Origin IGS: acgttattatttaaaaaaaattaggcggacaaatatagtgtttttttatttttacattgataattgttcgtggtgattttttttgtgtttattgcgttttttacaaatcaaaaaacaggatttttaatctgtctttttttacaaattgcaaatgagggttttataaacctttaatgttttctactcgtcagctgttcctttatatcagggaaataagcatggtttccggacccttatggcgtattcttttttcaagtataaaatacagcgttgcttca .........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 tgaagcaacgctgtattttatacttgaaaaaagaatacgccataagggtccggaaaccatgcttatttccctgatataaaggaacagctgacgagtagaaaacattaaaggtttataaaaccctcatttgcaatttgtaaaaaaagacagattaaaaatcctgttttttgatttgtaaaaaacgcaataaacacaaaaaaaatcaccacgaacaattatcaatgtaaaaataaaaaaacactatatttgtccgcctaattttttttaaataataacgt Mask Tandem Repeat Region ================================================ acgttattatttaaaaaaaattaggcggacaaatatagtgtttttttatttttacattgataattgttcgtggtgattttttttgtgtttattgcgttttttacaaatcaaaaaacaggatttttaatctgtctttttttacaaattgcaaatgagggttttataaacctttaatgttttctactcgtcagctgttcctttatatcagggaaataagcatggtttccggacccttatggcgtattcttttttcaagtataaaatacagcgttgcttca Find is-nt database================================================ Query_seq: TF0103:TF0104|TF0103:TF0104:rubredoxin:redox-sensitive transcriptional activator, OxyR:->->:112149..112426 278 acgttattatttaaaaaaaattaggcggacaaatatagtgtttttttatttttacattgataattgttcgtggtgattttttttgtgtttattgcgttttttacaaatcaaaaaacaggatttttaatctgtctttttttacaaattgcaaatgagggttttataaacctttaatgttttctactcgtcagctgttcctttatatcagggaaataagcatggtttccggacccttatggcgtattcttttttcaagtataaaatacagcgttgcttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0103:TF0104|TF0103:TF0104:rubredoxin:redox-sensitive transcriptional activator, OxyR:->->:112149..112426 278 acgttattatttaaaaaaaattaggcggacaaatatagtgtttttttatttttacattgataattgttcgtggtgattttttttgtgtttattgcgttttttacaaatcaaaaaacaggatttttaatctgtctttttttacaaattgcaaatgagggttttataaacctttaatgttttctactcgtcagctgttcctttatatcagggaaataagcatggtttccggacccttatggcgtattcttttttcaagtataaaatacagcgttgcttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0103:TF0104|TF0103:TF0104:rubredoxin:redox-sensitive transcriptional activator, OxyR:->->:112149..112426 278 acgttattatttaaaaaaaattaggcggacaaatatagtgtttttttatttttacattgataattgttcgtggtgattttttttgtgtttattgcgttttttacaaatcaaaaaacaggatttttaatctgtctttttttacaaattgcaaatgagggttttataaacctttaatgttttctactcgtcagctgttcctttatatcagggaaataagcatggtttccggacccttatggcgtattcttttttcaagtataaaatacagcgttgcttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgttattatttaaaaaaaattaggcggacaaatatagtgtttttttatttttacattgataattgttcgtggtgattttttttgtgtttattgcgttttttacaaatcaaaaaacaggatttttaatctgtctttttttacaaattgcaaatgagggttttataaacctttaatgttttctactcgtcagctgttcctttatatcagggaaataagcatggtttccggacccttatggcgtattcttttttcaagtataaaatacagcgttgcttca Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 48 End: 152 ............................................... M F T L I I V R G D F F C V Y C V F Y K S K N R I F N L S F F T N C K .............................................................................................................................. Protein_Len: 36 Strand: + Start: 64 End: 171 ............................................................... M F V V I F F V F I A F F T N Q K T G F L I C L F L Q I A N E G F I N L ........................................................................................................... Protein_Len: 35 Strand: + Start: 174 End: 278 ............................................................................................................................................................................. M F S T R Q L F L Y I R E I S M V S G P L W R I L F S S I K Y S V A S acgttattatttaaaaaaaattaggcggacaaatatagtgtttttttatttttacattgataattgttcgtggtgattttttttgtgtttattgcgttttttacaaatcaaaaaacaggatttttaatctgtctttttttacaaattgcaaatgagggttttataaacctttaatgttttctactcgtcagctgttcctttatatcagggaaataagcatggtttccggacccttatggcgtattcttttttcaagtataaaatacagcgttgcttca 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: 81 Start: 99 End: 128 ..................................................................................................TTTTACAAATCAAAAAACAGGATTTTTAAT...................