Origin IGS: cttccatcctcctcagagatattgtatcacagttctgccccttgtcaatccatccagtcgccaaagccctctgtcaacctaaacaaaaagaagagccgagattctcttcccgactctttcagttatattcaaaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctttgaatataactgaaagagtcgggaagagaatctcggctcttctttttgtttaggttgacagagggctttggcgactggatggattgacaaggggcagaactgtgatacaatatctctgaggaggatggaag Mask Tandem Repeat Region ================================================ cttccatcctcctcagagatattgtatcacagttctgccccttgtcaatccatccagtcgccaaagccctctgtcaacctaaacaaaaagaagagccgagattctcttcccgactctttcagttatattcaaaga Find is-nt database================================================ Query_seq: SSA_2243:SSA_2244|SSA_2243:SSA_2244:Conserved uncharacterized protein:Arsenate reductase, putative:<-<-:2239432..2239566 135 cttccatcctcctcagagatattgtatcacagttctgccccttgtcaatccatccagtcgccaaagccctctgtcaacctaaacaaaaagaagagccgagattctcttcccgactctttcagttatattcaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2243:SSA_2244|SSA_2243:SSA_2244:Conserved uncharacterized protein:Arsenate reductase, putative:<-<-:2239432..2239566 135 cttccatcctcctcagagatattgtatcacagttctgccccttgtcaatccatccagtcgccaaagccctctgtcaacctaaacaaaaagaagagccgagattctcttcccgactctttcagttatattcaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2243:SSA_2244|SSA_2243:SSA_2244:Conserved uncharacterized protein:Arsenate reductase, putative:<-<-:2239432..2239566 135 cttccatcctcctcagagatattgtatcacagttctgccccttgtcaatccatccagtcgccaaagccctctgtcaacctaaacaaaaagaagagccgagattctcttcccgactctttcagttatattcaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttccatcctcctcagagatattgtatcacagttctgccccttgtcaatccatccagtcgccaaagccctctgtcaacctaaacaaaaagaagagccgagattctcttcccgactctttcagttatattcaaaga Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 6 End: 134 ..... M L L R D I V S Q F C P L S I H P V A K A L C Q P K Q K E E P R F S S R L F Q L Y S K . Protein_Len: 39 Strand: + Start: 19 End: 135 .................. M L Y H S S A P C Q S I Q S P K P S V N L N K K K S R D S L P D S F S Y I Q R cttccatcctcctcagagatattgtatcacagttctgccccttgtcaatccatccagtcgccaaagccctctgtcaacctaaacaaaaagaagagccgagattctcttcccgactctttcagttatattcaaaga 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================================================ cttccatcctcctcagagatattgtatcacagttctgccccttgtcaatccatccagtcgccaaagccctctgtcaacctaaacaaaaagaagagccgagattctcttcccgactctttcagttatattcaaaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -2.3 Tail_Score: -3.85509 Start: 93 End: 116 Full_Region: CCTAAACAAAAAGAA GAGCCGAGA TTCTCT TCCCGACTC TTTCAGTTATATTCA ............................................................................................GAGCCGAGATTCTCTTCCCGACTC................... Find igs database================================================ Query_seq: SSA_2243:SSA_2244|SSA_2243:SSA_2244:Conserved uncharacterized protein:Arsenate reductase, putative:<-<-:2239432..2239566 135 cttccatcctcctcagagatattgtatcacagttctgccccttgtcaatccatccagtcgccaaagccctctgtcaacctaaacaaaaagaagagccgagattctcttcccgactctttcagttatattcaaaga Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: NC_009009_SSA_2243_SSA_2244|Conserved uncharacterized protein:Arsenate reductase, putative|NEGATIVE:NEGATIVE|[2239432,2239566]|135 HSP 1 e-value: 4.0E-71 bit: 268.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 cttccatcctcctcagagatattgtatcacagttctgccccttgtcaatccatccagtcgccaaagccctctgtcaacctaaacaaaaagaagagccgagattctcttcccgactctttcagttatattcaaaga cttccatcctcctcagagatattgtatcacagttctgccccttgtcaatccatccagtcgccaaagccctctgtcaacctaaacaaaaagaagagccgagattctcttcccgactctttcagttatattcaaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCCAUCCUCCUCAGAGAUAUUGUAUCACAGUUCUGCCCCUUGUCAAUCCAUCCAGUCGCCAAAGCCCUCUGUCAACCUAAACAAAAAGAAGAGCCGAGAUUCUCUUCCCGACUCUUUCAGUUAUAUUCAAAGA .............((((...((((.....))))))))....((((.........(((..((....))...))).........))))...((((((.((.((......)).)).))))))................ (-14.97) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUGAAUAUAACUGAAAGAGUCGGGAAGAGAAUCUCGGCUCUUCUUUUUGUUUAGGUUGACAGAGGGCUUUGGCGACUGGAUGGAUUGACAAGGGGCAGAACUGUGAUACAAUAUCUCUGAGGAGGAUGGAAG ((((((...........(((((((((((......)))))))))))(..((..(((((.(((.((((....)))).))))))))..))..).)))))).((((..(((......)))..))))............. (-32.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1041 80 31 171 122 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 369 79 32 223 180 NC_009009:SSA_1721|5end_DNA_polymerase_III,_delta'_subunit,_putative_1708028..1708258_NEGATIVE 362 76 31 90 36 NC_009009:SSA_1311|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_1328393..1328623_NEGATIVE 341 60 15 199 148 NC_009009:SSA_0878|5end_DNA_gyrase,_putative_871596..871826_POSITIVE 341 79 31 196 153 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 339 80 31 226 169 NC_009009:SSA_0422|5end_Phosphoglycerate_mutase_family_protein,_putative_420157..420387_POSITIVE 330 73 36 67 30 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 326 77 35 144 102 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 325 99 54 68 12 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 318 98 56 66 29 NC_009009:SSA_1873|5end_S-adenosyl-methyltransferase_mraW,_putative_1870144..1870374_NEGATIVE 317 76 31 183 109 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 313 69 28 212 168 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 311 80 32 71 13 NC_009009:SSA_0513|5end_ATP:cob(I)alamin_adenosyltransferase,_putative_511558..511788_POSITIVE 310 47 4 69 18 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 307 80 31 145 95 NC_009009:SSA_0402|5end_Histidine_kinase,_putative_399144..399374_POSITIVE 306 79 33 212 162 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 305 76 31 223 179 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 303 80 31 163 93 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 301 76 33 202 166 NC_009009:SSA_1424|5end_Hydrolase,_putative_1434479..1434709_NEGATIVE 301 83 41 69 29 NC_009009:SSA_1092|5end_Dihydrofolate_reductase,_putative_1109599..1109829_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 73 36 74 37 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 317 59 16 117 58 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 313 73 31 124 86 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 311 110 66 88 38 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 310 47 4 72 21 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 307 80 31 143 93 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE 300 68 21 138 95 NC_009009:SSA_1940|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_1926155..1926305_NEGATIVE 296 75 35 144 107 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 294 50 1 117 56 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 293 80 36 64 21 NC_009009:SSA_0313|3end_Conserved_uncharacterized_protein_308389..308539_NEGATIVE 290 74 37 78 47 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 288 119 71 75 31 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 288 80 31 69 3 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 286 119 71 59 4 NC_009009:SSA_2027|3end_P-type_ATPase-metal/cation_transport_(probably_copper),_putative_2033109..2033259_NEGATIVE 285 37 2 113 73 NC_009009:SSA_1929|3end_Macrophage_infectivity_potentiator_protein,_putative_1917029..1917179_NEGATIVE 285 80 33 58 1 NC_009009:SSA_0512|3end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_511625..511775_POSITIVE 284 70 25 87 29 NC_009009:SSA_1244|3end_hypothetical_protein_1268465..1268615_NEGATIVE 283 120 71 88 39 NC_009009:SSA_0748|3end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_730635..730785_POSITIVE 282 79 35 116 61 NC_009009:SSA_1191|3end_hypothetical_protein_1218222..1218372_NEGATIVE 279 50 4 70 23 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE