Origin IGS: tgaaacaaataacattttgcagcaataaccacgtcattttttactgttgaacagctgtacctaaaaagttttgtttttgctatcgacttgccttatctttgtcgtcacaaacaatatggg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cccatattgtttgtgacgacaaagataaggcaagtcgatagcaaaaacaaaactttttaggtacagctgttcaacagtaaaaaatgacgtggttattgctgcaaaatgttatttgtttca Mask Tandem Repeat Region ================================================ tgaaacaaataacattttgcagcaataaccacgtcattttttactgttgaacagctgtacctaaaaagttttgtttttgctatcgacttgccttatctttgtcgtcacaaacaatatggg Find is-nt database================================================ Query_seq: TF0770:TF0771|TF0770:TF0771:signal peptidase I:ABC transporter, ATP-binding/permease component:->->:816668..816787 120 tgaaacaaataacattttgcagcaataaccacgtcattttttactgttgaacagctgtacctaaaaagttttgtttttgctatcgacttgccttatctttgtcgtcacaaacaatatggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0770:TF0771|TF0770:TF0771:signal peptidase I:ABC transporter, ATP-binding/permease component:->->:816668..816787 120 tgaaacaaataacattttgcagcaataaccacgtcattttttactgttgaacagctgtacctaaaaagttttgtttttgctatcgacttgccttatctttgtcgtcacaaacaatatggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0770:TF0771|TF0770:TF0771:signal peptidase I:ABC transporter, ATP-binding/permease component:->->:816668..816787 120 tgaaacaaataacattttgcagcaataaccacgtcattttttactgttgaacagctgtacctaaaaagttttgtttttgctatcgacttgccttatctttgtcgtcacaaacaatatggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaacaaataacattttgcagcaataaccacgtcattttttactgttgaacagctgtacctaaaaagttttgtttttgctatcgacttgccttatctttgtcgtcacaaacaatatggg Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 25 End: 120 ........................ M T T S F F T V E Q L Y L K S F V F A I D L P Y L C R H K Q Y G tgaaacaaataacattttgcagcaataaccacgtcattttttactgttgaacagctgtacctaaaaagttttgtttttgctatcgacttgccttatctttgtcgtcacaaacaatatggg 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================================================ tgaaacaaataacattttgcagcaataaccacgtcattttttactgttgaacagctgtacctaaaaagttttgtttttgctatcgacttgccttatctttgtcgtcacaaacaatatggg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0770:TF0771|TF0770:TF0771:signal peptidase I:ABC transporter, ATP-binding/permease component:->->:816668..816787 120 tgaaacaaataacattttgcagcaataaccacgtcattttttactgttgaacagctgtacctaaaaagttttgtttttgctatcgacttgccttatctttgtcgtcacaaacaatatggg Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: tfor_TF0770_TF0771|signal peptidase I:ABC transporter, ATP-binding/permease component|POSITIVE:POSITIVE|[816668,816787]|120 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 tgaaacaaataacattttgcagcaataaccacgtcattttttactgttgaacagctgtacctaaaaagttttgtttttgctatcgacttgccttatctttgtcgtcacaaacaatatggg tgaaacaaataacattttgcagcaataaccacgtcattttttactgttgaacagctgtacctaaaaagttttgtttttgctatcgacttgccttatctttgtcgtcacaaacaatatggg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAACAAAUAACAUUUUGCAGCAAUAACCACGUCAUUUUUUACUGUUGAACAGCUGUACCUAAAAAGUUUUGUUUUUGCUAUCGACUUGCCUUAUCUUUGUCGUCACAAACAAUAUGGG ............(((.(((.(((((.....(((..(((((((((((.....))).......))))))))..)))..)))))..((((.............)))).......))).))).. (-14.23) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCAUAUUGUUUGUGACGACAAAGAUAAGGCAAGUCGAUAGCAAAAACAAAACUUUUUAGGUACAGCUGUUCAACAGUAAAAAAUGACGUGGUUAUUGCUGCAAAAUGUUAUUUGUUUCA ..((((.....))))..((((((((((..(((.(.(((((((....((...(((.....)))...((((.....))))..........)).)))))))))))....)))).))))))... (-19.