Origin IGS: taaatgtctattttttgactatcgaaaaaaaggcagcctttctcaaaaaaaggtggccttttttcgttatggccagtctacacgaaaaagaaccggctcctctcatattccgaaaaaaacaccctctcttgctcggttacgaaccggcaggacagaacaaatccctatctcacaggtttcccatagagacagggattttcattagcctacaaaaacactcaacggccgagatcaactgcccccccccttgtagttctgccttctcccgaaagccgataaacatctctttccgggaacaatcaatctttta .........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 taaaagattgattgttcccggaaagagatgtttatcggctttcgggagaaggcagaactacaagggggggggcagttgatctcggccgttgagtgtttttgtaggctaatgaaaatccctgtctctatgggaaacctgtgagatagggatttgttctgtcctgccggttcgtaaccgagcaagagagggtgtttttttcggaatatgagaggagccggttctttttcgtgtagactggccataacgaaaaaaggccacctttttttgagaaaggctgcctttttttcgatagtcaaaaaatagacattta Mask Tandem Repeat Region ================================================ taaatgtctattttttgactatcgaaaaaaaggcagcctttctcaaaaaaaggtggccttttttcgttatggccagtctacacgaaaaagaaccggctcctctcatattccgaaaaaaacaccctctcttgctcggttacgaaccggcaggacagaacaaatccctatctcacaggtttcccatagagacagggattttcattagcctacaaaaacactcaacggccgagatcaactgcccccccccttgtagttctgccttctcccgaaagccgataaacatctctttccgggaacaatcaatctttta Find is-nt database================================================ Query_seq: TF1527:TF1528|TF1527:TF1528:hypothetical protein:malate dehydrogenase:->->:1633117..1633426 310 taaatgtctattttttgactatcgaaaaaaaggcagcctttctcaaaaaaaggtggccttttttcgttatggccagtctacacgaaaaagaaccggctcctctcatattccgaaaaaaacaccctctcttgctcggttacgaaccggcaggacagaacaaatccctatctcacaggtttcccatagagacagggattttcattagcctacaaaaacactcaacggccgagatcaactgcccccccccttgtagttctgccttctcccgaaagccgataaacatctctttccgggaacaatcaatctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1527:TF1528|TF1527:TF1528:hypothetical protein:malate dehydrogenase:->->:1633117..1633426 310 taaatgtctattttttgactatcgaaaaaaaggcagcctttctcaaaaaaaggtggccttttttcgttatggccagtctacacgaaaaagaaccggctcctctcatattccgaaaaaaacaccctctcttgctcggttacgaaccggcaggacagaacaaatccctatctcacaggtttcccatagagacagggattttcattagcctacaaaaacactcaacggccgagatcaactgcccccccccttgtagttctgccttctcccgaaagccgataaacatctctttccgggaacaatcaatctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1527:TF1528|TF1527:TF1528:hypothetical protein:malate dehydrogenase:->->:1633117..1633426 310 taaatgtctattttttgactatcgaaaaaaaggcagcctttctcaaaaaaaggtggccttttttcgttatggccagtctacacgaaaaagaaccggctcctctcatattccgaaaaaaacaccctctcttgctcggttacgaaccggcaggacagaacaaatccctatctcacaggtttcccatagagacagggattttcattagcctacaaaaacactcaacggccgagatcaactgcccccccccttgtagttctgccttctcccgaaagccgataaacatctctttccgggaacaatcaatctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatgtctattttttgactatcgaaaaaaaggcagcctttctcaaaaaaaggtggccttttttcgttatggccagtctacacgaaaaagaaccggctcctctcatattccgaaaaaaacaccctctcttgctcggttacgaaccggcaggacagaacaaatccctatctcacaggtttcccatagagacagggattttcattagcctacaaaaacactcaacggccgagatcaactgcccccccccttgtagttctgccttctcccgaaagccgataaacatctctttccgggaacaatcaatctttta Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 53 End: 202 .................................................... M A F F R Y G Q S T R K R T G S S H I P K K T P S L A R L R T G R T E Q I P I S Q V S H R D R D F H ............................................................................................................ Protein_Len: 60 Strand: + Start: 15 End: 308 .............. M T I E K K A A F L K K R W P F F V M A S L H E K E P A P L I F R K K H P L L L G Y E P A G Q N K S L S H R F P I E T G .. Protein_Len: 44 Strand: - Start: 173 End: 304 ............................................................................................................................................................................ L N G M S V P I K M L R C F C E V A S I L Q G G G Q L E A K E R F G I F M E K R S C D M ...... Protein_Len: 32 Strand: - Start: 11 End: 106 .......... K K V I S F F A A K R L F L H G K K T I A L R C S F S G A G R M ............................................................................................................................................................................................................ taaatgtctattttttgactatcgaaaaaaaggcagcctttctcaaaaaaaggtggccttttttcgttatggccagtctacacgaaaaagaaccggctcctctcatattccgaaaaaaacaccctctcttgctcggttacgaaccggcaggacagaacaaatccctatctcacaggtttcccatagagacagggattttcattagcctacaaaaacactcaacggccgagatcaactgcccccccccttgtagttctgccttctcccgaaagccgataaacatctctttccgggaacaatcaatctttta 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================================================ taaatgtctattttttgactatcgaaaaaaaggcagcctttctcaaaaaaaggtggccttttttcgttatggccagtctacacgaaaaagaaccggctcctctcatattccgaaaaaaacaccctctcttgctcggttacgaaccggcaggacagaacaaatccctatctcacaggtttcccatagagacagggattttcattagcctacaaaaacactcaacggccgagatcaactgcccccccccttgtagttctgccttctcccgaaagccgataaacatctctttccgggaacaatcaatctttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 93 HP_score: -5.8 Tail_Score: -5.48825 Start: 32 End: 58 Full_Region: gccataacgaaaaaa ggccaccttttt ttg agaaaggctgcc tttttttcgatagtc ...............................ggccacctttttttgagaaaggctgcc............................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 86 HP_score: -9.7 Tail_Score: -4.41114 Start: 162 End: 195 Full_Region: gtaggctaatgaaaa tccctgtctctatggg aaa cctgtgagataggga tttgttctgtcctgc .................................................................................................................................................................tccctgtctctatgggaaacctgtgagataggga................................................................................................................... Find igs database================================================ Query_seq: TF1527:TF1528|TF1527:TF1528:hypothetical protein:malate dehydrogenase:->->:1633117..1633426 310 taaatgtctattttttgactatcgaaaaaaaggcagcctttctcaaaaaaaggtggccttttttcgttatggccagtctacacgaaaaagaaccggctcctctcatattccgaaaaaaacaccctctcttgctcggttacgaaccggcaggacagaacaaatccctatctcacaggtttcccatagagacagggattttcattagcctacaaaaacactcaacggccgagatcaactgcccccccccttgtagttctgccttctcccgaaagccgataaacatctctttccgggaacaatcaatctttta Intra-Species Hit: Count: 1 Min: 1 Max: 310 Len: 310 Subject: tfor_TF1527_TF1528|hypothetical protein:malate dehydrogenase|POSITIVE:POSITIVE|[1633117,1633426]|310 HSP 1 e-value: 1.0E-121 bit: 436.0 Len: 310 Query Start:1 Query End:310 Subject Strand: POSITIVE Subject Start: 1 Subject End: 310 taaatgtctattttttgactatcgnnnnnnnggcagcctttctcnnnnnnnggtggccttttttcgttatggccagtctacacgaaaaagaaccggctcctctcatattccgnnnnnnncaccctctcttgctcggttacgaaccggcaggacagaacaaatccctatctcacaggtttcccatagagacagggattttcattagcctacaaaaacactcaacggccgagatcaactgnnnnnnnnnttgtagttctgccttctcccgaaagccgataaacatctctttccgggaacaatcaatctttta taaatgtctattttttgactatcgaaaaaaaggcagcctttctcaaaaaaaggtggccttttttcgttatggccagtctacacgaaaaagaaccggctcctctcatattccgaaaaaaacaccctctcttgctcggttacgaaccggcaggacagaacaaatccctatctcacaggtttcccatagagacagggattttcattagcctacaaaaacactcaacggccgagatcaactgcccccccccttgtagttctgccttctcccgaaagccgataaacatctctttccgggaacaatcaatctttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUGUCUAUUUUUUGACUAUCGAAAAAAAGGCAGCCUUUCUCAAAAAAAGGUGGCCUUUUUUCGUUAUGGCCAGUCUACACGAAAAAGAACCGGCUCCUCUCAUAUUCCGAAAAAAACACCCUCUCUUGCUCGGUUACGAACCGGCAGGACAGAACAAAUCCCUAUCUCACAGGUUUCCCAUAGAGACAGGGAUUUUCAUUAGCCUACAAAAACACUCAACGGCCGAGAUCAACUGCCCCCCCCCUUGUAGUUCUGCCUUCUCCCGAAAGCCGAUAAACAUCUCUUUCCGGGAACAAUCAAUCUUUUA .....(((........)))...((((((((.(((.((((((.......)))))).)))))))))))....(((.((.(((((.(..........((((.........................((.((((((.((((.....)))))))))).))...((((((((.((((...((....))...)))).)))))))).....))))................(((.(.......).)))......).)))))..)))))...(((((((((..(((....))).)))).)))))............... (-79.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGAUUGAUUGUUCCCGGAAAGAGAUGUUUAUCGGCUUUCGGGAGAAGGCAGAACUACAAGGGGGGGGGCAGUUGAUCUCGGCCGUUGAGUGUUUUUGUAGGCUAAUGAAAAUCCCUGUCUCUAUGGGAAACCUGUGAGAUAGGGAUUUGUUCUGUCCUGCCGGUUCGUAACCGAGCAAGAGAGGGUGUUUUUUUCGGAAUAUGAGAGGAGCCGGUUCUUUUUCGUGUAGACUGGCCAUAACGAAAAAAGGCCACCUUUUUUUGAGAAAGGCUGCCUUUUUUUCGAUAGUCAAAAAAUAGACAUUUA ....