Origin IGS: gaaaatgagtctgggataaatttccagacttttttgtatagagccttaaaaaaattgaaagaagaaatttatatttcatctgtttatcaggcctgctttgtgctagaatattggtaaagtaacaatttagaggagattggga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcccaatctcctctaaattgttactttaccaatattctagcacaaagcaggcctgataaacagatgaaatataaatttcttctttcaatttttttaaggctctatacaaaaaagtctggaaatttatcccagactcattttc Mask Tandem Repeat Region ================================================ gaaaatgagtctgggataaatttccagacttttttgtatagagccttaaaaaaattgaaagaagaaatttatatttcatctgtttatcaggcctgctttgtgctagaatattggtaaagtaacaatttagaggagattggga Find is-nt database================================================ Query_seq: SSA_1127:SSA_1128|SSA_1127:SSA_1128:H2O-forming NADH dehydrogenase, putative:Voltage gated chloride channel EriC, putative:->->:1153248..1153389 142 gaaaatgagtctgggataaatttccagacttttttgtatagagccttaaaaaaattgaaagaagaaatttatatttcatctgtttatcaggcctgctttgtgctagaatattggtaaagtaacaatttagaggagattggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1127:SSA_1128|SSA_1127:SSA_1128:H2O-forming NADH dehydrogenase, putative:Voltage gated chloride channel EriC, putative:->->:1153248..1153389 142 gaaaatgagtctgggataaatttccagacttttttgtatagagccttaaaaaaattgaaagaagaaatttatatttcatctgtttatcaggcctgctttgtgctagaatattggtaaagtaacaatttagaggagattggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1127:SSA_1128|SSA_1127:SSA_1128:H2O-forming NADH dehydrogenase, putative:Voltage gated chloride channel EriC, putative:->->:1153248..1153389 142 gaaaatgagtctgggataaatttccagacttttttgtatagagccttaaaaaaattgaaagaagaaatttatatttcatctgtttatcaggcctgctttgtgctagaatattggtaaagtaacaatttagaggagattggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaaatgagtctgggataaatttccagacttttttgtatagagccttaaaaaaattgaaagaagaaatttatatttcatctgtttatcaggcctgctttgtgctagaatattggtaaagtaacaatttagaggagattggga Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 16 End: 114 ............... M N F Q T F L Y R A L K K L K E E I Y I S S V Y Q A C F V L E Y W ............................ Protein_Len: 36 Strand: - Start: 2 End: 109 . F H T Q S L N G S K K T Y L R L F I S L L F K Y K M Q K D P R S Q A L M ................................. gaaaatgagtctgggataaatttccagacttttttgtatagagccttaaaaaaattgaaagaagaaatttatatttcatctgtttatcaggcctgctttgtgctagaatattggtaaagtaacaatttagaggagattggga 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================================================ gaaaatgagtctgggataaatttccagacttttttgtatagagccttaaaaaaattgaaagaagaaatttatatttcatctgtttatcaggcctgctttgtgctagaatattggtaaagtaacaatttagaggagattggga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1127:SSA_1128|SSA_1127:SSA_1128:H2O-forming NADH dehydrogenase, putative:Voltage gated chloride channel EriC, putative:->->:1153248..1153389 142 gaaaatgagtctgggataaatttccagacttttttgtatagagccttaaaaaaattgaaagaagaaatttatatttcatctgtttatcaggcctgctttgtgctagaatattggtaaagtaacaatttagaggagattggga Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_009009_SSA_1127_SSA_1128|H2O-forming NADH dehydrogenase, putative:Voltage gated chloride channel EriC, putative|POSITIVE:POSITIVE|[1153248,1153389]|142 HSP 1 e-value: 1.0E-62 bit: 240.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 gaaaatgagtctgggataaatttccagacttttttgtatagagccttnnnnnnnttgaaagaagaaatttatatttcatctgtttatcaggcctgctttgtgctagaatattggtaaagtaacaatttagaggagattggga gaaaatgagtctgggataaatttccagacttttttgtatagagccttaaaaaaattgaaagaagaaatttatatttcatctgtttatcaggcctgctttgtgctagaatattggtaaagtaacaatttagaggagattggga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAUGAGUCUGGGAUAAAUUUCCAGACUUUUUUGUAUAGAGCCUUAAAAAAAUUGAAAGAAGAAAUUUAUAUUUCAUCUGUUUAUCAGGCCUGCUUUGUGCUAGAAUAUUGGUAAAGUAACAAUUUAGAGGAGAUUGGGA ..(((.((((((((((.....)))))))))).)))........((((....((((((..(((.(((((....))))).))).((((((((.(..((.....))..)....))))))))....)))))).))))......... (-31.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCAAUCUCCUCUAAAUUGUUACUUUACCAAUAUUCUAGCACAAAGCAGGCCUGAUAAACAGAUGAAAUAUAAAUUUCUUCUUUCAAUUUUUUUAAGGCUCUAUACAAAAAAGUCUGGAAAUUUAUCCCAGACUCAUUUUC .................