Origin IGS: tataatgtatacaatccttgagattattagcctttctatagattaattattaatttatagggattgatgagtcatcaatctagggagaacagattttcaagcctgtggataagaactattcatatttctctagaaagagcaatattcatagttcttatctgcaagaattgcgtcatttctcttctgagaaatgaccagatattattatgtaataatctcaaggaggataaaggagtgatatttt .........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 aaaatatcactcctttatcctccttgagattattacataataatatctggtcatttctcagaagagaaatgacgcaattcttgcagataagaactatgaatattgctctttctagagaaatatgaatagttcttatccacaggcttgaaaatctgttctccctagattgatgactcatcaatccctataaattaataattaatctatagaaaggctaataatctcaaggattgtatacattata Mask Tandem Repeat Region ================================================ tataatgtatacaatccttgagattattagcctttctatagattaattattaatttatagggattgatgagtcatcaatctagggagaacagattttcaagcctgtggataagaactattcatatttctctagaaagagcaatattcatagttcttatctgcaagaattgcgtcatttctcttctgagaaatgaccagatattattatgtaataatctcaaggaggataaaggagtgatatttt Find is-nt database================================================ Query_seq: FN0160:FN0161|FN0160:FN0161:hypothetical protein:RNA-directed DNA polymerase:->->:788659..788902 244 tataatgtatacaatccttgagattattagcctttctatagattaattattaatttatagggattgatgagtcatcaatctagggagaacagattttcaagcctgtggataagaactattcatatttctctagaaagagcaatattcatagttcttatctgcaagaattgcgtcatttctcttctgagaaatgaccagatattattatgtaataatctcaaggaggataaaggagtgatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0160:FN0161|FN0160:FN0161:hypothetical protein:RNA-directed DNA polymerase:->->:788659..788902 244 tataatgtatacaatccttgagattattagcctttctatagattaattattaatttatagggattgatgagtcatcaatctagggagaacagattttcaagcctgtggataagaactattcatatttctctagaaagagcaatattcatagttcttatctgcaagaattgcgtcatttctcttctgagaaatgaccagatattattatgtaataatctcaaggaggataaaggagtgatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0160:FN0161|FN0160:FN0161:hypothetical protein:RNA-directed DNA polymerase:->->:788659..788902 244 tataatgtatacaatccttgagattattagcctttctatagattaattattaatttatagggattgatgagtcatcaatctagggagaacagattttcaagcctgtggataagaactattcatatttctctagaaagagcaatattcatagttcttatctgcaagaattgcgtcatttctcttctgagaaatgaccagatattattatgtaataatctcaaggaggataaaggagtgatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataatgtatacaatccttgagattattagcctttctatagattaattattaatttatagggattgatgagtcatcaatctagggagaacagattttcaagcctgtggataagaactattcatatttctctagaaagagcaatattcatagttcttatctgcaagaattgcgtcatttctcttctgagaaatgaccagatattattatgtaataatctcaaggaggataaaggagtgatatttt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 93 End: 191 ............................................................................................ M F K P V D K N Y S Y F S R K S N I H S S Y L Q E L R H F S S E K ..................................................... Protein_Len: 60 Strand: + Start: 64 End: 243 ............................................................... M M S H Q S R E N R F S S L W I R T I H I S L E R A I F I V L I C K N C V I S L L R N D Q I L L C N N L K E D K G V I F . Protein_Len: 39 Strand: - Start: 123 End: 239 .......................................................................................................................... I E R S L A I N M T R I Q L F Q T M E R R L F S W I N N H L L R L S S L P T M ..... tataatgtatacaatccttgagattattagcctttctatagattaattattaatttatagggattgatgagtcatcaatctagggagaacagattttcaagcctgtggataagaactattcatatttctctagaaagagcaatattcatagttcttatctgcaagaattgcgtcatttctcttctgagaaatgaccagatattattatgtaataatctcaaggaggataaaggagtgatatttt 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================================================ tataatgtatacaatccttgagattattagcctttctatagattaattattaatttatagggattgatgagtcatcaatctagggagaacagattttcaagcctgtggataagaactattcatatttctctagaaagagcaatattcatagttcttatctgcaagaattgcgtcatttctcttctgagaaatgaccagatattattatgtaataatctcaaggaggataaaggagtgatatttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 76 HP_score: -9.8 Tail_Score: -2.77895 Start: 169 End: 197 Full_Region: ttacataataatatc tggtcatttctc agaa gagaaatgacgca attcttgcagataag ........................................................................................................................................................................tggtcatttctcagaagagaaatgacgca............................................... Find igs database================================================ Query_seq: FN0160:FN0161|FN0160:FN0161:hypothetical protein:RNA-directed DNA polymerase:->->:788659..788902 244 tataatgtatacaatccttgagattattagcctttctatagattaattattaatttatagggattgatgagtcatcaatctagggagaacagattttcaagcctgtggataagaactattcatatttctctagaaagagcaatattcatagttcttatctgcaagaattgcgtcatttctcttctgagaaatgaccagatattattatgtaataatctcaaggaggataaaggagtgatatttt Intra-Species Hit: Count: 1 Min: 1 Max: 244 Len: 244 Subject: NC_003454_FN0160_FN0161|hypothetical protein:RNA-directed DNA polymerase|POSITIVE:POSITIVE|[788659,788902]|244 HSP 1 e-value: 1.0E-136 bit: 484.0 Len: 244 Query Start:1 Query End:244 Subject Strand: POSITIVE Subject Start: 1 Subject End: 244 tataatgtatacaatccttgagattattagcctttctatagattaattattaatttatagggattgatgagtcatcaatctagggagaacagattttcaagcctgtggataagaactattcatatttctctagaaagagcaatattcatagttcttatctgcaagaattgcgtcatttctcttctgagaaatgaccagatattattatgtaataatctcaaggaggataaaggagtgatatttt tataatgtatacaatccttgagattattagcctttctatagattaattattaatttatagggattgatgagtcatcaatctagggagaacagattttcaagcctgtggataagaactattcatatttctctagaaagagcaatattcatagttcttatctgcaagaattgcgtcatttctcttctgagaaatgaccagatattattatgtaataatctcaaggaggataaaggagtgatatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAUGUAUACAAUCCUUGAGAUUAUUAGCCUUUCUAUAGAUUAAUUAUUAAUUUAUAGGGAUUGAUGAGUCAUCAAUCUAGGGAGAACAGAUUUUCAAGCCUGUGGAUAAGAACUAUUCAUAUUUCUCUAGAAAGAGCAAUAUUCAUAGUUCUUAUCUGCAAGAAUUGCGUCAUUUCUCUUCUGAGAAAUGACCAGAUAUUAUUAUGUAAUAAUCUCAAGGAGGAUAAAGGAGUGAUAUUUU .......(((....(((((((((((((((.((((.((((((((((.....)))))))))).((((((((...)))))))).))))..................((..((((((((((((..(((((.((((....)))).)))))..))))))))))))..))....(((.((((((((((....)))))))))))))...........)))))))))))))))..)))............... (-79.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAUCACUCCUUUAUCCUCCUUGAGAUUAUUACAUAAUAAUAUCUGGUCAUUUCUCAGAAGAGAAAUGACGCAAUUCUUGCAGAUAAGAACUAUGAAUAUUGCUCUUUCUAGAGAAAUAUGAAUAGUUCUUAUCCACAGGCUUGAAAAUCUGUUCUCCCUAGAUUGAUGACUCAUCAAUCCCUAUAAAUUAAUAAUUAAUCUAUAGAAAGGCUAAUAAUCUCAAGGAUUGUAUACAUUAUA ...............(((..(((((((((((((((..............((((((((((....)))))))))).(((..((((..((((((((((((..(((((.((((....)))).)))))..))))))))))))..)))).))).............(((.((((((((...)))))))).(((((.((((.....)))).)))))..))).)))))))))))))))..)))......... (-73.