Origin IGS: ctatttattcctcagtaaattgtaattctagagtgtactttggacatattatatcacaaccagataattgtgtaatcaatagaaatctagtataacaaaaacttttgaaaaatgagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagctatctaccaactctaacttaacaatcatttgctcacgacttgcaaattcagcaatttcttcttaacaaattgttatcatttccaaaatatttaaaagctata .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatagcttttaaatattttggaaatgataacaatttgttaagaagaaattgctgaatttgcaagtcgtgagcaaatgattgttaagttagagttggtagatagcttttttaaagcatgatgaatataattgatatacataaaacgaaaccatccaattcaaatggatggttttctcatttttcaaaagtttttgttatactagatttctattgattacacaattatctggttgtgatataatatgtccaaagtacactctagaattacaatttactgaggaataaatag Mask Tandem Repeat Region ================================================ ctatttattcctcagtaaattgtaattctagagtgtactttggacatattatatcacaaccagataattgtgtaatcaatagaaatctagtataacaaaaacttttgaaaaatgagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagctatctaccaactctaacttaacaatcatttgctcacgacttgcaaattcagcaatttcttcttaacaaattgttatcatttccaaaatatttaaaagctata Find is-nt database================================================ Query_seq: SSA_1285:SSA_1286|SSA_1285:SSA_1286:hypothetical protein:hypothetical protein:<-<-:1305560..1305848 289 ctatttattcctcagtaaattgtaattctagagtgtactttggacatattatatcacaaccagataattgtgtaatcaatagaaatctagtataacaaaaacttttgaaaaatgagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagctatctaccaactctaacttaacaatcatttgctcacgacttgcaaattcagcaatttcttcttaacaaattgttatcatttccaaaatatttaaaagctata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1285:SSA_1286|SSA_1285:SSA_1286:hypothetical protein:hypothetical protein:<-<-:1305560..1305848 289 ctatttattcctcagtaaattgtaattctagagtgtactttggacatattatatcacaaccagataattgtgtaatcaatagaaatctagtataacaaaaacttttgaaaaatgagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagctatctaccaactctaacttaacaatcatttgctcacgacttgcaaattcagcaatttcttcttaacaaattgttatcatttccaaaatatttaaaagctata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1285:SSA_1286|SSA_1285:SSA_1286:hypothetical protein:hypothetical protein:<-<-:1305560..1305848 289 ctatttattcctcagtaaattgtaattctagagtgtactttggacatattatatcacaaccagataattgtgtaatcaatagaaatctagtataacaaaaacttttgaaaaatgagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagctatctaccaactctaacttaacaatcatttgctcacgacttgcaaattcagcaatttcttcttaacaaattgttatcatttccaaaatatttaaaagctata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctatttattcctcagtaaattgtaattctagagtgtactttggacatattatatcacaaccagataattgtgtaatcaatagaaatctagtataacaaaaacttttgaaaaatgagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagctatctaccaactctaacttaacaatcatttgctcacgacttgcaaattcagcaatttcttcttaacaaattgttatcatttccaaaatatttaaaagctata Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 3 End: 92 .. M Y S S V N C N S R V Y F G H I I S Q P D N C V I N R N L V ..................................................................................................................................................................................................... Protein_Len: 32 Strand: + Start: 105 End: 200 ........................................................................................................ M K N E K T I H L N W M V S F Y V Y Q L Y S S C F K K A I Y Q L ......................................................................................... Protein_Len: 39 Strand: + Start: 133 End: 249 .................................................................................................................................... M G W F R F M Y I N Y I H H A L K K L S T N S N L T I I C S R L A N S A I S S ........................................ Protein_Len: 32 Strand: - Start: 79 End: 174 .............................................................................. Y F D L I V F V K S F H S F W G N S N S P K T K H I D I I N M M ................................................................................................................... Protein_Len: 44 Strand: - Start: 8 End: 139 ....... E E T F Q L E L T Y K P C I I D C G S L Q T I L L F R T Y C F S K F F S F V M W K F Q M ...................................................................................................................................................... ctatttattcctcagtaaattgtaattctagagtgtactttggacatattatatcacaaccagataattgtgtaatcaatagaaatctagtataacaaaaacttttgaaaaatgagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagctatctaccaactctaacttaacaatcatttgctcacgacttgcaaattcagcaatttcttcttaacaaattgttatcatttccaaaatatttaaaagctata 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: 48 End: 77 ...............................................GATTACACAATTATCTGGTTGTGATATAAT.................