Origin IGS: aaaaatttacctcctgattttttgttagcacttaattaagtagagtgctaaatttttataagacaataataatatattatttttcatttgtcaatagaaaaaacaacaatatttattttttaaaatataatttttagattctaataaaaattatggacttttataaaaaatatgataaaataaaatagaatctataaaaggaggagcaaaaatgttaaataaagtaaacaaaatgaattttaatccatcaactttgcctattattactcttatgaatagcataaaaaatgagaagagaagtggattagac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtctaatccacttctcttctcattttttatgctattcataagagtaataataggcaaagttgatggattaaaattcattttgtttactttatttaacatttttgctcctccttttatagattctattttattttatcatattttttataaaagtccataatttttattagaatctaaaaattatattttaaaaaataaatattgttgttttttctattgacaaatgaaaaataatatattattattgtcttataaaaatttagcactctacttaattaagtgctaacaaaaaatcaggaggtaaattttt Mask Tandem Repeat Region ================================================ aaaaatttacctcctgattttttgttagcacttaattaagtagagtgctaaatttttataagacaataataatatattatttttcatttgtcaatagaaaaaacaacaatatttattttttaaaatataatttttagattctaataaaaattatggacttttataaaaaatatgataaaataaaatagaatctataaaaggaggagcaaaaatgttaaataaagtaaacaaaatgaattttaatccatcaactttgcctattattactcttatgaatagcataaaaaatgagaagagaagtggattagac Find is-nt database================================================ Query_seq: FN0676:FN0677|FN0676:FN0677:10 kDa chaperonin GROES:hypothetical protein:<-->:1332471..1332780 310 aaaaatttacctcctgattttttgttagcacttaattaagtagagtgctaaatttttataagacaataataatatattatttttcatttgtcaatagaaaaaacaacaatatttattttttaaaatataatttttagattctaataaaaattatggacttttataaaaaatatgataaaataaaatagaatctataaaaggaggagcaaaaatgttaaataaagtaaacaaaatgaattttaatccatcaactttgcctattattactcttatgaatagcataaaaaatgagaagagaagtggattagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0676:FN0677|FN0676:FN0677:10 kDa chaperonin GROES:hypothetical protein:<-->:1332471..1332780 310 aaaaatttacctcctgattttttgttagcacttaattaagtagagtgctaaatttttataagacaataataatatattatttttcatttgtcaatagaaaaaacaacaatatttattttttaaaatataatttttagattctaataaaaattatggacttttataaaaaatatgataaaataaaatagaatctataaaaggaggagcaaaaatgttaaataaagtaaacaaaatgaattttaatccatcaactttgcctattattactcttatgaatagcataaaaaatgagaagagaagtggattagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0676:FN0677|FN0676:FN0677:10 kDa chaperonin GROES:hypothetical protein:<-->:1332471..1332780 310 aaaaatttacctcctgattttttgttagcacttaattaagtagagtgctaaatttttataagacaataataatatattatttttcatttgtcaatagaaaaaacaacaatatttattttttaaaatataatttttagattctaataaaaattatggacttttataaaaaatatgataaaataaaatagaatctataaaaggaggagcaaaaatgttaaataaagtaaacaaaatgaattttaatccatcaactttgcctattattactcttatgaatagcataaaaaatgagaagagaagtggattagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaatttacctcctgattttttgttagcacttaattaagtagagtgctaaatttttataagacaataataatatattatttttcatttgtcaatagaaaaaacaacaatatttattttttaaaatataatttttagattctaataaaaattatggacttttataaaaaatatgataaaataaaatagaatctataaaaggaggagcaaaaatgttaaataaagtaaacaaaatgaattttaatccatcaactttgcctattattactcttatgaatagcataaaaaatgagaagagaagtggattagac Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 45 End: 134 ............................................ M L N F Y K T I I I Y Y F S F V N R K N N N I Y F L K Y N F ................................................................................................................................................................................ Protein_Len: 42 Strand: + Start: 185 End: 310 ........................................................................................................................................................................................ M E S I K G G A K M L N K V N K M N F N P S T L P I I T L M N S I K N E K R S G L D Protein_Len: 43 Strand: - Start: 154 End: 282 ......................................................................................................................................................... P S K Y F I H Y F L I S D I F P P A F I N F L T F L I F K L G D V K G I I V R I F L M ............................ aaaaatttacctcctgattttttgttagcacttaattaagtagagtgctaaatttttataagacaataataatatattatttttcatttgtcaatagaaaaaacaacaatatttattttttaaaatataatttttagattctaataaaaattatggacttttataaaaaatatgataaaataaaatagaatctataaaaggaggagcaaaaatgttaaataaagtaaacaaaatgaattttaatccatcaactttgcctattattactcttatgaatagcataaaaaatgagaagagaagtggattagac 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: 89 Start: 66 End: 95 .................................................................ATTGACAAATGAAAAATAATATATTATTAT....................