Origin IGS: agaaaaaccacgatttttcatatcattccctcctaaaattattatgataaaagtaaatagttcccgctgagactgaatttttaatctaaaatgctaatcgttcgttaaaaagcaaaactcgttgataaatcaactcaaacagttgcttttcttaacactcactaacatagcatttcacgataaaattcgtcattcgcagttcacttattacttttacataaaactattgtttaattttaataattta .........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 taaattattaaaattaaacaatagttttatgtaaaagtaataagtgaactgcgaatgacgaattttatcgtgaaatgctatgttagtgagtgttaagaaaagcaactgtttgagttgatttatcaacgagttttgctttttaacgaacgattagcattttagattaaaaattcagtctcagcgggaactatttacttttatcataataattttaggagggaatgatatgaaaaatcgtggtttttct Mask Tandem Repeat Region ================================================ agaaaaaccacgatttttcatatcattccctcctaaaattattatgataaaagtaaatagttcccgctgagactgaatttttaatctaaaatgctaatcgttcgttaaaaagcaaaactcgttgataaatcaactcaaacagttgcttttcttaacactcactaacatagcatttcacgataaaattcgtcattcgcagttcacttattacttttacataaaactattgtttaattttaataattta Find is-nt database================================================ Query_seq: FN2093:FN2094|FN2093:FN2094:General secretion pathway protein G:General secretion pathway protein F:<-<-:603642..603888 247 agaaaaaccacgatttttcatatcattccctcctaaaattattatgataaaagtaaatagttcccgctgagactgaatttttaatctaaaatgctaatcgttcgttaaaaagcaaaactcgttgataaatcaactcaaacagttgcttttcttaacactcactaacatagcatttcacgataaaattcgtcattcgcagttcacttattacttttacataaaactattgtttaattttaataattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2093:FN2094|FN2093:FN2094:General secretion pathway protein G:General secretion pathway protein F:<-<-:603642..603888 247 agaaaaaccacgatttttcatatcattccctcctaaaattattatgataaaagtaaatagttcccgctgagactgaatttttaatctaaaatgctaatcgttcgttaaaaagcaaaactcgttgataaatcaactcaaacagttgcttttcttaacactcactaacatagcatttcacgataaaattcgtcattcgcagttcacttattacttttacataaaactattgtttaattttaataattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2093:FN2094|FN2093:FN2094:General secretion pathway protein G:General secretion pathway protein F:<-<-:603642..603888 247 agaaaaaccacgatttttcatatcattccctcctaaaattattatgataaaagtaaatagttcccgctgagactgaatttttaatctaaaatgctaatcgttcgttaaaaagcaaaactcgttgataaatcaactcaaacagttgcttttcttaacactcactaacatagcatttcacgataaaattcgtcattcgcagttcacttattacttttacataaaactattgtttaattttaataattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaaaaccacgatttttcatatcattccctcctaaaattattatgataaaagtaaatagttcccgctgagactgaatttttaatctaaaatgctaatcgttcgttaaaaagcaaaactcgttgataaatcaactcaaacagttgcttttcttaacactcactaacatagcatttcacgataaaattcgtcattcgcagttcacttattacttttacataaaactattgtttaattttaataattta Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 122 End: 247 ......................................................................................................................... M I N Q L K Q L L F L T L T N I A F H D K I R H S Q F T Y Y F Y I K L L F N F N N L agaaaaaccacgatttttcatatcattccctcctaaaattattatgataaaagtaaatagttcccgctgagactgaatttttaatctaaaatgctaatcgttcgttaaaaagcaaaactcgttgataaatcaactcaaacagttgcttttcttaacactcactaacatagcatttcacgataaaattcgtcattcgcagttcacttattacttttacataaaactattgtttaattttaataattta 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: 81 Start: 212 End: 241 ...................................................................................................................................................................................................................TTTTACATAAAACTATTGTTTAATTTTAAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaaaaaccacgatttttcatatcattccctcctaaaattattatgataaaagtaaatagttcccgctgagactgaatttttaatctaaaatgctaatcgttcgttaaaaagcaaaactcgttgataaatcaactcaaacagttgcttttcttaacactcactaacatagcatttcacgataaaattcgtcattcgcagttcacttattacttttacataaaactattgtttaattttaataattta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -4.3 Tail_Score: -3.38324 Start: 131 End: 145 Full_Region: AACTCGTTGATAAAT CAACT CAAAC AGTTG CTTTTCTTAACACTC ..................................................................................................................................CAACTCAAACAGTTG...................................................................................................... TransTerm Strand: - Conf: 48 HP_score: -4.3 Tail_Score: -2.91772 Start: 131 End: 145 Full_Region: gagtgttaagaaaag caact gtttg agttg atttatcaacgagtt ..................................................................................................................................caactgtttgagttg...................................................................................................... Find igs database================================================ Query_seq: FN2093:FN2094|FN2093:FN2094:General secretion pathway protein G:General secretion pathway protein F:<-<-:603642..603888 247 agaaaaaccacgatttttcatatcattccctcctaaaattattatgataaaagtaaatagttcccgctgagactgaatttttaatctaaaatgctaatcgttcgttaaaaagcaaaactcgttgataaatcaactcaaacagttgcttttcttaacactcactaacatagcatttcacgataaaattcgtcattcgcagttcacttattacttttacataaaactattgtttaattttaataattta Intra-Species Hit: Count: 2 Min: 1 Max: 247 Len: 247 Subject: NC_003454_FN2093_FN2094|General secretion pathway protein G:General secretion pathway protein F|NEGATIVE:NEGATIVE|[603642,603888]|247 HSP 1 e-value: 1.0E-137 bit: 490.0 Len: 247 Query Start:1 Query End:247 Subject Strand: POSITIVE Subject Start: 1 Subject End: 247 agaaaaaccacgatttttcatatcattccctcctaaaattattatgataaaagtaaatagttcccgctgagactgaatttttaatctaaaatgctaatcgttcgttaaaaagcaaaactcgttgataaatcaactcaaacagttgcttttcttaacactcactaacatagcatttcacgataaaattcgtcattcgcagttcacttattacttttacataaaactattgtttaattttaataattta agaaaaaccacgatttttcatatcattccctcctaaaattattatgataaaagtaaatagttcccgctgagactgaatttttaatctaaaatgctaatcgttcgttaaaaagcaaaactcgttgataaatcaactcaaacagttgcttttcttaacactcactaacatagcatttcacgataaaattcgtcattcgcagttcacttattacttttacataaaactattgtttaattttaataattta Subject: NC_003454_FN0579_FN0580|Hypothetical cytosolic protein:Penicillin-binding protein|POSITIVE:POSITIVE|[1234779,1235069]|291 HSP 1 e-value: 1.0E-44 bit: 180.0 Len: 127 Query Start:66 Query End:192 Subject Strand: NEGATIVE Subject Start: 50 Subject End: 176 .................................................................gctgagactgaatttttaatctaaaatgctaatcgttcgttaaaaagcaaaactcgttgataaatcaactcaaacagttgcttttcttaacactcactaacatagcatttcacgataaaattcgtca....................................................... .................................................................gctgagactgaattttaagtctaaaatgctaatcgttctctaaaaagcaaaactcgttgataaatcaactcaaacaattgcttttcttaacgctcactagcatagcatttaacgacaaaattcgtca....................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAAACCACGAUUUUUCAUAUCAUUCCCUCCUAAAAUUAUUAUGAUAAAAGUAAAUAGUUCCCGCUGAGACUGAAUUUUUAAUCUAAAAUGCUAAUCGUUCGUUAAAAAGCAAAACUCGUUGAUAAAUCAACUCAAACAGUUGCUUUUCUUAACACUCACUAACAUAGCAUUUCACGAUAAAAUUCGUCAUUCGCAGUUCACUUAUUACUUUUACAUAAAACUAUUGUUUAAUUUUAAUAAUUUA .((((((......))))))................(((((((((...(((((((((..(((....((((.(((.(((((((..(((..((((((((...((..((((((((((((.....(((((....)))))........)))))))..)))))....)).....))))))))...))))))))))))).....))))..)))..)))))))))....((((....)))).....))))))))). (-43.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUUAUUAAAAUUAAACAAUAGUUUUAUGUAAAAGUAAUAAGUGAACUGCGAAUGACGAAUUUUAUCGUGAAAUGCUAUGUUAGUGAGUGUUAAGAAAAGCAACUGUUUGAGUUGAUUUAUCAACGAGUUUUGCUUUUUAACGAACGAUUAGCAUUUUAGAUUAAAAAUUCAGUCUCAGCGGGAACUAUUUACUUUUAUCAUAAUAAUUUUAGGAGGGAAUGAUAUGAAAAAUCGUGGUUUUUCU .......(((((((((..........((((((((((((((..(((...((((....(((((((((((((.((((((((((.....((...((((((((..(((((........(((((....))))).....))))))))))))).))...)))))))))))))..))))))).)))...))))..)))..))))))))).)))))))))))))).((..((...(((((....)))))..))