Origin IGS: gttagcacctcctcaatatactttttttacaatacactgtattttatcatttaatttataaaaaatcaagaataaaaatctataaaattcttttttttattaaatggtaaaaaattcaacaaaataacttaaattttgatgattgattttgattgaaaaagaacgaaaatgattgtataatgaaataaactatattaatttatatattgctacttgccagccatta .........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 taatggctggcaagtagcaatatataaattaatatagtttatttcattatacaatcattttcgttctttttcaatcaaaatcaatcatcaaaatttaagttattttgttgaattttttaccatttaataaaaaaaagaattttatagatttttattcttgattttttataaattaaatgataaaatacagtgtattgtaaaaaaagtatattgaggaggtgctaac Mask Tandem Repeat Region ================================================ gttagcacctcctcaatatactttttttacaatacactgtattttatcatttaatttataaaaaatcaagaataaaaatctataaaattcttttttttattaaatggtaaaaaattcaacaaaataacttaaattttgatgattgattttgattgaaaaagaacgaaaatgattgtataatgaaataaactatattaatttatatattgctacttgccagccatta Find is-nt database================================================ Query_seq: FN1437:FN1438|FN1437:FN1438:LSU ribosomal protein L28P:hypothetical protein:<-->:2106238..2106463 226 gttagcacctcctcaatatactttttttacaatacactgtattttatcatttaatttataaaaaatcaagaataaaaatctataaaattcttttttttattaaatggtaaaaaattcaacaaaataacttaaattttgatgattgattttgattgaaaaagaacgaaaatgattgtataatgaaataaactatattaatttatatattgctacttgccagccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1437:FN1438|FN1437:FN1438:LSU ribosomal protein L28P:hypothetical protein:<-->:2106238..2106463 226 gttagcacctcctcaatatactttttttacaatacactgtattttatcatttaatttataaaaaatcaagaataaaaatctataaaattcttttttttattaaatggtaaaaaattcaacaaaataacttaaattttgatgattgattttgattgaaaaagaacgaaaatgattgtataatgaaataaactatattaatttatatattgctacttgccagccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1437:FN1438|FN1437:FN1438:LSU ribosomal protein L28P:hypothetical protein:<-->:2106238..2106463 226 gttagcacctcctcaatatactttttttacaatacactgtattttatcatttaatttataaaaaatcaagaataaaaatctataaaattcttttttttattaaatggtaaaaaattcaacaaaataacttaaattttgatgattgattttgattgaaaaagaacgaaaatgattgtataatgaaataaactatattaatttatatattgctacttgccagccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttagcacctcctcaatatactttttttacaatacactgtattttatcatttaatttataaaaaatcaagaataaaaatctataaaattcttttttttattaaatggtaaaaaattcaacaaaataacttaaattttgatgattgattttgattgaaaaagaacgaaaatgattgtataatgaaataaactatattaatttatatattgctacttgccagccatta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 18 End: 107 ................. M L F L Q Y T V F Y H L I Y K K S R I K I Y K I L F F I K W ....................................................................................................................... gttagcacctcctcaatatactttttttacaatacactgtattttatcatttaatttataaaaaatcaagaataaaaatctataaaattcttttttttattaaatggtaaaaaattcaacaaaataacttaaattttgatgattgattttgattgaaaaagaacgaaaatgattgtataatgaaataaactatattaatttatatattgctacttgccagccatta 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: 152 End: 181 .......................................................................................................................................................ATTGAAAAAGAACGAAAATGATTGTATAAT............................................. PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 41 End: 70 ........................................CTTGATTTTTTATAAATTAAATGATAAAAT............................