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 120 74 178 127 NC_003454:FN0268|5end_DNA_repair_protein_recN_894330..894560_POSITIVE 247 131 93 67 29 NC_003454:FN1476|5end_N-acetylmannosamine-6-phosphate_2-epimerase_2158672..2158902_POSITIVE 243 189 141 105 54 NC_003454:FN1379|5end_Citrate_lyase_beta_chain_2026355..2026585_POSITIVE 241 219 171 135 89 NC_003454:FN1278|5end_Acetyltransferase_1937174..1937404_NEGATIVE 231 187 146 88 33 NC_003454:FN0575|5end_hypothetical_protein_1225331..1225561_POSITIVE 226 107 70 197 154 NC_003454:FN1053|5end_hypothetical_protein_1701023..1701253_POSITIVE 223 197 151 78 16 NC_003454:FN0393|5end_Polysaccharide_deacetylase_1030528..1030758_POSITIVE 222 132 96 162 123 NC_003454:FN1182|5end_hypothetical_protein_1845438..1845668_NEGATIVE 218 210 161 159 100 NC_003454:FN0704|5end_hypothetical_protein_1361855..1362085_NEGATIVE 218 203 162 92 46 NC_003454:FN1645|5end_LSU_ribosomal_protein_L3P_141301..141531_NEGATIVE 214 194 159 79 40 NC_003454:FN0699|5end_Protein_translocase_subunit_secD_1357051..1357281_POSITIVE 214 177 131 82 19 NC_003454:FN2072|5end_Guanine-hypoxanthine_permease_582506..582736_POSITIVE 211 109 69 107 57 NC_003454:FN1355|5end_Integral_membrane_protein_2007575..2007805_NEGATIVE 211 198 158 179 143 NC_003454:FN0595|5end_UDP-N-acetylglucosamine_acyltransferase_1249228..1249458_POSITIVE 211 187 148 55 18 NC_003454:FN1971|5end_Hemin_receptor_471106..471336_NEGATIVE 207 174 138 180 133 NC_003454:FN0656|5end_hypothetical_protein_1313725..1313955_POSITIVE 206 176 131 54 7 NC_003454:FN1357|5end_Transposase_2008189..2008419_POSITIVE 206 176 131 54 7 NC_003454:FN0509|5end_Transposase_1160059..1160289_NEGATIVE 206 176 131 54 7 NC_003454:FN1883|5end_Transposase_368863..369093_POSITIVE 205 78 31 152 105 NC_003454:FN0361|5end_ATP_synthase_delta_chain,_sodium_ion_specific_992905..993135_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 219 176 143 97 NC_003454:FN1441|3end_PTS_system,_fructose-specific_IIABC_component_2110123..2110273_POSITIVE 247 131 93 52 14 NC_003454:FN1475|3end_N-acetylneuraminate_lyase_2158737..2158887_POSITIVE 243 189 141 96 45 NC_003454:FN1378|3end_Citrate_lyase_acyl_carrier_protein_2026426..2026576_POSITIVE 239 78 33 73 28 NC_003454:FN0160|3end_hypothetical_protein_788598..788748_POSITIVE 223 197 151 67 5 NC_003454:FN0392|3end_Oxygen-independent_coproporphyrinogen_III_oxidase_1030597..1030747_POSITIVE 218 185 145 130 90 NC_003454:FN2087|3end_hypothetical_protein_599039..599189_NEGATIVE 214 194 159 55 16 NC_003454:FN0698|3end_DNA_integration/recombination/invertion_protein_1357107..1357257_POSITIVE 213 239 195 64 11 NC_003454:FN0115|3end_hypothetical_protein_748215..748365_NEGATIVE 207 189 145 151 110 NC_003454:FN2098|3end_MRP-family_nucleotide-binding_protein_607373..607523_NEGATIVE 205 199 159 147 120 NC_003454:FN0317|3end_tryptophan_synthase_subunit_beta_953819..953969_NEGATIVE 203 168 121 135 92 NC_003454:FN2042|3end_Protein_translocase_subunit_SecE_549656..549806_NEGATIVE 202 189 148 128 80 NC_003454:FN0102|3end_Ribonucleoside-diphosphate_reductase_alpha_chain_738580..738730_POSITIVE 198 75 35 105 69 NC_003454:FN0206|3end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_833635..833785_POSITIVE 198 198 151 55 1 NC_003454:FN0157|3end_DNA_repair_protein_RadA_786336..786486_POSITIVE 198 226 182 76 48 NC_003454:FN1680|3end_Transposase_175971..176121_NEGATIVE 197 144 104 121 78 NC_003454:FN1445|3end_DNA_helicase_2115953..2116103_POSITIVE 197 127 81 149 117 NC_003454:FN1639|3end_SSU_ribosomal_protein_S3P_137504..137654_NEGATIVE 196 180 131 145 96 NC_003454:FN1164|3end_Glucokinase_1822781..1822931_POSITIVE 195 77 32 139 84 NC_003454:FN0913|3end_Cobinamide_kinase_1570172..1570322_NEGATIVE 195 178 158 145 125 NC_003454:FN0594|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase_1249290..1249440_POSITIVE