Origin IGS: taaacaaatctctgaaggggacactaaaattctataaaaccgatccgatgtaggcggcaaagaaaaaaaatttctacttttgtgctctaattttacagcataataatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattattatgctgtaaaattagagcacaaaagtagaaattttttttctttgccgcctacatcggatcggttttatagaattttagtgtccccttcagagatttgttta Mask Tandem Repeat Region ================================================ taaacaaatctctgaaggggacactaaaattctataaaaccgatccgatgtaggcggcaaagaaaaaaaatttctacttttgtgctctaattttacagcataataatt Find is-nt database================================================ Query_seq: TF2446:TF2447|TF2446:TF2447:riboflavin-specific deaminase:lipoprotein:->->:2623581..2623688 108 taaacaaatctctgaaggggacactaaaattctataaaaccgatccgatgtaggcggcaaagaaaaaaaatttctacttttgtgctctaattttacagcataataatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2446:TF2447|TF2446:TF2447:riboflavin-specific deaminase:lipoprotein:->->:2623581..2623688 108 taaacaaatctctgaaggggacactaaaattctataaaaccgatccgatgtaggcggcaaagaaaaaaaatttctacttttgtgctctaattttacagcataataatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2446:TF2447|TF2446:TF2447:riboflavin-specific deaminase:lipoprotein:->->:2623581..2623688 108 taaacaaatctctgaaggggacactaaaattctataaaaccgatccgatgtaggcggcaaagaaaaaaaatttctacttttgtgctctaattttacagcataataatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaacaaatctctgaaggggacactaaaattctataaaaccgatccgatgtaggcggcaaagaaaaaaaatttctacttttgtgctctaattttacagcataataatt Predict ORF larger than 30AA ================================================ taaacaaatctctgaaggggacactaaaattctataaaaccgatccgatgtaggcggcaaagaaaaaaaatttctacttttgtgctctaattttacagcataataatt 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================================================ taaacaaatctctgaaggggacactaaaattctataaaaccgatccgatgtaggcggcaaagaaaaaaaatttctacttttgtgctctaattttacagcataataatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2446:TF2447|TF2446:TF2447:riboflavin-specific deaminase:lipoprotein:->->:2623581..2623688 108 taaacaaatctctgaaggggacactaaaattctataaaaccgatccgatgtaggcggcaaagaaaaaaaatttctacttttgtgctctaattttacagcataataatt Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: tfor_TF2446_TF2447|riboflavin-specific deaminase:lipoprotein|POSITIVE:POSITIVE|[2623581, 2623688]|108 HSP 1 e-value: 9.0E-41 bit: 167.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 taaacaaatctctgaaggggacactaaaattctataaaaccgatccgatgtaggcggcaaagnnnnnnnntttctacttttgtgctctaattttacagcataataatt taaacaaatctctgaaggggacactaaaattctataaaaccgatccgatgtaggcggcaaagaaaaaaaatttctacttttgtgctctaattttacagcataataatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACAAAUCUCUGAAGGGGACACUAAAAUUCUAUAAAACCGAUCCGAUGUAGGCGGCAAAGAAAAAAAAUUUCUACUUUUGUGCUCUAAUUUUACAGCAUAAUAAUU ........((((.....))))..................(((..((......)))))...(((((.....)))))....(((((((.((....)).)))))))..... (-13.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAUUAUGCUGUAAAAUUAGAGCACAAAAGUAGAAAUUUUUUUUCUUUGCCGCCUACAUCGGAUCGGUUUUAUAGAAUUUUAGUGUCCCCUUCAGAGAUUUGUUUA ........((((.((....)).))))...(((..((.(((....((((..((((((......))..)))).....))))....))).))..))).............. (-14.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 87 41 179 136 tfor:TF1286|5end_hypothetical_protein_1369199..1369429_POSITIVE 303 64 39 61 29 tfor:TF0389|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_408774..409004_POSITIVE 283 59 39 151 130 tfor:TF1070|5end_hydrolase_1139704..1139934_POSITIVE 276 87 41 202 154 tfor:TF1799|5end_quinolinate_synthetase_1940276..1940506_POSITIVE 272 58 12 225 164 tfor:TF2311|5end_conserved_hypothetical_protein_2471290..2471520_POSITIVE 269 56 12 175 127 tfor:TF0890|5end_transfer_region-related_protein,_TraQ_940014..940244_POSITIVE 265 84 41 144 106 tfor:TF0322|5end_possible_YngK_protein_348345..348575_POSITIVE 263 58 12 143 91 tfor:TF2445|5end_protoporphyrinogen_oxidase_2621457..2621687_POSITIVE 263 59 39 49 30 tfor:TF1778|5end_conserved_hypothetical_protein_1917712..1917942_POSITIVE 262 57 13 127 81 tfor:TF1161|5end_large_conductance_mechanosensitive_channel_protein_1240931..1241161_POSITIVE 261 59 12 151 99 tfor:TF1260|5end_chaperone_protein_DnaJ_1345325..1345555_POSITIVE 259 59 12 142 103 tfor:TF1975|5end_uridylate_kinase_2121536..2121766_POSITIVE 258 58 14 218 174 tfor:TF2001|5end_conserved_hypothetical_protein_2155384..2155614_POSITIVE 258 87 53 196 163 tfor:TF1555|5end_hypothetical_protein_1661061..1661291_POSITIVE 258 59 34 201 175 tfor:TF0178|5end_ferritin_187613..187843_POSITIVE 254 63 31 60 32 tfor:TF2545|5end_hypothetical_protein_2729053..2729283_POSITIVE 254 70 39 114 75 tfor:TF2223|5end_CTn_excision__protein_2394247..2394477_POSITIVE 253 64 40 107 83 tfor:TF2916|5end_conserved_hypothetical_protein_3111559..3111789_POSITIVE 249 58 11 192 132 tfor:TF0944|5end_TonB-dependent_receptor_986340..986570_POSITIVE 246 60 39 144 121 tfor:TF1547|5end_conserved_hypothetical_protein_1651459..1651689_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 87 41 145 102 tfor:TF1285|3end_hypothetical_protein_1369245..1369395_POSITIVE 308 56 13 52 10 tfor:TF2848|3end_cobalamin_biosynthesis_protein_3037389..3037539_POSITIVE 303 64 39 53 21 tfor:TF0388|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_408846..408996_POSITIVE 287 57 11 129 74 tfor:TF0134|3end_transposase_element_146044..146194_POSITIVE 276 59 13 147 92 tfor:TF2644|3end_possible_thiamine_pyrophosphokinase_2813779..2813929_POSITIVE 272 58 12 138 77 tfor:TF2310|3end_dehydrogenase,_possible_3-oxoacyl-[acyl-carrier-protein]_reductase_2471283..2471433_POSITIVE 262 57 13 124 78 tfor:TF1160|3end_MutT/nudix_family_protein_1241008..1241158_POSITIVE 258 87 53 68 35 tfor:TF1554|3end_UDP-glucose_dehydrogenase_1661013..1661163_POSITIVE 253 64 40 46 22 tfor:TF2915|3end_hypothetical_protein_3111578..3111728_POSITIVE 253 88 44 37 2 tfor:TF0813|3end_glycosyl_hydrolase,_secreted_872181..872331_POSITIVE 251 60 12 47 4 tfor:TF0958|3end_conserved_hypothetical_protein_1004909..1005059_POSITIVE 246 60 39 151 128 tfor:TF1545|3end_conserved_hypothetical_protein_1651546..1651696_POSITIVE 243 59 13 112 59 tfor:TF2618|3end_integral_membrane_protein,_possible_zinc_transporter_2796113..2796263_POSITIVE 241 60 16 134 90 tfor:TF1145|3end_anaerobic_C4-dicarboxylate_membrane_transporter_1227180..1227330_POSITIVE 241 100 53 65 23 tfor:TF0324|3end_conserved_hypothetical_protein_351997..352147_POSITIVE 240 98 65 73 42 tfor:TF0219|3end_threonyl-tRNA_synthetase_245878..246028_POSITIVE 238 80 39 74 24 tfor:TF1717|3end_DNA_mismatch_repair_protein_1840494..1840644_POSITIVE 236 60 16 120 67 tfor:TF0614|3end_UDP-glucose_6-dehydrogenase/UDP-N-acetyl-D-mannosaminuronate_dehydrogenase_648863..649013_POSITIVE 232 63 24 132 92 tfor:TF2318|3end_conserved_hypothetical_protein_2476312..2476462_POSITIVE 232 57 14 103 53 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE