Origin IGS: atatgtctccttaacaaagttatgctttcaacattgtaacagaaaaactaattattagcaagataggacttgacaatttttttaaatttattataattataaatgaacatatgagcatttgttcatatgaataggtgatagaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attctatcacctattcatatgaacaaatgctcatatgttcatttataattataataaatttaaaaaaattgtcaagtcctatcttgctaataattagtttttctgttacaatgttgaaagcataactttgttaaggagacatat Mask Tandem Repeat Region ================================================ atatgtctccttaacaaagttatgctttcaacattgtaacagaaaaactaattattagcaagataggacttgacaatttttttaaatttattataattataaatgaacatatgagcatttgttcatatgaataggtgatagaat Find is-nt database================================================ Query_seq: TDE1381:TDE1382|TDE1381:TDE1382:V-type ATP synthase subunit E:transcriptional regulator, ArsR family:<-->:1421996..1422139 144 atatgtctccttaacaaagttatgctttcaacattgtaacagaaaaactaattattagcaagataggacttgacaatttttttaaatttattataattataaatgaacatatgagcatttgttcatatgaataggtgatagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1381:TDE1382|TDE1381:TDE1382:V-type ATP synthase subunit E:transcriptional regulator, ArsR family:<-->:1421996..1422139 144 atatgtctccttaacaaagttatgctttcaacattgtaacagaaaaactaattattagcaagataggacttgacaatttttttaaatttattataattataaatgaacatatgagcatttgttcatatgaataggtgatagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1381:TDE1382|TDE1381:TDE1382:V-type ATP synthase subunit E:transcriptional regulator, ArsR family:<-->:1421996..1422139 144 atatgtctccttaacaaagttatgctttcaacattgtaacagaaaaactaattattagcaagataggacttgacaatttttttaaatttattataattataaatgaacatatgagcatttgttcatatgaataggtgatagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatgtctccttaacaaagttatgctttcaacattgtaacagaaaaactaattattagcaagataggacttgacaatttttttaaatttattataattataaatgaacatatgagcatttgttcatatgaataggtgatagaat Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 33 End: 131 ................................ M V T E K L I I S K I G L D N F F K F I I I I N E H M S I C S Y E ............. Protein_Len: 39 Strand: - Start: 23 End: 139 ...................... A K L M T V S F S I I L L I P S S L K K L N I I I I F S C I L M Q E Y S Y T M ..... atatgtctccttaacaaagttatgctttcaacattgtaacagaaaaactaattattagcaagataggacttgacaatttttttaaatttattataattataaatgaacatatgagcatttgttcatatgaataggtgatagaat 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: 87 Start: 33 End: 62 ................................CTTGCTAATAATTAGTTTTTCTGTTACAAT.................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atatgtctccttaacaaagttatgctttcaacattgtaacagaaaaactaattattagcaagataggacttgacaatttttttaaatttattataattataaatgaacatatgagcatttgttcatatgaataggtgatagaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1381:TDE1382|TDE1381:TDE1382:V-type ATP synthase subunit E:transcriptional regulator, ArsR family:<-->:1421996..1422139 144 atatgtctccttaacaaagttatgctttcaacattgtaacagaaaaactaattattagcaagataggacttgacaatttttttaaatttattataattataaatgaacatatgagcatttgttcatatgaataggtgatagaat Intra-Species Hit: Count: 1 Min: 1 Max: 144 Len: 144 Subject: NC_002967_TDE1381_TDE1382|V-type ATP synthase subunit E:transcriptional regulator, ArsR family|NEGATIVE:POSITIVE|[1421996,1422139]|144 HSP 1 e-value: 7.0E-64 bit: 244.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 atatgtctccttaacaaagttatgctttcaacattgtaacagaaaaactaattattagcaagataggacttgacaannnnnnnaaatttattataattataaatgaacatatgagcatttgttcatatgaataggtgatagaat atatgtctccttaacaaagttatgctttcaacattgtaacagaaaaactaattattagcaagataggacttgacaatttttttaaatttattataattataaatgaacatatgagcatttgttcatatgaataggtgatagaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUGUCUCCUUAACAAAGUUAUGCUUUCAACAUUGUAACAGAAAAACUAAUUAUUAGCAAGAUAGGACUUGACAAUUUUUUUAAAUUUAUUAUAAUUAUAAAUGAACAUAUGAGCAUUUGUUCAUAUGAAUAGGUGAUAGAAU ...((((.(((....((((.....))))....(((((((.(((......((..(((..((((......))))..)))..)).....))).)))))))..........(((((((((....)))))))))...))).)))).... (-22.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUAUCACCUAUUCAUAUGAACAAAUGCUCAUAUGUUCAUUUAUAAUUAUAAUAAAUUUAAAAAAAUUGUCAAGUCCUAUCUUGCUAAUAAUUAGUUUUUCUGUUACAAUGUUGAAAGCAUAACUUUGUUAAGGAGACAUAU ...............