Origin IGS: ttgtatgtcctccctcgtcgtttaagtcgtttaatttaaaaataaaaaaagaatcccggtcaagaaagaatgtttcgaccggaatccagttgtttaccacttattatattcggatgcaaaaataggagatattttacatatatccaaattccgaaatactgctttataacatcataccctatttcttttcttta .........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 taaagaaaagaaatagggtatgatgttataaagcagtatttcggaatttggatatatgtaaaatatctcctatttttgcatccgaatataataagtggtaaacaactggattccggtcgaaacattctttcttgaccgggattctttttttatttttaaattaaacgacttaaacgacgagggaggacatacaa Mask Tandem Repeat Region ================================================ ttgtatgtcctccctcgtcgtttaagtcgtttaatttaaaaataaaaaaagaatcccggtcaagaaagaatgtttcgaccggaatccagttgtttaccacttattatattcggatgcaaaaataggagatattttacatatatccaaattccgaaatactgctttataacatcataccctatttcttttcttta Find is-nt database================================================ Query_seq: TF2040:TF2041|TF2040:TF2041:transcription elongation factor:conserved hypothetical protein:->->:2200341..2200534 194 ttgtatgtcctccctcgtcgtttaagtcgtttaatttaaaaataaaaaaagaatcccggtcaagaaagaatgtttcgaccggaatccagttgtttaccacttattatattcggatgcaaaaataggagatattttacatatatccaaattccgaaatactgctttataacatcataccctatttcttttcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2040:TF2041|TF2040:TF2041:transcription elongation factor:conserved hypothetical protein:->->:2200341..2200534 194 ttgtatgtcctccctcgtcgtttaagtcgtttaatttaaaaataaaaaaagaatcccggtcaagaaagaatgtttcgaccggaatccagttgtttaccacttattatattcggatgcaaaaataggagatattttacatatatccaaattccgaaatactgctttataacatcataccctatttcttttcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2040:TF2041|TF2040:TF2041:transcription elongation factor:conserved hypothetical protein:->->:2200341..2200534 194 ttgtatgtcctccctcgtcgtttaagtcgtttaatttaaaaataaaaaaagaatcccggtcaagaaagaatgtttcgaccggaatccagttgtttaccacttattatattcggatgcaaaaataggagatattttacatatatccaaattccgaaatactgctttataacatcataccctatttcttttcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgtatgtcctccctcgtcgtttaagtcgtttaatttaaaaataaaaaaagaatcccggtcaagaaagaatgtttcgaccggaatccagttgtttaccacttattatattcggatgcaaaaataggagatattttacatatatccaaattccgaaatactgctttataacatcataccctatttcttttcttta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 53 End: 166 .................................................... M P V K K E C F D R N P V V Y H L L Y S D A K I G D I L H I S K F R N T A L ............................ Protein_Len: 41 Strand: + Start: 70 End: 192 ..................................................................... M F R P E S S C L P L I I F G C K N R R Y F T Y I Q I P K Y C F I T S Y P I S F L .. Protein_Len: 40 Strand: - Start: 63 End: 182 .............................................................. S L I N R G S D L Q K G S I I N P H L F L L Y K V Y I W I G F Y Q K I V D Y G M ............ Protein_Len: 33 Strand: - Start: 2 End: 100 . T H G G E D N L D N L K F I F F S D R D L F F T E V P I W N N V M .............................................................................................. ttgtatgtcctccctcgtcgtttaagtcgtttaatttaaaaataaaaaaagaatcccggtcaagaaagaatgtttcgaccggaatccagttgtttaccacttattatattcggatgcaaaaataggagatattttacatatatccaaattccgaaatactgctttataacatcataccctatttcttttcttta 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================================================ ttgtatgtcctccctcgtcgtttaagtcgtttaatttaaaaataaaaaaagaatcccggtcaagaaagaatgtttcgaccggaatccagttgtttaccacttattatattcggatgcaaaaataggagatattttacatatatccaaattccgaaatactgctttataacatcataccctatttcttttcttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -7.3 Tail_Score: -6.20267 