Origin IGS: gaggttcctcctaatatgatttgattaacagccaataggaatttagactgttagtttgatgattttccaaatggtagttttagttacatactgaccgttcggtacaattataataacatctagaattgaatttgtaaatcaatttgctcagaacaaaaattttaatgataaaacagtggcaaaaggaggtggtttcaattgtttggtctcagactctgaatctgctataataggaaaaaagagaggtgagcag .........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 ctgctcacctctcttttttcctattatagcagattcagagtctgagaccaaacaattgaaaccacctccttttgccactgttttatcattaaaatttttgttctgagcaaattgatttacaaattcaattctagatgttattataattgtaccgaacggtcagtatgtaactaaaactaccatttggaaaatcatcaaactaacagtctaaattcctattggctgttaatcaaatcatattaggaggaacctc Mask Tandem Repeat Region ================================================ gaggttcctcctaatatgatttgattaacagccaataggaatttagactgttagtttgatgattttccaaatggtagttttagttacatactgaccgttcggtacaattataataacatctagaattgaatttgtaaatcaatttgctcagaacaaaaattttaatgataaaacagtggcaaaaggaggtggtttcaattgtttggtctcagactctgaatctgctataataggaaaaaagagaggtgagcag Find is-nt database================================================ Query_seq: SMT_436:SMT_437|SMT_436:SMT_437:amidase related to nicotinamidase:transcriptional regulator, TetR family:<-->:378289..378541 253 gaggttcctcctaatatgatttgattaacagccaataggaatttagactgttagtttgatgattttccaaatggtagttttagttacatactgaccgttcggtacaattataataacatctagaattgaatttgtaaatcaatttgctcagaacaaaaattttaatgataaaacagtggcaaaaggaggtggtttcaattgtttggtctcagactctgaatctgctataataggaaaaaagagaggtgagcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_436:SMT_437|SMT_436:SMT_437:amidase related to nicotinamidase:transcriptional regulator, TetR family:<-->:378289..378541 253 gaggttcctcctaatatgatttgattaacagccaataggaatttagactgttagtttgatgattttccaaatggtagttttagttacatactgaccgttcggtacaattataataacatctagaattgaatttgtaaatcaatttgctcagaacaaaaattttaatgataaaacagtggcaaaaggaggtggtttcaattgtttggtctcagactctgaatctgctataataggaaaaaagagaggtgagcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_436:SMT_437|SMT_436:SMT_437:amidase related to nicotinamidase:transcriptional regulator, TetR family:<-->:378289..378541 253 gaggttcctcctaatatgatttgattaacagccaataggaatttagactgttagtttgatgattttccaaatggtagttttagttacatactgaccgttcggtacaattataataacatctagaattgaatttgtaaatcaatttgctcagaacaaaaattttaatgataaaacagtggcaaaaggaggtggtttcaattgtttggtctcagactctgaatctgctataataggaaaaaagagaggtgagcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaggttcctcctaatatgatttgattaacagccaataggaatttagactgttagtttgatgattttccaaatggtagttttagttacatactgaccgttcggtacaattataataacatctagaattgaatttgtaaatcaatttgctcagaacaaaaattttaatgataaaacagtggcaaaaggaggtggtttcaattgtttggtctcagactctgaatctgctataataggaaaaaagagaggtgagcag Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 138 End: 227 ......................................................................................................................................... M N L L R T K I L M I K Q W Q K E V V S I V W S Q T L N L L .......................... Protein_Len: 49 Strand: + Start: 107 End: 253 .......................................................................................................... M I I T S R I E F V N Q F A Q N K N F N D K T V A K G G G F N C L V S D S E S A I I G K K R G E Q Protein_Len: 39 Strand: - Start: 83 End: 199 .................................................................................. N C V S R E T C N Y Y C R S N F K Y I L K S L V F I K I I F C H C F S T T E M ...................................................... gaggttcctcctaatatgatttgattaacagccaataggaatttagactgttagtttgatgattttccaaatggtagttttagttacatactgaccgttcggtacaattataataacatctagaattgaatttgtaaatcaatttgctcagaacaaaaattttaatgataaaacagtggcaaaaggaggtggtttcaattgtttggtctcagactctgaatctgctataataggaaaaaagagaggtgagcag 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: 88 Start: 110 End: 139 .............................................................................................................ATTTACAAATTCAATTCTAGATGTTATTAT.................