((((..................((.....)).(((((...(((.(((.(((((....))))).))).......)))...)))))....))))...(((((((.........)))))))....... (-19.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 110 61 195 136 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 282 128 90 156 122 NC_009009:SSA_1854|5end_Conserved_uncharacterized_protein_1850884..1851114_NEGATIVE 269 128 83 44 5 NC_009009:SSA_1955|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1952602..1952832_NEGATIVE 265 140 91 134 94 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 263 113 76 65 24 NC_009009:SSA_0831|5end_Nucleotide_sugar_synthetase-like_protein,_putative_815671..815901_POSITIVE 260 120 76 175 118 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 253 47 6 137 96 NC_009009:SSA_0860|5end_N-acetylmuramidase/lysin,_putative_847615..847845_POSITIVE 250 98 52 231 176 NC_009009:SSA_0379|5end_PTS_system,_beta-glucoside-specific_EII_component,_putative_368822..369052_POSITIVE 248 107 75 47 9 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 247 114 75 192 155 NC_009009:SSA_2073|5end_Undecaprenyl_pyrophosphate_synthetase,_putative_2076371..2076601_NEGATIVE 247 120 78 197 149 NC_009009:SSA_1804|5end_NADPH-flavin_oxidoreductase,_putative_1788668..1788898_NEGATIVE 246 116 87 27 1 NC_009009:SSA_1959|5end_Undecaprenyl-diphosphatase,_putative_1956431..1956661_NEGATIVE 246 104 74 187 159 NC_009009:SSA_1574|5end_Glycosyl_transferase,_family_1,_putative_1577930..1578160_NEGATIVE 244 130 81 216 154 NC_009009:SSA_1513|5end_Glycosyltransferase,_putative_1520976..1521206_NEGATIVE 243 136 91 77 24 NC_009009:SSA_1086|5end_TRNA_nucleotidyltransferase,_putative_1103328..1103558_POSITIVE 242 118 78 119 82 NC_009009:SSA_1776|5end_Potassium_uptake_protein,_Trk_family,_putative_1762639..1762869_POSITIVE 242 117 75 176 142 NC_009009:SSA_1445|5end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447886..1448116_NEGATIVE 239 49 7 219 176 NC_009009:SSA_0221|5end_PTS_system,_mannose-specific_IIC_component,_putative_216370..216600_POSITIVE 235 113 77 62 17 NC_009009:SSA_0759|5end_Acetylglutamate_kinase,_putative_741841..742071_POSITIVE 234 36 5 161 135 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 39 2 86 46 NC_009009:SSA_1301|3end_Conserved_uncharacterized_protein,_possible_surface_protein_1319010..1319160_NEGATIVE 327 49 1 116 52 NC_009009:SSA_1535|3end_hypothetical_protein_1542457..1542607_NEGATIVE 282 128 90 143 109 NC_009009:SSA_1855|3end_hypothetical_protein_1850897..1851047_NEGATIVE 269 47 1 91 50 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE 265 140 91 134 94 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 263 113 76 48 7 NC_009009:SSA_0830|3end_Glycosyltransferase,_putative_815734..815884_POSITIVE 260 44 7 65 23 NC_009009:SSA_1964|3end_conserved_uncharacterized_protein_1960996..1961146_NEGATIVE 259 37 4 27 1 NC_009009:SSA_1529|3end_Lysyl-tRNA_synthetase,_putative_1537441..1537591_POSITIVE 243 136 91 80 27 NC_009009:SSA_1085|3end_Dihydrodipicolinate_reductase,_putative_1103411..1103561_POSITIVE 242 118 78 113 76 NC_009009:SSA_1775|3end_Potassium_uptake_protein,_Trk_family,_putative_1762713..1762863_POSITIVE 240 38 9 54 25 NC_009009:SSA_2201|3end_hypothetical_protein_2202237..2202387_POSITIVE 237 116 78 133 88 NC_009009:SSA_1594|3end_Metalloendopeptidase,_putative_1598457..1598607_NEGATIVE 235 113 77 50 5 NC_009009:SSA_0758|3end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_741909..742059_POSITIVE 231 117 76 75 31 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 229 48 4 118 67 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 228 98 53 68 24 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE 226 107 68 66 21 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 224 37 9 65 37 NC_009009:SSA_2202|3end_Elongation_factor_Ts,_putative_2202307..2202457_NEGATIVE 222 116 74 147 105 NC_009009:SSA_1648|3end_hypothetical_protein_1647166..1647316_NEGATIVE 221 38 1 68 28 NC_009009:SSA_0708|3end_hypothetical_protein_694757..694907_POSITIVE