Origin IGS: ttttatagtaatgaactctttaattttatatgcaatctgttatttttaaaaggagagggctaacctctcctttttttaaaaattatattatgaaaaatggactttggtattaaaattttaggaggcttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataagcctcctaaaattttaataccaaagtccatttttcataatataatttttaaaaaaaggagaggttagccctctccttttaaaaataacagattgcatataaaattaaagagttcattactataaaa Mask Tandem Repeat Region ================================================ ttttatagtaatgaactctttaattttatatgcaatctgttatttttaaaaggagagggctaacctctcctttttttaaaaattatattatgaaaaatggactttggtattaaaattttaggaggcttat Find is-nt database================================================ Query_seq: FN1988:FN1989|FN1988:FN1989:Tyrosine phenol-lyase:Sodium-dependent tyrosine transporter:->->:492441..492570 130 ttttatagtaatgaactctttaattttatatgcaatctgttatttttaaaaggagagggctaacctctcctttttttaaaaattatattatgaaaaatggactttggtattaaaattttaggaggcttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1988:FN1989|FN1988:FN1989:Tyrosine phenol-lyase:Sodium-dependent tyrosine transporter:->->:492441..492570 130 ttttatagtaatgaactctttaattttatatgcaatctgttatttttaaaaggagagggctaacctctcctttttttaaaaattatattatgaaaaatggactttggtattaaaattttaggaggcttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1988:FN1989|FN1988:FN1989:Tyrosine phenol-lyase:Sodium-dependent tyrosine transporter:->->:492441..492570 130 ttttatagtaatgaactctttaattttatatgcaatctgttatttttaaaaggagagggctaacctctcctttttttaaaaattatattatgaaaaatggactttggtattaaaattttaggaggcttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttatagtaatgaactctttaattttatatgcaatctgttatttttaaaaggagagggctaacctctcctttttttaaaaattatattatgaaaaatggactttggtattaaaattttaggaggcttat Predict ORF larger than 30AA ================================================ ttttatagtaatgaactctttaattttatatgcaatctgttatttttaaaaggagagggctaacctctcctttttttaaaaattatattatgaaaaatggactttggtattaaaattttaggaggcttat 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================================================ ttttatagtaatgaactctttaattttatatgcaatctgttatttttaaaaggagagggctaacctctcctttttttaaaaattatattatgaaaaatggactttggtattaaaattttaggaggcttat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.3 Tail_Score: -5.43866 Start: 52 End: 70 Full_Region: CTGTTATTTTTAAAA GGAGAGG GCTAA CCTCTCC TTTTTTTAAAAATTA ...................................................GGAGAGGGCTAACCTCTCC............................................................ TransTerm Strand: - Conf: 88 HP_score: -10.3 Tail_Score: -4.11216 Start: 52 End: 70 Full_Region: taatttttaaaaaaa ggagagg ttagc cctctcc ttttaaaaataacag ...................................................ggagaggttagccctctcc............................................................ Find igs database================================================ Query_seq: FN1988:FN1989|FN1988:FN1989:Tyrosine phenol-lyase:Sodium-dependent tyrosine transporter:->->:492441..492570 130 ttttatagtaatgaactctttaattttatatgcaatctgttatttttaaaaggagagggctaacctctcctttttttaaaaattatattatgaaaaatggactttggtattaaaattttaggaggcttat Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_003454_FN1988_FN1989|Tyrosine phenol-lyase:Sodium-dependent tyrosine transporter|POSITIVE:POSITIVE|[492441,492570]|130 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 ttttatagtaatgaactctttaattttatatgcaatctgttatttttaaaaggagagggctaacctctccnnnnnnnaaaaattatattatgaaaaatggactttggtattaaaattttaggaggcttat ttttatagtaatgaactctttaattttatatgcaatctgttatttttaaaaggagagggctaacctctcctttttttaaaaattatattatgaaaaatggactttggtattaaaattttaggaggcttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUAGUAAUGAACUCUUUAAUUUUAUAUGCAAUCUGUUAUUUUUAAAAGGAGAGGGCUAACCUCUCCUUUUUUUAAAAAUUAUAUUAUGAAAAAUGGACUUUGGUAUUAAAAUUUUAGGAGGCUUAU ...............(((((.(((((((.((((......(((((((((((((((((((.....)))))))))))..................))))))))......)))))))))))..)))))...... (-29.66) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAGCCUCCUAAAAUUUUAAUACCAAAGUCCAUUUUUCAUAAUAUAAUUUUUAAAAAAAGGAGAGGUUAGCCCUCUCCUUUUAAAAAUAACAGAUUGCAUAUAAAAUUAAAGAGUUCAUUACUAUAAAA ......