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 202 End: 231 .........................................................................................................................................................................................................TTTGGTCTCAGACTCTGAATCTGCTATAAT...................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaggttcctcctaatatgatttgattaacagccaataggaatttagactgttagtttgatgattttccaaatggtagttttagttacatactgaccgttcggtacaattataataacatctagaattgaatttgtaaatcaatttgctcagaacaaaaattttaatgataaaacagtggcaaaaggaggtggtttcaattgtttggtctcagactctgaatctgctataataggaaaaaagagaggtgagcag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_436:SMT_437|SMT_436:SMT_437:amidase related to nicotinamidase:transcriptional regulator, TetR family:<-->:378289..378541 253 gaggttcctcctaatatgatttgattaacagccaataggaatttagactgttagtttgatgattttccaaatggtagttttagttacatactgaccgttcggtacaattataataacatctagaattgaatttgtaaatcaatttgctcagaacaaaaattttaatgataaaacagtggcaaaaggaggtggtttcaattgtttggtctcagactctgaatctgctataataggaaaaaagagaggtgagcag Intra-Species Hit: Count: 1 Min: 1 Max: 253 Len: 253 Subject: smit_SMT_436_SMT_437|amidase related to nicotinamidase:transcriptional regulator, TetR family|NEGATIVE:POSITIVE|[378289,378541]|253 HSP 1 e-value: 1.0E-141 bit: 502.0 Len: 253 Query Start:1 Query End:253 Subject Strand: POSITIVE Subject Start: 1 Subject End: 253 gaggttcctcctaatatgatttgattaacagccaataggaatttagactgttagtttgatgattttccaaatggtagttttagttacatactgaccgttcggtacaattataataacatctagaattgaatttgtaaatcaatttgctcagaacaaaaattttaatgataaaacagtggcaaaaggaggtggtttcaattgtttggtctcagactctgaatctgctataataggaaaaaagagaggtgagcag gaggttcctcctaatatgatttgattaacagccaataggaatttagactgttagtttgatgattttccaaatggtagttttagttacatactgaccgttcggtacaattataataacatctagaattgaatttgtaaatcaatttgctcagaacaaaaattttaatgataaaacagtggcaaaaggaggtggtttcaattgtttggtctcagactctgaatctgctataataggaaaaaagagaggtgagcag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGUUCCUCCUAAUAUGAUUUGAUUAACAGCCAAUAGGAAUUUAGACUGUUAGUUUGAUGAUUUUCCAAAUGGUAGUUUUAGUUACAUACUGACCGUUCGGUACAAUUAUAAUAACAUCUAGAAUUGAAUUUGUAAAUCAAUUUGCUCAGAACAAAAAUUUUAAUGAUAAAACAGUGGCAAAAGGAGGUGGUUUCAAUUGUUUGGUCUCAGACUCUGAAUCUGCUAUAAUAGGAAAAAAGAGAGGUGAGCAG (((....)))..........((((((.(((.((....))..((((((.(((((.....((((((..((.(((((((((...........))).)))))).))...))))))..)))))))))))........))).))))))..((((((.........(((((....)))))..((((((...((((.(((..((((....))))..)))..)))).....))))))..................)))))). (-50.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGCUCACCUCUCUUUUUUCCUAUUAUAGCAGAUUCAGAGUCUGAGACCAAACAAUUGAAACCACCUCCUUUUGCCACUGUUUUAUCAUUAAAAUUUUUGUUCUGAGCAAAUUGAUUUACAAAUUCAAUUCUAGAUGUUAUUAUAAUUGUACCGAACGGUCAGUAUGUAACUAAAACUACCAUUUGGAAAAUCAUCAAACUAACAGUCUAAAUUCCUAUUGGCUGUUAAUCAAAUCAUAUUAGGAGGAACCUC ...((((...((((..(((.(((...))).)))...))))..))))..................(((((((((((((..((((((....))))))........)).))))).((((((..........(((((((((.(((((((((((.(((....))))))).))))).......)).)))))))))...........((((((((............))))))))...))))))....))))))