Origin IGS: tataactattacaataaaagtaaaaagtgaaagtctaaccaatcattttttacttttattttttattgacaagtaaaaaaaattatggtatatattatttgaaattattagccattaatatataagagtgctaaaaggaggaaaagtaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttacttttcctccttttagcactcttatatattaatggctaataatttcaaataatatataccataattttttttacttgtcaataaaaaataaaagtaaaaaatgattggttagactttcactttttacttttattgtaatagttata Mask Tandem Repeat Region ================================================ tataactattacaataaaagtaaaaagtgaaagtctaaccaatcattttttacttttattttttattgacaagtaaaaaaaattatggtatatattatttgaaattattagccattaatatataagagtgctaaaaggaggaaaagtaaaa Find is-nt database================================================ Query_seq: FN0320:FN0321|FN0320:FN0321:Hypothetical cytosolic protein:heat shock protein 90:->->:957623..957773 151 tataactattacaataaaagtaaaaagtgaaagtctaaccaatcattttttacttttattttttattgacaagtaaaaaaaattatggtatatattatttgaaattattagccattaatatataagagtgctaaaaggaggaaaagtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0320:FN0321|FN0320:FN0321:Hypothetical cytosolic protein:heat shock protein 90:->->:957623..957773 151 tataactattacaataaaagtaaaaagtgaaagtctaaccaatcattttttacttttattttttattgacaagtaaaaaaaattatggtatatattatttgaaattattagccattaatatataagagtgctaaaaggaggaaaagtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0320:FN0321|FN0320:FN0321:Hypothetical cytosolic protein:heat shock protein 90:->->:957623..957773 151 tataactattacaataaaagtaaaaagtgaaagtctaaccaatcattttttacttttattttttattgacaagtaaaaaaaattatggtatatattatttgaaattattagccattaatatataagagtgctaaaaggaggaaaagtaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataactattacaataaaagtaaaaagtgaaagtctaaccaatcattttttacttttattttttattgacaagtaaaaaaaattatggtatatattatttgaaattattagccattaatatataagagtgctaaaaggaggaaaagtaaaa Predict ORF larger than 30AA ================================================ tataactattacaataaaagtaaaaagtgaaagtctaaccaatcattttttacttttattttttattgacaagtaaaaaaaattatggtatatattatttgaaattattagccattaatatataagagtgctaaaaggaggaaaagtaaaa 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: 82 Start: 65 End: 94 ................................................................ATTGACAAGTAAAAAAAATTATGGTATATA......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tataactattacaataaaagtaaaaagtgaaagtctaaccaatcattttttacttttattttttattgacaagtaaaaaaaattatggtatatattatttgaaattattagccattaatatataagagtgctaaaaggaggaaaagtaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0320:FN0321|FN0320:FN0321:Hypothetical cytosolic protein:heat shock protein 90:->->:957623..957773 151 tataactattacaataaaagtaaaaagtgaaagtctaaccaatcattttttacttttattttttattgacaagtaaaaaaaattatggtatatattatttgaaattattagccattaatatataagagtgctaaaaggaggaaaagtaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 151 Len: 151 Subject: NC_003454_FN0320_FN0321|Hypothetical cytosolic protein:heat shock protein 90|POSITIVE:POSITIVE|[957623,957773]|151 HSP 1 e-value: 1.0E-31 bit: 137.0 Len: 69 Query Start:83 Query End:151 Subject Strand: POSITIVE Subject Start: 83 Subject End: 151 ..................................................................................ttatggtatatattatttgaaattattagccattaatatataagagtgctaaaaggaggaaaagtaaaa ..................................................................................ttatggtatatattatttgaaattattagccattaatatataagagtgctaaaaggaggaaaagtaaaa HSP 2 e-value: 2.0E-17 bit: 89.7 Len: 45 Query Start:1 Query End:45 Subject Strand: POSITIVE Subject Start: 1 Subject End: 45 tataactattacaataaaagtaaaaagtgaaagtctaaccaatca.......................................................................................................... tataactattacaataaaagtaaaaagtgaaagtctaaccaatca.......................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAACUAUUACAAUAAAAGUAAAAAGUGAAAGUCUAACCAAUCAUUUUUUACUUUUAUUUUUUAUUGACAAGUAAAAAAAAUUAUGGUAUAUAUUAUUUGAAAUUAUUAGCCAUUAAUAUAUAAGAGUGCUAAAAGGAGGAAAAGUAAAA ....(((((....(((((((((((((((((............)))))))))))))))))((((((((....)))))))).....))))).....((((((....((.((((((.(((.....)))..).)))))...))....)))))).. (-24.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUACUUUUCCUCCUUUUAGCACUCUUAUAUAUUAAUGGCUAAUAAUUUCAAAUAAUAUAUACCAUAAUUUUUUUUACUUGUCAAUAAAAAAUAAAAGUAAAAAAUGAUUGGUUAGACUUUCACUUUUUACUUUUAUUGUAAUAGUUAUA ..................