Origin IGS: gcttgcatcctttttattagtaaaattttattagaccgacagtcggtttattctttcctttatcgtacatcttttctaaatcaatgtcaagaataaagacagttcctctattttttgatataataagtctaatcaaaattgaaggagtatatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatatactccttcaattttgattagacttattatatcaaaaaatagaggaactgtctttattcttgacattgatttagaaaagatgtacgataaaggaaagaataaaccgactgtcggtctaataaaattttactaataaaaaggatgcaagc Mask Tandem Repeat Region ================================================ gcttgcatcctttttattagtaaaattttattagaccgacagtcggtttattctttcctttatcgtacatcttttctaaatcaatgtcaagaataaagacagttcctctattttttgatataataagtctaatcaaaattgaaggagtatatc Find is-nt database================================================ Query_seq: SSA_0609:SSA_0610|SSA_0609:SSA_0610:Transcriptional regulator, TetR/AcrR family, putative:LemA-like protein, putative:<-->:598955..599107 153 gcttgcatcctttttattagtaaaattttattagaccgacagtcggtttattctttcctttatcgtacatcttttctaaatcaatgtcaagaataaagacagttcctctattttttgatataataagtctaatcaaaattgaaggagtatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0609:SSA_0610|SSA_0609:SSA_0610:Transcriptional regulator, TetR/AcrR family, putative:LemA-like protein, putative:<-->:598955..599107 153 gcttgcatcctttttattagtaaaattttattagaccgacagtcggtttattctttcctttatcgtacatcttttctaaatcaatgtcaagaataaagacagttcctctattttttgatataataagtctaatcaaaattgaaggagtatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0609:SSA_0610|SSA_0609:SSA_0610:Transcriptional regulator, TetR/AcrR family, putative:LemA-like protein, putative:<-->:598955..599107 153 gcttgcatcctttttattagtaaaattttattagaccgacagtcggtttattctttcctttatcgtacatcttttctaaatcaatgtcaagaataaagacagttcctctattttttgatataataagtctaatcaaaattgaaggagtatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcttgcatcctttttattagtaaaattttattagaccgacagtcggtttattctttcctttatcgtacatcttttctaaatcaatgtcaagaataaagacagttcctctattttttgatataataagtctaatcaaaattgaaggagtatatc Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 30 End: 152 ............................. M R P T V G L F F P L S Y I F S K S M S R I K T V P L F F D I I S L I K I E G V Y . Protein_Len: 40 Strand: - Start: 20 End: 139 ................... Y F K I L G V T P K N K G K D Y M K E L D I D L I F V T G R N K S I I L R I L M .............. gcttgcatcctttttattagtaaaattttattagaccgacagtcggtttattctttcctttatcgtacatcttttctaaatcaatgtcaagaataaagacagttcctctattttttgatataataagtctaatcaaaattgaaggagtatatc 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: 83 Start: 62 End: 91 .............................................................CTTGACATTGATTTAGAAAAGATGTACGAT.............................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 95 End: 124 ..............................................................................................AAAGACAGTTCCTCTATTTTTTGATATAAT............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcttgcatcctttttattagtaaaattttattagaccgacagtcggtttattctttcctttatcgtacatcttttctaaatcaatgtcaagaataaagacagttcctctattttttgatataataagtctaatcaaaattgaaggagtatatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0609:SSA_0610|SSA_0609:SSA_0610:Transcriptional regulator, TetR/AcrR family, putative:LemA-like protein, putative:<-->:598955..599107 153 gcttgcatcctttttattagtaaaattttattagaccgacagtcggtttattctttcctttatcgtacatcttttctaaatcaatgtcaagaataaagacagttcctctattttttgatataataagtctaatcaaaattgaaggagtatatc Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: NC_009009_SSA_0609_SSA_0610|Transcriptional regulator, TetR/AcrR family, putative:LemA-like protein, putative|NEGATIVE:POSITIVE|[598955,599107]|153 HSP 1 e-value: 9.0E-82 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 gcttgcatcctttttattagtaaaattttattagaccgacagtcggtttattctttcctttatcgtacatcttttctaaatcaatgtcaagaataaagacagttcctctattttttgatataataagtctaatcaaaattgaaggagtatatc gcttgcatcctttttattagtaaaattttattagaccgacagtcggtttattctttcctttatcgtacatcttttctaaatcaatgtcaagaataaagacagttcctctattttttgatataataagtctaatcaaaattgaaggagtatatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUGCAUCCUUUUUAUUAGUAAAAUUUUAUUAGACCGACAGUCGGUUUAUUCUUUCCUUUAUCGUACAUCUUUUCUAAAUCAAUGUCAAGAAUAAAGACAGUUCCUCUAUUUUUUGAUAUAAUAAGUCUAAUCAAAAUUGAAGGAGUAUAUC ...(((.((((((..........(((((((((((((.....((((((..............)))).))...............((((((((((...(((.......)))