(((((((.(....).)))))))........(((((((....(((((....)))))..((((......))))...)))))))..((((((...((((.((((......)))).))))..))))))..... (-17.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 746 70 21 161 112 NC_002967:TDE1381|5end_V-type_ATP_synthase_subunit_E_1421905..1422135_NEGATIVE 251 44 5 231 193 NC_002967:TDE0544|5end_hypothetical_protein_583854..584084_POSITIVE 230 60 13 63 14 NC_002967:TDE0269|5end_hypothetical_protein_300687..300917_NEGATIVE 212 50 7 203 161 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 202 36 7 75 47 NC_002967:TDE2087|5end_translation_initiation_factor_IF-1_2115686..2115916_NEGATIVE 201 40 20 174 153 NC_002967:TDE0410|5end_peptidase,_M48_family_462053..462283_POSITIVE 183 139 112 144 113 NC_002967:TDE1151|5end_hypothetical_protein_1188534..1188764_NEGATIVE 181 49 5 148 96 NC_002967:TDE1073|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1103515..1103745_POSITIVE 181 138 100 159 120 NC_002967:TDE0751|5end_magnesium_chelatase,_subunit_D/I_family_791051..791281_NEGATIVE 179 70 21 169 106 NC_002967:TDE0841|5end_hypothetical_protein_861598..861828_NEGATIVE 179 138 110 46 23 NC_002967:TDE0045|5end_ABC_transporter,_ATP-binding_protein_55113..55343_NEGATIVE 177 64 22 75 31 NC_002967:TDE1828|5end_hypothetical_protein_1861752..1861982_NEGATIVE 177 64 22 75 31 NC_002967:TDE1776|5end_hypothetical_protein_1819232..1819462_NEGATIVE 177 40 5 79 48 NC_002967:TDE0153|5end_coenzyme_A_disulfide_reductase,_putative_176185..176415_NEGATIVE 175 136 96 157 119 NC_002967:TDE1773|5end_hypothetical_protein_1817101..1817331_NEGATIVE 175 60 19 80 44 NC_002967:TDE0315|5end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_346938..347168_POSITIVE 174 94 57 69 27 NC_002967:TDE0664|5end_OmpA_family_protein_698380..698610_POSITIVE 171 72 35 157 116 NC_002967:TDE0936|5end_hypothetical_protein_959979..960209_NEGATIVE 170 38 2 174 125 NC_002967:TDE2059|5end_hypothetical_protein_2086509..2086739_NEGATIVE 167 37 1 131 93 NC_002967:TDE2362|5end_hypothetical_protein_2397472..2397702_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 44 5 150 112 NC_002967:TDE0543|3end_hypothetical_protein_583853..584003_POSITIVE 218 80 33 87 38 NC_002967:TDE1741|3end_penicillin-binding_protein_1795412..1795562_POSITIVE 188 38 1 141 101 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 183 139 112 151 120 NC_002967:TDE1152|3end_head-to-tail_joining_protein,_putative_1188527..1188677_NEGATIVE 177 40 5 56 25 NC_002967:TDE0154|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_176208..176358_NEGATIVE 171 82 54 84 58 NC_002967:TDE0964|3end_hypothetical_protein_990578..990728_POSITIVE 169 92 51 129 85 NC_002967:TDE0370|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_422594..422744_POSITIVE 167 37 1 131 93 NC_002967:TDE2363|3end_high-affinity_branched_chain_amino_acid_ABC_transporter,_ATP-binding_protein_2397472..2397622_NEGATIVE 164 130 112 148 128 NC_002967:TDE0687|3end_phosphoribosylaminoimidazole_carboxylase,_PurE_protein_724233..724383_POSITIVE 162 72 31 143 116 NC_002967:TDE2406|3end_TldD/PmbA_family_protein_2432047..2432197_NEGATIVE 161 73 41 126 96 NC_002967:TDE1343|3end_trypsin_domain/PDZ_domain_protein_1382236..1382386_POSITIVE 160 68 24 65 28 NC_002967:TDE2095|3end_hypothetical_protein_2123283..2123433_POSITIVE 160 22 2 81 61 NC_002967:TDE1108|3end_hypothetical_protein_1142413..1142563_NEGATIVE 159 46 1 120 76 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 159 66 21 127 85 NC_002967:TDE0354|3end_general_stress_protein_14_399001..399151_POSITIVE 158 45 17 116 93 NC_002967:TDE0615|3end_cobalamin_biosynthesis_protein_CbiG_649856..650006_POSITIVE 158 43 1 103 69 NC_002967:TDE0002|3end_DNA_gyrase,_B_subunit_3540..3690_POSITIVE 157 69 26 60 12 NC_002967:TDE2298|3end_galactokinase,_putative_2337113..2337263_NEGATIVE 155 42 8 110 83 NC_002967:TDE2782|3end_ABC_transporter,_ATP-binding/permease_protein_2832486..2832636_NEGATIVE 155 139 108 149 112 NC_002967:TDE2626|3end_ABC_transporter,_ATP-binding/permease_protein_2666657..2666807_NEGATIVE