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 253 End: 282 ............................................................................................................................................................................................................................................................TTTGCCTATTATTACTCTTATGAATAGCAT............................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaatttacctcctgattttttgttagcacttaattaagtagagtgctaaatttttataagacaataataatatattatttttcatttgtcaatagaaaaaacaacaatatttattttttaaaatataatttttagattctaataaaaattatggacttttataaaaaatatgataaaataaaatagaatctataaaaggaggagcaaaaatgttaaataaagtaaacaaaatgaattttaatccatcaactttgcctattattactcttatgaatagcataaaaaatgagaagagaagtggattagac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0676:FN0677|FN0676:FN0677:10 kDa chaperonin GROES:hypothetical protein:<-->:1332471..1332780 310 aaaaatttacctcctgattttttgttagcacttaattaagtagagtgctaaatttttataagacaataataatatattatttttcatttgtcaatagaaaaaacaacaatatttattttttaaaatataatttttagattctaataaaaattatggacttttataaaaaatatgataaaataaaatagaatctataaaaggaggagcaaaaatgttaaataaagtaaacaaaatgaattttaatccatcaactttgcctattattactcttatgaatagcataaaaaatgagaagagaagtggattagac Intra-Species Hit: Count: 1 Min: 1 Max: 310 Len: 310 Subject: NC_003454_FN0676_FN0677|10 kDa chaperonin GROES:hypothetical protein|NEGATIVE:POSITIVE|[1332471,1332780]|310 HSP 1 e-value: 2.0E-35 bit: 151.0 Len: 76 Query Start:235 Query End:310 Subject Strand: POSITIVE Subject Start: 235 Subject End: 310 ..........................................................................................................................................................................................................................................gaattttaatccatcaactttgcctattattactcttatgaatagcataaaaaatgagaagagaagtggattagac ..........................................................................................................................................................................................................................................gaattttaatccatcaactttgcctattattactcttatgaatagcataaaaaatgagaagagaagtggattagac HSP 2 e-value: 2.0E-28 bit: 127.0 Len: 64 Query Start:1 Query End:64 Subject Strand: POSITIVE Subject Start: 1 Subject End: 64 aaaaatttacctcctgattttttgttagcacttaattaagtagagtgctaaatttttataagac...................................................................................................................................................................................................................................................... aaaaatttacctcctgattttttgttagcacttaattaagtagagtgctaaatttttataagac...................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUUUACCUCCUGAUUUUUUGUUAGCACUUAAUUAAGUAGAGUGCUAAAUUUUUAUAAGACAAUAAUAAUAUAUUAUUUUUCAUUUGUCAAUAGAAAAAACAACAAUAUUUAUUUUUUAAAAUAUAAUUUUUAGAUUCUAAUAAAAAUUAUGGACUUUUAUAAAAAAUAUGAUAAAAUAAAAUAGAAUCUAUAAAAGGAGGAGCAAAAAUGUUAAAUAAAGUAAACAAAAUGAAUUUUAAUCCAUCAACUUUGCCUAUUAUUACUCUUAUGAAUAGCAUAAAAAAUGAGAAGAGAAGUGGAUUAGAC ...((((((((((((.(((((((((((((((((.........))))))))....(((((((((...((((((((..((((((..(((((.((.................................(((((((((((........)))))))))))..((((((((.....(((...........))).....))))))))...))....)))))..)))))).(((((....(((..........)))....))))).)))))))).)))))))))....))))))))).))..)))..))))))).... (-49.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUAAUCCACUUCUCUUCUCAUUUUUUAUGCUAUUCAUAAGAGUAAUAAUAGGCAAAGUUGAUGGAUUAAAAUUCAUUUUGUUUACUUUAUUUAACAUUUUUGCUCCUCCUUUUAUAGAUUCUAUUUUAUUUUAUCAUAUUUUUUAUAAAAGUCCAUAAUUUUUAUUAGAAUCUAAAAAUUAUAUUUUAAAAAAUAAAUAUUGUUGUUUUUUCUAUUGACAAAUGAAAAAUAAUAUAUUAUUAUUGUCUUAUAAAAAUUUAGCACUCUACUUAAUUAAGUGCUAACAAAAAAUCAGGAGGUAAAUUUUU ..............((((((.(((((((.........((((((.(((((((((.....((..(((((..(((...((.(((((((.........................((((((((((.......................))))))))))