Origin IGS: caaatattaagaattattatagaataaatgaaattaaatatatttccttttaagagagtccagagaggctaacaagggtgtgaaagactaattttttagtctatgtttttgtatgtttacctaaagcctttggttttaggtttttttataccttaataaattttataaaagttgtgttatggtatccattaatattgatggaaagattccagaaatattaatggttgtcaagcacag .........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 ctgtgcttgacaaccattaatatttctggaatctttccatcaatattaatggataccataacacaacttttataaaatttattaaggtataaaaaaacctaaaaccaaaggctttaggtaaacatacaaaaacatagactaaaaaattagtctttcacacccttgttagcctctctggactctcttaaaaggaaatatatttaatttcatttattctataataattcttaatatttg Mask Tandem Repeat Region ================================================ caaatattaagaattattatagaataaatgaaattaaatatatttccttttaagagagtccagagaggctaacaagggtgtgaaagactaattttttagtctatgtttttgtatgtttacctaaagcctttggttttaggtttttttataccttaataaattttataaaagttgtgttatggtatccattaatattgatggaaagattccagaaatattaatggttgtcaagcacag Find is-nt database================================================ Query_seq: FN0417:FN0418|FN0417:FN0418:Type III restriction-modification system restriction subunit:pyrimidine regulatory protein PyrR:->->:1059021..1059257 237 caaatattaagaattattatagaataaatgaaattaaatatatttccttttaagagagtccagagaggctaacaagggtgtgaaagactaattttttagtctatgtttttgtatgtttacctaaagcctttggttttaggtttttttataccttaataaattttataaaagttgtgttatggtatccattaatattgatggaaagattccagaaatattaatggttgtcaagcacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0417:FN0418|FN0417:FN0418:Type III restriction-modification system restriction subunit:pyrimidine regulatory protein PyrR:->->:1059021..1059257 237 caaatattaagaattattatagaataaatgaaattaaatatatttccttttaagagagtccagagaggctaacaagggtgtgaaagactaattttttagtctatgtttttgtatgtttacctaaagcctttggttttaggtttttttataccttaataaattttataaaagttgtgttatggtatccattaatattgatggaaagattccagaaatattaatggttgtcaagcacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0417:FN0418|FN0417:FN0418:Type III restriction-modification system restriction subunit:pyrimidine regulatory protein PyrR:->->:1059021..1059257 237 caaatattaagaattattatagaataaatgaaattaaatatatttccttttaagagagtccagagaggctaacaagggtgtgaaagactaattttttagtctatgtttttgtatgtttacctaaagcctttggttttaggtttttttataccttaataaattttataaaagttgtgttatggtatccattaatattgatggaaagattccagaaatattaatggttgtcaagcacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caaatattaagaattattatagaataaatgaaattaaatatatttccttttaagagagtccagagaggctaacaagggtgtgaaagactaattttttagtctatgtttttgtatgtttacctaaagcctttggttttaggtttttttataccttaataaattttataaaagttgtgttatggtatccattaatattgatggaaagattccagaaatattaatggttgtcaagcacag Predict ORF larger than 30AA ================================================ caaatattaagaattattatagaataaatgaaattaaatatatttccttttaagagagtccagagaggctaacaagggtgtgaaagactaattttttagtctatgtttttgtatgtttacctaaagcctttggttttaggtttttttataccttaataaattttataaaagttgtgttatggtatccattaatattgatggaaagattccagaaatattaatggttgtcaagcacag 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: 81 Start: 203 End: 232 ..........................................................................................................................................................................................................CTTGACAACCATTAATATTTCTGGAATCTT..... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caaatattaagaattattatagaataaatgaaattaaatatatttccttttaagagagtccagagaggctaacaagggtgtgaaagactaattttttagtctatgtttttgtatgtttacctaaagcctttggttttaggtttttttataccttaataaattttataaaagttgtgttatggtatccattaatattgatggaaagattccagaaatattaatggttgtcaagcacag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.5 Tail_Score: -5.66684 Start: 120 End: 140 Full_Region: GTTTTTGTATGTTTA CCTAAAGCC TTT GGTTTTAGG TTTTTTTATACCTTA .......................................................................................................................CCTAAAGCCTTTGGTTTTAGG................................................................................................. Find igs database================================================ Query_seq: FN0417:FN0418|FN0417:FN0418:Type III restriction-modification system restriction subunit:pyrimidine regulatory protein PyrR:->->:1059021..1059257 237 caaatattaagaattattatagaataaatgaaattaaatatatttccttttaagagagtccagagaggctaacaagggtgtgaaagactaattttttagtctatgtttttgtatgtttacctaaagcctttggttttaggtttttttataccttaataaattttataaaagttgtgttatggtatccattaatattgatggaaagattccagaaatattaatggttgtcaagcacag Intra-Species Hit: Count: 1 Min: 1 Max: 237 Len: 237 Subject: NC_003454_FN0417_FN0418|Type III restriction-modification system restriction subunit:pyrimidine regulatory protein PyrR|POSITIVE:POSITIVE|[1059021,1059257]|237 HSP 1 e-value: 1.0E-44 bit: 180.0 Len: 91 Query Start:1 Query End:91 Subject Strand: POSITIVE Subject Start: 1 Subject End: 91 caaatattaagaattattatagaataaatgaaattaaatatatttccttttaagagagtccagagaggctaacaagggtgtgaaagactaa.................................................................................................................................................. caaatattaagaattattatagaataaatgaaattaaatatatttccttttaagagagtccagagaggctaacaagggtgtgaaagactaa.................................................................................................................................................. HSP 2 e-value: 2.0E-43 bit: 176.0 Len: 89 Query Start:149 Query End:237 Subject Strand: POSITIVE Subject Start: 149 Subject End: 237 ....................................................................................................................................................taccttaataaattttataaaagttgtgttatggtatccattaatattgatggaaagattccagaaatattaatggttgtcaagcacag ....................................................................................................................................................taccttaataaattttataaaagttgtgttatggtatccattaatattgatggaaagattccagaaatattaatggttgtcaagcacag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAUAUUAAGAAUUAUUAUAGAAUAAAUGAAAUUAAAUAUAUUUCCUUUUAAGAGAGUCCAGAGAGGCUAACAAGGGUGUGAAAGACUAAUUUUUUAGUCUAUGUUUUUGUAUGUUUACCUAAAGCCUUUGGUUUUAGGUUUUUUUAUACCUUAAUAAAUUUUAUAAAAGUUGUGUUAUGGUAUCCAUUAAUAUUGAUGGAAAGAUUCCAGAAAUAUUAAUGGUUGUCAAGCACAG ................(((((((((....................((((((..(.....)..))))))......(((((((((((((((((....)))))))................((((((((((...))))))))))...)))))))))).....)))))))))....((((((.((..(.(((((((((((..((((.....))))..))))))))))).)..)))))))). (-62.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUGCUUGACAACCAUUAAUAUUUCUGGAAUCUUUCCAUCAAUAUUAAUGGAUACCAUAACACAACUUUUAUAAAAUUUAUUAAGGUAUAAAAAAACCUAAAACCAAAGGCUUUAGGUAAACAUACAAAAACAUAGACUAAAAAAUUAGUCUUUCACACCCUUGUUAGCCUCUCUGGACUCUCUUAAAAGGAAAUAUAUUUAAUUUCAUUUAUUCUAUAAUAAUUCUUAAUAUUUG .((((..((....(((((((((((..((((.....))))..)))))))))))....))...))))..............((((((((.................(((.((.....((((.((((...........(((((((....)))))))..........)))).)))))).))).............(((((.......))))).................)))))))).... (-41.