Origin IGS: agttggtctccctaatctgaatttataaatattatatcaaattatccactcatttgcattatttaattaaaaaaagagcaagtagttttttcttccacctgctctaaatattttttttgttctctctcgcaccagtagactttaactttaactcttcataaatatatgaatcaatcataaaagctgagccaattatagatttttttgctttcattttaggttcacttacaaaatgcactttacaccctattccaa .........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 ttggaatagggtgtaaagtgcattttgtaagtgaacctaaaatgaaagcaaaaaaatctataattggctcagcttttatgattgattcatatatttatgaagagttaaagttaaagtctactggtgcgagagagaacaaaaaaaatatttagagcaggtggaagaaaaaactacttgctctttttttaattaaataatgcaaatgagtggataatttgatataatatttataaattcagattagggagaccaact Mask Tandem Repeat Region ================================================ agttggtctccctaatctgaatttataaatattatatcaaattatccactcatttgcattatttaattaaaaaaagagcaagtagttttttcttccacctgctctaaatattttttttgttctctctcgcaccagtagactttaactttaactcttcataaatatatgaatcaatcataaaagctgagccaattatagatttttttgctttcattttaggttcacttacaaaatgcactttacaccctattccaa Find is-nt database================================================ Query_seq: FN1247:FN1248|FN1247:FN1248:LOS biosynthesis enzyme LBGB:Hypothetical cytosolic protein:<-<-:1904435..1904689 255 agttggtctccctaatctgaatttataaatattatatcaaattatccactcatttgcattatttaattaaaaaaagagcaagtagttttttcttccacctgctctaaatattttttttgttctctctcgcaccagtagactttaactttaactcttcataaatatatgaatcaatcataaaagctgagccaattatagatttttttgctttcattttaggttcacttacaaaatgcactttacaccctattccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1247:FN1248|FN1247:FN1248:LOS biosynthesis enzyme LBGB:Hypothetical cytosolic protein:<-<-:1904435..1904689 255 agttggtctccctaatctgaatttataaatattatatcaaattatccactcatttgcattatttaattaaaaaaagagcaagtagttttttcttccacctgctctaaatattttttttgttctctctcgcaccagtagactttaactttaactcttcataaatatatgaatcaatcataaaagctgagccaattatagatttttttgctttcattttaggttcacttacaaaatgcactttacaccctattccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1247:FN1248|FN1247:FN1248:LOS biosynthesis enzyme LBGB:Hypothetical cytosolic protein:<-<-:1904435..1904689 255 agttggtctccctaatctgaatttataaatattatatcaaattatccactcatttgcattatttaattaaaaaaagagcaagtagttttttcttccacctgctctaaatattttttttgttctctctcgcaccagtagactttaactttaactcttcataaatatatgaatcaatcataaaagctgagccaattatagatttttttgctttcattttaggttcacttacaaaatgcactttacaccctattccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agttggtctccctaatctgaatttataaatattatatcaaattatccactcatttgcattatttaattaaaaaaagagcaagtagttttttcttccacctgctctaaatattttttttgttctctctcgcaccagtagactttaactttaactcttcataaatatatgaatcaatcataaaagctgagccaattatagatttttttgctttcattttaggttcacttacaaaatgcactttacaccctattccaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 162 End: 254 ................................................................................................................................................................. M Y E S I I K A E P I I D F F A F I L G S L T K C T L H P I P . Protein_Len: 48 Strand: - Start: 107 End: 250 .......................................................................................................... I N K K N E R A G T S K L K L E E Y I Y S D I M F A S G I I S K K A K M K P E S V F H V K C G M ..... agttggtctccctaatctgaatttataaatattatatcaaattatccactcatttgcattatttaattaaaaaaagagcaagtagttttttcttccacctgctctaaatattttttttgttctctctcgcaccagtagactttaactttaactcttcataaatatatgaatcaatcataaaagctgagccaattatagatttttttgctttcattttaggttcacttacaaaatgcactttacaccctattccaa 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: 31 End: 60 ..............................AATGCAAATGAGTGGATAATTTGATATAAT................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agttggtctccctaatctgaatttataaatattatatcaaattatccactcatttgcattatttaattaaaaaaagagcaagtagttttttcttccacctgctctaaatattttttttgttctctctcgcaccagtagactttaactttaactcttcataaatatatgaatcaatcataaaagctgagccaattatagatttttttgctttcattttaggttcacttacaaaatgcactttacaccctattccaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 82 HP_score: -4.6 Tail_Score: -5.64006 Start: 76 End: 104 Full_Region: caaaaaaaatattta gagcaggtgg aagaaaaaa ctacttgctc tttttttaattaaat ...........................................................................gagcaggtggaagaaaaaactacttgctc....................................................................................................................................................... TransTerm Strand: - Conf: 49 HP_score: -2.9 Tail_Score: -3.52678 Start: 165 End: 179 Full_Region: aattggctcagcttt tatga ttgat tcata tatttatgaagagtt ....................................................................................................................................................................tatgattgattcata............................................................................ Find igs database================================================ Query_seq: FN1247:FN1248|FN1247:FN1248:LOS biosynthesis enzyme LBGB:Hypothetical cytosolic protein:<-<-:1904435..1904689 255 agttggtctccctaatctgaatttataaatattatatcaaattatccactcatttgcattatttaattaaaaaaagagcaagtagttttttcttccacctgctctaaatattttttttgttctctctcgcaccagtagactttaactttaactcttcataaatatatgaatcaatcataaaagctgagccaattatagatttttttgctttcattttaggttcacttacaaaatgcactttacaccctattccaa Intra-Species Hit: Count: 1 Min: 1 Max: 255 Len: 255 Subject: NC_003454_FN1247_FN1248|LOS biosynthesis enzyme LBGB:Hypothetical cytosolic protein|NEGATIVE:NEGATIVE|[1904435,1904689]|255 HSP 1 e-value: 1.0E-103 bit: 375.0 Len: 255 Query Start:1 Query End:255 Subject Strand: POSITIVE Subject Start: 1 Subject End: 255 agttggtctccctaatctgaatttataaatattatatcaaattatccactcatttgcattatttaattnnnnnnngagcaagtagttttttcttccacctgctctaaatannnnnnnngttctctctcgcaccagtagactttaactttaactcttcataaatatatgaatcaatcataaaagctgagccaattatagannnnnnngctttcattttaggttcacttacaaaatgcactttacaccctattccaa agttggtctccctaatctgaatttataaatattatatcaaattatccactcatttgcattatttaattaaaaaaagagcaagtagttttttcttccacctgctctaaatattttttttgttctctctcgcaccagtagactttaactttaactcttcataaatatatgaatcaatcataaaagctgagccaattatagatttttttgctttcattttaggttcacttacaaaatgcactttacaccctattccaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUGGUCUCCCUAAUCUGAAUUUAUAAAUAUUAUAUCAAAUUAUCCACUCAUUUGCAUUAUUUAAUUAAAAAAAGAGCAAGUAGUUUUUUCUUCCACCUGCUCUAAAUAUUUUUUUUGUUCUCUCUCGCACCAGUAGACUUUAACUUUAACUCUUCAUAAAUAUAUGAAUCAAUCAUAAAAGCUGAGCCAAUUAUAGAUUUUUUUGCUUUCAUUUUAGGUUCACUUACAAAAUGCACUUUACACCCUAUUCCAA .((.(((...(((((..((((....((((((......(((((.........)))))...))))))..((((((.((((((.((((......))...)).))))))..........(((((.....(((((...(((........))).......((((((....))))))............)).)))......)))))..))))))..))))..)))))...))).)).......................... (-27.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGGAAUAGGGUGUAAAGUGCAUUUUGUAAGUGAACCUAAAAUGAAAGCAAAAAAAUCUAUAAUUGGCUCAGCUUUUAUGAUUGAUUCAUAUAUUUAUGAAGAGUUAAAGUUAAAGUCUACUGGUGCGAGAGAGAACAAAAAAAAUAUUUAGAGCAGGUGGAAGAAAAAACUACUUGCUCUUUUUUUAAUUAAAUAAUGCAAAUGAGUGGAUAAUUUGAUAUAAUAUUUAUAAAUUCAGAUUAGGGAGACCAACU ((((.(((((((((.....))))))))).......(((((..((((.................(((((((..(...(((((.....))))).......)..))))))).(((((((((((((..((((..(...((..((((((......(((((((((((.........)))))))))))))))))..))...)..))))....)))))))..))))))..............))))..)))))....)))).. (-52.