((((.....(((((((((.(((.........)))..)))))))))............................((((((((((((((.(((..(......)..))).))))))))))))))......)))).. (-20.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 225 135 105 108 78 NC_003454:FN0113|5end_Heat-inducible_transcription_repressor_hrcA_746557..746787_POSITIVE 194 67 34 175 131 NC_003454:FN1694|5end_UDP-N-acetyl-D-quinovosamine_4-epimerase_190169..190399_NEGATIVE 189 148 117 45 18 NC_003454:FN0186|5end_Cytochrome_c-type_biogenesis_protein_ccdA_810853..811083_POSITIVE 186 69 28 134 92 NC_003454:FN0114|5end_GrpE_protein_747623..747853_POSITIVE 180 142 122 231 212 NC_003454:FN0537|5end_Hypothetical_membrane-spanning_protein_1191753..1191983_NEGATIVE 179 73 38 70 41 NC_003454:FN1451|5end_cell_division_protein_FtsZ_2132710..2132940_NEGATIVE 179 72 43 117 88 NC_003454:FN1668|5end_Cholinephosphate_cytidylyltransferase_165563..165793_NEGATIVE 178 116 72 92 45 NC_003454:FN0166|5end_hypothetical_protein_793732..793962_POSITIVE 177 150 125 69 42 NC_003454:FN1659|5end_hypothetical_protein_155036..155266_POSITIVE 174 66 30 112 74 NC_003454:FN0384|5end_hypothetical_protein_1015571..1015801_POSITIVE 173 55 35 120 98 NC_003454:FN0258|5end_Zinc-transporting_ATPase_886009..886239_NEGATIVE 172 135 98 58 23 NC_003454:FN0394|5end_Outer_membrane_protein_1032327..1032557_POSITIVE 172 74 49 93 63 NC_003454:FN1612|5end_coproporphyrinogen_III_oxidase_122533..122763_NEGATIVE 171 69 33 58 18 NC_003454:FN0553|5end_D-serine_dehydratase_1206060..1206290_NEGATIVE 169 74 43 123 88 NC_003454:FN2064|5end_hypothetical_protein_575716..575946_NEGATIVE 168 140 91 179 142 NC_003454:FN1077|5end_hypothetical_protein_1724005..1724235_NEGATIVE 168 60 14 105 60 NC_003454:FN0912|5end_Cobalamin_[5'-phosphate]_synthase_1570159..1570389_NEGATIVE 167 76 33 122 72 NC_003454:FN1095|5end_hypothetical_protein_1740232..1740462_POSITIVE 167 139 92 156 95 NC_003454:FN1838|5end_Glycerol_uptake_facilitator_protein_327489..327719_POSITIVE 162 65 24 231 187 NC_003454:FN1898|5end_Sugar_transport_ATP-binding_protein_386569..386799_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 60 13 78 31 NC_003454:FN0320|3end_Hypothetical_cytosolic_protein_957562..957712_POSITIVE 225 135 105 71 41 NC_003454:FN0112|3end_hypothetical_protein_746600..746750_POSITIVE 187 130 89 142 105 NC_003454:FN1291|3end_hypothetical_protein_1947972..1948122_NEGATIVE 186 69 28 123 81 NC_003454:FN0113|3end_Heat-inducible_transcription_repressor_hrcA_747692..747842_POSITIVE 184 67 24 88 42 NC_003454:FN1899|3end_Hypothetical_lipoprotein_386714..386864_NEGATIVE 179 73 38 47 18 NC_003454:FN1452|3end_Cell_division_protein_ftsA_2132733..2132883_NEGATIVE 179 57 15 61 10 NC_003454:FN1428|3end_Branched-chain_amino_acid_transport_ATP-binding_protein_livF_2096860..2097010_NEGATIVE 179 72 43 120 91 NC_003454:FN1669|3end_Choline_transport_protein_165560..165710_NEGATIVE 178 116 72 78 31 NC_003454:FN0165|3end_hypothetical_protein_793798..793948_POSITIVE 176 57 11 105 58 NC_003454:FN1616|3end_transcription_antitermination_protein_NusB_125976..126126_NEGATIVE 174 66 30 110 72 NC_003454:FN0383|3end_Lipopolysaccharide_N-acetylglucosaminyltransferase_1015649..1015799_POSITIVE 173 55 35 92 70 NC_003454:FN0259|3end_Zinc-transporting_ATPase_886037..886187_NEGATIVE 172 135 98 55 20 NC_003454:FN0393|3end_Polysaccharide_deacetylase_1032404..1032554_POSITIVE 172 74 49 90 60 NC_003454:FN1613|3end_hypothetical_protein_122536..122686_NEGATIVE 168 60 14 92 47 NC_003454:FN0913|3end_Cobinamide_kinase_1570172..1570322_NEGATIVE 162 136 110 73 36 NC_003454:FN1561|3end_Hypothetical_cytosolic_protein_83032..83182_NEGATIVE 160 88 42 88 46 NC_003454:FN0064|3end_Hypothetical_cytosolic_protein_699922..700072_POSITIVE 156 128 82 47 1 NC_003454:FN1879|3end_SSU_ribosomal_protein_S20P_367507..367657_POSITIVE 155 113 80 80 46 NC_003454:FN2073|3end_adenine_phosphoribosyltransferase_584198..584348_POSITIVE 154 146 110 77 36 NC_003454:FN0798|3end_Fructose-1,6-bisphosphatase_1457852..1458002_POSITIVE