Origin IGS: tttttcctccttagaaattttatatattttatatttttaaagtcattttaaaaataacttccatctaatataatgatataacaaagtcacaattaaatcaagtaaatatttttattttatagaaatttttaaaaaattgctattttttccttaatagtgtaaaatatattgattgaagaaaatttttaagtgataaggaatagtgaaaagtata .........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 tatacttttcactattccttatcacttaaaaattttcttcaatcaatatattttacactattaaggaaaaaatagcaattttttaaaaatttctataaaataaaaatatttacttgatttaattgtgactttgttatatcattatattagatggaagttatttttaaaatgactttaaaaatataaaatatataaaatttctaaggaggaaaaa Mask Tandem Repeat Region ================================================ tttttcctccttagaaattttatatattttatatttttaaagtcattttaaaaataacttccatctaatataatgatataacaaagtcacaattaaatcaagtaaatatttttattttatagaaatttttaaaaaattgctattttttccttaatagtgtaaaatatattgattgaagaaaatttttaagtgataaggaatagtgaaaagtata Find is-nt database================================================ Query_seq: FN0741:FN0742|FN0741:FN0742:Glutamate formiminotransferase:hypothetical protein:<-->:1400047..1400260 214 tttttcctccttagaaattttatatattttatatttttaaagtcattttaaaaataacttccatctaatataatgatataacaaagtcacaattaaatcaagtaaatatttttattttatagaaatttttaaaaaattgctattttttccttaatagtgtaaaatatattgattgaagaaaatttttaagtgataaggaatagtgaaaagtata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0741:FN0742|FN0741:FN0742:Glutamate formiminotransferase:hypothetical protein:<-->:1400047..1400260 214 tttttcctccttagaaattttatatattttatatttttaaagtcattttaaaaataacttccatctaatataatgatataacaaagtcacaattaaatcaagtaaatatttttattttatagaaatttttaaaaaattgctattttttccttaatagtgtaaaatatattgattgaagaaaatttttaagtgataaggaatagtgaaaagtata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0741:FN0742|FN0741:FN0742:Glutamate formiminotransferase:hypothetical protein:<-->:1400047..1400260 214 tttttcctccttagaaattttatatattttatatttttaaagtcattttaaaaataacttccatctaatataatgatataacaaagtcacaattaaatcaagtaaatatttttattttatagaaatttttaaaaaattgctattttttccttaatagtgtaaaatatattgattgaagaaaatttttaagtgataaggaatagtgaaaagtata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttcctccttagaaattttatatattttatatttttaaagtcattttaaaaataacttccatctaatataatgatataacaaagtcacaattaaatcaagtaaatatttttattttatagaaatttttaaaaaattgctattttttccttaatagtgtaaaatatattgattgaagaaaatttttaagtgataaggaatagtgaaaagtata Predict ORF larger than 30AA ================================================ tttttcctccttagaaattttatatattttatatttttaaagtcattttaaaaataacttccatctaatataatgatataacaaagtcacaattaaatcaagtaaatatttttattttatagaaatttttaaaaaattgctattttttccttaatagtgtaaaatatattgattgaagaaaatttttaagtgataaggaatagtgaaaagtata 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: 86 Start: 136 End: 165 .......................................................................................................................................ATTGCTATTTTTTCCTTAATAGTGTAAAAT................................................. PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 73 End: 102 ........................................................................CTTGATTTAATTGTGACTTTGTTATATCAT................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 45 End: 74 ............................................ATTTTAAAAATAACTTCCATCTAATATAAT............................