Origin IGS: taatccgtccgtctgcctgaagcagcgtaaaaaaagggcgttcttgcaaaagagcgtccttttttcagttcatccagcacaggtatcagcccttgtaaaacttacggtttatctgaccgctgatcaacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagttgatcagcggtcagataaaccgtaagttttacaagggctgatacctgtgctggatgaactgaaaaaaggacgctcttttgcaagaacgccctttttttacgctgcttcaggcagacggacggatta Mask Tandem Repeat Region ================================================ taatccgtccgtctgcctgaagcagcgtaaaaaaagggcgttcttgcaaaagagcgtccttttttcagttcatccagcacaggtatcagcccttgtaaaacttacggtttatctgaccgctgatcaacta Find is-nt database================================================ Query_seq: TF1943:TF1944|TF1943:TF1944:phosphoenolpyruvate carboxykinase:conserved hypothetical protein:->->:2092526..2092655 130 taatccgtccgtctgcctgaagcagcgtaaaaaaagggcgttcttgcaaaagagcgtccttttttcagttcatccagcacaggtatcagcccttgtaaaacttacggtttatctgaccgctgatcaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1943:TF1944|TF1943:TF1944:phosphoenolpyruvate carboxykinase:conserved hypothetical protein:->->:2092526..2092655 130 taatccgtccgtctgcctgaagcagcgtaaaaaaagggcgttcttgcaaaagagcgtccttttttcagttcatccagcacaggtatcagcccttgtaaaacttacggtttatctgaccgctgatcaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1943:TF1944|TF1943:TF1944:phosphoenolpyruvate carboxykinase:conserved hypothetical protein:->->:2092526..2092655 130 taatccgtccgtctgcctgaagcagcgtaaaaaaagggcgttcttgcaaaagagcgtccttttttcagttcatccagcacaggtatcagcccttgtaaaacttacggtttatctgaccgctgatcaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatccgtccgtctgcctgaagcagcgtaaaaaaagggcgttcttgcaaaagagcgtccttttttcagttcatccagcacaggtatcagcccttgtaaaacttacggtttatctgaccgctgatcaacta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 17 End: 130 ................ M K Q R K K R A F L Q K S V L F S V H P A Q V S A L V K L T V Y L T A D Q L taatccgtccgtctgcctgaagcagcgtaaaaaaagggcgttcttgcaaaagagcgtccttttttcagttcatccagcacaggtatcagcccttgtaaaacttacggtttatctgaccgctgatcaacta 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================================================ taatccgtccgtctgcctgaagcagcgtaaaaaaagggcgttcttgcaaaagagcgtccttttttcagttcatccagcacaggtatcagcccttgtaaaacttacggtttatctgaccgctgatcaacta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 84 HP_score: -5.2 Tail_Score: -5.44721 Start: 36 End: 59 Full_Region: gatgaactgaaaaaa ggacgctctt ttgc aagaacgccc tttttttacgctgct ...................................ggacgctcttttgcaagaacgccc....................................................................... Find igs database================================================ Query_seq: TF1943:TF1944|TF1943:TF1944:phosphoenolpyruvate carboxykinase:conserved hypothetical protein:->->:2092526..2092655 130 taatccgtccgtctgcctgaagcagcgtaaaaaaagggcgttcttgcaaaagagcgtccttttttcagttcatccagcacaggtatcagcccttgtaaaacttacggtttatctgaccgctgatcaacta Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: tfor_TF1943_TF1944|phosphoenolpyruvate carboxykinase:conserved hypothetical protein|POSITIVE:POSITIVE|[2092526,2092655]|130 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 taatccgtccgtctgcctgaagcagcgtnnnnnnngggcgttcttgcaaaagagcgtccttttttcagttcatccagcacaggtatcagcccttgtaaaacttacggtttatctgaccgctgatcaacta taatccgtccgtctgcctgaagcagcgtaaaaaaagggcgttcttgcaaaagagcgtccttttttcagttcatccagcacaggtatcagcccttgtaaaacttacggtttatctgaccgctgatcaacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCCGUCCGUCUGCCUGAAGCAGCGUAAAAAAAGGGCGUUCUUGCAAAAGAGCGUCCUUUUUUCAGUUCAUCCAGCACAGGUAUCAGCCCUUGUAAAACUUACGGUUUAUCUGACCGCUGAUCAACUA .........((.((((.....))))))..((((((((((((((((....)))))))))))))))).((((.(((.(((.((((((..((((...(((.....)))))))))))))...)))))).)))). (-40.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUGAUCAGCGGUCAGAUAAACCGUAAGUUUUACAAGGGCUGAUACCUGUGCUGGAUGAACUGAAAAAAGGACGCUCUUUUGCAAGAACGCCCUUUUUUUACGCUGCUUCAGGCAGACGGACGGAUUA .