...... (-45.51) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 828 50 1 141 92 smit:SMT_436|5end_amidase_related_to_nicotinamidase_378198..378428_NEGATIVE 318 227 182 178 134 smit:SMT_1370|5end_K06217_phosphate_starvation-inducible_protein_PhoH_and_related_proteins_1350494..1350724_NEGATIVE 298 97 51 94 48 smit:SMT_1660|5end_serine_protease_1650634..1650864_NEGATIVE 286 227 186 231 184 smit:SMT_507|5end_hypothetical_protein_438216..438446_NEGATIVE 275 226 185 204 170 smit:SMT_908|5end_hypothetical_protein_857230..857460_NEGATIVE 274 250 206 224 171 smit:SMT_1899|5end_hypothetical_protein_1850018..1850248_POSITIVE 265 226 181 220 169 smit:SMT_162|5end_hypothetical_protein_106593..106823_POSITIVE 264 50 1 182 131 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 262 219 173 113 51 smit:SMT_1407|5end_ribonuclease_HII_1386309..1386539_NEGATIVE 261 230 181 222 154 smit:SMT_1217|5end_hypothetical_protein_1176603..1176833_NEGATIVE 258 78 31 160 113 smit:SMT_1557|5end_hypothetical_protein_1541939..1542169_POSITIVE 254 218 177 178 132 smit:SMT_874|5end_dipeptidase_822765..822995_NEGATIVE 253 216 175 88 42 smit:SMT_446|5end_ABC-type_cobalt_transport_system,_ATPase_component_384870..385100_POSITIVE 252 216 173 223 177 smit:SMT_1057|5end_replicative_DNA_helicase_995316..995546_POSITIVE 250 230 184 57 9 smit:SMT_1612|5end_K06024_segregation_and_condensation_protein_B_1600052..1600282_POSITIVE 246 226 187 192 151 smit:SMT_1922|5end_exonuclease_RexA_1865998..1866228_NEGATIVE 245 227 189 133 93 smit:SMT_877|5end_hypothetical_protein_824412..824642_NEGATIVE 245 218 177 54 17 smit:SMT_832|5end_hypothetical_protein_775104..775334_NEGATIVE 243 233 191 189 146 smit:SMT_759|5end_K01992_ABC-2_type_transport_system_permease_protein_665712..665942_NEGATIVE 242 227 187 144 106 smit:SMT_479|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416656..416886_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 227 182 93 49 smit:SMT_1371|3end_hypothetical_protein_1350579..1350729_NEGATIVE 304 226 188 108 73 smit:SMT_1665|3end_cell_wall_surface_anchor_family_protein_1656021..1656171_NEGATIVE 265 226 181 133 82 smit:SMT_161|3end_putative_folyl-polyglutamate_synthetase_106586..106736_POSITIVE 264 50 1 126 75 smit:SMT_2045|3end_K+_transport_system,_NAD-binding_component_1956758..1956908_POSITIVE 264 50 1 126 75 smit:SMT_1668|3end_K+_transport_system,_NAD-binding_component_1657623..1657773_NEGATIVE 262 219 173 126 64 smit:SMT_1408|3end_GTP-binding_protein_1386296..1386446_NEGATIVE 261 230 181 137 69 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 258 78 31 107 60 smit:SMT_1556|3end_phosphoglycerate_mutase_1541966..1542116_POSITIVE 257 227 183 151 108 smit:SMT_1494|3end_nucleoside_diphosphate_kinase_1480221..1480371_POSITIVE 253 216 175 87 41 smit:SMT_445|3end_hypothetical_protein_384949..385099_POSITIVE 252 226 184 112 70 smit:SMT_150|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_99400..99550_POSITIVE 247 213 174 138 105 smit:SMT_1476|3end_thiol_peroxidase_1458728..1458878_NEGATIVE 245 227 189 143 103 smit:SMT_878|3end_excinuclease_ABC,_subunit_C_824402..824552_NEGATIVE 240 191 166 42 16 smit:SMT_794|3end_hypothetical_protein_703245..703395_NEGATIVE 237 218 174 71 25 smit:SMT_531|3end_hypothetical_protein_predicted_by_Glimmer/Critica_453075..453225_POSITIVE 237 220 175 102 48 smit:SMT_132|3end_L-serine_dehydratase_alpha_subunit_83685..83835_NEGATIVE 235 226 184 115 83 smit:SMT_2097|3end_type_I_restriction_enzyme_M_protein_1990475..1990625_NEGATIVE 232 225 183 117 60 smit:SMT_788|3end_hypothetical_protein_699153..699303_NEGATIVE 230 210 176 107 72 smit:SMT_1174|3end_acylneuraminate_cytidylyltransferase_1125617..1125767_NEGATIVE 230 247 202 74 34 smit:SMT_1092|3end_transcription_antitermination_factor_1033160..1033310_NEGATIVE