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttagcacctcctcaatatactttttttacaatacactgtattttatcatttaatttataaaaaatcaagaataaaaatctataaaattcttttttttattaaatggtaaaaaattcaacaaaataacttaaattttgatgattgattttgattgaaaaagaacgaaaatgattgtataatgaaataaactatattaatttatatattgctacttgccagccatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -2.4 Tail_Score: -3.75718 Start: 116 End: 142 Full_Region: TAAATGGTAAAAAAT TCAACAAAAT AACTTAA ATTTTGATGA TTGATTTTGATTGAA ...................................................................................................................TCAACAAAATAACTTAAATTTTGATGA.................................................................................... TransTerm Strand: - Conf: 43 HP_score: -2.4 Tail_Score: -3.6654 Start: 116 End: 142 Full_Region: ttcaatcaaaatcaa tcatcaaaat ttaagtt attttgttga attttttaccattta ...................................................................................................................tcatcaaaatttaagttattttgttga.................................................................................... Find igs database================================================ Query_seq: FN1437:FN1438|FN1437:FN1438:LSU ribosomal protein L28P:hypothetical protein:<-->:2106238..2106463 226 gttagcacctcctcaatatactttttttacaatacactgtattttatcatttaatttataaaaaatcaagaataaaaatctataaaattcttttttttattaaatggtaaaaaattcaacaaaataacttaaattttgatgattgattttgattgaaaaagaacgaaaatgattgtataatgaaataaactatattaatttatatattgctacttgccagccatta Intra-Species Hit: Count: 1 Min: 1 Max: 226 Len: 226 Subject: NC_003454_FN1437_FN1438|LSU ribosomal protein L28P:hypothetical protein|NEGATIVE:POSITIVE|[2106238,2106463]|226 HSP 1 e-value: 2.0E-31 bit: 137.0 Len: 90 Query Start:1 Query End:90 Subject Strand: POSITIVE Subject Start: 1 Subject End: 90 gttagcacctcctcaatatacnnnnnnnacaatacactgtattttatcatttaatttataaaaaatcaagaataaaaatctataaaattc........................................................................................................................................ gttagcacctcctcaatatactttttttacaatacactgtattttatcatttaatttataaaaaatcaagaataaaaatctataaaattc........................................................................................................................................ HSP 2 e-value: 2.0E-22 bit: 107.0 Len: 54 Query Start:173 Query End:226 Subject Strand: POSITIVE Subject Start: 173 Subject End: 226 ............................................................................................................................................................................ttgtataatgaaataaactatattaatttatatattgctacttgccagccatta ............................................................................................................................................................................ttgtataatgaaataaactatattaatttatatattgctacttgccagccatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUAGCACCUCCUCAAUAUACUUUUUUUACAAUACACUGUAUUUUAUCAUUUAAUUUAUAAAAAAUCAAGAAUAAAAAUCUAUAAAAUUCUUUUUUUUAUUAAAUGGUAAAAAAUUCAACAAAAUAACUUAAAUUUUGAUGAUUGAUUUUGAUUGAAAAAGAACGAAAAUGAUUGUAUAAUGAAAUAAACUAUAUUAAUUUAUAUAUUGCUACUUGCCAGCCAUUA ..(((((.....(((.((((((((((((.((((.((.....((((((((((((....((((((((..((((((.............))))))))))))))))))))))))))...(((.((((((.......)))))).))).......)))))).)))))))...........))))).))).......(((((......))))).))))).............. (-30.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGGCUGGCAAGUAGCAAUAUAUAAAUUAAUAUAGUUUAUUUCAUUAUACAAUCAUUUUCGUUCUUUUUCAAUCAAAAUCAAUCAUCAAAAUUUAAGUUAUUUUGUUGAAUUUUUUACCAUUUAAUAAAAAAAAGAAUUUUAUAGAUUUUUAUUCUUGAUUUUUUAUAAAUUAAAUGAUAAAAUACAGUGUAUUGUAAAAAAAGUAUAUUGAGGAGGUGCUAAC .......(((((.(((....))).....((((((((.(((.(((((.(((((................................(((.((((((.......)))))).)))...(((((.((((((((.....((((((((....(((.......))).))))))))....)))))))).)))))....))))).)).))).))).)))))))).....))))).. (-33.