Origin IGS: caagaactcctctatcaattaatataaagattataacaaaaaagagcaaaatctacacgattaagctctaaatagattttaatgttcgggaaaaacaaaaaacttggaaatttttgttctctaaactataagattttagagtcacttctccgctgtgacactctgcaattagaattattttactaaatttcttttttcttgtaaaatagtgct .........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 agcactattttacaagaaaaaagaaatttagtaaaataattctaattgcagagtgtcacagcggagaagtgactctaaaatcttatagtttagagaacaaaaatttccaagttttttgtttttcccgaacattaaaatctatttagagcttaatcgtgtagattttgctcttttttgttataatctttatattaattgatagaggagttcttg Mask Tandem Repeat Region ================================================ caagaactcctctatcaattaatataaagattataacaaaaaagagcaaaatctacacgattaagctctaaatagattttaatgttcgggaaaaacaaaaaacttggaaatttttgttctctaaactataagattttagagtcacttctccgctgtgacactctgcaattagaattattttactaaatttcttttttcttgtaaaatagtgct Find is-nt database================================================ Query_seq: SSA_1200:SSA_1201|SSA_1200:SSA_1201:Formate--tetrahydrofolate ligase, putative:hypothetical protein:<-->:1225682..1225894 213 caagaactcctctatcaattaatataaagattataacaaaaaagagcaaaatctacacgattaagctctaaatagattttaatgttcgggaaaaacaaaaaacttggaaatttttgttctctaaactataagattttagagtcacttctccgctgtgacactctgcaattagaattattttactaaatttcttttttcttgtaaaatagtgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1200:SSA_1201|SSA_1200:SSA_1201:Formate--tetrahydrofolate ligase, putative:hypothetical protein:<-->:1225682..1225894 213 caagaactcctctatcaattaatataaagattataacaaaaaagagcaaaatctacacgattaagctctaaatagattttaatgttcgggaaaaacaaaaaacttggaaatttttgttctctaaactataagattttagagtcacttctccgctgtgacactctgcaattagaattattttactaaatttcttttttcttgtaaaatagtgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1200:SSA_1201|SSA_1200:SSA_1201:Formate--tetrahydrofolate ligase, putative:hypothetical protein:<-->:1225682..1225894 213 caagaactcctctatcaattaatataaagattataacaaaaaagagcaaaatctacacgattaagctctaaatagattttaatgttcgggaaaaacaaaaaacttggaaatttttgttctctaaactataagattttagagtcacttctccgctgtgacactctgcaattagaattattttactaaatttcttttttcttgtaaaatagtgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caagaactcctctatcaattaatataaagattataacaaaaaagagcaaaatctacacgattaagctctaaatagattttaatgttcgggaaaaacaaaaaacttggaaatttttgttctctaaactataagattttagagtcacttctccgctgtgacactctgcaattagaattattttactaaatttcttttttcttgtaaaatagtgct Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 76 End: 183 ........................................................................... M L M F G K N K K L G N F C S L N Y K I L E S L L R C D T L Q L E L F Y .............................. Protein_Len: 36 Strand: - Start: 71 End: 178 ...................................................................... I S K L T R S F C F V Q F N K N E L S Y S K L T V E G S H C E A I L I M ................................... caagaactcctctatcaattaatataaagattataacaaaaaagagcaaaatctacacgattaagctctaaatagattttaatgttcgggaaaaacaaaaaacttggaaatttttgttctctaaactataagattttagagtcacttctccgctgtgacactctgcaattagaattattttactaaatttcttttttcttgtaaaatagtgct 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: 86 Start: 178 End: 207 .................................................................................................................................................................................TTTTACTAAATTTCTTTTTTCTTGTAAAAT...... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 21 End: 50 ....................TTTGCTCTTTTTTGTTATAATCTTTATATT................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 30 End: 59 .............................CGTGTAGATTTTGCTCTTTTTTGTTATAAT.......................