Start: 51 End: 87 Full_Region: aagtggtaaacaact ggattccggtcgaaaca ttc tttcttgaccgggattc tttttttatttttaa ..................................................ggattccggtcgaaacattctttcttgaccgggattc........................................................................................................... TransTerm Strand: - Conf: 51 HP_score: -2.6 Tail_Score: -3.94812 Start: 125 End: 145 Full_Region: agtatttcggaattt ggatatat gtaaa atatctcc tatttttgcatccga ............................................................................................................................ggatatatgtaaaatatctcc................................................. Find igs database================================================ Query_seq: TF2040:TF2041|TF2040:TF2041:transcription elongation factor:conserved hypothetical protein:->->:2200341..2200534 194 ttgtatgtcctccctcgtcgtttaagtcgtttaatttaaaaataaaaaaagaatcccggtcaagaaagaatgtttcgaccggaatccagttgtttaccacttattatattcggatgcaaaaataggagatattttacatatatccaaattccgaaatactgctttataacatcataccctatttcttttcttta Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: tfor_TF2040_TF2041|transcription elongation factor:conserved hypothetical protein|POSITIVE:POSITIVE|[2200341,2200534]|194 HSP 1 e-value: 3.0E-76 bit: 285.0 Len: 144 Query Start:51 Query End:194 Subject Strand: POSITIVE Subject Start: 51 Subject End: 194 ..................................................gaatcccggtcaagaaagaatgtttcgaccggaatccagttgtttaccacttattatattcggatgcaaaaataggagatattttacatatatccaaattccgaaatactgctttataacatcataccctatttcttttcttta ..................................................gaatcccggtcaagaaagaatgtttcgaccggaatccagttgtttaccacttattatattcggatgcaaaaataggagatattttacatatatccaaattccgaaatactgctttataacatcataccctatttcttttcttta HSP 2 e-value: 2.0E-12 bit: 73.8 Len: 37 Query Start:1 Query End:37 Subject Strand: POSITIVE Subject Start: 1 Subject End: 37 ttgtatgtcctccctcgtcgtttaagtcgtttaattt............................................................................................................................................................. ttgtatgtcctccctcgtcgtttaagtcgtttaattt............................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUAUGUCCUCCCUCGUCGUUUAAGUCGUUUAAUUUAAAAAUAAAAAAAGAAUCCCGGUCAAGAAAGAAUGUUUCGACCGGAAUCCAGUUGUUUACCACUUAUUAUAUUCGGAUGCAAAAAUAGGAGAUAUUUUACAUAUAUCCAAAUUCCGAAAUACUGCUUUAUAACAUCAUACCCUAUUUCUUUUCUUUA ..(((((.............(((((((......))))))).......((((....((((((..((((.....))))))))))..........................((((((..........(((.((((.....)))).)))....))))))......)))).......)))))................. (-25.14) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGAAAAGAAAUAGGGUAUGAUGUUAUAAAGCAGUAUUUCGGAAUUUGGAUAUAUGUAAAAUAUCUCCUAUUUUUGCAUCCGAAUAUAAUAAGUGGUAAACAACUGGAUUCCGGUCGAAACAUUCUUUCUUGACCGGGAUUCUUUUUUUAUUUUUAAAUUAAACGACUUAAACGACGAGGGAGGACAUACAA .................(((((.((((....))))...(((((..(((((((....(((((((..........))))))))))))))....(((((.((........(((((((((((((...........)))))))))))))....((((....))))....)).))))).....))))).....))))).. (-41.