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 738 50 1 141 92 NC_003454:FN1437|5end_LSU_ribosomal_protein_L28P_2106147..2106377_NEGATIVE 239 50 4 124 87 NC_003454:FN1842|5end_Dihydroxyacetone_kinase_phosphotransfer_protein_331491..331721_POSITIVE 230 50 7 144 102 NC_003454:FN1797|5end_Spermidine/putrescine_transport_ATP-binding_protein_potA_278821..279051_POSITIVE 213 50 1 202 147 NC_003454:FN1764|5end_Enolase_257997..258227_NEGATIVE 205 32 1 120 95 NC_003454:FN1625|5end_LSU_ribosomal_protein_L15P_132864..133094_NEGATIVE 198 50 8 134 99 NC_003454:FN0181|5end_hypothetical_protein_805801..806031_NEGATIVE 194 49 3 139 91 NC_003454:FN1348|5end_ABC_transporter_ATP-binding_protein_2001141..2001371_NEGATIVE 193 46 1 171 136 NC_003454:FN1113|5end_Dipeptide_transport_system_permease_protein_dppB_1757915..1758145_NEGATIVE 191 53 11 66 27 NC_003454:FN1840|5end_Dihydroxyacetone_kinase_329835..330065_POSITIVE 181 14 3 105 94 NC_003454:FN1416|5end_AMINOTRANSFERASE_CLASS-I_2076893..2077123_POSITIVE 181 47 4 128 74 NC_003454:FN1823|5end_Transcriptional_regulator,_TetR_family_311720..311950_POSITIVE 179 40 1 131 92 NC_003454:FN1136|5end_Phosphonates_transport_ATP-binding_protein_phnC_1783057..1783287_POSITIVE 178 96 53 119 76 NC_003454:FN0018|5end_hypothetical_protein_656448..656678_NEGATIVE 174 45 8 173 134 NC_003454:FN1168|5end_Macrolide-efflux_protein_1827559..1827789_NEGATIVE 173 45 7 139 100 NC_003454:FN0279|5end_Lipoprotein_906479..906709_NEGATIVE 172 150 131 191 172 NC_003454:FN0811|5end_hypothetical_protein_1470075..1470305_POSITIVE 171 49 5 137 93 NC_003454:FN0938|5end_hypothetical_protein_1591125..1591355_NEGATIVE 168 49 8 189 152 NC_003454:FN0445|5end_hypothetical_protein_1084816..1085046_POSITIVE 166 64 21 78 31 NC_003454:FN0930|5end_Glycerol-3-phosphate_cytidylyltransferase_1583964..1584194_NEGATIVE 165 50 3 132 93 NC_003454:FN0613|5end_hypothetical_protein_1270890..1271120_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 50 4 120 83 NC_003454:FN1841|3end_Dihydroxyacetone_kinase_331567..331717_POSITIVE 205 32 1 120 95 NC_003454:FN1626|3end_LSU_ribosomal_protein_L30P_132864..133014_NEGATIVE 198 50 8 134 99 NC_003454:FN0182|3end_Sarcosine_oxidase_alpha_subunit_805801..805951_NEGATIVE 194 49 3 130 82 NC_003454:FN1349|3end_ABC_transporter_permease_protein_2001150..2001300_NEGATIVE 181 47 4 65 11 NC_003454:FN1822|3end_Flavodoxin_311737..311887_POSITIVE 179 40 1 53 14 NC_003454:FN1135|3end_Phosphonates-binding_protein_1783059..1783209_POSITIVE 173 45 7 149 110 NC_003454:FN0280|3end_hypothetical_protein_906469..906619_NEGATIVE 167 108 69 99 63 NC_003454:FN0812|3end_Hypothetical_cytosolic_protein_1471397..1471547_POSITIVE 166 64 21 109 62 NC_003454:FN0931|3end_Phosphohydrolase_(MUTT/NUDIX_family_protein)_1583933..1584083_NEGATIVE 165 44 8 151 113 NC_003454:FN1169|3end_L-lactate_dehydrogenase_1827580..1827730_NEGATIVE 162 50 7 113 76 NC_003454:FN1586|3end_O-succinylbenzoate-CoA_synthase_97415..97565_NEGATIVE 161 50 7 122 70 NC_003454:FN1106|3end_L-serine_dehydratase_1751873..1752023_POSITIVE 157 57 19 137 100 NC_003454:FN1685|3end_dTDP-4-dehydrorhamnose_reductase_180135..180285_NEGATIVE 155 44 9 92 65 NC_003454:FN1384|3end_IAA_acetyltransferase_2037888..2038038_NEGATIVE 154 50 2 120 66 NC_003454:FN1088|3end_NADH_oxidase_1733095..1733245_POSITIVE 154 58 13 145 104 NC_003454:FN0942|3end_Sensory_Transduction_Protein_Kinase_1596890..1597040_POSITIVE 154 171 133 47 13 NC_003454:FN0331|3end_hypothetical_protein_966168..966318_POSITIVE 154 43 1 119 74 NC_003454:FN1994|3end_hypothetical_protein_498091..498241_POSITIVE 153 219 171 47 4 NC_003454:FN1179|3end_ATP-dependent_RNA_helicase_1839330..1839480_NEGATIVE 152 219 176 145 102 NC_003454:FN1279|3end_Zinc_metallohydrolase,_glyoxalase_II_family_1937290..1937440_NEGATIVE