Origin IGS: aacaatcctattatatcacaagtgctttgaaagataggctattttagaactatttagtactatttgtacaaaaaaatttagggtaaattaacgacaaagggtctcttatgtctcaaaatttcattttttgataattggtagtataatagaattattattttagaaatgaggtgccttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaggcacctcatttctaaaataataattctattatactaccaattatcaaaaaatgaaattttgagacataagagaccctttgtcgttaatttaccctaaatttttttgtacaaatagtactaaatagttctaaaatagcctatctttcaaagcacttgtgatataataggattgtt Mask Tandem Repeat Region ================================================ aacaatcctattatatcacaagtgctttgaaagataggctattttagaactatttagtactatttgtacaaaaaaatttagggtaaattaacgacaaagggtctcttatgtctcaaaatttcattttttgataattggtagtataatagaattattattttagaaatgaggtgccttt Find is-nt database================================================ Query_seq: SSA_1551:SSA_1552|SSA_1551:SSA_1552:Transcriptional accessory ribonuclease (YqgFc, S1), putative:hypothetical protein:<-->:1554875..1555052 178 aacaatcctattatatcacaagtgctttgaaagataggctattttagaactatttagtactatttgtacaaaaaaatttagggtaaattaacgacaaagggtctcttatgtctcaaaatttcattttttgataattggtagtataatagaattattattttagaaatgaggtgccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1551:SSA_1552|SSA_1551:SSA_1552:Transcriptional accessory ribonuclease (YqgFc, S1), putative:hypothetical protein:<-->:1554875..1555052 178 aacaatcctattatatcacaagtgctttgaaagataggctattttagaactatttagtactatttgtacaaaaaaatttagggtaaattaacgacaaagggtctcttatgtctcaaaatttcattttttgataattggtagtataatagaattattattttagaaatgaggtgccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1551:SSA_1552|SSA_1551:SSA_1552:Transcriptional accessory ribonuclease (YqgFc, S1), putative:hypothetical protein:<-->:1554875..1555052 178 aacaatcctattatatcacaagtgctttgaaagataggctattttagaactatttagtactatttgtacaaaaaaatttagggtaaattaacgacaaagggtctcttatgtctcaaaatttcattttttgataattggtagtataatagaattattattttagaaatgaggtgccttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacaatcctattatatcacaagtgctttgaaagataggctattttagaactatttagtactatttgtacaaaaaaatttagggtaaattaacgacaaagggtctcttatgtctcaaaatttcattttttgataattggtagtataatagaattattattttagaaatgaggtgccttt Predict ORF larger than 30AA ================================================ aacaatcctattatatcacaagtgctttgaaagataggctattttagaactatttagtactatttgtacaaaaaaatttagggtaaattaacgacaaagggtctcttatgtctcaaaatttcattttttgataattggtagtataatagaattattattttagaaatgaggtgccttt 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: 83 Start: 118 End: 147 .....................................................................................................................ATTTCATTTTTTGATAATTGGTAGTATAAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacaatcctattatatcacaagtgctttgaaagataggctattttagaactatttagtactatttgtacaaaaaaatttagggtaaattaacgacaaagggtctcttatgtctcaaaatttcattttttgataattggtagtataatagaattattattttagaaatgaggtgccttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -2.6 Tail_Score: -5.61596 Start: 77 End: 87 Full_Region: accctttgtcgttaa ttta ccc taaa tttttttgtacaaat ............................................................................tttaccctaaa........................................................................................... Find igs database================================================ Query_seq: SSA_1551:SSA_1552|SSA_1551:SSA_1552:Transcriptional accessory ribonuclease (YqgFc, S1), putative:hypothetical protein:<-->:1554875..1555052 178 aacaatcctattatatcacaagtgctttgaaagataggctattttagaactatttagtactatttgtacaaaaaaatttagggtaaattaacgacaaagggtctcttatgtctcaaaatttcattttttgataattggtagtataatagaattattattttagaaatgaggtgccttt Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: NC_009009_SSA_1551_SSA_1552|Transcriptional accessory ribonuclease (YqgFc, S1), putative:hypothetical protein|NEGATIVE:POSITIVE|[1554875,1555052]|178 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 aacaatcctattatatcacaagtgctttgaaagataggctattttagaactatttagtactatttgtacnnnnnnntttagggtaaattaacgacaaagggtctcttatgtctcaaaatttcattttttgataattggtagtataatagaattattattttagaaatgaggtgccttt aacaatcctattatatcacaagtgctttgaaagataggctattttagaactatttagtactatttgtacaaaaaaatttagggtaaattaacgacaaagggtctcttatgtctcaaaatttcattttttgataattggtagtataatagaattattattttagaaatgaggtgccttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAUCCUAUUAUAUCACAAGUGCUUUGAAAGAUAGGCUAUUUUAGAACUAUUUAGUACUAUUUGUACAAAAAAAUUUAGGGUAAAUUAACGACAAAGGGUCUCUUAUGUCUCAAAAUUUCAUUUUUUGAUAAUUGGUAGUAUAAUAGAAUUAUUAUUUUAGAAAUGAGGUGCCUUU .......