Origin IGS: ttttttgtcattgctgcccgataaaagtatttgattaggataaaaaacagaacgtctcgttaaaatactttatggtgaaagtgcccataccatcttgatattattcagttttatcgggaaataaattctaataaagattctcccgaatttatatgattgggcggaggcttatccatcgtttttaacggacaacaatgaataaataagaaggggcaggcttttgaaggcttggttaaataagtttggcttttcgttgtacatcttttatctttgtcgcccatagatgtaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttacatctatgggcgacaaagataaaagatgtacaacgaaaagccaaacttatttaaccaagccttcaaaagcctgccccttcttatttattcattgttgtccgttaaaaacgatggataagcctccgcccaatcatataaattcgggagaatctttattagaatttatttcccgataaaactgaataatatcaagatggtatgggcactttcaccataaagtattttaacgagacgttctgttttttatcctaatcaaatacttttatcgggcagcaatgacaaaaaa Mask Tandem Repeat Region ================================================ ttttttgtcattgctgcccgataaaagtatttgattaggataaaaaacagaacgtctcgttaaaatactttatggtgaaagtgcccataccatcttgatattattcagttttatcgggaaataaattctaataaagattctcccgaatttatatgattgggcggaggcttatccatcgtttttaacggacaacaatgaataaataagaaggggcaggcttttgaaggcttggttaaataagtttggcttttcgttgtacatcttttatctttgtcgcccatagatgtaaa Find is-nt database================================================ Query_seq: TF0297:TF0298|TF0297:TF0298:RNA polymerase sigma-70 factor, ECF subfamily:dipeptidase:->->:322977..323266 290 ttttttgtcattgctgcccgataaaagtatttgattaggataaaaaacagaacgtctcgttaaaatactttatggtgaaagtgcccataccatcttgatattattcagttttatcgggaaataaattctaataaagattctcccgaatttatatgattgggcggaggcttatccatcgtttttaacggacaacaatgaataaataagaaggggcaggcttttgaaggcttggttaaataagtttggcttttcgttgtacatcttttatctttgtcgcccatagatgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0297:TF0298|TF0297:TF0298:RNA polymerase sigma-70 factor, ECF subfamily:dipeptidase:->->:322977..323266 290 ttttttgtcattgctgcccgataaaagtatttgattaggataaaaaacagaacgtctcgttaaaatactttatggtgaaagtgcccataccatcttgatattattcagttttatcgggaaataaattctaataaagattctcccgaatttatatgattgggcggaggcttatccatcgtttttaacggacaacaatgaataaataagaaggggcaggcttttgaaggcttggttaaataagtttggcttttcgttgtacatcttttatctttgtcgcccatagatgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0297:TF0298|TF0297:TF0298:RNA polymerase sigma-70 factor, ECF subfamily:dipeptidase:->->:322977..323266 290 ttttttgtcattgctgcccgataaaagtatttgattaggataaaaaacagaacgtctcgttaaaatactttatggtgaaagtgcccataccatcttgatattattcagttttatcgggaaataaattctaataaagattctcccgaatttatatgattgggcggaggcttatccatcgtttttaacggacaacaatgaataaataagaaggggcaggcttttgaaggcttggttaaataagtttggcttttcgttgtacatcttttatctttgtcgcccatagatgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttttgtcattgctgcccgataaaagtatttgattaggataaaaaacagaacgtctcgttaaaatactttatggtgaaagtgcccataccatcttgatattattcagttttatcgggaaataaattctaataaagattctcccgaatttatatgattgggcggaggcttatccatcgtttttaacggacaacaatgaataaataagaaggggcaggcttttgaaggcttggttaaataagtttggcttttcgttgtacatcttttatctttgtcgcccatagatgtaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 172 End: 261 ........................................................................................................................................................................... G D N K V S L L S Y I L L P L S K F A Q N F L N P K E N Y M ............................. Protein_Len: 56 Strand: - Start: 114 End: 281 ................................................................................................................. R S I F E L L S E G S N I H N P P P K D M T K L P C C H I F L F P C A K S P K T L Y T Q S K T T C R K D K D G M ......... ttttttgtcattgctgcccgataaaagtatttgattaggataaaaaacagaacgtctcgttaaaatactttatggtgaaagtgcccataccatcttgatattattcagttttatcgggaaataaattctaataaagattctcccgaatttatatgattgggcggaggcttatccatcgtttttaacggacaacaatgaataaataagaaggggcaggcttttgaaggcttggttaaataagtttggcttttcgttgtacatcttttatctttgtcgcccatagatgtaaa 