Origin IGS: aaaaagtaaaaaataatatggtagtgagtaaaataaacgaactgtgaattgacgaattttgtcgttaaatgctatgctagtgagcgttaagaaaagcaattgtttgagttgatttatcaacgagttttgctttttagagaacgattagcattttagacttaaaattcagtctcagcagagagttattttactcctactatttaaaaggagaaaagagttatgttaaaaaatattaattttaagaaagtgattatttttttcataactctttttatattgctttttatttat .........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 ataaataaaaagcaatataaaaagagttatgaaaaaaataatcactttcttaaaattaatattttttaacataactcttttctccttttaaatagtaggagtaaaataactctctgctgagactgaattttaagtctaaaatgctaatcgttctctaaaaagcaaaactcgttgataaatcaactcaaacaattgcttttcttaacgctcactagcatagcatttaacgacaaaattcgtcaattcacagttcgtttattttactcactaccatattattttttacttttt Mask Tandem Repeat Region ================================================ aaaaagtaaaaaataatatggtagtgagtaaaataaacgaactgtgaattgacgaattttgtcgttaaatgctatgctagtgagcgttaagaaaagcaattgtttgagttgatttatcaacgagttttgctttttagagaacgattagcattttagacttaaaattcagtctcagcagagagttattttactcctactatttaaaaggagaaaagagttatgttaaaaaatattaattttaagaaagtgattatttttttcataactctttttatattgctttttatttat Find is-nt database================================================ Query_seq: FN0579:FN0580|FN0579:FN0580:Hypothetical cytosolic protein:Penicillin-binding protein:->->:1234779..1235069 291 aaaaagtaaaaaataatatggtagtgagtaaaataaacgaactgtgaattgacgaattttgtcgttaaatgctatgctagtgagcgttaagaaaagcaattgtttgagttgatttatcaacgagttttgctttttagagaacgattagcattttagacttaaaattcagtctcagcagagagttattttactcctactatttaaaaggagaaaagagttatgttaaaaaatattaattttaagaaagtgattatttttttcataactctttttatattgctttttatttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0579:FN0580|FN0579:FN0580:Hypothetical cytosolic protein:Penicillin-binding protein:->->:1234779..1235069 291 aaaaagtaaaaaataatatggtagtgagtaaaataaacgaactgtgaattgacgaattttgtcgttaaatgctatgctagtgagcgttaagaaaagcaattgtttgagttgatttatcaacgagttttgctttttagagaacgattagcattttagacttaaaattcagtctcagcagagagttattttactcctactatttaaaaggagaaaagagttatgttaaaaaatattaattttaagaaagtgattatttttttcataactctttttatattgctttttatttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0579:FN0580|FN0579:FN0580:Hypothetical cytosolic protein:Penicillin-binding protein:->->:1234779..1235069 291 aaaaagtaaaaaataatatggtagtgagtaaaataaacgaactgtgaattgacgaattttgtcgttaaatgctatgctagtgagcgttaagaaaagcaattgtttgagttgatttatcaacgagttttgctttttagagaacgattagcattttagacttaaaattcagtctcagcagagagttattttactcctactatttaaaaggagaaaagagttatgttaaaaaatattaattttaagaaagtgattatttttttcataactctttttatattgctttttatttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaagtaaaaaataatatggtagtgagtaaaataaacgaactgtgaattgacgaattttgtcgttaaatgctatgctagtgagcgttaagaaaagcaattgtttgagttgatttatcaacgagttttgctttttagagaacgattagcattttagacttaaaattcagtctcagcagagagttattttactcctactatttaaaaggagaaaagagttatgttaaaaaatattaattttaagaaagtgattatttttttcataactctttttatattgctttttatttat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 144 End: 233 ............................................................................................................................................... M S I L D L K F S L S R E L F Y S Y Y L K G E K S Y V K K Y .......................................................... Protein_Len: 40 Strand: - Start: 1 End: 120 F L L F Y Y P L S Y F L R V T F Q R I K D N F A I S T L T L F L L Q K L Q N I M ........................................................................................................................................................................... aaaaagtaaaaaataatatggtagtgagtaaaataaacgaactgtgaattgacgaattttgtcgttaaatgctatgctagtgagcgttaagaaaagcaattgtttgagttgatttatcaacgagttttgctttttagagaacgattagcattttagacttaaaattcagtctcagcagagagttattttactcctactatttaaaaggagaaaagagttatgttaaaaaatattaattttaagaaagtgattatttttttcataactctttttatattgctttttatttat 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================================================ aaaaagtaaaaaataatatggtagtgagtaaaataaacgaactgtgaattgacgaattttgtcgttaaatgctatgctagtgagcgttaagaaaagcaattgtttgagttgatttatcaacgagttttgctttttagagaacgattagcattttagacttaaaattcagtctcagcagagagttattttactcctactatttaaaaggagaaaagagttatgttaaaaaatattaattttaagaaagtgattatttttttcataactctttttatattgctttttatttat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 75 HP_score: -4.3 Tail_Score: -5.16206 Start: 215 End: 268 Full_Region: TTTAAAAGGAGAAAA GAGTTATGTTAAAAAATATTAATTTT AAG AAAGTGATTATTTTTTTCATAACTC TTTTTATATTGCTTT ......................................................................................................................................................................................................................GAGTTATGTTAAAAAATATTAATTTTAAGAAAGTGATTATTTTTTTCATAACTC....................... Find igs database================================================ Query_seq: FN0579:FN0580|FN0579:FN0580:Hypothetical cytosolic protein:Penicillin-binding protein:->->:1234779..1235069 291 aaaaagtaaaaaataatatggtagtgagtaaaataaacgaactgtgaattgacgaattttgtcgttaaatgctatgctagtgagcgttaagaaaagcaattgtttgagttgatttatcaacgagttttgctttttagagaacgattagcattttagacttaaaattcagtctcagcagagagttattttactcctactatttaaaaggagaaaagagttatgttaaaaaatattaattttaagaaagtgattatttttttcataactctttttatattgctttttatttat Intra-Species Hit: Count: 3 Min: 14 Max: 291 Len: 278 Subject: NC_003454_FN0579_FN0580|Hypothetical cytosolic protein:Penicillin-binding protein|POSITIVE:POSITIVE|[1234779,1235069]|291 HSP 1 e-value: 1.0E-143 bit: 509.0 Len: 278 Query Start:14 Query End:291 Subject Strand: POSITIVE Subject Start: 14 Subject End: 291 .............taatatggtagtgagtaaaataaacgaactgtgaattgacgaattttgtcgttaaatgctatgctagtgagcgttaagaaaagcaattgtttgagttgatttatcaacgagttttgctttttagagaacgattagcattttagacttaaaattcagtctcagcagagagttattttactcctactatttaaaaggagaaaagagttatgttaaaaaatattaattttaagaaagtgattannnnnnncataactctttttatattgctttttatttat .............taatatggtagtgagtaaaataaacgaactgtgaattgacgaattttgtcgttaaatgctatgctagtgagcgttaagaaaagcaattgtttgagttgatttatcaacgagttttgctttttagagaacgattagcattttagacttaaaattcagtctcagcagagagttattttactcctactatttaaaaggagaaaagagttatgttaaaaaatattaattttaagaaagtgattatttttttcataactctttttatattgctttttatttat Subject: NC_003454_FN2093_FN2094|General secretion pathway protein G:General secretion pathway protein F|NEGATIVE:NEGATIVE|[603642,603888]|247 HSP 1 e-value: 2.0E-44 bit: 180.0 Len: 127 Query Start:50 Query End:176 Subject Strand: NEGATIVE Subject Start: 66 Subject End: 192 .................................................tgacgaattttgtcgttaaatgctatgctagtgagcgttaagaaaagcaattgtttgagttgatttatcaacgagttttgctttttagagaacgattagcattttagacttaaaattcagtctcagc................................................................................................................... .................................................tgacgaattttatcgtgaaatgctatgttagtgagtgttaagaaaagcaactgtttgagttgatttatcaacgagttttgctttttaacgaacgattagcattttagattaaaaattcagtctcagc................................................................................................................... Subject: NC_003454_FN0071_FN0072|GTP cyclohydrolase I:2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase|POSITIVE:POSITIVE|[711666,711854]|189 HSP 1 e-value: 3.0E-18 bit: 93.7 Len: 79 Query Start:29 Query End:107 Subject Strand: NEGATIVE Subject Start: 88 Subject End: 166 ............................taaaataaacgaactgtgaattgacgaattttgtcgttaaatgctatgctagtgagcgttaagaaaagcaattgtttga........................................................................................................................................................................................ ............................taaaacaaacgaactgcgaattgacgaattttgccgttaaatgctatgctaatgagcatcaaaaaaagcagttgtttga........................................................................................................................................................................................ HSP 2 e-value: 5.0E-14 bit: 79.8 Len: 56 Query Start:122 Query End:177 Subject Strand: NEGATIVE Subject Start: 25 Subject End: 80 .........................................................................................................................gagttttgctttttagagaacgattagcattttagacttaaaattcagtctcagca.................................................................................................................. .........................................................................................................................gagttctgctttttagcgaatgattagcattttaggcttaaaattcagtctcagca.................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUGGUAGUGAGUAAAAUAAACGAACUGUGAAUUGACGAAUUUUGUCGUUAAAUGCUAUGCUAGUGAGCGUUAAGAAAAGCAAUUGUUUGAGUUGAUUUAUCAACGAGUUUUGCUUUUUAGAGAACGAUUAGCAUUUUAGACUUAAAAUUCAGUCUCAGCAGAGAGUUAUUUUACUCCUACUAUUUAAAAGGAGAAAAGAGUUAUGUUAAAAAAUAUUAAUUUUAAGAAAGUGAUUAUUUUUUUCAUAACUCUUUUUAUAUUGCUUUUUAUUUAU ....(((((((.(((((((((((.(...((((.....(((((((((((((...((((((((.(((....))).....(((((((((........(((((....))))).....)))))))))..........))))))))..)))..))))))).)))...))))...))))))))))))))))))).(((((((.(((((((((((((..((((((((...((((.....))))...)))))))).)))))))))))))......)))))))..... (-79.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAUAAAAAGCAAUAUAAAAAGAGUUAUGAAAAAAAUAAUCACUUUCUUAAAAUUAAUAUUUUUUAACAUAACUCUUUUCUCCUUUUAAAUAGUAGGAGUAAAAUAACUCUCUGCUGAGACUGAAUUUUAAGUCUAAAAUGCUAAUCGUUCUCUAAAAAGCAAAACUCGUUGAUAAAUCAACUCAAACAAUUGCUUUUCUUAACGCUCACUAGCAUAGCAUUUAACGACAAAAUUCGUCAAUUCACAGUUCGUUUAUUUUACUCACUACCAUAUUA .......(((((.......((((((((((((.((((((((...................))))))))..))))))))))))...))))).....((((((((((((((((...(((.((((((.(((((((..(((..((((((((...........((((((((.....(((((....)))))........))))))))......(((....))).))))))))...)))))))))))))...))))))...).))))))))))).))))....... (-60.83) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 746 80 31 179 130 NC_003454:FN0072|5end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_711715..711945_POSITIVE 368 187 148 227 179 NC_003454:FN2125|5end_DNA_gyrase_subunit_A_636160..636390_NEGATIVE 270 197 162 45 9 NC_003454:FN0057|5end_Endonuclease_III_693215..693445_POSITIVE 256 118 79 62 17 NC_003454:FN2038|5end_LSU_ribosomal_protein_L10P_547696..547926_NEGATIVE 253 190 159 51 21 NC_003454:FN1972|5end_hypothetical_protein_472071..472301_NEGATIVE 246 269 235 98 62 NC_003454:FN0311|5end_anaerobic_ribonucleoside_triphosphate_reductase_947125..947355_POSITIVE 