUAUUUCCAUACCGAUCUGUCAUUCUACAGUUUAUCUUACCUUCAUCUUAUUACUGAAGUCUCCCUA ..(((((((((..(((....((((....(((((((.((((((.((........(((....)))....(((((((((((.((((....))))..)))))))))))..................))))).))).)))))))....))))..))).))))..))))).......... (-26.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 70 21 143 82 tfor:TF1824|5end_ABC_transporter,_ATP-binding_protein_1972537..1972767_POSITIVE 295 73 32 59 19 tfor:TF1552|5end_conserved_hypothetical_protein_1657097..1657327_POSITIVE 279 69 21 166 124 tfor:TF2213|5end_glycyl-tRNA_synthetase_2385319..2385549_POSITIVE 265 83 47 105 63 tfor:TF1741|5end_conserved_hypothetical_protein_1869304..1869534_POSITIVE 265 69 21 103 46 tfor:TF0981|5end_possible_hydrolase_1038112..1038342_POSITIVE 261 70 29 53 6 tfor:TF2594|5end_hypothetical_protein_2764176..2764406_POSITIVE 260 85 45 152 117 tfor:TF3145|5end_conserved_hypothetical_protein;_possible_GTP_cyclohydrolase_I_family_3381254..3381484_POSITIVE 258 84 42 45 3 tfor:TF0628|5end_conserved_hypothetical_protein_664305..664535_POSITIVE 257 40 3 114 72 tfor:TF1465|5end_modulator_of_DNA_gyrase_1554148..1554378_POSITIVE 256 142 101 101 57 tfor:TF2283|5end_hypothetical_protein_2440266..2440496_POSITIVE 253 49 4 108 59 tfor:TF0704|5end_TPR-repeat-containing_protein_747888..748118_POSITIVE 251 134 97 229 188 tfor:TF2419|5end_conserved_hypothetical_protein;_possible_DNA_uptake-related_protein_2598358..2598588_POSITIVE 248 130 81 130 78 tfor:TF1329|5end_glucose-1-phosphate_thymidyltransferase_1408578..1408808_POSITIVE 245 83 42 126 89 tfor:TF2717|5end_glycosyltransferase_2889995..2890225_POSITIVE 240 60 17 201 156 tfor:TF0144|5end_hypothetical_protein_151209..151439_POSITIVE 237 69 21 104 58 tfor:TF0619|5end_ubiquinone_biosynthesis_methyltransferase_653943..654173_POSITIVE 236 68 24 152 106 tfor:TF2186|5end_outer_membrane_protein_2360291..2360521_POSITIVE 233 70 23 134 102 tfor:TF2420|5end_hypothetical_protein_2599235..2599465_POSITIVE 233 70 21 132 83 tfor:TF1419|5end_cell_division_protein_1501413..1501643_POSITIVE 232 62 27 142 112 tfor:TF2243|5end_possible_mobilization_protein_2417384..2417614_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 70 21 115 54 tfor:TF1823|3end_xanthan_lyase_XalB_precursor_1972589..1972739_POSITIVE 280 70 21 140 99 tfor:TF0498|3end_hypothetical_protein_525955..526105_POSITIVE 279 69 21 81 39 tfor:TF2211|3end_conserved_hypothetical_protein_2385314..2385464_POSITIVE 253 49 4 95 46 tfor:TF0703|3end_conserved_hypothetical_protein_747955..748105_POSITIVE 248 130 81 122 70 tfor:TF1328|3end_possible_cytidylyltransferase_1408650..1408800_POSITIVE 245 83 42 126 89 tfor:TF2716|3end_glycosyltransferase_2890075..2890225_POSITIVE 245 69 21 145 100 tfor:TF2530|3end_conserved_hypothetical_protein_2712926..2713076_POSITIVE 237 69 21 104 58 tfor:TF0618|3end_shikimate_5-dehydrogenase_654023..654173_POSITIVE 236 68 24 137 91 tfor:TF2185|3end_outer_membrane_protein,_TonB_dependent_receptor_2360356..2360506_POSITIVE 233 70 21 116 67 tfor:TF1418|3end_cell_division_protein_1501477..1501627_POSITIVE 232 62 27 94 64 tfor:TF2242|3end_hypothetical_protein_2417416..2417566_POSITIVE 232 68 21 139 94 tfor:TF1955|3end_amino_acid_exporter,_possible_threonine_efflux_protein_2107649..2107799_POSITIVE 232 70 21 115 56 tfor:TF1035|3end_iron(III)_ABC_transporter,_periplasmic-binding_protein_1097240..1097390_POSITIVE 232 60 13 121 74 tfor:TF0904|3end_conserved_hypothetical_protein_949156..949306_POSITIVE 229 88 42 87 42 tfor:TF0879|3end_TraG_family_protein_934085..934235_POSITIVE 228 70 43 39 8 tfor:TF2593|3end_amino_acid_transport_protein_2764242..2764392_POSITIVE 225 55 14 103 62 tfor:TF0581|3end_single_stranded_DNA-binding_protein_611932..612082_POSITIVE 224 73 38 35 5 tfor:TF1551|3end_hypothetical_protein_1657153..1657303_POSITIVE 223 45 2 49 12 tfor:TF2055|3end_UDP-N-acetyl-D-mannosaminuronic_acid_dehydrogenase_2220784..2220934_POSITIVE 223 69 24 146 103 tfor:TF0006|3end_3-oxyacyl_[acyl-carrier_protein]_reductase_2580..2730_POSITIVE