((((.(((.(((((.......)))))......((((.((.......))))))...))).))))(((((((((.((.((((....)))).)).))))))))).((((((.....)))).))......... (-33.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 92 58 190 141 tfor:TF2758|5end_hypothetical_protein_2942392..2942622_POSITIVE 341 60 12 171 134 tfor:TF2808|5end_bacterial_sugar_transferase_2998432..2998662_POSITIVE 341 46 5 164 131 tfor:TF1070|5end_hydrolase_1139704..1139934_POSITIVE 332 92 55 198 162 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 329 49 3 176 117 tfor:TF3097|5end_conserved_hypothetical_protein_3328661..3328891_POSITIVE 321 47 4 55 13 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 321 47 4 48 6 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 319 30 4 231 207 tfor:TF2690|5end_possible_permease_2865466..2865696_POSITIVE 319 47 4 156 104 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 312 60 13 55 5 tfor:TF3105|5end_hypothetical_protein_3338068..3338298_POSITIVE 311 59 13 117 72 tfor:TF2296|5end_hypothetical_protein_2448892..2449122_POSITIVE 308 39 2 222 186 tfor:TF2516|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2692071..2692301_POSITIVE 308 60 11 56 3 tfor:TF1465|5end_modulator_of_DNA_gyrase_1554148..1554378_POSITIVE 308 124 86 57 22 tfor:TF1088|5end_transposase_fragment_1158060..1158290_POSITIVE 308 59 13 41 1 tfor:TF0421|5end_alpha-L-fucosidase_436021..436251_POSITIVE 307 73 35 69 22 tfor:TF1064|5end_ampG_permease_1134004..1134234_POSITIVE 305 43 3 40 3 tfor:TF0463|5end_precorrin-6Y_C5,15-methyltransferase_479015..479245_POSITIVE 302 47 3 68 22 tfor:TF1935|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2082002..2082232_POSITIVE 301 92 51 186 139 tfor:TF3096|5end_conserved_hypothetical_protein_3327963..3328193_POSITIVE 301 55 17 181 138 tfor:TF1555|5end_hypothetical_protein_1661061..1661291_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 422 60 14 56 6 tfor:TF1943|3end_phosphoenolpyruvate_carboxykinase_2092465..2092615_POSITIVE 350 92 58 53 4 tfor:TF2757|3end_hypothetical_protein_2942335..2942485_POSITIVE 333 45 4 52 5 tfor:TF1762|3end_hypothetical_protein_1899648..1899798_POSITIVE 329 49 3 149 90 tfor:TF3096|3end_conserved_hypothetical_protein_3328714..3328864_POSITIVE 315 123 98 76 51 tfor:TF1535|3end_possible_outer_membrane_receptor_protein_1642209..1642359_POSITIVE 314 80 34 74 18 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 313 43 4 151 104 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 308 124 86 142 107 tfor:TF1087|3end_ISPg4_transposase_1158225..1158375_POSITIVE 307 56 11 125 73 tfor:TF1653|3end_hypothetical_protein_1766481..1766631_POSITIVE 307 73 35 49 2 tfor:TF1063|3end_possible_amidase_enhancer_precursor;_sporulation-related_protein_1134064..1134214_POSITIVE 307 56 11 125 73 tfor:TF0979|3end_hypothetical_protein_1033118..1033268_POSITIVE 306 60 14 69 12 tfor:TF2922|3end_surface_antigen_BspA_3121538..3121688_POSITIVE 305 40 6 118 72 tfor:TF2921|3end_hypothetical_protein_3118790..3118940_POSITIVE 305 40 6 118 72 tfor:TF2438|3end_hypothetical_protein_2616157..2616307_POSITIVE 305 40 6 118 72 tfor:TF1167|3end_hypothetical_protein_1248932..1249082_POSITIVE 305 43 3 40 3 tfor:TF0462|3end_possible_cobalamin_biosynthesis_precorrin-3_methylase_479095..479245_POSITIVE 301 55 17 53 10 tfor:TF1554|3end_UDP-glucose_dehydrogenase_1661013..1661163_POSITIVE 300 94 52 113 64 tfor:TF2656|3end_valyl-tRNA_synthetase_2829822..2829972_POSITIVE 300 60 13 132 73 tfor:TF2081|3end_phosphopantetheine_adenylyltransferase_2249031..2249181_POSITIVE 299 28 4 49 20 tfor:TF1040|3end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_1102118..1102268_POSITIVE