232 108 61 225 182 NC_003454:FN2093|5end_General_secretion_pathway_protein_G_603551..603781_NEGATIVE 227 106 62 80 29 NC_003454:FN0196|5end_Transcriptional_regulator,_FUR_family_822317..822547_POSITIVE 226 106 66 231 189 NC_003454:FN1486|5end_Integral_membrane_protein_with_CBS_domains_2169299..2169529_NEGATIVE 226 270 222 113 62 NC_003454:FN0556|5end_hypothetical_protein_1209000..1209230_NEGATIVE 220 91 56 211 183 NC_003454:FN0739|5end_Formiminotetrahydrofolate_cyclodeaminase_1397655..1397885_NEGATIVE 220 158 112 141 97 NC_003454:FN0044|5end_Shikimate_5-dehydrogenase_682701..682931_POSITIVE 219 110 63 227 179 NC_003454:FN0047|5end_Exodeoxyribonuclease_III_684427..684657_POSITIVE 217 147 104 82 39 NC_003454:FN1631|5end_SSU_ribosomal_protein_S14P_135247..135477_NEGATIVE 212 55 17 180 142 NC_003454:FN2080|5end_ABC_transporter_integral_membrane_protein_591957..592187_NEGATIVE 210 210 161 219 163 NC_003454:FN1399|5end_Hypothetical_cytosolic_protein_2054355..2054585_POSITIVE 210 166 129 227 185 NC_003454:FN0269|5end_Transposase_896041..896271_POSITIVE 208 268 226 155 118 NC_003454:FN0569|5end_Hypothetical_membrane-spanning_protein_1220732..1220962_NEGATIVE 208 182 142 83 34 NC_003454:FN1683|5end_Acetyltransferase_179082..179312_NEGATIVE 206 90 44 179 130 NC_003454:FN0702|5end_N-acyl-L-amino_acid_amidohydrolase_1361002..1361232_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 557 160 111 62 13 NC_003454:FN0071|3end_GTP_cyclohydrolase_I_711605..711755_POSITIVE 368 187 148 81 33 NC_003454:FN2126|3end_DNA_gyrase_subunit_B_636306..636456_NEGATIVE 248 180 131 65 10 NC_003454:FN0579|3end_Hypothetical_cytosolic_protein_1234718..1234868_POSITIVE 239 157 112 78 32 NC_003454:FN1801|3end_Sodium/glutamate_symport_carrier_protein_282636..282786_NEGATIVE 227 106 62 90 39 NC_003454:FN0195|3end_Dipeptide_transport_ATP-binding_protein_dppD_822407..822557_POSITIVE 217 147 104 61 18 NC_003454:FN1632|3end_LSU_ribosomal_protein_L5P_135268..135418_NEGATIVE 212 55 17 62 24 NC_003454:FN2081|3end_ABC_transporter_substrate-binding_protein_592075..592225_NEGATIVE 211 179 133 55 11 NC_003454:FN2094|3end_General_secretion_pathway_protein_F_603799..603949_NEGATIVE 210 210 161 84 28 NC_003454:FN1398|3end_Amino_acid_carrier_protein_alsT_2054300..2054450_POSITIVE 208 182 142 82 33 NC_003454:FN1684|3end_N-acetylneuraminate_synthase_179083..179233_NEGATIVE 206 128 83 44 5 NC_003454:FN0907|3end_Ribosomal_RNA_small_subunit_methyltransferase_C_1565324..1565474_NEGATIVE 206 90 44 113 64 NC_003454:FN0703|3end_N-acyl-L-amino_acid_amidohydrolase_1361068..1361218_NEGATIVE 206 130 89 36 3 NC_003454:FN0025|3end_Hypothetical_exported_24-amino_acid_repeat_protein_664326..664476_POSITIVE 204 68 30 95 49 NC_003454:FN2040|3end_LSU_ribosomal_protein_L11P_548618..548768_NEGATIVE 197 58 12 60 6 NC_003454:FN1363|3end_Dipeptide_transport_ATP-binding_protein_dppF_2015333..2015483_POSITIVE 196 264 228 45 4 NC_003454:FN1942|3end_Hypothetical_cytosolic_protein_444000..444150_NEGATIVE 195 192 155 99 61 NC_003454:FN1811|3end_Manganese_transport_system_ATP-binding_protein_mntA_292161..292311_NEGATIVE 191 97 62 99 56 NC_003454:FN1045|3end_hypothetical_protein_1695178..1695328_NEGATIVE 191 100 56 83 38 NC_003454:FN2044|3end_LSU_ribosomal_protein_L33P_549957..550107_NEGATIVE 188 72 31 77 31 NC_003454:FN1487|3end_hypothetical_protein_2169559..2169709_NEGATIVE