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 177 End: 206 ................................................................................................................................................................................TTTTACAAGAAAAAAGAAATTTAGTAAAAT....... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caagaactcctctatcaattaatataaagattataacaaaaaagagcaaaatctacacgattaagctctaaatagattttaatgttcgggaaaaacaaaaaacttggaaatttttgttctctaaactataagattttagagtcacttctccgctgtgacactctgcaattagaattattttactaaatttcttttttcttgtaaaatagtgct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -2.8 Tail_Score: -5.58179 Start: 44 End: 68 Full_Region: attaaaatctattta gagcttaatc gtgta gattttgctc ttttttgttataatc ...........................................gagcttaatcgtgtagattttgctc................................................................................................................................................. TransTerm Strand: + Conf: 44 HP_score: -3.5 Tail_Score: -2.60257 Start: 119 End: 141 Full_Region: TTGGAAATTTTTGTT CTCTAAACT ATAAG ATTTTAGAG TCACTTCTCCGCTGT ......................................................................................................................CTCTAAACTATAAGATTTTAGAG........................................................................ Find igs database================================================ Query_seq: SSA_1200:SSA_1201|SSA_1200:SSA_1201:Formate--tetrahydrofolate ligase, putative:hypothetical protein:<-->:1225682..1225894 213 caagaactcctctatcaattaatataaagattataacaaaaaagagcaaaatctacacgattaagctctaaatagattttaatgttcgggaaaaacaaaaaacttggaaatttttgttctctaaactataagattttagagtcacttctccgctgtgacactctgcaattagaattattttactaaatttcttttttcttgtaaaatagtgct Intra-Species Hit: Count: 1 Min: 1 Max: 213 Len: 213 Subject: NC_009009_SSA_1200_SSA_1201|Formate--tetrahydrofolate ligase, putative:hypothetical protein|NEGATIVE:POSITIVE|[1225682,1225894]|213 HSP 1 e-value: 6.0E-96 bit: 351.0 Len: 213 Query Start:1 Query End:213 Subject Strand: POSITIVE Subject Start: 1 Subject End: 213 caagaactcctctatcaattaatataaagattataacaaaaaagagcaaaatctacacgattaagctctaaatagattttaatgttcgggnnnnnnnnnnnncttggaaatttttgttctctaaactataagattttagagtcacttctccgctgtgacactctgcaattagaattattttactaaatttcttttttcttgtaaaatagtgct caagaactcctctatcaattaatataaagattataacaaaaaagagcaaaatctacacgattaagctctaaatagattttaatgttcgggaaaaacaaaaaacttggaaatttttgttctctaaactataagattttagagtcacttctccgctgtgacactctgcaattagaattattttactaaatttcttttttcttgtaaaatagtgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGAACUCCUCUAUCAAUUAAUAUAAAGAUUAUAACAAAAAAGAGCAAAAUCUACACGAUUAAGCUCUAAAUAGAUUUUAAUGUUCGGGAAAAACAAAAAACUUGGAAAUUUUUGUUCUCUAAACUAUAAGAUUUUAGAGUCACUUCUCCGCUGUGACACUCUGCAAUUAGAAUUAUUUUACUAAAUUUCUUUUUUCUUGUAAAAUAGUGCU ...((((......(((......((((.....)))).......(((((..((((.....))))..))))).....)))......)))).(((..((((((((.........)))))))).))).........((((.(((((((((.........)))))..)))).))))...((((((((((.................))))))))))... (-32.33) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCACUAUUUUACAAGAAAAAAGAAAUUUAGUAAAAUAAUUCUAAUUGCAGAGUGUCACAGCGGAGAAGUGACUCUAAAAUCUUAUAGUUUAGAGAACAAAAAUUUCCAAGUUUUUUGUUUUUCCCGAACAUUAAAAUCUAUUUAGAGCUUAAUCGUGUAGAUUUUGCUCUUUUUUGUUAUAAUCUUUAUAUUAAUUGAUAGAGGAGUUCUUG .((..((((((((.(((.........))).))))))))(((((......)))))......)).(((((.(..(((((...((...((((.(((((((((((((........(((..(((((.....)))))..)))........(((((..((((.....))))..)))))))))))).....)))))).))))...))))))).).))))). (-37.