(((((((((.((...(((((((((((((((............)))))).((((.....)))).......))))))))).......((((.(((....))).))))((((((.......))))))......)).)))))))))......(((((((....)))))))..... (-30.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGGCACCUCAUUUCUAAAAUAAUAAUUCUAUUAUACUACCAAUUAUCAAAAAAUGAAAUUUUGAGACAUAAGAGACCCUUUGUCGUUAAUUUACCCUAAAUUUUUUUGUACAAAUAGUACUAAAUAGUUCUAAAAUAGCCUAUCUUUCAAAGCACUUGUGAUAUAAUAGGAUUGUU ......................(((((((((((((((..........((((((.......))))))..((((((.(((.....)))..............((((.(((.((((.....)))).))).)))).........................)))))).))))))))))))))) (-25.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 766 50 1 141 92 NC_009009:SSA_1551|5end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1554784..1555014_NEGATIVE 263 41 5 166 117 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 253 129 81 115 59 NC_009009:SSA_0005|5end_GTP-binding_protein,_putative_3821..4051_POSITIVE 242 139 92 61 20 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 230 130 86 97 47 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 224 60 19 195 139 NC_009009:SSA_1343|5end_Aspartate_carbamoyltransferase,_putative_1361959..1362189_NEGATIVE 222 48 5 174 141 NC_009009:SSA_1322|5end_Glycosyl_transferase,_putative_1339819..1340049_NEGATIVE 218 58 12 181 124 NC_009009:SSA_2078|5end_hypothetical_protein_2083837..2084067_NEGATIVE 217 140 92 191 146 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 216 57 21 171 143 NC_009009:SSA_1365|5end_FmtA-like_protein,_putative_1382299..1382529_NEGATIVE 210 59 11 200 147 NC_009009:SSA_1235|5end_Dihydroorotase,_putative_1261227..1261457_NEGATIVE 209 84 49 143 107 NC_009009:SSA_2363|5end_Phosphoglycolate_phosphatase,_putative_2365632..2365862_POSITIVE 208 130 96 63 31 NC_009009:SSA_2051|5end_Oligoendopeptidase,_putative_2054731..2054961_POSITIVE 208 45 15 199 166 NC_009009:SSA_0643|5end_hypothetical_protein_630194..630424_NEGATIVE 205 41 2 165 124 NC_009009:SSA_1395|5end_hypothetical_protein_1409773..1410003_NEGATIVE 201 46 7 90 46 NC_009009:SSA_1326|5end_Peptidase_T,_putative_1342432..1342662_POSITIVE 198 128 81 190 146 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 197 39 8 149 121 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 196 40 8 158 126 NC_009009:SSA_1405|5end_Copper_homeostasis_protein_CutC,_putative_1419393..1419623_NEGATIVE 195 46 8 153 106 NC_009009:SSA_0289|5end_Leucyl-tRNA_synthetase,_putative_281406..281636_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 230 130 86 100 50 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 229 42 1 94 59 NC_009009:SSA_1733|3end_hypothetical_protein_1717678..1717828_POSITIVE 224 60 19 85 29 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 217 140 92 106 61 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 209 84 49 91 55 NC_009009:SSA_2362|3end_L-serine_dehydratase_alpha_subunit_2365660..2365810_POSITIVE 209 55 23 96 58 NC_009009:SSA_0345|3end_hypothetical_protein_339209..339359_POSITIVE 207 140 99 55 11 NC_009009:SSA_2235|3end_Conserved_uncharacterized_protein_2234971..2235121_NEGATIVE 205 41 2 148 107 NC_009009:SSA_1396|3end_hypothetical_protein_1409790..1409940_NEGATIVE 204 45 19 138 108 NC_009009:SSA_1739|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1727065..1727215_POSITIVE 196 40 8 96 64 NC_009009:SSA_1406|3end_Histone_acetyltransferase_HPA2,_putative_1419455..1419605_NEGATIVE 196 51 14 148 117 NC_009009:SSA_0683|3end_DNA-binding_protein_HU,_putative_664739..664889_POSITIVE 195 137 103 147 116 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 193 154 121 148 116 NC_009009:SSA_1709|3end_hypothetical_protein_1698313..1698463_NEGATIVE 191 137 91 84 34 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 190 122 81 60 27 NC_009009:SSA_1003|3end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1005214..1005364_POSITIVE 188 139 91 142 93 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE 185 48 4 80 30 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 185 62 24 51 3 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 185 50 12 51 11 NC_009009:SSA_1096|3end_Methyltransferase,_putative_1114099..1114249_POSITIVE 184 61 22 64 15 NC_009009:SSA_0548|3end_Alanine_racemase,_putative_543529..543679_POSITIVE