..)))))))))).....))))))).))))))))))))))).... (-24.74) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAUACUCCUUCAAUUUUGAUUAGACUUAUUAUAUCAAAAAAUAGAGGAACUGUCUUUAUUCUUGACAUUGAUUUAGAAAAGAUGUACGAUAAAGGAAAGAAUAAACCGACUGUCGGUCUAAUAAAAUUUUACUAAUAAAAAGGAUGCAAGC .......(((((.(((((((.((((((....((((((......((((..((.((((.........))))))..)))).....))))))(((((..((..........))...))))))))))))))))))...........)))))....... (-20.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 802 80 31 171 122 NC_009009:SSA_0609|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_598864..599094_NEGATIVE 312 78 33 105 51 NC_009009:SSA_1730|5end_hypothetical_protein_1716057..1716287_NEGATIVE 275 66 36 85 56 NC_009009:SSA_0172|5end_Transcriptional_regulator,_XRE_family,_putative_169140..169370_POSITIVE 271 77 35 110 62 NC_009009:SSA_1013|5end_Phosphatidylserine_synthase,_putative_1017221..1017451_POSITIVE 265 146 103 76 35 NC_009009:SSA_1733|5end_hypothetical_protein_1717494..1717724_POSITIVE 250 90 43 132 81 NC_009009:SSA_1545|5end_Conserved_uncharacterized_protein_1549210..1549440_NEGATIVE 249 77 38 104 65 NC_009009:SSA_1117|5end_hypothetical_protein_1142743..1142973_POSITIVE 242 76 35 102 50 NC_009009:SSA_1952|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1949624..1949854_NEGATIVE 241 99 51 156 104 NC_009009:SSA_0367|5end_hypothetical_protein_358309..358539_POSITIVE 241 79 35 219 179 NC_009009:SSA_0245|5end_hypothetical_protein_239136..239366_POSITIVE 235 134 96 66 27 NC_009009:SSA_0211|5end_hypothetical_protein_208041..208271_POSITIVE 233 86 41 129 86 NC_009009:SSA_2102|5end_Conserved_uncharacterized_protein_2106410..2106640_NEGATIVE 233 148 103 225 175 NC_009009:SSA_0663|5end_Acetyltransferase,_putative_648352..648582_POSITIVE 232 67 29 182 143 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 227 118 72 156 114 NC_009009:SSA_1798|5end_hypothetical_protein_1780513..1780743_NEGATIVE 227 78 43 76 37 NC_009009:SSA_1502|5end_Conserved_uncharacterized_protein_(contains_LysM,_Lysin_motif)_1506219..1506449_NEGATIVE 227 90 45 159 105 NC_009009:SSA_0623|5end_hypothetical_protein_614512..614742_POSITIVE 227 80 34 228 192 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 224 47 10 192 157 NC_009009:SSA_2176|5end_hypothetical_protein_2175159..2175389_NEGATIVE 224 80 34 122 74 NC_009009:SSA_0575|5end_Hydrolase,_HAD_superfamily,_putative_569527..569757_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 77 35 123 75 NC_009009:SSA_1012|3end_Phosphoenolpyruvate_synthase,_putative_1017314..1017464_POSITIVE 250 90 43 75 24 NC_009009:SSA_1546|3end_Prolipoprotein_diacylglyceryl_transferase,_putative_1549267..1549417_NEGATIVE 242 76 35 84 32 NC_009009:SSA_1953|3end_NifU_family_protein,_putative_1949642..1949792_NEGATIVE 235 134 96 69 30 NC_009009:SSA_0210|3end_hypothetical_protein_208124..208274_POSITIVE 232 65 26 133 89 NC_009009:SSA_1253|3end_hypothetical_protein_1280976..1281126_NEGATIVE 231 49 1 133 80 NC_009009:SSA_0392|3end_hypothetical_protein_388303..388453_POSITIVE 224 47 10 119 84 NC_009009:SSA_2177|3end_hypothetical_protein_2175232..2175382_NEGATIVE 223 48 2 81 26 NC_009009:SSA_1745|3end_General_stress_response_protein_CsbD,_putative_1731997..1732147_NEGATIVE 222 86 51 39 3 NC_009009:SSA_2103|3end_hypothetical_protein_2106500..2106650_NEGATIVE 218 50 1 149 110 NC_009009:SSA_1754|3end_hypothetical_protein_1743125..1743275_NEGATIVE 216 80 33 68 29 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE 214 111 72 149 114 NC_009009:SSA_1799|3end_Acetyltransferase,_putative_1780513..1780663_NEGATIVE 213 50 1 134 73 NC_009009:SSA_0332|3end_hypothetical_protein_326924..327074_POSITIVE 212 83 41 87 38 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE 212 73 33 118 75 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 211 90 41 61 11 NC_009009:SSA_1076|3end_hypothetical_protein_1095047..1095197_POSITIVE 208 76 36 117 83 NC_009009:SSA_1558|3end_Hydrolase,_HAD_superfamily_1560044..1560194_NEGATIVE 207 105 62 73 30 NC_009009:SSA_2074|3end_Preprotein_translocase_subunit_YajC,_putative_2076600..2076750_NEGATIVE 205 77 34 98 58 NC_009009:SSA_0063|3end_Holliday_junction_DNA_helicase_ruvB,_putative_66413..66563_POSITIVE 203 77 37 124 74 NC_009009:SSA_0088|3end_V-type_sodium_ATPase,_subunit_C,_putative_90023..90173_POSITIVE