Origin IGS: tgacgcagcttgcaacagctgtccgccgcccgtatctcctccgttcgcaggcgtaaaaatatcggctgccggttgtcggttggtaattattttatacctttgcacatcgcttggaaaaacaggcggataaacattcgcaacatttaatattcgataaattcaatcatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgattgaatttatcgaatattaaatgttgcgaatgtttatccgcctgtttttccaagcgatgtgcaaaggtataaaataattaccaaccgacaaccggcagccgatatttttacgcctgcgaacggaggagatacgggcggcggacagctgttgcaagctgcgtca Mask Tandem Repeat Region ================================================ tgacgcagcttgcaacagctgtccgccgcccgtatctcctccgttcgcaggcgtaaaaatatcggctgccggttgtcggttggtaattattttatacctttgcacatcgcttggaaaaacaggcggataaacattcgcaacatttaatattcgataaattcaatcatt Find is-nt database================================================ Query_seq: TF1247:TF1249|TF1247:TF1249:alanyl-tRNA synthetase (alanine--tRNA ligase):phosphoglycerate kinase (cytosolic phosphoglycerate kinase):->->:1330989..1331156 168 tgacgcagcttgcaacagctgtccgccgcccgtatctcctccgttcgcaggcgtaaaaatatcggctgccggttgtcggttggtaattattttatacctttgcacatcgcttggaaaaacaggcggataaacattcgcaacatttaatattcgataaattcaatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1247:TF1249|TF1247:TF1249:alanyl-tRNA synthetase (alanine--tRNA ligase):phosphoglycerate kinase (cytosolic phosphoglycerate kinase):->->:1330989..1331156 168 tgacgcagcttgcaacagctgtccgccgcccgtatctcctccgttcgcaggcgtaaaaatatcggctgccggttgtcggttggtaattattttatacctttgcacatcgcttggaaaaacaggcggataaacattcgcaacatttaatattcgataaattcaatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1247:TF1249|TF1247:TF1249:alanyl-tRNA synthetase (alanine--tRNA ligase):phosphoglycerate kinase (cytosolic phosphoglycerate kinase):->->:1330989..1331156 168 tgacgcagcttgcaacagctgtccgccgcccgtatctcctccgttcgcaggcgtaaaaatatcggctgccggttgtcggttggtaattattttatacctttgcacatcgcttggaaaaacaggcggataaacattcgcaacatttaatattcgataaattcaatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgacgcagcttgcaacagctgtccgccgcccgtatctcctccgttcgcaggcgtaaaaatatcggctgccggttgtcggttggtaattattttatacctttgcacatcgcttggaaaaacaggcggataaacattcgcaacatttaatattcgataaattcaatcatt Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 10 End: 144 ......... M Q Q L S A A R I S S V R R R K N I G C R L S V G N Y F I P L H I A W K N R R I N I R N I ........................ Protein_Len: 53 Strand: - Start: 1 End: 159 S A A Q L L Q G G G T D G G N A P T F I D A A P Q R N T I I K Y R Q V D S P F V P P Y V N A V N L I R Y M ......... tgacgcagcttgcaacagctgtccgccgcccgtatctcctccgttcgcaggcgtaaaaatatcggctgccggttgtcggttggtaattattttatacctttgcacatcgcttggaaaaacaggcggataaacattcgcaacatttaatattcgataaattcaatcatt 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================================================ tgacgcagcttgcaacagctgtccgccgcccgtatctcctccgttcgcaggcgtaaaaatatcggctgccggttgtcggttggtaattattttatacctttgcacatcgcttggaaaaacaggcggataaacattcgcaacatttaatattcgataaattcaatcatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1247:TF1249|TF1247:TF1249:alanyl-tRNA synthetase (alanine--tRNA ligase):phosphoglycerate kinase (cytosolic phosphoglycerate kinase):->->:1330989..1331156 168 tgacgcagcttgcaacagctgtccgccgcccgtatctcctccgttcgcaggcgtaaaaatatcggctgccggttgtcggttggtaattattttatacctttgcacatcgcttggaaaaacaggcggataaacattcgcaacatttaatattcgataaattcaatcatt Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: tfor_TF1247_TF1249|alanyl-tRNA synthetase (alanine--tRNA ligase):phosphoglycerate kinase (cytosolic phosphoglycerate kinase)|POSITIVE:POSITIVE|[1330989,1331156]|168 HSP 1 e-value: 1.0E-90 bit: 333.0 Len: 168 Query Start:1 Query End:168 Subject Strand: POSITIVE Subject Start: 1 Subject End: 168 tgacgcagcttgcaacagctgtccgccgcccgtatctcctccgttcgcaggcgtaaaaatatcggctgccggttgtcggttggtaattattttatacctttgcacatcgcttggaaaaacaggcggataaacattcgcaacatttaatattcgataaattcaatcatt tgacgcagcttgcaacagctgtccgccgcccgtatctcctccgttcgcaggcgtaaaaatatcggctgccggttgtcggttggtaattattttatacctttgcacatcgcttggaaaaacaggcggataaacattcgcaacatttaatattcgataaattcaatcatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACGCAGCUUGCAACAGCUGUCCGCCGCCCGUAUCUCCUCCGUUCGCAGGCGUAAAAAUAUCGGCUGCCGGUUGUCGGUUGGUAAUUAUUUUAUACCUUUGCACAUCGCUUGGAAAAACAGGCGGAUAAACAUUCGCAACAUUUAAUAUUCGAUAAAUUCAAUCAUU (((.((((((......))))))...(((((.((.(.(((..((...(((((.(((((((((...(((((((.....))).))))...)))))).))).)))))....))...))).).)).))))).................................)))...... (-37.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUUGAAUUUAUCGAAUAUUAAAUGUUGCGAAUGUUUAUCCGCCUGUUUUUCCAAGCGAUGUGCAAAGGUAUAAAAUAAUUACCAACCGACAACCGGCAGCCGAUAUUUUUACGCCUGCGAACGGAGGAGAUACGGGCGGCGGACAGCUGUUGCAAGCUGCGUCA ((((.((((.....)))).)))).....((((((.(((((..((((((((.(((((..((.....))...((((.........)))).........(((((((.((.((....)))).))))...))).))))).)))))))).)))))....))))))......... (-45.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 492 53 13 80 35 tfor:TF1240|5end_conserved_hypothetical_protein_1324304..1324534_POSITIVE 455 69 21 64 32 tfor:TF0146|5end_glutamine-dependent_NAD(+)_synthetase_154855..155085_POSITIVE 441 80 31 165 113 tfor:TF1507|5end_outer_membrane_receptor,_TonB-dependent_1614536..1614766_POSITIVE 441 49 1 196 146 tfor:TF1329|5end_glucose-1-phosphate_thymidyltransferase_1408578..1408808_POSITIVE 441 70 21 160 106 tfor:TF0038|5end_conserved_hypothetical_protein_39907..40137_POSITIVE 434 70 23 211 166 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 424 48 7 207 163 tfor:TF2294|5end_hypothetical_protein_2448012..2448242_POSITIVE 419 49 1 169 120 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 419 80 31 59 6 tfor:TF1814|5end_conserved_hypothetical_protein;_possible_biotin_synthase_related_domain_containing_protein_1955325..1955555_POSITIVE 416 49 4 74 20 tfor:TF2097|5end_glucose_inhibited_division_protein_A_2269137..2269367_POSITIVE 414 50 6 144 111 tfor:TF2487|5end_transposase_2663010..2663240_POSITIVE 414 69 25 176 127 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 414 85 41 68 26 tfor:TF1970|5end_oxaloacetate_decarboxylase,_beta_subunit_2116804..2117034_POSITIVE 409 50 2 206 146 tfor:TF2025|5end_hypothetical_protein_2181933..2182163_POSITIVE 406 44 5 169 128 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 406 126 96 49 19 tfor:TF1286|5end_hypothetical_protein_1369199..1369429_POSITIVE 401 48 4 202 149 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 400 84 42 51 7 tfor:TF2546|5end_S-adenosylmethionine_synthetase_2729237..2729467_POSITIVE 398 49 1 133 69 tfor:TF0600|5end_oxidoreductase/dehydrogenase_630083..630313_POSITIVE 397 79 31 210 159 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 419 49 1 147 98 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 405 58 17 150 100 tfor:TF0896|3end_hypothetical_protein_945213..945363_POSITIVE 399 86 48 146 100 tfor:TF1215|3end_haloacid_dehalogenase-like_hydrolase_1303216..1303366_POSITIVE 398 49 1 100 36 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 397 79 31 121 70 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 397 70 21 102 53 tfor:TF0010|3end_conserved_hypothetical_protein_4790..4940_POSITIVE 387 80 31 99 29 tfor:TF0788|3end_protein-export_membrane_protein_841370..841520_POSITIVE 386 49 3 115 59 tfor:TF2547|3end_hypothetical_protein_2730947..2731097_POSITIVE 382 110 63 65 18 tfor:TF2583|3end_possible_ABC_transporter,__permease_component_2751026..2751176_POSITIVE 375 79 31 122 70 tfor:TF3126|3end_glycosyltransferase,_group_2_family_3361685..3361835_POSITIVE 373 82 41 143 97 tfor:TF2022|3end_conserved_hypothetical_protein_2180670..2180820_POSITIVE 369 76 31 66 19 tfor:TF2343|3end_ribosome_recycling_factor_2507502..2507652_POSITIVE 366 48 4 151 97 tfor:TF0037|3end_sialic_acid-specific_9-O-acetylesterase_39991..40141_POSITIVE 360 46 5 57 12 tfor:TF3095|3end_ABC_transporter,_ATP-binding_protein_3328033..3328183_POSITIVE 358 54 16 137 97 tfor:TF2454|3end_D-alanyl-D-alanine_dipeptidase_2632025..2632175_POSITIVE 357 48 4 140 89 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 357 86 41 151 111 tfor:TF0808|3end_cation_efflux_system_protein_865421..865571_POSITIVE 354 48 1 65 27 tfor:TF0776|3end_ABC_transporter,_permease_component_826173..826323_POSITIVE 351 82 42 87 47 tfor:TF2527|3end_RNA_polymerase_ECF-type_sigma_factor_2710749..2710899_POSITIVE 350 44 2 146 112 tfor:TF2024|3end_conserved_hypothetical_protein_2181979..2182129_POSITIVE