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acgttattatttaaaaaaaattaggcggacaaatatagtgtttttttatttttacattgataattgttcgtggtgattttttttgtgtttattgcgttttttacaaatcaaaaaacaggatttttaatctgtctttttttacaaattgcaaatgagggttttataaacctttaatgttttctactcgtcagctgttcctttatatcagggaaataagcatggtttccggacccttatggcgtattcttttttcaagtataaaatacagcgttgcttca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -6.3 Tail_Score: -4.10958 Start: 157 End: 169 Full_Region: CAAATTGCAAATGAG GGTTT TAT AAACC TTTAATGTTTTCTAC ............................................................................................................................................................GGTTTTATAAACC............................................................................................................. Find igs database================================================ Query_seq: TF0103:TF0104|TF0103:TF0104:rubredoxin:redox-sensitive transcriptional activator, OxyR:->->:112149..112426 278 acgttattatttaaaaaaaattaggcggacaaatatagtgtttttttatttttacattgataattgttcgtggtgattttttttgtgtttattgcgttttttacaaatcaaaaaacaggatttttaatctgtctttttttacaaattgcaaatgagggttttataaacctttaatgttttctactcgtcagctgttcctttatatcagggaaataagcatggtttccggacccttatggcgtattcttttttcaagtataaaatacagcgttgcttca Intra-Species Hit: Count: 1 Min: 142 Max: 278 Len: 137 Subject: tfor_TF0103_TF0104|rubredoxin:redox-sensitive transcriptional activator, OxyR|POSITIVE:POSITIVE|[112149,112426]|278 HSP 1 e-value: 6.0E-72 bit: 272.0 Len: 137 Query Start:142 Query End:278 Subject Strand: POSITIVE Subject Start: 142 Subject End: 278 .............................................................................................................................................caaattgcaaatgagggttttataaacctttaatgttttctactcgtcagctgttcctttatatcagggaaataagcatggtttccggacccttatggcgtattcttttttcaagtataaaatacagcgttgcttca .............................................................................................................................................caaattgcaaatgagggttttataaacctttaatgttttctactcgtcagctgttcctttatatcagggaaataagcatggtttccggacccttatggcgtattcttttttcaagtataaaatacagcgttgcttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAUUGCAAAUGAGGGUUUUAUAAACCUUUAAUGUUUUCUACUCGUCAGCUGUUCCUUUAUAUCAGGGAAAUAAGCAUGGUUUCCGGACCCUUAUGGCGUAUUCUUUUUUCAAGUAUAAAAUACAGCGUUGCUUCA ......(((.((((((((((...(((((......((.....))......(((.((((((......))))))...)))..)))))..)))))))))).(((((((................))))).))..))).... (-29.59) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAGCAACGCUGUAUUUUAUACUUGAAAAAAGAAUACGCCAUAAGGGUCCGGAAACCAUGCUUAUUUCCCUGAUAUAAAGGAACAGCUGACGAGUAGAAAACAUUAAAGGUUUAUAAAACCCUCAUUUGCAAUUUG ....((((.((.(((((((............)))))))))....(((((....(((((..(((...((((.(......).)))).)))......((.....))......))))).....)))))...))))...... (-23.