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctatttattcctcagtaaattgtaattctagagtgtactttggacatattatatcacaaccagataattgtgtaatcaatagaaatctagtataacaaaaacttttgaaaaatgagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagctatctaccaactctaacttaacaatcatttgctcacgacttgcaaattcagcaatttcttcttaacaaattgttatcatttccaaaatatttaaaagctata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 81 HP_score: -8.3 Tail_Score: -4.31065 Start: 121 End: 141 Full_Region: TGAAAAATGAGAAAA CCATCCATT TGA ATTGGATGG TTTCGTTTTATGTAT ........................................................................................................................CCATCCATTTGAATTGGATGG.................................................................................................................................................... TransTerm Strand: - Conf: 87 HP_score: -8.3 Tail_Score: -4.72556 Start: 121 End: 141 Full_Region: atacataaaacgaaa ccatccaat tca aatggatgg ttttctcatttttca ........................................................................................................................ccatccaattcaaatggatgg.................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1285:SSA_1286|SSA_1285:SSA_1286:hypothetical protein:hypothetical protein:<-<-:1305560..1305848 289 ctatttattcctcagtaaattgtaattctagagtgtactttggacatattatatcacaaccagataattgtgtaatcaatagaaatctagtataacaaaaacttttgaaaaatgagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagctatctaccaactctaacttaacaatcatttgctcacgacttgcaaattcagcaatttcttcttaacaaattgttatcatttccaaaatatttaaaagctata Intra-Species Hit: Count: 2 Min: 1 Max: 289 Len: 289 Subject: NC_009009_SSA_1285_SSA_1286|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1305560,1305848]|289 HSP 1 e-value: 1.0E-162 bit: 573.0 Len: 289 Query Start:1 Query End:289 Subject Strand: POSITIVE Subject Start: 1 Subject End: 289 ctatttattcctcagtaaattgtaattctagagtgtactttggacatattatatcacaaccagataattgtgtaatcaatagaaatctagtataacaaaaacttttgaaaaatgagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagctatctaccaactctaacttaacaatcatttgctcacgacttgcaaattcagcaatttcttcttaacaaattgttatcatttccaaaatatttaaaagctata ctatttattcctcagtaaattgtaattctagagtgtactttggacatattatatcacaaccagataattgtgtaatcaatagaaatctagtataacaaaaacttttgaaaaatgagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagctatctaccaactctaacttaacaatcatttgctcacgacttgcaaattcagcaatttcttcttaacaaattgttatcatttccaaaatatttaaaagctata Subject: NC_009009_SSA_1287_SSA_1288|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1306828,1307185]|358 HSP 1 e-value: 5.0E-57 bit: 222.0 Len: 120 Query Start:83 Query End:202 Subject Strand: POSITIVE Subject Start: 174 Subject End: 293 ..................................................................................aaatctagtataacaaaaacttttgaaaaatgagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagctatctaccaactcta....................................................................................... ..................................................................................aaatctagtataacaaaaacttttgaaaaaagagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagttatctaccaactcta....................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUUUAUUCCUCAGUAAAUUGUAAUUCUAGAGUGUACUUUGGACAUAUUAUAUCACAACCAGAUAAUUGUGUAAUCAAUAGAAAUCUAGUAUAACAAAAACUUUUGAAAAAUGAGAAAACCAUCCAUUUGAAUUGGAUGGUUUCGUUUUAUGUAUAUCAAUUAUAUUCAUCAUGCUUUAAAAAAGCUAUCUACCAACUCUAACUUAACAAUCAUUUGCUCACGACUUGCAAAUUCAGCAAUUUCUUCUUAACAAAUUGUUAUCAUUUCCAAAAUAUUUAAAAGCUAUA ...................((((.((.(((((.......(((((((((...((((.......))))..)))))..))))......))))).)).))))....(((((((..((((..((((((((((.......))))))))))........(((((.....)))))...))))..))))))).((((.........................((((((.........))))))..((((((((.........)))))))).....................))))... (-44.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAGCUUUUAAAUAUUUUGGAAAUGAUAACAAUUUGUUAAGAAGAAAUUGCUGAAUUUGCAAGUCGUGAGCAAAUGAUUGUUAAGUUAGAGUUGGUAGAUAGCUUUUUUAAAGCAUGAUGAAUAUAAUUGAUAUACAUAAAACGAAACCAUCCAAUUCAAAUGGAUGGUUUUCUCAUUUUUCAAAAGUUUUUGUUAUACUAGAUUUCUAUUGAUUACACAAUUAUCUGGUUGUGAUAUAAUAUGUCCAAAGUACACUCUAGAAUUACAAUUUACUGAGGAAUAAAUAG .............(((((((((..((((((..(((((((..((.....((((.......)))).))...)))))))..))))))......(((..(((((..((((.....)))).(((..((.((..((((............(((((((((((.......)))))))))))........))))..)).))..))).........)))))..))).(((((((....)))))))..........)))))))))..(((..((((....))))...))).......... (-57.35) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 767 70 21 161 112 NC_009009:SSA_1285|5end_hypothetical_protein_1305469..1305699_NEGATIVE 304 250 209 103 68 NC_009009:SSA_0900|5end_Tetratricopeptide_repeat_(TPR)_family_protein_891068..891298_POSITIVE 300 233 195 64 25 NC_009009:SSA_2049|5end_Polyribonucleotide_nucleotidyltransferase,_putative_2052894..2053124_NEGATIVE 280 247 208 43 3 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 264 270 230 167 128 NC_009009:SSA_1044|5end_Homoserine_kinase,_putative_1059853..1060083_POSITIVE 249 230 193 164 128 NC_009009:SSA_2240|5end_Holliday_junction_resolvase,_putative_2237677..2237907_NEGATIVE 248 249 203 128 81 NC_009009:SSA_1996|5end_DNA-directed_RNA_polymerase_delta_subunit,_putative_1994024..1994254_NEGATIVE 241 249 223 29 5 NC_009009:SSA_0569|5end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563613..563843_POSITIVE 232 269 221 145 97 NC_009009:SSA_0667|5end_Transcriptional_regulator,_putative_649778..650008_POSITIVE 230 159 112 122 78 NC_009009:SSA_2135|5end_Transcriptional_repressor,_DeoR_family_(possibly_truncated),_putative_2136777..2137007_POSITIVE 229 140 121 22 4 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 228 188 142 112 56 NC_009009:SSA_1910|5end_hypothetical_protein_1902672..1902902_NEGATIVE 227 246 210 38 4 NC_009009:SSA_1747|5end_hypothetical_protein_1733450..1733680_NEGATIVE 227 268 222 74 36 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 226 43 1 131 92 NC_009009:SSA_1289|5end_hypothetical_protein_1308385..1308615_NEGATIVE 225 230 184 65 17 NC_009009:SSA_0308|5end_hypothetical_protein_304385..304615_POSITIVE 224 220 171 186 128 NC_009009:SSA_1864|5end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1860870..1861100_NEGATIVE 222 229 188 159 116 NC_009009:SSA_0716|5end_Competence_protein,_putative_701390..701620_POSITIVE 221 250 208 69 25 NC_009009:SSA_0812|5end_hypothetical_protein_793443..793673_POSITIVE 220 230 183 152 78 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 144 102 68 25 NC_009009:SSA_1289|3end_hypothetical_protein_1307909..1308059_NEGATIVE 304 250 209 116 81 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 242 202 178 25 1 NC_009009:SSA_1288|3end_hypothetical_protein_1307096..1307246_NEGATIVE 229 84 51 128 88 NC_009009:SSA_1284|3end_hypothetical_protein_1304446..1304596_NEGATIVE 229 140 121 20 2 NC_009009:SSA_0463|3end_Cobyrinic_acid_A,C-diamide_synthase,_putative_468303..468453_POSITIVE 228 188 142 119 63 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 224 220 171 78 20 NC_009009:SSA_1865|3end_Thioredoxin_reductase,_putative_1860978..1861128_NEGATIVE 221 250 208 72 28 NC_009009:SSA_0811|3end_hypothetical_protein_793526..793676_POSITIVE 218 239 207 78 48 NC_009009:SSA_0460|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_463146..463296_POSITIVE 216 248 209 92 65 NC_009009:SSA_2227|3end_Acetyl_transferase,_putative_2227716..2227866_NEGATIVE 212 249 201 130 84 NC_009009:SSA_1096|3end_Methyltransferase,_putative_1114099..1114249_POSITIVE 211 247 214 125 93 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 211 240 196 76 30 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 208 244 212 146 119 NC_009009:SSA_2283|3end_Conserved_uncharacterized_protein_2285537..2285687_NEGATIVE 207 248 209 135 88 NC_009009:SSA_1934|3end_Biotin_carboxyl_carrier_protein_of_acetyl-CoA_carboxylase,_putative_1921312..1921462_NEGATIVE 207 34 2 117 81 NC_009009:SSA_1356|3end_Helicase_subunit_of_the_DNA_excision_repair_complex,_subunit_B,_putative_1369927..1370077_NEGATIVE 205 230 182 148 97 NC_009009:SSA_1447|3end_ATP_phosphoribosyltransferase,_putative_1449187..1449337_NEGATIVE 204 229 185 146 106 NC_009009:SSA_1179|3end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1206640..1206790_NEGATIVE 203 252 213 94 54 NC_009009:SSA_1405|3end_Copper_homeostasis_protein_CutC,_putative_1418758..1418908_NEGATIVE 203 237 192 106 67 NC_009009:SSA_1198|3end_ATPase_(PilT_family),_putative_1222703..1222853_NEGATIVE