Origin IGS: gacgcggtcttgtttaatttttggagagacaaatttaaacaaaagttccgacaatttcaaacagcatccattaaaataatgttcaacaatttatcgccttaccctgacctgaaaaacgtcaaaacctttttacagaaacaaggaccaacagacatcagtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taactgatgtctgttggtccttgtttctgtaaaaaggttttgacgtttttcaggtcagggtaaggcgataaattgttgaacattattttaatggatgctgtttgaaattgtcggaacttttgtttaaatttgtctctccaaaaattaaacaagaccgcgtc Mask Tandem Repeat Region ================================================ gacgcggtcttgtttaatttttggagagacaaatttaaacaaaagttccgacaatttcaaacagcatccattaaaataatgttcaacaatttatcgccttaccctgacctgaaaaacgtcaaaacctttttacagaaacaaggaccaacagacatcagtta Find is-nt database================================================ Query_seq: TF0225:TF0227|TF0225:TF0227:iron-containing alcohol dehydrogenase:transcriptional regulator, Crp/Fnr family:->->:252799..252959 161 gacgcggtcttgtttaatttttggagagacaaatttaaacaaaagttccgacaatttcaaacagcatccattaaaataatgttcaacaatttatcgccttaccctgacctgaaaaacgtcaaaacctttttacagaaacaaggaccaacagacatcagtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0225:TF0227|TF0225:TF0227:iron-containing alcohol dehydrogenase:transcriptional regulator, Crp/Fnr family:->->:252799..252959 161 gacgcggtcttgtttaatttttggagagacaaatttaaacaaaagttccgacaatttcaaacagcatccattaaaataatgttcaacaatttatcgccttaccctgacctgaaaaacgtcaaaacctttttacagaaacaaggaccaacagacatcagtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0225:TF0227|TF0225:TF0227:iron-containing alcohol dehydrogenase:transcriptional regulator, Crp/Fnr family:->->:252799..252959 161 gacgcggtcttgtttaatttttggagagacaaatttaaacaaaagttccgacaatttcaaacagcatccattaaaataatgttcaacaatttatcgccttaccctgacctgaaaaacgtcaaaacctttttacagaaacaaggaccaacagacatcagtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacgcggtcttgtttaatttttggagagacaaatttaaacaaaagttccgacaatttcaaacagcatccattaaaataatgttcaacaatttatcgccttaccctgacctgaaaaacgtcaaaacctttttacagaaacaaggaccaacagacatcagtta Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 10 End: 159 ......... M F N F W R D K F K Q K F R Q F Q T A S I K I M F N N L S P Y P D L K N V K T F L Q K Q G P T D I S .. Protein_Len: 30 Strand: - Start: 1 End: 90 V R D Q K I K P S V F K F L L E S L K L C C G N F Y H E V M ....................................................................... gacgcggtcttgtttaatttttggagagacaaatttaaacaaaagttccgacaatttcaaacagcatccattaaaataatgttcaacaatttatcgccttaccctgacctgaaaaacgtcaaaacctttttacagaaacaaggaccaacagacatcagtta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 32 End: 61 ...............................TTTGAAATTGTCGGAACTTTTGTTTAAATT.................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacgcggtcttgtttaatttttggagagacaaatttaaacaaaagttccgacaatttcaaacagcatccattaaaataatgttcaacaatttatcgccttaccctgacctgaaaaacgtcaaaacctttttacagaaacaaggaccaacagacatcagtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0225:TF0227|TF0225:TF0227:iron-containing alcohol dehydrogenase:transcriptional regulator, Crp/Fnr family:->->:252799..252959 161 gacgcggtcttgtttaatttttggagagacaaatttaaacaaaagttccgacaatttcaaacagcatccattaaaataatgttcaacaatttatcgccttaccctgacctgaaaaacgtcaaaacctttttacagaaacaaggaccaacagacatcagtta Intra-Species Hit: Count: 1 Min: 1 Max: 161 Len: 161 Subject: tfor_TF0225_TF0227|iron-containing alcohol dehydrogenase:transcriptional regulator, Crp/Fnr family|POSITIVE:POSITIVE|[252799,252959]|161 HSP 1 e-value: 2.0E-86 bit: 319.0 Len: 161 Query Start:1 Query End:161 Subject Strand: POSITIVE Subject Start: 1 Subject End: 161 gacgcggtcttgtttaatttttggagagacaaatttaaacaaaagttccgacaatttcaaacagcatccattaaaataatgttcaacaatttatcgccttaccctgacctgaaaaacgtcaaaacctttttacagaaacaaggaccaacagacatcagtta gacgcggtcttgtttaatttttggagagacaaatttaaacaaaagttccgacaatttcaaacagcatccattaaaataatgttcaacaatttatcgccttaccctgacctgaaaaacgtcaaaacctttttacagaaacaaggaccaacagacatcagtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACGCGGUCUUGUUUAAUUUUUGGAGAGACAAAUUUAAACAAAAGUUCCGACAAUUUCAAACAGCAUCCAUUAAAAUAAUGUUCAACAAUUUAUCGCCUUACCCUGACCUGAAAAACGUCAAAACCUUUUUACAGAAACAAGGACCAACAGACAUCAGUUA .....((((((((((((..((((......)))).)))))))...(((..(((..(((((..(((...............((.....))...............)))...)))))...)))..)))................)))))