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 88 44 163 115 tfor:TF2580|5end_RNA_polymerase,_alpha_subunit_2747815..2748045_POSITIVE 341 112 71 203 156 tfor:TF2560|5end_30S_ribosomal_protein_S3_2737897..2738127_POSITIVE 335 98 53 230 188 tfor:TF2796|5end_cytochrome_D_ubiquinol_oxidase,_subunit_II_2981269..2981499_POSITIVE 312 110 66 150 96 tfor:TF2550|5end_translation_elongation_factor_G_2732268..2732498_POSITIVE 311 107 64 132 77 tfor:TF1746|5end_histidine_ammonia-lyase_1879529..1879759_POSITIVE 305 102 65 203 166 tfor:TF1068|5end_conserved_hypothetical_protein;_possible_N-acetylglucosamine_kinase_1138036..1138266_POSITIVE 303 108 74 61 28 tfor:TF2118|5end_conserved_hypothetical_protein_2289961..2290191_POSITIVE 303 107 67 217 171 tfor:TF0963|5end_acyltransferase_1012374..1012604_POSITIVE 299 89 42 207 147 tfor:TF0379|5end_conserved_hypothetical_protein,_nif3_family_399458..399688_POSITIVE 297 110 78 126 93 tfor:TF0920|5end_conserved_hypothetical_protein_958148..958378_POSITIVE 295 99 51 204 159 tfor:TF2683|5end_translation_initiation_factor_IF-2_2857722..2857952_POSITIVE 293 100 52 98 41 tfor:TF0841|5end_NADH_dehydrogenase/NAD(P)H_nitroreductase_892165..892395_POSITIVE 292 92 52 154 99 tfor:TF3122|5end_ABC_transporter,_ATP-binding_protein_3356047..3356277_POSITIVE 291 110 61 193 140 tfor:TF1416|5end_outer_membrane_protein_1497576..1497806_POSITIVE 289 88 43 222 173 tfor:TF1754|5end_conserved_hypothetical_protein_1890937..1891167_POSITIVE 289 89 41 115 61 tfor:TF1620|5end_TPR_domain_protein_1734454..1734684_POSITIVE 289 89 44 216 170 tfor:TF1236|5end_L-rhamnose_isomerase_1320743..1320973_POSITIVE 288 100 54 189 140 tfor:TF2582|5end_ABC_transporter,_ATP-binding_protein_2749433..2749663_POSITIVE 286 99 51 231 175 tfor:TF3027|5end_zinc_metalloprotease_3250223..3250453_POSITIVE 286 99 52 163 125 tfor:TF0772|5end_conserved_hypothetical_protein_818568..818798_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 85 44 150 104 tfor:TF2579|3end_30S_ribosomal_protein_S4_2747884..2748034_POSITIVE 312 110 66 147 93 tfor:TF2549|3end_30S_ribosomal_protein_S7_2732345..2732495_POSITIVE 311 107 64 125 70 tfor:TF1745|3end_hypothetical_protein_1879602..1879752_POSITIVE 292 92 52 151 96 tfor:TF3121|3end_nicotinate_phosphoribosyltransferase_3356124..3356274_POSITIVE 289 89 41 109 55 tfor:TF1619|3end_riboflavin_synthase,_beta_subunit_1734528..1734678_POSITIVE 286 99 52 87 49 tfor:TF0771|3end_ABC_transporter,_ATP-binding/permease_component_818572..818722_POSITIVE 282 101 62 131 89 tfor:TF2472|3end_GAF_domain-containing_protein_2650468..2650618_POSITIVE 279 69 27 80 28 tfor:TF2840|3end_hypothetical_protein_3031289..3031439_POSITIVE 276 117 73 70 32 tfor:TF2454|3end_D-alanyl-D-alanine_dipeptidase_2632025..2632175_POSITIVE 276 99 56 95 43 tfor:TF1163|3end_two-component_system_response_regulator_1243771..1243921_POSITIVE 274 130 84 107 49 tfor:TF1459|3end_possible_protease_1549320..1549470_POSITIVE 273 106 65 53 13 tfor:TF2581|3end_50S_ribosomal_protein_L17_2749370..2749520_POSITIVE 269 130 84 102 59 tfor:TF0282|3end_probable_tonB-linked_outer_membrane_receptor_311376..311526_POSITIVE 268 99 56 49 5 tfor:TF3122|3end_ABC_transporter,_ATP-binding_protein_3357743..3357893_POSITIVE 266 101 66 145 95 tfor:TF2737|3end_conserved_hypothetical_protein;_TPR-repeat-containing_protein_2919304..2919454_POSITIVE 265 113 78 81 49 tfor:TF1034|3end_conserved_hypothetical_protein_1095901..1096051_POSITIVE 264 99 51 137 66 tfor:TF0858|3end_conserved_hypothetical_protein_911833..911983_POSITIVE 256 99 52 69 6 tfor:TF1680|3end_peptide_chain_release_factor_3_1794969..1795119_POSITIVE 255 90 42 69 17 tfor:TF3131|3end_uracil-DNA_glycosylase_3365248..3365398_POSITIVE 252 101 64 53 13 tfor:TF2818|3end_acetylornithine_aminotransferase_3008949..3009099_POSITIVE