Origin IGS: agcctactcctgtttacattatagtttcattatatcacgcctaagaaagcaattcaaatctaggagaaggccatcaagtagcttgccaatcaaaaagaacaggttgccctgctctttctgaaaaatataaggagactaatttaaaatacctgcggttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaccgcaggtattttaaattagtctccttatatttttcagaaagagcagggcaacctgttctttttgattggcaagctacttgatggccttctcctagatttgaattgctttcttaggcgtgatataatgaaactataatgtaaacaggagtaggct Mask Tandem Repeat Region ================================================ agcctactcctgtttacattatagtttcattatatcacgcctaagaaagcaattcaaatctaggagaaggccatcaagtagcttgccaatcaaaaagaacaggttgccctgctctttctgaaaaatataaggagactaatttaaaatacctgcggttc Find is-nt database================================================ Query_seq: SSA_1892:SSA_1893|SSA_1892:SSA_1893:hypothetical protein:N-acetylglucosamine-6-phosphate deacetylase, putative:<-<-:1889353..1889510 158 agcctactcctgtttacattatagtttcattatatcacgcctaagaaagcaattcaaatctaggagaaggccatcaagtagcttgccaatcaaaaagaacaggttgccctgctctttctgaaaaatataaggagactaatttaaaatacctgcggttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1892:SSA_1893|SSA_1892:SSA_1893:hypothetical protein:N-acetylglucosamine-6-phosphate deacetylase, putative:<-<-:1889353..1889510 158 agcctactcctgtttacattatagtttcattatatcacgcctaagaaagcaattcaaatctaggagaaggccatcaagtagcttgccaatcaaaaagaacaggttgccctgctctttctgaaaaatataaggagactaatttaaaatacctgcggttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1892:SSA_1893|SSA_1892:SSA_1893:hypothetical protein:N-acetylglucosamine-6-phosphate deacetylase, putative:<-<-:1889353..1889510 158 agcctactcctgtttacattatagtttcattatatcacgcctaagaaagcaattcaaatctaggagaaggccatcaagtagcttgccaatcaaaaagaacaggttgccctgctctttctgaaaaatataaggagactaatttaaaatacctgcggttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcctactcctgtttacattatagtttcattatatcacgcctaagaaagcaattcaaatctaggagaaggccatcaagtagcttgccaatcaaaaagaacaggttgccctgctctttctgaaaaatataaggagactaatttaaaatacctgcggttc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 29 End: 118 ............................ M I S R L R K Q F K S R R R P S S S L P I K K N R L P C S F ........................................ Protein_Len: 35 Strand: - Start: 22 End: 126 ..................... L K M I D R R L F C N L D L L L G D L L K G I L F F L N G Q E K Q F M ................................ agcctactcctgtttacattatagtttcattatatcacgcctaagaaagcaattcaaatctaggagaaggccatcaagtagcttgccaatcaaaaagaacaggttgccctgctctttctgaaaaatataaggagactaatttaaaatacctgcggttc 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: 85 Start: 29 End: 58 ............................TTTGAATTGCTTTCTTAGGCGTGATATAAT.................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: - Score: 81 Start: 73 End: 89 ........................................................................TTGGCAAGCTACTTGAT..................................................................... agcctactcctgtttacattatagtttcattatatcacgcctaagaaagcaattcaaatctaggagaaggccatcaagtagcttgccaatcaaaaagaacaggttgccctgctctttctgaaaaatataaggagactaatttaaaatacctgcggttc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 86 HP_score: -7.7 Tail_Score: -4.8622 Start: 97 End: 114 Full_Region: tatatttttcagaaa gagcagg gcaa cctgttc tttttgattggcaag ................................................................................................gagcagggcaacctgttc............................................ Find igs database================================================ Query_seq: SSA_1892:SSA_1893|SSA_1892:SSA_1893:hypothetical protein:N-acetylglucosamine-6-phosphate deacetylase, putative:<-<-:1889353..1889510 158 agcctactcctgtttacattatagtttcattatatcacgcctaagaaagcaattcaaatctaggagaaggccatcaagtagcttgccaatcaaaaagaacaggttgccctgctctttctgaaaaatataaggagactaatttaaaatacctgcggttc Intra-Species Hit: Count: 1 Min: 1 Max: 158 Len: 158 Subject: NC_009009_SSA_1892_SSA_1893|hypothetical protein:N-acetylglucosamine-6-phosphate deacetylase, putative|NEGATIVE:NEGATIVE|[1889353,1889510]|158 HSP 1 e-value: 9.0E-85 bit: 313.0 Len: 158 Query Start:1 Query End:158 Subject Strand: POSITIVE Subject Start: 1 Subject End: 158 agcctactcctgtttacattatagtttcattatatcacgcctaagaaagcaattcaaatctaggagaaggccatcaagtagcttgccaatcaaaaagaacaggttgccctgctctttctgaaaaatataaggagactaatttaaaatacctgcggttc agcctactcctgtttacattatagtttcattatatcacgcctaagaaagcaattcaaatctaggagaaggccatcaagtagcttgccaatcaaaaagaacaggttgccctgctctttctgaaaaatataaggagactaatttaaaatacctgcggttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCUACUCCUGUUUACAUUAUAGUUUCAUUAUAUCACGCCUAAGAAAGCAAUUCAAAUCUAGGAGAAGGCCAUCAAGUAGCUUGCCAAUCAAAAAGAACAGGUUGCCCUGCUCUUUCUGAAAAAUAUAAGGAGACUAAUUUAAAAUACCUGCGGUUC .