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 341 96 56 70 24 tfor:TF0597|5end_hypothetical_protein_628788..629018_POSITIVE 315 98 56 193 149 tfor:TF0497|5end_conserved_hypothetical_protein_524058..524288_POSITIVE 312 90 56 52 15 tfor:TF0658|5end_2-amino-3-ketobutyrate_coenzyme_A_ligase_703912..704142_POSITIVE 303 128 85 55 18 tfor:TF1794|5end_possible_glucose-1-phosphatase_1934453..1934683_POSITIVE 302 30 2 192 166 tfor:TF2584|5end_hypothetical_protein_2751180..2751410_POSITIVE 289 98 56 113 61 tfor:TF1599|5end_ribonuclease_P_protein_component_1713564..1713794_POSITIVE 276 131 102 40 9 tfor:TF1253|5end_hypothetical_protein_1335982..1336212_POSITIVE 273 99 54 54 2 tfor:TF0426|5end_conserved_hypothetical_protein_444728..444958_POSITIVE 271 119 71 183 126 tfor:TF2158|5end_conserved_hypothetical_protein_2333857..2334087_POSITIVE 270 89 54 56 14 tfor:TF3063|5end_ferredoxin-type_protein_3288179..3288409_POSITIVE 268 91 52 191 150 tfor:TF1109|5end_lipoprotein_1178784..1179014_POSITIVE 265 99 57 160 105 tfor:TF2022|5end_conserved_hypothetical_protein_2178524..2178754_POSITIVE 263 91 54 159 118 tfor:TF1745|5end_hypothetical_protein_1879154..1879384_POSITIVE 262 98 56 228 181 tfor:TF1246|5end_protease,_with_chaperone_function_1329390..1329620_POSITIVE 260 90 48 87 36 tfor:TF2684|5end_conserved_hypothetical_protein;_possible_CvpA_family_protein_2860692..2860922_POSITIVE 260 98 57 178 123 tfor:TF0440|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_2_463655..463885_POSITIVE 259 60 12 87 44 tfor:TF2419|5end_conserved_hypothetical_protein;_possible_DNA_uptake-related_protein_2598358..2598588_POSITIVE 257 117 79 107 68 tfor:TF1995|5end_exonuclease_2147148..2147378_POSITIVE 256 97 54 67 12 tfor:TF1800|5end_conserved_hypothetical_protein_1941214..1941444_POSITIVE 255 99 57 169 136 tfor:TF2615|5end_conserved_hypothetical_protein_2790569..2790799_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 98 56 128 76 tfor:TF1598|3end_conserved_hypothetical_protein_1713659..1713809_POSITIVE 276 98 58 60 9 tfor:TF2146|3end_secreted_sulfatase_ydeN_precursor_2321858..2322008_POSITIVE 276 131 102 62 31 tfor:TF1252|3end_phosphofructokinase;_pyrophosphate-fructose_6-phosphate_1-phosphotransferase_(probable_beta_subunit)_1336084..1336234_POSITIVE 274 98 55 72 30 tfor:TF0616|3end_conserved_hypothetical_protein_650658..650808_POSITIVE 265 99 57 144 89 tfor:TF2021|3end_hypothetical_protein_2178588..2178738_POSITIVE 263 91 54 143 102 tfor:TF1744|3end_phenylacetate-CoA_ligase_1879218..1879368_POSITIVE 260 90 48 71 20 tfor:TF2683|3end_translation_initiation_factor_IF-2_2860756..2860906_POSITIVE 260 98 57 132 77 tfor:TF0439|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_1_463689..463839_POSITIVE 259 120 76 45 1 tfor:TF2402|3end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2576224..2576374_POSITIVE 257 117 79 107 68 tfor:TF1994|3end_acyl-CoA_synthetase_2147228..2147378_POSITIVE 256 97 54 67 12 tfor:TF1799|3end_quinolinate_synthetase_1941294..1941444_POSITIVE 253 98 53 69 11 tfor:TF2456|3end_ABC_transporter,_ATP-binding_protein_2633208..2633358_POSITIVE 250 95 53 86 31 tfor:TF0038|3end_conserved_hypothetical_protein_41213..41363_POSITIVE 247 116 71 119 67 tfor:TF2586|3end_conserved_hypothetical_protein_2752064..2752214_POSITIVE 247 82 50 87 49 tfor:TF2473|3end_poly(A)_polymerase/tRNA_nucleotidyltransferase_2652010..2652160_POSITIVE 246 152 112 55 15 tfor:TF1121|3end_ABC_transporter_ATP-binding/permease_component,_bacteriocin/lantibiotic_exporter_1196507..1196657_POSITIVE 242 100 52 148 90 tfor:TF1333|3end_probable_acylaminoacyl_peptidase;_alanyl_dipeptidyl_peptidase_1416014..1416164_POSITIVE 240 190 141 79 20 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 238 100 53 74 15 tfor:TF2366|3end_conserved_hypothetical_protein_2531892..2532042_POSITIVE 238 168 123 81 30 tfor:TF1107|3end_ABC_transporter_ATP-binding/permease_component,_bacteriocin/lantibiotic_exporter_1177625..1177775_POSITIVE