(((....(((((((.......((((.(((......)))...(((((((((...((((((((.....)))))))))))))))))....)))).....)))))))...)))............... (-19.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 231 103 63 130 87 NC_003454:FN0307|5end_Iron(III)_dicitrate_transport_ATP-binding_protein_fecE_942095..942325_POSITIVE 225 100 52 228 182 NC_003454:FN0160|5end_hypothetical_protein_788279..788509_POSITIVE 214 58 15 179 128 NC_003454:FN1333|5end_hypothetical_protein_1987580..1987810_NEGATIVE 208 90 58 125 87 NC_003454:FN0643|5end_hypothetical_protein_1299871..1300101_NEGATIVE 202 79 31 46 2 NC_003454:FN1380|5end_Citrate_lyase_beta_chain_2027248..2027478_POSITIVE 202 90 46 207 165 NC_003454:FN1759|5end_Hydroxymethylpyrimidine_kinase_254765..254995_NEGATIVE 201 62 30 173 141 NC_003454:FN1046|5end_hypothetical_protein_1696371..1696601_POSITIVE 200 105 61 141 98 NC_003454:FN0006|5end_tRNA_modification_GTPase_644505..644735_POSITIVE 199 83 45 184 147 NC_003454:FN0664|5end_2-nitropropane_dioxygenase_1319758..1319988_POSITIVE 199 69 31 198 160 NC_003454:FN1995|5end_hypothetical_protein_498245..498475_POSITIVE 197 61 37 104 79 NC_003454:FN2091|5end_hypothetical_protein_602481..602711_NEGATIVE 195 83 50 146 109 NC_003454:FN1228|5end_hypothetical_protein_1886190..1886420_NEGATIVE 193 47 6 217 162 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 192 68 27 216 173 NC_003454:FN2102|5end_ABC_transporter_ATP-binding_protein_611177..611407_POSITIVE 191 105 61 56 7 NC_003454:FN0328|5end_Na(+)-linked_D-alanine_glycine_permease_963771..964001_NEGATIVE 190 79 36 114 66 NC_003454:FN0201|5end_Glutaconyl-COA_decarboxylase_beta_subunit_826542..826772_POSITIVE 187 96 51 181 135 NC_003454:FN1024|5end_DNA-binding_protein_HU_1678480..1678710_NEGATIVE 186 80 32 74 24 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 185 55 16 72 35 NC_003454:FN0692|5end_Nitrogen_regulation_protein_NIFR3_1346428..1346658_POSITIVE 184 79 31 183 134 NC_003454:FN0628|5end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing]_1288257..1288487_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 83 42 49 8 NC_003454:FN1988|3end_Tyrosine_phenol-lyase_492380..492530_POSITIVE 231 103 63 136 93 NC_003454:FN0306|3end_Iron(III)_dicitrate_transport_system_permease_protein_fecD_942181..942331_POSITIVE 215 127 98 53 15 NC_003454:FN1006|3end_Acetyltransferase_1660998..1661148_NEGATIVE 208 90 58 109 71 NC_003454:FN0644|3end_UROPORPHYRINOGEN-III_SYNTHASE_1299887..1300037_NEGATIVE 200 56 20 115 80 NC_003454:FN0173|3end_hypothetical_protein_799304..799454_POSITIVE 200 105 61 135 92 NC_003454:FN0005|3end_Jag_protein_644579..644729_POSITIVE 199 83 45 143 106 NC_003454:FN0663|3end_hypothetical_protein_1319797..1319947_POSITIVE 197 86 49 98 60 NC_003454:FN1894|3end_BAX_protein_381731..381881_NEGATIVE 195 83 50 76 39 NC_003454:FN1229|3end_hypothetical_protein_1886260..1886410_NEGATIVE 193 47 6 98 43 NC_003454:FN1069|3end_DNA_topoisomerase_I_1717082..1717232_POSITIVE 191 70 46 79 47 NC_003454:FN1986|3end_hypothetical_protein_490007..490157_POSITIVE 190 79 36 99 51 NC_003454:FN0200|3end_Biotin_carboxyl_carrier_protein_of_glutaconyl-COA_decarboxylase_826607..826757_POSITIVE 187 74 42 71 36 NC_003454:FN1059|3end_Branched_chain_amino_acid_transport_system_II_carrier_protein_1707020..1707170_POSITIVE 185 79 52 94 62 NC_003454:FN1987|3end_Transcriptional_regulator,_GntR_family_490018..490168_NEGATIVE 183 46 11 104 67 NC_003454:FN1101|3end_ATPase_1746039..1746189_POSITIVE 180 56 15 150 105 NC_003454:FN1334|3end_N-acetylmuramoyl-L-alanine_amidase_1987603..1987753_NEGATIVE 177 127 85 92 43 NC_003454:FN1477|3end_Hypothetical_membrane-spanning_protein_2160297..2160447_POSITIVE 176 87 52 65 18 NC_003454:FN1724|3end_Potassium_uptake_protein_KtrA_222654..222804_NEGATIVE 176 47 6 85 45 NC_003454:FN1563|3end_hypothetical_protein_84777..84927_NEGATIVE 173 82 62 64 42 NC_003454:FN0043|3end_Hypothetical_exported_24-amino_acid_repeat_protein_682818..682968_POSITIVE