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================================================ ttttttgtcattgctgcccgataaaagtatttgattaggataaaaaacagaacgtctcgttaaaatactttatggtgaaagtgcccataccatcttgatattattcagttttatcgggaaataaattctaataaagattctcccgaatttatatgattgggcggaggcttatccatcgtttttaacggacaacaatgaataaataagaaggggcaggcttttgaaggcttggttaaataagtttggcttttcgttgtacatcttttatctttgtcgcccatagatgtaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0297:TF0298|TF0297:TF0298:RNA polymerase sigma-70 factor, ECF subfamily:dipeptidase:->->:322977..323266 290 ttttttgtcattgctgcccgataaaagtatttgattaggataaaaaacagaacgtctcgttaaaatactttatggtgaaagtgcccataccatcttgatattattcagttttatcgggaaataaattctaataaagattctcccgaatttatatgattgggcggaggcttatccatcgtttttaacggacaacaatgaataaataagaaggggcaggcttttgaaggcttggttaaataagtttggcttttcgttgtacatcttttatctttgtcgcccatagatgtaaa Intra-Species Hit: Count: 1 Min: 1 Max: 290 Len: 290 Subject: tfor_TF0297_TF0298|RNA polymerase sigma-70 factor, ECF subfamily:dipeptidase|POSITIVE:POSITIVE|[322977, 323266]|290 HSP 1 e-value: 1.0E-163 bit: 575.0 Len: 290 Query Start:1 Query End:290 Subject Strand: POSITIVE Subject Start: 1 Subject End: 290 ttttttgtcattgctgcccgataaaagtatttgattaggataaaaaacagaacgtctcgttaaaatactttatggtgaaagtgcccataccatcttgatattattcagttttatcgggaaataaattctaataaagattctcccgaatttatatgattgggcggaggcttatccatcgtttttaacggacaacaatgaataaataagaaggggcaggcttttgaaggcttggttaaataagtttggcttttcgttgtacatcttttatctttgtcgcccatagatgtaaa ttttttgtcattgctgcccgataaaagtatttgattaggataaaaaacagaacgtctcgttaaaatactttatggtgaaagtgcccataccatcttgatattattcagttttatcgggaaataaattctaataaagattctcccgaatttatatgattgggcggaggcttatccatcgtttttaacggacaacaatgaataaataagaaggggcaggcttttgaaggcttggttaaataagtttggcttttcgttgtacatcttttatctttgtcgcccatagatgtaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUUGUCAUUGCUGCCCGAUAAAAGUAUUUGAUUAGGAUAAAAAACAGAACGUCUCGUUAAAAUACUUUAUGGUGAAAGUGCCCAUACCAUCUUGAUAUUAUUCAGUUUUAUCGGGAAAUAAAUUCUAAUAAAGAUUCUCCCGAAUUUAUAUGAUUGGGCGGAGGCUUAUCCAUCGUUUUUAACGGACAACAAUGAAUAAAUAAGAAGGGGCAGGCUUUUGAAGGCUUGGUUAAAUAAGUUUGGCUUUUCGUUGUACAUCUUUUAUCUUUGUCGCCCAUAGAUGUAAA ...((((((((((.((.(((.((((((....((((..((((((..........(((((.......((((....)))).....(((((...(((.((((......)))).....((((((.......(((.....)))...))))))......)))..))))).))))))))))))))))))))).))).)).))))).)))))...((((((.(((((((((((........))))..))))))).))))))....(((((((..................))))))).. (-64.47) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACAUCUAUGGGCGACAAAGAUAAAAGAUGUACAACGAAAAGCCAAACUUAUUUAACCAAGCCUUCAAAAGCCUGCCCCUUCUUAUUUAUUCAUUGUUGUCCGUUAAAAACGAUGGAUAAGCCUCCGCCCAAUCAUAUAAAUUCGGGAGAAUCUUUAUUAGAAUUUAUUUCCCGAUAAAACUGAAUAAUAUCAAGAUGGUAUGGGCACUUUCACCAUAAAGUAUUUUAACGAGACGUUCUGUUUUUUAUCCUAAUCAAAUACUUUUAUCGGGCAGCAAUGACAAAAAA ...........(((((.........................(((.....)))..........((........)).)))))............(((((((((((((.(((((..(((((((((......((((((((((......((((((((.(((.....))).....))))))))......(((......)))..))))).)))))........................(((((.....)))))))))))..)))......))))).)))))))))))))....... (-57.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 46 4 120 84 tfor:TF2972|5end_conserved_hypothetical_protein_3180197..3180427_POSITIVE 334 256 211 82 40 tfor:TF2208|5end_conserved_hypothetical_protein_2382349..2382579_POSITIVE 327 190 141 80 25 tfor:TF2540|5end_conserved_hypothetical_protein_2723058..2723288_POSITIVE 322 288 245 188 137 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 321 220 173 192 145 tfor:TF3028|5end_1-deoxy-d-xylulose-5-phosphate_reductoisomerase_3251642..3251872_POSITIVE 311 286 241 136 76 tfor:TF0930|5end_conserved_hypothetical_protein;_possible_prophage_protein_968782..969012_POSITIVE 308 199 156 95 52 tfor:TF0094|5end_alpha-glucosidase_103561..103791_POSITIVE 305 189 141 221 169 tfor:TF0280|5end_hypothetical_protein_308807..309037_POSITIVE 304 247 205 104 48 tfor:TF2999|5end_conserved_hypothetical_protein_3215566..3215796_POSITIVE 303 174 142 48 21 tfor:TF0687|5end_hypothetical_protein_732226..732456_POSITIVE 301 250 207 104 64 tfor:TF1499|5end_3-oxyacyl-[acyl-carrier_protein]_synthase_1598394..1598624_POSITIVE 300 189 143 68 27 tfor:TF2349|5end_conserved_hypothetical_protein_2513192..2513422_POSITIVE 300 188 142 71 19 tfor:TF0617|5end_alpha-1,2-mannosidase_650862..651092_POSITIVE 299 190 143 176 123 tfor:TF1243|5end_periplasmic_protease_1327243..1327473_POSITIVE 298 190 145 63 6 tfor:TF1214|5end_conserved_hypothetical_protein_1301213..1301443_POSITIVE 298 230 184 151 95 tfor:TF1027|5end_hypothetical_protein_1085641..1085871_POSITIVE 296 247 209 173 121 tfor:TF1198|5end_conserved_hypothetical_protein_1281464..1281694_POSITIVE 295 191 155 206 171 tfor:TF1179|5end_two-component_sensor_histidine_kinase_1266057..1266287_POSITIVE 293 188 141 75 28 tfor:TF1534|5end_conserved_hypothetical_protein_1639485..1639715_POSITIVE 293 256 213 231 173 tfor:TF0789|5end_preprotein_translocase,_secDF_family_841293..841523_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 190 141 58 3 tfor:TF2539|3end_hypothetical_protein_2723116..2723266_POSITIVE 321 220 173 89 42 tfor:TF3027|3end_zinc_metalloprotease_3251619..3251769_POSITIVE 313 39 3 74 36 tfor:TF2896|3end_conserved_hypothetical_protein;_possible_ATPase,_AAA_superfamily_3085687..3085837_POSITIVE 311 286 241 136 76 tfor:TF0929|3end_conserved_hypothetical_protein_968862..969012_POSITIVE 308 199 156 72 29 tfor:TF0093|3end_outer_membrane_protein,_TonB_dependent_receptor_103618..103768_POSITIVE 301 250 207 120 80 tfor:TF1498|3end_GTP-binding_protein_1598490..1598640_POSITIVE 300 189 143 48 7 tfor:TF2348|3end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2513252..2513402_POSITIVE 298 230 184 69 13 tfor:TF1026|3end_beta-N-acetylglucosaminidase;_beta_lactamase_1085639..1085789_POSITIVE 289 189 141 68 12 tfor:TF0079|3end_conserved_hypothetical_protein_86273..86423_POSITIVE 287 252 211 136 91 tfor:TF0203|3end_PhoH-like_protein_230660..230810_POSITIVE 283 178 135 139 90 tfor:TF3022|3end_chorismate_synthase_3247301..3247451_POSITIVE 282 290 261 30 3 tfor:TF2532|3end_ferric-uptake_regulator_2715708..2715858_POSITIVE 282 189 152 120 89 tfor:TF0429|3end_ABC_transporter,_ATP-binding_protein_452227..452377_POSITIVE 281 188 142 112 65 tfor:TF3004|3end_phosphoribosylformylglycinamidine_(FGAM)_synthase_3224576..3224726_POSITIVE 281 246 204 119 75 tfor:TF2458|3end_ribosome-binding_factor_A_2635645..2635795_POSITIVE 281 246 209 140 107 tfor:TF0815|3end_conserved_hypothetical_protein_873974..874124_POSITIVE 275 179 137 129 99 tfor:TF2230|3end_CTn_excision_protein_2400394..2400544_POSITIVE 274 247 205 117 75 tfor:TF0991|3end_probable_NAD(FAD)-dependent_dehydrogenase_1048334..1048484_POSITIVE 271 191 158 50 18 tfor:TF3159|3end_conserved_hypothetical_protein;_possible_transcriptional_regulator_3395611..3395761_POSITIVE 270 195 157 69 18 tfor:TF0212|3end_DNA/pantothenate_metabolism_flavoprotein_239001..239151_POSITIVE