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 230 181 207 151 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 257 230 181 103 47 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 257 227 185 230 181 NC_003454:FN1740|5end_ATP_synthase_subunit_K_238400..238630_NEGATIVE 244 83 49 135 107 NC_003454:FN1678|5end_hypothetical_protein_174287..174517_POSITIVE 221 70 38 59 22 NC_003454:FN1749|5end_Pyruvate-flavodoxin_oxidoreductase_247461..247691_POSITIVE 217 132 92 215 181 NC_003454:FN1753|5end_thiamine_biosynthesis_protein_ThiH_250344..250574_NEGATIVE 214 113 72 51 14 NC_003454:FN1002|5end_Adenosylmethionine-8-amino-7-oxononanoate_aminotransferase_1656738..1656968_POSITIVE 214 130 89 145 115 NC_003454:FN1519|5end_23S_rRNA_methyltransferase_24792..25022_NEGATIVE 213 100 56 84 41 NC_003454:FN0027|5end_hypothetical_protein_664891..665121_NEGATIVE 211 109 64 170 116 NC_003454:FN0334|5end_Aspartate/aromatic_aminotransferase_969066..969296_NEGATIVE 208 230 185 227 175 NC_003454:FN1142|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1791529..1791759_POSITIVE 205 230 184 164 115 NC_003454:FN1762|5end_Protein_yaaA_256004..256234_NEGATIVE 203 148 102 202 147 NC_003454:FN1628|5end_LSU_ribosomal_protein_L18P_133948..134178_NEGATIVE 202 97 56 96 59 NC_003454:FN1509|5end_hypothetical_protein_14176..14406_NEGATIVE 197 100 54 92 43 NC_003454:FN0057|5end_Endonuclease_III_693215..693445_POSITIVE 197 149 104 129 83 NC_003454:FN2020|5end_translation_initiation_factor_IF-2_524522..524752_NEGATIVE 196 152 120 228 197 NC_003454:FN1380|5end_Citrate_lyase_beta_chain_2027248..2027478_POSITIVE 195 78 38 109 67 NC_003454:FN1426|5end_Serine_protease_2095462..2095692_NEGATIVE 195 69 42 57 27 NC_003454:FN2102|5end_ABC_transporter_ATP-binding_protein_611177..611407_POSITIVE 195 70 26 132 80 NC_003454:FN2042|5end_Protein_translocase_subunit_SecE_549832..550062_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 230 185 72 20 NC_003454:FN1741|3end_ATP_synthase_subunit_I_238561..238711_NEGATIVE 222 54 16 86 46 NC_003454:FN0100|3end_Flavodoxins/hemoproteins_735119..735269_NEGATIVE 221 70 38 77 40 NC_003454:FN1748|3end_Pyruvate-flavodoxin_oxidoreductase_247559..247709_POSITIVE 214 130 89 135 105 NC_003454:FN1520|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_24802..24952_NEGATIVE 211 109 64 79 25 NC_003454:FN0335|3end_Outer_membrane_porin_F_969157..969307_NEGATIVE 207 137 91 132 86 NC_003454:FN0405|3end_tryptophanyl-tRNA_synthetase_1042465..1042615_NEGATIVE 206 74 50 71 47 NC_003454:FN1986|3end_hypothetical_protein_490007..490157_POSITIVE 202 97 56 41 4 NC_003454:FN0404|3end_hypothetical_protein_1042373..1042523_POSITIVE 202 97 56 41 4 NC_003454:FN1510|3end_hypothetical_protein_14231..14381_NEGATIVE 201 155 121 63 22 NC_003454:FN1675|3end_Transposase_172206..172356_NEGATIVE 198 66 45 108 86 NC_003454:FN0587|3end_Hypothetical_membrane-spanning_protein_1241963..1242113_NEGATIVE 197 149 104 102 56 NC_003454:FN2021|3end_ABC1_family_protein_524549..524699_NEGATIVE 195 69 42 31 1 NC_003454:FN2101|3end_Transporter_611231..611381_POSITIVE 193 136 93 127 88 NC_003454:FN1503|3end_Nickel_transport_system_permease_protein_nikB_7503..7653_NEGATIVE 191 219 175 115 68 NC_003454:FN0917|3end_hypothetical_protein_1573643..1573793_POSITIVE 190 100 54 48 6 NC_003454:FN0056|3end_Acetyltransferase_693251..693401_POSITIVE 189 100 62 41 1 NC_003454:FN0894|3end_hypothetical_protein_1554893..1555043_POSITIVE 189 107 62 62 10 NC_003454:FN2085|3end_hypothetical_protein_596560..596710_NEGATIVE 187 135 92 55 5 NC_003454:FN0953|3end_hypothetical_protein_1609515..1609665_NEGATIVE 186 230 181 69 13 NC_003454:FN1077|3end_hypothetical_protein_1723754..1723904_NEGATIVE