((((..(((((((((.......(((....))).((((((....))))))..............)))))))))..)))).(((((((..........((((((......(((((((((((((...((....))...))))))))))))).....).)))))..(((((....)))))..(((((((.((((((((((.....)))))))))).....))))))).....))).))))....(((((((((((..((((((.....))))))..))).))))))))...(((........)))..... (-110.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 409 267 225 80 31 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 403 295 252 69 18 tfor:TF2128|5end_3-oxoacyl-(acyl-carrier_protein)_synthase_2304258..2304488_POSITIVE 396 268 223 54 1 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 395 290 241 75 29 tfor:TF2336|5end_conserved_hypothetical_protein_2496169..2496399_POSITIVE 381 269 223 69 23 tfor:TF1240|5end_conserved_hypothetical_protein_1324304..1324534_POSITIVE 373 267 241 225 200 tfor:TF0830|5end_hypothetical_protein_887610..887840_POSITIVE 369 167 130 196 152 tfor:TF1581|5end_hypothetical_protein_1689199..1689429_POSITIVE 368 268 224 55 2 tfor:TF2511|5end_RNA_binding_protein_2689910..2690140_POSITIVE 367 170 122 180 141 tfor:TF2504|5end_peptidyl-prolyl_cis-trans_isomerase_2680031..2680261_POSITIVE 364 275 239 225 177 tfor:TF1594|5end_hypothetical_protein_1709903..1710133_POSITIVE 358 100 52 53 2 tfor:TF1775|5end_oxidoreductase,_Gfo/Idh/MocA_family_1913135..1913365_POSITIVE 354 156 120 35 1 tfor:TF2515|5end_outer_membrane_protein,_TonB_dependent_receptor_2692854..2693084_POSITIVE 349 100 52 166 121 tfor:TF1995|5end_exonuclease_2147148..2147378_POSITIVE 345 259 220 227 180 tfor:TF0763|5end_chromate_transport_protein_809675..809905_POSITIVE 340 208 166 83 37 tfor:TF2844|5end_possible_phosphatase_or_hydrolase_3033680..3033910_POSITIVE 340 166 128 199 158 tfor:TF2207|5end_exo-alpha-sialidase_(neuraminidase)_2380907..2381137_POSITIVE 338 169 124 225 177 tfor:TF0338|5end_alkaline_phosphatase_361788..362018_POSITIVE 337 157 119 90 48 tfor:TF2932|5end_capsule_biosynthesis_protein_3135514..3135744_POSITIVE 335 267 222 220 172 tfor:TF2653|5end_hypothetical_protein_2822093..2822323_POSITIVE 335 226 181 49 10 tfor:TF1028|5end_1-acyl-sn-glycerol-3-phosphate_acyltransferase_1085937..1086167_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 409 267 225 149 100 tfor:TF3106|3end_hypothetical_protein_3338608..3338758_POSITIVE 389 150 101 58 15 tfor:TF2646|3end_conserved_hypothetical_protein_2816697..2816847_POSITIVE 373 267 241 43 18 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 347 166 122 77 37 tfor:TF3009|3end_RNA_polymerase_ECF-type_sigma_factor_3229709..3229859_POSITIVE 340 208 166 83 37 tfor:TF2843|3end_conserved_hypothetical_protein;_possible_lipoprotein_3033760..3033910_POSITIVE 337 157 119 80 38 tfor:TF2931|3end_3-deoxy-D-manno-2-octulosonic_acid_(Kdo_transferase)_3135584..3135734_POSITIVE 335 267 222 61 13 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 333 275 232 106 61 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 333 170 125 86 33 tfor:TF2184|3end_conserved_hypothetical_protein_2357043..2357193_POSITIVE 331 268 223 142 95 tfor:TF1443|3end_hypothetical_protein_1528203..1528353_POSITIVE 331 270 223 62 8 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 325 260 215 51 7 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 324 277 234 83 35 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 322 163 131 143 98 tfor:TF0041|3end_outer_membrane_protein,_TonB_dependent_receptor_45942..46092_POSITIVE 320 248 207 44 4 tfor:TF2603|3end_transcriptional_regulator,_AraC_family_2777272..2777422_POSITIVE 320 276 237 83 32 tfor:TF1682|3end_hydrolase_1797343..1797493_POSITIVE 318 246 215 44 10 tfor:TF2999|3end_conserved_hypothetical_protein_3215891..3216041_POSITIVE 316 170 123 71 22 tfor:TF1420|3end_cell_division_protein_1503545..1503695_POSITIVE 315 176 131 72 28 tfor:TF1342|3end_possible_lipoprotein_1424620..1424770_POSITIVE 314 289 243 51 1 tfor:TF0821|3end_hypothetical_protein_880195..880345_POSITIVE