...((((((((((........))))))))))........)))))))...))...)))..)))))..))...(....)........)))))))))))))))......((((((((...........)))))))).))))))).))))))......... (-48.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 739 50 1 141 92 NC_003454:FN0676|5end_10_kDa_chaperonin_GROES_1332380..1332610_NEGATIVE 432 68 21 125 77 NC_003454:FN0113|5end_Heat-inducible_transcription_repressor_hrcA_746557..746787_POSITIVE 247 46 8 210 168 NC_003454:FN2123|5end_Phenylalanyl-tRNA_synthetase_alpha_chain_633224..633454_NEGATIVE 245 49 4 139 92 NC_003454:FN0409|5end_Acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_alpha_1046277..1046507_POSITIVE 229 204 162 55 18 NC_003454:FN0141|5end_hypothetical_protein_773265..773495_NEGATIVE 227 204 162 55 18 NC_003454:FN1356|5end_hypothetical_protein_2007922..2008152_POSITIVE 227 204 162 55 18 NC_003454:FN0510|5end_hypothetical_protein_1160326..1160556_NEGATIVE 222 45 10 140 101 NC_003454:FN1869|5end_hypothetical_protein_360839..361069_NEGATIVE 218 309 276 165 132 NC_003454:FN0822|5end_Shikimate_kinase_1481828..1482058_POSITIVE 216 50 5 143 94 NC_003454:FN2020|5end_translation_initiation_factor_IF-2_524522..524752_NEGATIVE 216 281 244 62 23 NC_003454:FN1602|5end_Hypothetical_cytosolic_protein_111492..111722_NEGATIVE 215 39 6 139 95 NC_003454:FN1391|5end_Acetyltransferase_2048784..2049014_POSITIVE 208 267 233 33 5 NC_003454:FN0859|5end_hypothetical_protein_1521229..1521459_NEGATIVE 206 60 11 80 16 NC_003454:FN0099|5end_Inorganic_pyrophosphatase_734682..734912_POSITIVE 205 281 242 228 187 NC_003454:FN1278|5end_Acetyltransferase_1937174..1937404_NEGATIVE 205 282 242 55 13 NC_003454:FN0187|5end_Thiol:disulfide_interchange_protein_tlpA_811590..811820_POSITIVE 203 52 11 187 138 NC_003454:FN0770|5end_Hemin_transport_system_ATP-binding_protein_hmuV_1426672..1426902_POSITIVE 203 280 237 73 27 NC_003454:FN0349|5end_D-tyrosyl-tRNA_deacylase_981792..982022_POSITIVE 201 49 4 224 172 NC_003454:FN0660|5end_ABC_transporter_ATP-binding_protein_1317388..1317618_NEGATIVE 199 90 41 123 72 NC_003454:FN1834|5end_Biopolymer_transport_exbB_protein_323239..323469_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 432 68 21 88 40 NC_003454:FN0112|3end_hypothetical_protein_746600..746750_POSITIVE 245 49 4 127 80 NC_003454:FN0408|3end_Acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_1046345..1046495_POSITIVE 229 204 162 117 80 NC_003454:FN0141|3end_hypothetical_protein_773203..773353_NEGATIVE 226 248 201 146 96 NC_003454:FN1310|3end_TonB_protein_1965148..1965298_NEGATIVE 225 67 26 102 62 NC_003454:FN0104|3end_Acetyltransferase_739618..739768_NEGATIVE 218 309 276 62 29 NC_003454:FN0821|3end_hypothetical_protein_1481805..1481955_POSITIVE 216 50 5 116 67 NC_003454:FN2021|3end_ABC1_family_protein_524549..524699_NEGATIVE 205 281 242 112 71 NC_003454:FN1279|3end_Zinc_metallohydrolase,_glyoxalase_II_family_1937290..1937440_NEGATIVE 198 50 5 61 15 NC_003454:FN1505|3end_6,7-dimethyl-8-ribityllumazine_synthase_10949..11099_POSITIVE 196 206 166 55 7 NC_003454:FN1589|3end_LexA_repressor_100531..100681_POSITIVE 193 309 269 50 8 NC_003454:FN1382|3end_ATPase_2034437..2034587_POSITIVE 190 46 10 118 75 NC_003454:FN0863|3end_hypothetical_protein_1522398..1522548_NEGATIVE 189 280 244 109 73 NC_003454:FN1368|3end_COMF_operon_protein_3_2018157..2018307_NEGATIVE 188 230 187 79 30 NC_003454:FN0566|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1217502..1217652_NEGATIVE 185 41 2 107 63 NC_003454:FN1954|3end_Glycerophosphoryl_diester_phosphodiesterase_459777..459927_NEGATIVE 181 280 237 138 93 NC_003454:FN0467|3end_murein_hydrolase_exporter_1113300..1113450_POSITIVE 179 44 5 36 4 NC_003454:FN1528|3end_hypothetical_protein_42588..42738_NEGATIVE 178 47 12 116 83 NC_003454:FN1444|3end_GMP_synthase_[glutamine-hydrolyzing]_2113203..2113353_POSITIVE 178 109 73 121 87 NC_003454:FN0053|3end_Branched-chain_amino_acid_transport_system_carrier_protein_690694..690844_POSITIVE 178 33 9 61 36 NC_003454:FN1799|3end_Spermidine/putrescine_transport_system_permease_protein_potC_281650..281800_POSITIVE