Origin IGS: tgtctgaccggtgagagaaacccgcttcaaataaatattttatagaggctgtgactgggattttgtctagaaattctagtcacagcttttttatatcttggtcgattttgtaaacaacagtcttgactttgctgcggaattccttatataataaattgtattattaaattttaggaggtctt .........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 aagacctcctaaaatttaataatacaatttattatataaggaattccgcagcaaagtcaagactgttgtttacaaaatcgaccaagatataaaaaagctgtgactagaatttctagacaaaatcccagtcacagcctctataaaatatttatttgaagcgggtttctctcaccggtcagaca Mask Tandem Repeat Region ================================================ tgtctgaccggtgagagaaacccgcttcaaataaatattttatagaggctgtgactgggattttgtctagaaattctagtcacagcttttttatatcttggtcgattttgtaaacaacagtcttgactttgctgcggaattccttatataataaattgtattattaaattttaggaggtctt Find is-nt database================================================ Query_seq: SSA_0707:SSA_0708|SSA_0707:SSA_0708:Lactose phosphotransferase system transcriptional repressor, putative:hypothetical protein:->->:694102..694283 182 tgtctgaccggtgagagaaacccgcttcaaataaatattttatagaggctgtgactgggattttgtctagaaattctagtcacagcttttttatatcttggtcgattttgtaaacaacagtcttgactttgctgcggaattccttatataataaattgtattattaaattttaggaggtctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0707:SSA_0708|SSA_0707:SSA_0708:Lactose phosphotransferase system transcriptional repressor, putative:hypothetical protein:->->:694102..694283 182 tgtctgaccggtgagagaaacccgcttcaaataaatattttatagaggctgtgactgggattttgtctagaaattctagtcacagcttttttatatcttggtcgattttgtaaacaacagtcttgactttgctgcggaattccttatataataaattgtattattaaattttaggaggtctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0707:SSA_0708|SSA_0707:SSA_0708:Lactose phosphotransferase system transcriptional repressor, putative:hypothetical protein:->->:694102..694283 182 tgtctgaccggtgagagaaacccgcttcaaataaatattttatagaggctgtgactgggattttgtctagaaattctagtcacagcttttttatatcttggtcgattttgtaaacaacagtcttgactttgctgcggaattccttatataataaattgtattattaaattttaggaggtctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtctgaccggtgagagaaacccgcttcaaataaatattttatagaggctgtgactgggattttgtctagaaattctagtcacagcttttttatatcttggtcgattttgtaaacaacagtcttgactttgctgcggaattccttatataataaattgtattattaaattttaggaggtctt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 30 End: 140 ............................. I F I K Y L S H S P N Q R S I R T V A K K Y R P R N Q L C C D Q S Q Q P M .......................................... tgtctgaccggtgagagaaacccgcttcaaataaatattttatagaggctgtgactgggattttgtctagaaattctagtcacagcttttttatatcttggtcgattttgtaaacaacagtcttgactttgctgcggaattccttatataataaattgtattattaaattttaggaggtctt 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================================================ tgtctgaccggtgagagaaacccgcttcaaataaatattttatagaggctgtgactgggattttgtctagaaattctagtcacagcttttttatatcttggtcgattttgtaaacaacagtcttgactttgctgcggaattccttatataataaattgtattattaaattttaggaggtctt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 52 HP_score: -5.5 Tail_Score: -2.92449 Start: 47 End: 87 Full_Region: accaagatataaaaa agctgtgactagaattt ctagaca aaatcccagtcacagcc tctataaaatattta ..............................................agctgtgactagaatttctagacaaaatcccagtcacagcc............................................................................................... TransTerm Strand: + Conf: 