Origin IGS: tgaggtaggtgttagggattgggtatggggttgttcttgcctaatacccaacacctaatatctcttaaaaataaacagcgtaataatatgtatatatagaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attctatatatacatattattacgctgtttatttttaagagatattaggtgttgggtattaggcaagaacaaccccatacccaatccctaacacctacctca Mask Tandem Repeat Region ================================================ tgaggtaggtgttagggattgggtatggggttgttcttgcctaatacccaacacctaatatctcttaaaaataaacagcgtaataatatgtatatatagaat Find is-nt database================================================ Query_seq: TF2604:TF2605|TF2604:TF2605:possible membrane transport protein:outer membrane protein, TonB dependent receptor:->->:2779893..2779994 102 tgaggtaggtgttagggattgggtatggggttgttcttgcctaatacccaacacctaatatctcttaaaaataaacagcgtaataatatgtatatatagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2604:TF2605|TF2604:TF2605:possible membrane transport protein:outer membrane protein, TonB dependent receptor:->->:2779893..2779994 102 tgaggtaggtgttagggattgggtatggggttgttcttgcctaatacccaacacctaatatctcttaaaaataaacagcgtaataatatgtatatatagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2604:TF2605|TF2604:TF2605:possible membrane transport protein:outer membrane protein, TonB dependent receptor:->->:2779893..2779994 102 tgaggtaggtgttagggattgggtatggggttgttcttgcctaatacccaacacctaatatctcttaaaaataaacagcgtaataatatgtatatatagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaggtaggtgttagggattgggtatggggttgttcttgcctaatacccaacacctaatatctcttaaaaataaacagcgtaataatatgtatatatagaat Predict ORF larger than 30AA ================================================ tgaggtaggtgttagggattgggtatggggttgttcttgcctaatacccaacacctaatatctcttaaaaataaacagcgtaataatatgtatatatagaat 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================================================ tgaggtaggtgttagggattgggtatggggttgttcttgcctaatacccaacacctaatatctcttaaaaataaacagcgtaataatatgtatatatagaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2604:TF2605|TF2604:TF2605:possible membrane transport protein:outer membrane protein, TonB dependent receptor:->->:2779893..2779994 102 tgaggtaggtgttagggattgggtatggggttgttcttgcctaatacccaacacctaatatctcttaaaaataaacagcgtaataatatgtatatatagaat Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: tfor_TF2604_TF2605|possible membrane transport protein:outer membrane protein, TonB dependent receptor|POSITIVE:POSITIVE|[2779893,2779994]|102 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 tgaggtaggtgttagggattgggtatggggttgttcttgcctaatacccaacacctaatatctcttaaaaataaacagcgtaataatatgtatatatagaat tgaggtaggtgttagggattgggtatggggttgttcttgcctaatacccaacacctaatatctcttaaaaataaacagcgtaataatatgtatatatagaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGGUAGGUGUUAGGGAUUGGGUAUGGGGUUGUUCUUGCCUAAUACCCAACACCUAAUAUCUCUUAAAAAUAAACAGCGUAAUAAUAUGUAUAUAUAGAAU ..(((.((((((((((..((((((((.((((.......)))).))))))))..)))))))))))))...........(((((....)))))........... (-34.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUAUAUAUACAUAUUAUUACGCUGUUUAUUUUUAAGAGAUAUUAGGUGUUGGGUAUUAGGCAAGAACAACCCCAUACCCAAUCCCUAACACCUACCUCA ......................................(((.(((((((..((((((((..((.........))..))))))))..)))))....)).))). (-20.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 483 56 12 151 108 tfor:TF2629|5end_conserved_hypothetical_protein;_possible_lactoylglutathione_lyase_2801296..2801526_POSITIVE 459 60 15 163 117 tfor:TF2612|5end_conserved_hypothetical_protein_2788070..2788300_POSITIVE 330 50 1 129 92 tfor:TF1433|5end_ribose_5-phosphate_isomerase_1517031..1517261_POSITIVE 325 54 16 166 130 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 320 41 4 215 185 tfor:TF0755|5end_conserved_hypothetical_protein_802763..802993_POSITIVE 313 66 21 179 129 tfor:TF1015|5end_conserved_hypothetical_protein_1072512..1072742_POSITIVE 303 60 16 57 9 tfor:TF1490|5end_hypothetical_protein_1590238..1590468_POSITIVE 302 50 1 210 150 tfor:TF1285|5end_hypothetical_protein_1369004..1369234_POSITIVE 298 42 4 218 163 tfor:TF2410|5end_possible_endo-1,4-beta-xylanase_2584000..2584230_POSITIVE 296 60 13 215 173 tfor:TF2721|5end_conserved_hypothetical_protein_2895590..2895820_POSITIVE 294 32 4 114 90 tfor:TF3145|5end_conserved_hypothetical_protein;_possible_GTP_cyclohydrolase_I_family_3381254..3381484_POSITIVE 276 49 2 67 20 tfor:TF0665|5end_conserved_hypothetical_protein_709497..709727_POSITIVE 272 50 1 130 70 tfor:TF1601|5end_conserved_hypothetical_protein_1714731..1714961_POSITIVE 272 50 3 201 145 tfor:TF0653|5end_hypothetical_protein_696544..696774_POSITIVE 271 33 1 134 98 tfor:TF2613|5end_conserved_hypothetical_protein_2788477..2788707_POSITIVE 271 49 7 154 105 tfor:TF0582|5end_hemolysin-related_protein,_with_CBS_domains;_possible_gliding-motility_related_protein_611885..612115_POSITIVE 270 49 1 165 109 tfor:TF2631|5end_conserved_hypothetical_protein_2801694..2801924_POSITIVE 270 50 2 139 95 tfor:TF0912|5end_transposase_954329..954559_POSITIVE 267 56 14 203 166 tfor:TF2794|5end_possible_transcriptional_regulator_2979938..2980168_POSITIVE 267 50 3 203 167 tfor:TF1833|5end_2-isopropylmalate_synthase_1981511..1981741_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 483 56 12 151 108 tfor:TF2628|3end_conserved_hypothetical_protein_2801376..2801526_POSITIVE 459 60 15 82 36 tfor:TF2611|3end_conserved_hypothetical_protein_2788069..2788219_POSITIVE 320 41 4 147 117 tfor:TF0754|3end_GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-redu_ctase_(GDP-L-fucose_synthetase)_802775..802925_POSITIVE 318 42 9 82 53 tfor:TF0175|3end_hypothetical_protein_185907..186057_POSITIVE 315 80 38 108 61 tfor:TF2615|3end_conserved_hypothetical_protein_2791209..2791359_POSITIVE 313 66 21 61 11 tfor:TF1014|3end_glucose-6-phosphate_isomerase_1072474..1072624_POSITIVE 310 50 1 71 24 tfor:TF2604|3end_possible_membrane_transport_protein_2779832..2779982_POSITIVE 303 60 16 57 9 tfor:TF1489|3end_argininosuccinate_lyase_1590318..1590468_POSITIVE 300 49 16 151 118 tfor:TF2264|3end_transfer_region-related_protein,_TraO_2433542..2433692_POSITIVE 299 42 2 84 30 tfor:TF1167|3end_hypothetical_protein_1248932..1249082_POSITIVE 285 49 1 151 92 tfor:TF1284|3end_glyceraldehyde_3-phosphate_dehydrogenase_1369026..1369176_POSITIVE 283 48 1 46 3 tfor:TF1483|3end_glycosyltransferase_family_protein_1578825..1578975_POSITIVE 276 49 2 60 13 tfor:TF0664|3end_small_protein_B_(SMPB)_709570..709720_POSITIVE 275 42 1 142 92 tfor:TF0613|3end_conserved_hypothetical_protein_647421..647571_POSITIVE 272 50 1 136 76 tfor:TF1600|3end_uroporphyrinogen-III_synthase_1714817..1714967_POSITIVE 272 50 3 99 43 tfor:TF0652|3end_conserved_hypothetical_protein_696522..696672_POSITIVE 271 33 1 134 98 tfor:TF2612|3end_conserved_hypothetical_protein_2788557..2788707_POSITIVE 271 49 7 121 72 tfor:TF0581|3end_single_stranded_DNA-binding_protein_611932..612082_POSITIVE 268 40 4 150 109 tfor:TF1294|3end_conserved_hypothetical_protein_1378331..1378481_POSITIVE 267 56 14 73 36 tfor:TF2793|3end_possible_L-lysine_2,3-aminomutase_2979888..2980038_POSITIVE