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 90 43 219 174 tfor:TF0285|5end_conserved_hypothetical_protein_314465..314695_POSITIVE 299 110 64 93 39 tfor:TF2487|5end_transposase_2663010..2663240_POSITIVE 294 115 71 151 110 tfor:TF1202|5end_antitermination_factor,_NusB_family_1284152..1284382_POSITIVE 290 115 72 231 190 tfor:TF1144|5end_ABC_transporter,_ATP-binding/permease_component_1223527..1223757_POSITIVE 288 119 71 60 9 tfor:TF1353|5end_conserved_hypothetical_protein;_possible_penicillinase_repressor_1432908..1433138_POSITIVE 281 109 68 212 161 tfor:TF0640|5end_outer_membrane_protein,_TonB_dependent_receptor_678087..678317_POSITIVE 269 108 63 178 133 tfor:TF0970|5end_2-keto-3-deoxygluconate_kinase_1020396..1020626_POSITIVE 267 118 88 180 147 tfor:TF3067|5end_conserved_hypothetical_protein_3292432..3292662_POSITIVE 267 119 71 220 170 tfor:TF1673|5end_ATP_synthase,_C_subunit_1787238..1787468_POSITIVE 267 107 68 47 9 tfor:TF1016|5end_30S_ribosomal_protein_S6_1074151..1074381_POSITIVE 265 59 13 191 132 tfor:TF2552|5end_50S_ribosomal_protein_L3_2734758..2734988_POSITIVE 263 111 71 211 167 tfor:TF1914|5end_conserved_hypothetical_protein_2066599..2066829_POSITIVE 260 80 33 212 161 tfor:TF0258|5end_hypothetical_protein_288561..288791_POSITIVE 258 107 68 163 132 tfor:TF2525|5end_conserved_hypothetical_protein_2704027..2704257_POSITIVE 258 109 68 158 117 tfor:TF2504|5end_peptidyl-prolyl_cis-trans_isomerase_2680031..2680261_POSITIVE 252 107 66 108 70 tfor:TF2295|5end_hypothetical_protein_2448164..2448394_POSITIVE 252 114 72 81 33 tfor:TF0052|5end_hypothetical_protein_57611..57841_POSITIVE 250 85 53 87 56 tfor:TF1094|5end_conserved_hypothetical_protein_1163076..1163306_POSITIVE 245 90 48 133 92 tfor:TF0780|5end_alpha-L-arabinofuranosidase,_precursor_A_831944..832174_POSITIVE 244 94 52 195 151 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 115 71 66 25 tfor:TF1201|3end_possible_preprotein_translocase_1284147..1284297_POSITIVE 269 108 63 141 96 tfor:TF0969|3end_oxidoreductase_1020439..1020589_POSITIVE 267 118 88 80 47 tfor:TF3065|3end_enolase_3292412..3292562_POSITIVE 258 107 68 146 115 tfor:TF2524|3end_conserved_hypothetical_protein;_possible_endonuclease/exonuclease/phosphatase_family_protein_2704090..2704240_POSITIVE 252 107 66 114 76 tfor:TF2294|3end_hypothetical_protein_2448250..2448400_POSITIVE 244 94 52 118 74 tfor:TF2245|3end_conserved_hypothetical_protein_2421291..2421441_POSITIVE 239 109 67 128 77 tfor:TF2550|3end_translation_elongation_factor_G_2734492..2734642_POSITIVE 238 120 73 55 10 tfor:TF1582|3end_hypothetical_protein_1690506..1690656_POSITIVE 237 105 65 137 90 tfor:TF1215|3end_haloacid_dehalogenase-like_hydrolase_1303216..1303366_POSITIVE 235 58 16 85 34 tfor:TF2046|3end_polyribonucleotide_nucleotidyltransferase_2210152..2210302_POSITIVE 233 90 44 63 4 tfor:TF0112|3end_outer_membrane_protein_123027..123177_POSITIVE 231 89 41 65 15 tfor:TF0372|3end_transcriptional_regulator_391118..391268_POSITIVE 230 119 71 104 67 tfor:TF2773|3end_S-adenosylmethionine_tRNA_ribosyltransferase_2959243..2959393_POSITIVE 224 92 51 110 79 tfor:TF2607|3end_conserved_hypothetical_protein_2784645..2784795_POSITIVE 223 90 44 145 105 tfor:TF1656|3end_possible_2-methylthioadenine_synthetase_1772505..1772655_POSITIVE 222 60 11 63 19 tfor:TF2827|3end_conserved_hypothetical_protein_3019642..3019792_POSITIVE 221 107 67 123 64 tfor:TF2563|3end_30S_ribosomal_protein_S17_2739679..2739829_POSITIVE 221 111 71 65 27 tfor:TF1601|3end_conserved_hypothetical_protein_1715539..1715689_POSITIVE 220 119 74 139 96 tfor:TF0439|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_1_463689..463839_POSITIVE 219 57 11 149 96 tfor:TF0229|3end_beta-galactosidase_257003..257153_POSITIVE