............... (-19.31) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUGAUGUCUGUUGGUCCUUGUUUCUGUAAAAAGGUUUUGACGUUUUUCAGGUCAGGGUAAGGCGAUAAAUUGUUGAACAUUAUUUUAAUGGAUGCUGUUUGAAAUUGUCGGAACUUUUGUUUAAAUUUGUCUCUCCAAAAAUUAAACAAGACCGCGUC .....(((((.....((((.((((((......(((((((((((((..(((((((.(((.((..(((((....)))))...(((((...))))).)).)))))))))).))))))))))))).......((((......))))....))))))))))))))) (-36.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 110 62 172 130 tfor:TF0449|5end_transposase_467891..468121_POSITIVE 282 110 61 227 184 tfor:TF2120|5end_holliday_junction_endonuclease_2292108..2292338_POSITIVE 271 126 89 81 28 tfor:TF3159|5end_conserved_hypothetical_protein;_possible_transcriptional_regulator_3395220..3395450_POSITIVE 263 156 113 183 135 tfor:TF2929|5end_conserved_hypothetical_protein_3131484..3131714_POSITIVE 251 133 91 196 148 tfor:TF2810|5end_conserved_hypothetical_protein_3000583..3000813_POSITIVE 243 124 81 124 77 tfor:TF2121|5end_phosphoenolpyruvate_synthase_2294167..2294397_POSITIVE 234 118 88 81 51 tfor:TF3071|5end_integral_membrane_protein,_possible_MotA/TolQ/ExbB_proton_channel_family_3294703..3294933_POSITIVE 234 135 94 222 190 tfor:TF0136|5end_transposase_element_145627..145857_POSITIVE 234 135 94 137 105 tfor:TF0134|5end_transposase_element_145542..145772_POSITIVE 233 124 91 71 39 tfor:TF2655|5end_DNA_topoisomerase_I_2824543..2824773_POSITIVE 230 128 96 169 134 tfor:TF2629|5end_conserved_hypothetical_protein;_possible_lactoylglutathione_lyase_2801296..2801526_POSITIVE 229 121 94 219 195 tfor:TF3044|5end_two-component_system_sensor_kinase_3272691..3272921_POSITIVE 229 135 94 226 190 tfor:TF3003|5end_hypothetical_protein_3220382..3220612_POSITIVE 229 50 1 231 183 tfor:TF0809|5end_cation_efflux_protein_865358..865588_POSITIVE 227 50 3 139 92 tfor:TF2772|5end_tRNA_pseudouridine_synthase_B_2957383..2957613_POSITIVE 226 150 102 53 1 tfor:TF2684|5end_conserved_hypothetical_protein;_possible_CvpA_family_protein_2860692..2860922_POSITIVE 225 90 44 169 114 tfor:TF0664|5end_small_protein_B_(SMPB)_709029..709259_POSITIVE 224 126 94 75 44 tfor:TF1611|5end_conserved_hypothetical_protein;_possible_glycosyl_transferase_1729620..1729850_POSITIVE 224 127 82 63 9 tfor:TF0814|5end_conserved_hypothetical_protein_872546..872776_POSITIVE 224 148 102 69 7 tfor:TF0778|5end_outer_membrane_protein,_TonB_dependent_receptor_827284..827514_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 110 62 112 70 tfor:TF0448|3end_hypothetical_protein_467911..468061_POSITIVE 263 156 113 58 10 tfor:TF2928|3end_predicted_DNA_repair__protein_3131439..3131589_POSITIVE 234 118 88 81 51 tfor:TF3070|3end_conserved_hypothetical_protein_3294783..3294933_POSITIVE 234 135 94 71 39 tfor:TF0133|3end_transposase_element_145556..145706_POSITIVE 232 132 95 46 1 tfor:TF2999|3end_conserved_hypothetical_protein_3215891..3216041_POSITIVE 227 50 3 124 77 tfor:TF2771|3end_undecaprenol_kinase,_bacitracin_resistance_protein_2957448..2957598_POSITIVE 224 126 94 49 18 tfor:TF1610|3end_peptide_chain_release_factor_RF-2_1729674..1729824_POSITIVE 221 127 86 79 36 tfor:TF2615|3end_conserved_hypothetical_protein_2791209..2791359_POSITIVE 216 118 97 28 3 tfor:TF2020|3end_muconate_cycloisomerase_2177552..2177702_POSITIVE 216 107 63 151 104 tfor:TF0284|3end_alanine_racemase_314542..314692_POSITIVE 215 145 105 129 92 tfor:TF0201|3end_permease,_major_facilitator_superfamily_227773..227923_POSITIVE 213 122 94 42 7 tfor:TF0722|3end_pyruvate_dehydrogenase_E3_component(dihydrolipoamide_dehydrogenase)_774308..774458_POSITIVE 211 127 95 44 4 tfor:TF0812|3end_conserved_hypothetical_protein_872607..872757_POSITIVE 209 118 92 41 16 tfor:TF1934|3end_hypothetical_protein_2084079..2084229_POSITIVE 209 118 90 117 87 tfor:TF1443|3end_hypothetical_protein_1528203..1528353_POSITIVE 209 125 94 143 116 tfor:TF0454|3end_xanthine/uracil_permease_family_protein_473453..473603_POSITIVE 208 120 81 150 123 tfor:TF2683|3end_translation_initiation_factor_IF-2_2860756..2860906_POSITIVE 207 97 51 47 1 tfor:TF1473|3end_hypothetical_protein_1566966..1567116_POSITIVE 207 155 117 117 70 tfor:TF0002|3end_hypothetical_protein_647..797_POSITIVE 203 88 44 151 98 tfor:TF0663|3end_conserved_hypothetical_protein_709093..709243_POSITIVE