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttcctccttagaaattttatatattttatatttttaaagtcattttaaaaataacttccatctaatataatgatataacaaagtcacaattaaatcaagtaaatatttttattttatagaaatttttaaaaaattgctattttttccttaatagtgtaaaatatattgattgaagaaaatttttaagtgataaggaatagtgaaaagtata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -5.0 Tail_Score: -5.30155 Start: 120 End: 142 Full_Region: AATATTTTTATTTTA TAGAAATTTT TAA AAAATTGCTA TTTTTTCCTTAATAG .......................................................................................................................TAGAAATTTTTAAAAAATTGCTA........................................................................ Find igs database================================================ Query_seq: FN0741:FN0742|FN0741:FN0742:Glutamate formiminotransferase:hypothetical protein:<-->:1400047..1400260 214 tttttcctccttagaaattttatatattttatatttttaaagtcattttaaaaataacttccatctaatataatgatataacaaagtcacaattaaatcaagtaaatatttttattttatagaaatttttaaaaaattgctattttttccttaatagtgtaaaatatattgattgaagaaaatttttaagtgataaggaatagtgaaaagtata Intra-Species Hit: Count: 1 Min: 55 Max: 214 Len: 160 Subject: NC_003454_FN0741_FN0742|Glutamate formiminotransferase:hypothetical protein|NEGATIVE:POSITIVE|[1400047,1400260]|214 HSP 1 e-value: 1.0E-29 bit: 131.0 Len: 66 Query Start:149 Query End:214 Subject Strand: POSITIVE Subject Start: 149 Subject End: 214 ....................................................................................................................................................ccttaatagtgtaaaatatattgattgaagaaaatttttaagtgataaggaatagtgaaaagtata ....................................................................................................................................................ccttaatagtgtaaaatatattgattgaagaaaatttttaagtgataaggaatagtgaaaagtata HSP 2 e-value: 1.0E-19 bit: 97.6 Len: 49 Query Start:55 Query End:103 Subject Strand: POSITIVE Subject Start: 55 Subject End: 103 ......................................................taacttccatctaatataatgatataacaaagtcacaattaaatcaagt............................................................................................................... ......................................................taacttccatctaatataatgatataacaaagtcacaattaaatcaagt............................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUUCCAUCUAAUAUAAUGAUAUAACAAAGUCACAAUUAAAUCAAGUAAAUAUUUUUAUUUUAUAGAAAUUUUUAAAAAAUUGCUAUUUUUUCCUUAAUAGUGUAAAAUAUAUUGAUUGAAGAAAAUUUUUAAGUGAUAAGGAAUAGUGAAAAGUAUA ....((((.....((((....))))......(((((.........(((((((....)))))))..(((((((((((....((((..(((.(((((((....)).).)))).)))..))))...))))))))))).)))))..)))).............. (-18.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUACUUUUCACUAUUCCUUAUCACUUAAAAAUUUUCUUCAAUCAAUAUAUUUUACACUAUUAAGGAAAAAAUAGCAAUUUUUUAAAAAUUUCUAUAAAAUAAAAAUAUUUACUUGAUUUAAUUGUGACUUUGUUAUAUCAUUAUAUUAGAUGGAAGUUA ..............(((((((.......(((((................))))).......)))))))...................(((((((((.(((((....)))))...((((.((((((((((...))))))..)))).)))).))))))))). (-14.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 679 50 1 195 146 NC_003454:FN0741|5end_Glutamate_formiminotransferase_1399956..1400186_NEGATIVE 219 110 66 118 79 NC_003454:FN1313|5end_Oligopeptide-binding_protein_oppA_1967053..1967283_POSITIVE 212 145 101 171 124 NC_003454:FN0614|5end_Export_ABC_transporter_1271447..1271677_POSITIVE 199 130 90 191 153 NC_003454:FN1179|5end_ATP-dependent_RNA_helicase_1841768..1841998_NEGATIVE 195 50 4 107 58 NC_003454:FN1575|5end_Hypothetical_cytosolic_protein_86495..86725_NEGATIVE 185 76 40 177 136 NC_003454:FN1308|5end_Phosphatidate_cytidylyltransferase_1964140..1964370_POSITIVE 184 128 84 216 173 NC_003454:FN0633|5end_Replication_protein_1290928..1291158_POSITIVE 181 28 1 129 95 NC_003454:FN1645|5end_LSU_ribosomal_protein_L3P_141301..141531_NEGATIVE 180 135 102 127 93 NC_003454:FN0529|5end_Transposase_1186369..1186599_NEGATIVE 180 135 102 127 93 NC_003454:FN0403|5end_Transposase_1042307..1042537_NEGATIVE 180 135 102 127 93 NC_003454:FN0372|5end_Transposase_1002479..1002709_NEGATIVE 180 135 102 127 93 NC_003454:FN0028|5end_Transposase_664913..665143_POSITIVE 180 135 102 222 188 NC_003454:FN1815|5end_Transposase_295961..296191_NEGATIVE 180 135 102 127 93 NC_003454:FN1511|5end_Transposase_14217..14447_POSITIVE 178 87 43 71 26 NC_003454:FN0569|5end_Hypothetical_membrane-spanning_protein_1220732..1220962_NEGATIVE 178 137 97 231 186 NC_003454:FN1871|5end_hypothetical_protein_362551..362781_NEGATIVE 176 47 4 155 98 NC_003454:FN2073|5end_adenine_phosphoribosyltransferase_583585..583815_POSITIVE 161 107 62 155 116 NC_003454:FN0953|5end_hypothetical_protein_1610246..1610476_NEGATIVE 160 59 13 66 17 NC_003454:FN0122|5end_hypothetical_protein_753401..753631_POSITIVE 157 155 114 88 47 NC_003454:FN0567|5end_hypothetical_protein_1218389..1218619_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 203 145 112 45 9 NC_003454:FN0613|3end_hypothetical_protein_1271401..1271551_POSITIVE 199 130 90 102 64 NC_003454:FN1180|3end_hypothetical_protein_1841857..1842007_NEGATIVE 195 50 4 97 48 NC_003454:FN1576|3end_ATPase_and_helicase_subunits_involved_in_DNA_replication_86505..86655_NEGATIVE 180 135 102 44 10 NC_003454:FN1816|3end_hypothetical_protein_296139..296289_NEGATIVE 176 47 4 143 86 NC_003454:FN2072|3end_Guanine-hypoxanthine_permease_583653..583803_POSITIVE 156 98 78 82 59 NC_003454:FN1455|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_2135674..2135824_NEGATIVE 156 100 54 94 37 NC_003454:FN1240|3end_Lipopolysaccharide_core_biosynthesis_protein_rfaY_1897057..1897207_NEGATIVE 154 158 114 53 5 NC_003454:FN1277|3end_Aminoacyl-histidine_dipeptidase_1935294..1935444_NEGATIVE 154 154 134 42 22 NC_003454:FN0699|3end_Protein_translocase_subunit_secD_1358366..1358516_POSITIVE 153 115 74 85 40 NC_003454:FN1026|3end_tRNA_pseudouridine_synthase_A_1679954..1680104_NEGATIVE 151 120 88 114 82 NC_003454:FN1223|3end_Dihydropteridine_reductase_1881984..1882134_NEGATIVE 151 158 119 54 12 NC_003454:FN1136|3end_Phosphonates_transport_ATP-binding_protein_phnC_1783880..1784030_POSITIVE 151 114 84 62 28 NC_003454:FN1803|3end_Transcriptional_regulator,_TetR_family_284947..285097_POSITIVE 150 102 61 151 112 NC_003454:FN2123|3end_Phenylalanyl-tRNA_synthetase_alpha_chain_632208..632358_NEGATIVE 150 99 54 121 87 NC_003454:FN1914|3end_Anti-sigma_F_factor_antagonist_411643..411793_NEGATIVE 149 160 117 137 89 NC_003454:FN0246|3end_hypothetical_protein_870633..870783_NEGATIVE 148 38 5 151 117 NC_003454:FN0931|3end_Phosphohydrolase_(MUTT/NUDIX_family_protein)_1583933..1584083_NEGATIVE 145 159 115 79 25 NC_003454:FN2097|3end_hypothetical_protein_606449..606599_NEGATIVE 144 116 86 45 19 NC_003454:FN1420|3end_NA+/H+_antiporter_NHAC_2083316..2083466_POSITIVE 144 49 29 126 106 NC_003454:FN1005|3end_hypothetical_protein_1660975..1661125_POSITIVE