((((.((((((.......((((((...))))))....((........))..........)))))).))))......((((........(((.(((((.((((....)))).))))).)))........((....))............))))..... (-33.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAACCGCAGGUAUUUUAAAUUAGUCUCCUUAUAUUUUUCAGAAAGAGCAGGGCAACCUGUUCUUUUUGAUUGGCAAGCUACUUGAUGGCCUUCUCCUAGAUUUGAAUUGCUUUCUUAGGCGUGAUAUAAUGAAACUAUAAUGUAAACAGGAGUAGGCU ......((((((.(((......(((............((((((((((((((....))))))))))))))..)))))).))))))..(((((.(((((...........((((....))))...((((.(((....))).))))....))))).))))) (-43.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 951 110 61 201 152 NC_009009:SSA_1892|5end_hypothetical_protein_1889262..1889492_NEGATIVE 342 110 62 66 2 NC_009009:SSA_2038|5end_hypothetical_protein_2041627..2041857_POSITIVE 324 109 61 183 143 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 316 110 61 99 39 NC_009009:SSA_0815|5end_hypothetical_protein_796975..797205_POSITIVE 313 110 62 177 128 NC_009009:SSA_0632|5end_Anthranilate_synthase_component_I,_putative_621458..621688_POSITIVE 312 120 71 199 142 NC_009009:SSA_1649|5end_hypothetical_protein_1648886..1649116_NEGATIVE 309 110 69 71 23 NC_009009:SSA_2312|5end_hypothetical_protein_2315281..2315511_NEGATIVE 302 109 67 220 170 NC_009009:SSA_1639|5end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1642031..1642261_NEGATIVE 299 138 96 219 171 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 294 108 69 71 27 NC_009009:SSA_1493|5end_hypothetical_protein_1499480..1499710_NEGATIVE 292 108 66 186 147 NC_009009:SSA_0410|5end_hypothetical_protein_406442..406672_NEGATIVE 289 114 71 48 1 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 289 113 71 218 186 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 285 110 62 193 134 NC_009009:SSA_1608|5end_hypothetical_protein_1613753..1613983_NEGATIVE 284 119 71 88 39 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 283 119 79 106 52 NC_009009:SSA_1037|5end_Cytidine_deaminase,_putative_1052118..1052348_POSITIVE 283 86 47 137 95 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 278 108 61 64 26 NC_009009:SSA_0784|5end_Proton-translocating_ATPase,_F0_sector,_subunit_b,_putative_767550..767780_POSITIVE 276 120 71 203 151 NC_009009:SSA_1035|5end_Pyrimidine_nucleoside_phosphorylase,_putative_1050174..1050404_POSITIVE 274 76 31 169 124 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 109 67 143 93 NC_009009:SSA_1640|3end_hypothetical_protein_1642108..1642258_NEGATIVE 292 108 66 148 109 NC_009009:SSA_0411|3end_hypothetical_protein_406480..406630_NEGATIVE 284 119 71 95 46 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 283 117 71 75 12 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 283 119 79 119 65 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 283 86 47 140 98 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 282 119 72 87 24 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 278 108 61 45 7 NC_009009:SSA_0783|3end_Proton-translocating_ATPase,_F0_sector,_subunit_a,_putative_767611..767761_POSITIVE 272 88 44 131 96 NC_009009:SSA_2208|3end_Preprotein_translocase_secE_component,_putative_2207734..2207884_NEGATIVE 267 118 73 92 51 NC_009009:SSA_1601|3end_VacB-like_protein,_putative_1606592..1606742_NEGATIVE 267 120 73 76 14 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 266 137 91 66 24 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 265 89 53 141 110 NC_009009:SSA_1112|3end_Cell_wall_surface_anchor_family_protein,_putative_1139738..1139888_POSITIVE 260 124 90 80 41 NC_009009:SSA_0849|3end_Signal_peptidase_I,_putative_836764..836914_POSITIVE 259 110 63 128 66 NC_009009:SSA_0346|3end_hypothetical_protein_340322..340472_POSITIVE 258 87 46 151 93 NC_009009:SSA_2226|3end_Organic_radical_activating_chaperone,_putative_2227151..2227301_NEGATIVE 257 110 61 143 95 NC_009009:SSA_0351|3end_Signal_peptidase_I,_putative_344278..344428_NEGATIVE 255 118 81 75 29 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 255 107 62 66 21 NC_009009:SSA_1330|3end_hypothetical_protein_1345901..1346051_NEGATIVE 251 109 72 133 92 NC_009009:SSA_1247|3end_hypothetical_protein_1271222..1271372_NEGATIVE