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 871 140 91 231 182 NC_003454:FN1247|5end_LOS_biosynthesis_enzyme_LBGB_1904344..1904574_NEGATIVE 265 134 91 53 8 NC_003454:FN2032|5end_DNA-directed_RNA_polymerase_omega_chain_537315..537545_NEGATIVE 264 128 86 141 104 NC_003454:FN0979|5end_hypothetical_protein_1632096..1632326_POSITIVE 257 159 114 91 55 NC_003454:FN1552|5end_hypothetical_protein_67145..67375_NEGATIVE 255 130 84 102 41 NC_003454:FN1323|5end_Thymidylate_kinase_1979152..1979382_NEGATIVE 255 128 86 192 149 NC_003454:FN0608|5end_Exoribonuclease_II_1262142..1262372_POSITIVE 254 144 102 182 134 NC_003454:FN1370|5end_Endonuclease_2019349..2019579_NEGATIVE 248 108 72 74 45 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 241 137 96 212 166 NC_003454:FN1901|5end_Transcription_regulator,_CRP_family_390017..390247_NEGATIVE 240 249 205 158 117 NC_003454:FN0914|5end_hypothetical_protein_1571528..1571758_NEGATIVE 237 226 181 202 159 NC_003454:FN0780|5end_Hypothetical_membrane-spanning_protein_1437490..1437720_NEGATIVE 235 116 91 185 164 NC_003454:FN1069|5end_DNA_topoisomerase_I_1714732..1714962_POSITIVE 235 137 92 110 62 NC_003454:FN1698|5end_dTDP-4-dehydrorhamnose_reductase_194593..194823_NEGATIVE 234 159 111 111 59 NC_003454:FN0464|5end_hypothetical_protein_1109675..1109905_POSITIVE 230 159 118 91 54 NC_003454:FN0981|5end_phosphoribosylamine--glycine_ligase_1634120..1634350_NEGATIVE 230 130 83 224 173 NC_003454:FN0269|5end_Transposase_896041..896271_POSITIVE 227 138 100 51 20 NC_003454:FN0832|5end_hypothetical_protein_1494305..1494535_POSITIVE 227 217 184 94 61 NC_003454:FN1929|5end_Competence-damage_protein_cinA_429733..429963_NEGATIVE 225 138 91 66 29 NC_003454:FN0121|5end_hypothetical_protein_753300..753530_NEGATIVE 225 131 93 159 115 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 257 159 114 86 50 NC_003454:FN1553|3end_Transporter_67150..67300_NEGATIVE 255 130 84 114 53 NC_003454:FN1324|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_1979140..1979290_NEGATIVE 252 138 93 58 8 NC_003454:FN0426|3end_Orotidine_5'-phosphate_decarboxylase_1069513..1069663_POSITIVE 240 249 205 143 102 NC_003454:FN0915|3end_PTS_system,_N-acetylglucosamine-specific_IIA_component_1571543..1571693_NEGATIVE 235 116 91 130 109 NC_003454:FN1068|3end_Smf_protein_1714757..1714907_POSITIVE 235 137 92 100 52 NC_003454:FN1699|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_194603..194753_NEGATIVE 230 159 118 74 37 NC_003454:FN0982|3end_bifunctional_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1634137..1634287_NEGATIVE 228 243 206 40 3 NC_003454:FN1998|3end_HIPA_protein_500391..500541_POSITIVE 227 217 184 83 50 NC_003454:FN1930|3end_Phosphatidylglycerophosphatase_A_429744..429894_NEGATIVE 225 131 93 83 39 NC_003454:FN1835|3end_hypothetical_protein_323315..323465_NEGATIVE 221 105 77 144 118 NC_003454:FN1555|3end_Protein_Translation_Elongation_Factor_Tu_76252..76402_NEGATIVE 220 128 82 74 17 NC_003454:FN0302|3end_Iron(III)_dicitrate_transport_ATP-binding_protein_fecE_937578..937728_POSITIVE 218 133 93 91 51 NC_003454:FN1458|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_2138977..2139127_NEGATIVE 218 137 92 87 31 NC_003454:FN1639|3end_SSU_ribosomal_protein_S3P_137504..137654_NEGATIVE 217 100 53 136 95 NC_003454:FN0495|3end_Acetyl-CoA_acetyltransferase_1140855..1141005_POSITIVE 213 249 202 114 67 NC_003454:FN1370|3end_Endonuclease_2018990..2019140_NEGATIVE 209 225 184 67 23 NC_003454:FN0933|3end_3-phosphoshikimate_1-carboxyvinyltransferase_1586536..1586686_POSITIVE 208 133 91 150 110 NC_003454:FN2112|3end_hypothetical_protein_623169..623319_NEGATIVE 207 131 96 56 4 NC_003454:FN1969|3end_Hemin_transport_system_permease_protein_hmuU_467186..467336_NEGATIVE 206 193 151 126 80 NC_003454:FN0135|3end_Transposase_770605..770755_POSITIVE