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 784 90 41 181 132 NC_009009:SSA_1200|5end_Formate--tetrahydrofolate_ligase,_putative_1225591..1225821_NEGATIVE 285 167 133 205 160 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 266 167 130 142 104 NC_009009:SSA_2036|5end_Conserved_hypothetical_cytosolic_protein_2040799..2041029_NEGATIVE 250 200 151 105 50 NC_009009:SSA_1122|5end_Thioredoxin_family_protein,_putative_1147871..1148101_POSITIVE 249 160 119 65 17 NC_009009:SSA_2053|5end_hypothetical_protein_2057747..2057977_NEGATIVE 247 164 122 95 45 NC_009009:SSA_2161|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160600..2160830_NEGATIVE 245 167 124 164 125 NC_009009:SSA_1069|5end_Lipoprotein_signal_peptidase,_putative_1088291..1088521_POSITIVE 242 170 122 209 154 NC_009009:SSA_1330|5end_hypothetical_protein_1346368..1346598_NEGATIVE 238 186 147 191 155 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 236 172 137 133 91 NC_009009:SSA_1059|5end_hypothetical_protein_1076153..1076383_POSITIVE 236 168 121 210 157 NC_009009:SSA_0990|5end_hypothetical_protein_991733..991963_POSITIVE 234 172 133 128 90 NC_009009:SSA_0942|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_949939..950169_POSITIVE 233 172 144 54 21 NC_009009:SSA_1729|5end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1715699..1715929_NEGATIVE 233 166 132 216 184 NC_009009:SSA_0939|5end_Inositol_monophosphatase_(Mg++_dependent),_putative_946810..947040_POSITIVE 232 166 132 88 45 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 230 100 56 62 19 NC_009009:SSA_0955|5end_Aminopeptidase_N,_putative_958519..958749_POSITIVE 230 177 137 60 11 NC_009009:SSA_0691|5end_D-ala,D-ala_ligase,_putative_675233..675463_POSITIVE 230 155 113 50 7 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 229 170 145 201 174 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 227 172 137 201 159 NC_009009:SSA_0835|5end_Accessory_secretory_protein_Asp3,_putative_821036..821266_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 167 130 145 107 NC_009009:SSA_2037|3end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2040796..2040946_NEGATIVE 254 165 127 125 85 NC_009009:SSA_0857|3end_hypothetical_protein_845482..845632_POSITIVE 250 200 151 90 35 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE 247 166 127 130 83 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 242 170 122 104 49 NC_009009:SSA_1331|3end_Conserved_uncharacterized_protein_1346473..1346623_NEGATIVE 239 166 127 119 84 NC_009009:SSA_0793|3end_DNA-entry_nuclease,_putative_775799..775949_POSITIVE 238 166 131 68 28 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 237 167 135 151 122 NC_009009:SSA_2245|3end_RecA_protein,_putative_2239961..2240111_NEGATIVE 236 172 137 111 69 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE 234 172 133 131 93 NC_009009:SSA_0941|3end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_950022..950172_POSITIVE 232 166 132 95 52 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 229 171 140 128 87 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 222 167 124 143 93 NC_009009:SSA_0936|3end_FAD_synthase,_putative_946151..946301_POSITIVE 218 47 6 66 15 NC_009009:SSA_2235|3end_Conserved_uncharacterized_protein_2234971..2235121_NEGATIVE 217 184 144 50 9 NC_009009:SSA_0766|3end_hypothetical_protein_746975..747125_POSITIVE 215 156 113 107 68 NC_009009:SSA_1860|3end_Penicillin-binding_protein_1A,_putative_1856520..1856670_POSITIVE 215 174 133 31 1 NC_009009:SSA_0858|3end_DTDP-L-rhamnose_synthase,_putative_846446..846596_POSITIVE 214 199 151 55 11 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 213 172 136 67 18 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 212 174 138 143 117 NC_009009:SSA_2020|3end_hypothetical_protein_2022471..2022621_POSITIVE