100 HP_score: -14.1 Tail_Score: -5.47431 Start: 48 End: 86 Full_Region: AAATATTTTATAGAG GCTGTGACTGGGATTTT GTCTA GAAATTCTAGTCACAGC TTTTTTATATCTTGG ...............................................GCTGTGACTGGGATTTTGTCTAGAAATTCTAGTCACAGC................................................................................................ Find igs database================================================ Query_seq: SSA_0707:SSA_0708|SSA_0707:SSA_0708:Lactose phosphotransferase system transcriptional repressor, putative:hypothetical protein:->->:694102..694283 182 tgtctgaccggtgagagaaacccgcttcaaataaatattttatagaggctgtgactgggattttgtctagaaattctagtcacagcttttttatatcttggtcgattttgtaaacaacagtcttgactttgctgcggaattccttatataataaattgtattattaaattttaggaggtctt Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: NC_009009_SSA_0707_SSA_0708|Lactose phosphotransferase system transcriptional repressor, putative:hypothetical protein|POSITIVE:POSITIVE|[694102,694283]|182 HSP 1 e-value: 5.0E-99 bit: 361.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 182 tgtctgaccggtgagagaaacccgcttcaaataaatattttatagaggctgtgactgggattttgtctagaaattctagtcacagcttttttatatcttggtcgattttgtaaacaacagtcttgactttgctgcggaattccttatataataaattgtattattaaattttaggaggtctt tgtctgaccggtgagagaaacccgcttcaaataaatattttatagaggctgtgactgggattttgtctagaaattctagtcacagcttttttatatcttggtcgattttgtaaacaacagtcttgactttgctgcggaattccttatataataaattgtattattaaattttaggaggtctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCUGACCGGUGAGAGAAACCCGCUUCAAAUAAAUAUUUUAUAGAGGCUGUGACUGGGAUUUUGUCUAGAAAUUCUAGUCACAGCUUUUUUAUAUCUUGGUCGAUUUUGUAAACAACAGUCUUGACUUUGCUGCGGAAUUCCUUAUAUAAUAAAUUGUAUUAUUAAAUUUUAGGAGGUCUU .....((((.(((((.(((..((((..(((..........((.(((((((((((((((((((((.....))))))))))))))))))))).))......((((((..((((.....))))..)))))))))..))))..)))))))).((((((......))))))..........)))).. (-57.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGACCUCCUAAAAUUUAAUAAUACAAUUUAUUAUAUAAGGAAUUCCGCAGCAAAGUCAAGACUGUUGUUUACAAAAUCGACCAAGAUAUAAAAAAGCUGUGACUAGAAUUUCUAGACAAAAUCCCAGUCACAGCCUCUAUAAAAUAUUUAUUUGAAGCGGGUUUCUCUCACCGGUCAGACA ..((((..........((((((......)))))).....((((..((((..((((....((((....)))).....(((......)))........(((((((((.(.((((.......)))).).)))))))))................))))..))))..))))......))))..... (-38.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 67 21 167 122 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 301 90 42 193 145 NC_009009:SSA_1249|5end_hypothetical_protein_1273985..1274215_NEGATIVE 280 59 11 78 21 NC_009009:SSA_0153|5end_hypothetical_protein_148677..148907_POSITIVE 279 84 42 57 9 NC_009009:SSA_0756|5end_Alanyl-tRNA_synthetase,_putative_736736..736966_POSITIVE 276 90 42 154 110 NC_009009:SSA_1173|5end_Lipoate_protein_ligase_A,_putative_1201081..1201311_NEGATIVE 268 89 42 209 151 NC_009009:SSA_1213|5end_Pyridoxal-phosphate_dependent_aminotransferase,_putative_1236290..1236520_POSITIVE 267 70 41 154 129 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 266 89 43 181 132 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 266 90 47 57 11 NC_009009:SSA_0261|5end_ABC-type_Mn2+/Zn2+_transport_systems,_permease_component,_putative_255468..255698_NEGATIVE 263 89 43 183 134 