..)) (-60.92) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 784 100 51 191 142 NC_003454:FN2093|5end_General_secretion_pathway_protein_G_603551..603781_NEGATIVE 304 90 52 231 191 NC_003454:FN0580|5end_Penicillin-binding_protein_1234930..1235160_POSITIVE 279 46 1 225 171 NC_003454:FN1264|5end_hypothetical_protein_1920766..1920996_POSITIVE 275 48 9 115 76 NC_003454:FN1433|5end_Short_chain_dehydrogenase_2102520..2102750_NEGATIVE 242 147 101 109 61 NC_003454:FN1604|5end_hypothetical_protein_113822..114052_NEGATIVE 221 52 11 121 79 NC_003454:FN1165|5end_D-galactose-binding_protein_1822898..1823128_POSITIVE 217 34 9 104 79 NC_003454:FN1884|5end_hypothetical_protein_370507..370737_NEGATIVE 215 205 162 52 14 NC_003454:FN1578|5end_hypothetical_protein_88796..89026_NEGATIVE 212 44 14 112 84 NC_003454:FN2118|5end_Hypothetical_exported_24-amino_acid_repeat_protein_627024..627254_NEGATIVE 212 34 5 105 72 NC_003454:FN1597|5end_peptidyl-tRNA_hydrolase_107810..108040_NEGATIVE 210 68 29 139 97 NC_003454:FN0939|5end_Hypothetical_membrane-spanning_protein_1592919..1593149_NEGATIVE 209 43 7 80 36 NC_003454:FN1263|5end_Cobalt_chelatase_1920576..1920806_NEGATIVE 206 147 106 50 15 NC_003454:FN1192|5end_hypothetical_protein_1854679..1854909_POSITIVE 206 57 13 218 182 NC_003454:FN1186|5end_Amidohydrolase_1848756..1848986_POSITIVE 204 48 6 217 173 NC_003454:FN0312|5end_Anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_949316..949546_POSITIVE 203 95 59 154 113 NC_003454:FN0642|5end_hypothetical_protein_1299461..1299691_NEGATIVE 203 54 14 142 99 NC_003454:FN0018|5end_hypothetical_protein_656448..656678_NEGATIVE 200 33 12 102 82 NC_003454:FN1412|5end_5-methylthioribose_kinase_2073206..2073436_NEGATIVE 199 230 184 70 15 NC_003454:FN0363|5end_ATP_synthase_C_chain,_sodium_ion_specific_993703..993933_NEGATIVE 196 100 60 166 122 NC_003454:FN0703|5end_N-acyl-L-amino_acid_amidohydrolase_1361724..1361954_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 550 200 152 50 1 NC_003454:FN0579|3end_Hypothetical_cytosolic_protein_1234718..1234868_POSITIVE 275 48 9 97 58 NC_003454:FN1434|3end_Tetratricopeptide_repeat_family_protein_2102538..2102688_NEGATIVE 223 195 157 132 101 NC_003454:FN1691|3end_Hypothetical_membrane-spanning_protein_186632..186782_NEGATIVE 215 205 162 64 26 NC_003454:FN1579|3end_Cysteinyl-tRNA_synthetase_88784..88934_NEGATIVE 214 216 173 48 2 NC_003454:FN1652|3end_Oligopeptide-binding_protein_oppA_146041..146191_NEGATIVE 212 44 14 100 72 NC_003454:FN2119|3end_Hypothetical_exported_24-amino_acid_repeat_protein_627036..627186_NEGATIVE 210 68 29 83 41 NC_003454:FN0940|3end_hypothetical_protein_1592975..1593125_NEGATIVE 200 33 12 87 67 NC_003454:FN1413|3end_translation_initiation_factor_IF-2B_subunit_alpha_2073221..2073371_NEGATIVE 195 163 141 151 127 NC_003454:FN0828|3end_ABC_transporter_permease_protein_1489505..1489655_POSITIVE 195 220 173 74 25 NC_003454:FN0319|3end_Citrate_(pro-3S)-lyase_ligase_955818..955968_NEGATIVE 193 56 15 113 70 NC_003454:FN1034|3end_Transcriptional_regulator,_TetR_family_1688345..1688495_POSITIVE 193 210 173 36 4 NC_003454:FN0184|3end_hypothetical_protein_808656..808806_NEGATIVE 193 164 131 146 112 NC_003454:FN1834|3end_Biopolymer_transport_exbB_protein_322676..322826_NEGATIVE 191 49 5 116 70 NC_003454:FN1898|3end_Sugar_transport_ATP-binding_protein_384986..385136_NEGATIVE 190 35 1 93 60 NC_003454:FN1178|3end_Hypothetical_cytosolic_protein_1838793..1838943_NEGATIVE 190 43 14 82 53 NC_003454:FN2122|3end_Phenylalanyl-tRNA_synthetase_beta_chain_629798..629948_NEGATIVE 190 45 10 53 10 NC_003454:FN1735|3end_V-type_ATP_synthase_subunit_A_234251..234401_NEGATIVE 189 34 2 78 42 NC_003454:FN2035|3end_DNA-directed_RNA_polymerase_beta'_chain_538822..538972_NEGATIVE 188 47 10 96 59 NC_003454:FN1838|3end_Glycerol_uptake_facilitator_protein_328333..328483_POSITIVE 188 65 23 119 79 NC_003454:FN1608|3end_Ribosomal_protein_L11_methyltransferase_117909..118059_NEGATIVE