NC_009009:SSA_0421|5end_Phosphoglycerate_mutase_family_protein,_putative_419564..419794_POSITIVE 262 130 83 86 49 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 257 146 101 161 122 NC_009009:SSA_1649|5end_hypothetical_protein_1648886..1649116_NEGATIVE 255 89 47 58 22 NC_009009:SSA_2041|5end_Leucine-rich_protein,_putative_2046682..2046912_NEGATIVE 255 92 56 37 3 NC_009009:SSA_1715|5end_Phosphoserine_aminotransferase,_putative_1702488..1702718_NEGATIVE 254 76 43 231 186 NC_009009:SSA_2065|5end_hypothetical_protein_2065743..2065973_NEGATIVE 253 42 1 195 145 NC_009009:SSA_0071|5end_N-acetylmannosamine-6-p_hosphate_2-epimerase_1,_putative_75210..75440_POSITIVE 250 85 46 48 3 NC_009009:SSA_1734|5end_Cation_(Mg/Ni_uptake)_transport_ATPase,_putative_1720303..1720533_NEGATIVE 250 148 118 130 96 NC_009009:SSA_0990|5end_hypothetical_protein_991733..991963_POSITIVE 249 146 101 167 125 NC_009009:SSA_0431|5end_hypothetical_protein_433275..433505_NEGATIVE 248 137 103 63 29 NC_009009:SSA_2094|5end_Conserved_uncharacterized_protein_2098247..2098477_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 559 90 44 47 1 NC_009009:SSA_0707|3end_Lactose_phosphotransferase_system_transcriptional_repressor,_putative_694041..694191_POSITIVE 276 90 42 87 43 NC_009009:SSA_1174|3end_Dihydrolipoamide_dehydrogenase,_putative_1201148..1201298_NEGATIVE 266 90 47 70 24 NC_009009:SSA_0262|3end_ABC-type_Mn/Zn_transporter,_ATP-ase_component,_putative_255455..255605_NEGATIVE 258 67 22 63 7 NC_009009:SSA_0152|3end_hypothetical_protein_148731..148881_POSITIVE 257 146 101 151 112 NC_009009:SSA_1650|3end_3-Ketoacyl-ACP_reductase,_putative_1648896..1649046_NEGATIVE 255 89 47 71 35 NC_009009:SSA_2042|3end_hypothetical_protein_2046669..2046819_NEGATIVE 254 139 94 146 102 NC_009009:SSA_1053|3end_Pyruvate_phosphate_dikinase,_putative_1067447..1067597_NEGATIVE 250 148 118 133 99 NC_009009:SSA_0989|3end_Conserved_protein,_possible_transcriptional_regulator_(sigma-70,_region_4),_putative_991816..991966_POSITIVE 247 90 42 80 32 NC_009009:SSA_1259|3end_Purine_nucleoside_phosphorylase,_putative_1284910..1285060_NEGATIVE 247 145 115 147 118 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 246 70 22 149 102 NC_009009:SSA_2068|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_2070931..2071081_NEGATIVE 245 86 41 81 38 NC_009009:SSA_2293|3end_hypothetical_protein_2295955..2296105_POSITIVE 242 135 96 43 3 NC_009009:SSA_1187|3end_Transcriptional_antiterminator,_BglG_family,_putative_1215195..1215345_NEGATIVE 242 138 116 88 61 NC_009009:SSA_0935|3end_tRNA_pseudouridine_synthase_B,_putative_944973..945123_POSITIVE 238 99 55 58 2 NC_009009:SSA_2336|3end_Transcriptional_regulator,_PadR_family,_putative_2338785..2338935_POSITIVE 235 82 44 75 36 NC_009009:SSA_0955|3end_Aminopeptidase_N,_putative_961139..961289_POSITIVE 235 105 62 151 111 NC_009009:SSA_0078|3end_N-acetylneuraminate_lyase,_putative_82901..83051_POSITIVE 234 28 5 25 4 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 233 137 96 72 29 NC_009009:SSA_2349|3end_DTDP-4-dehydrorhamnose_3,5-epimerase,_putative_2350677..2350827_NEGATIVE 233 145 118 34 11 NC_009009:SSA_1578|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1582929..1583079_POSITIVE