Origin IGS: tcccctttttctccattctccttttttatatttgaagttatacaactttattatacagcattcccaccaccatgtaaatatgaattatcgcctcagtaacaagcttctaagcgattacaagaaaattaattagaacgaaaaagagcttgatttagtatcaggctctgatttgtctatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatagacaaatcagagcctgatactaaatcaagctctttttcgttctaattaattttcttgtaatcgcttagaagcttgttactgaggcgataattcatatttacatggtggtgggaatgctgtataataaagttgtataacttcaaatataaaaaaggagaatggagaaaaagggga Mask Tandem Repeat Region ================================================ tcccctttttctccattctccttttttatatttgaagttatacaactttattatacagcattcccaccaccatgtaaatatgaattatcgcctcagtaacaagcttctaagcgattacaagaaaattaattagaacgaaaaagagcttgatttagtatcaggctctgatttgtctatt Find is-nt database================================================ Query_seq: SSA_2259:SSA_2260|SSA_2259:SSA_2260:hypothetical protein:DNA mismatch repair protein hexA, putative:<-<-:2255513..2255690 178 tcccctttttctccattctccttttttatatttgaagttatacaactttattatacagcattcccaccaccatgtaaatatgaattatcgcctcagtaacaagcttctaagcgattacaagaaaattaattagaacgaaaaagagcttgatttagtatcaggctctgatttgtctatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2259:SSA_2260|SSA_2259:SSA_2260:hypothetical protein:DNA mismatch repair protein hexA, putative:<-<-:2255513..2255690 178 tcccctttttctccattctccttttttatatttgaagttatacaactttattatacagcattcccaccaccatgtaaatatgaattatcgcctcagtaacaagcttctaagcgattacaagaaaattaattagaacgaaaaagagcttgatttagtatcaggctctgatttgtctatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2259:SSA_2260|SSA_2259:SSA_2260:hypothetical protein:DNA mismatch repair protein hexA, putative:<-<-:2255513..2255690 178 tcccctttttctccattctccttttttatatttgaagttatacaactttattatacagcattcccaccaccatgtaaatatgaattatcgcctcagtaacaagcttctaagcgattacaagaaaattaattagaacgaaaaagagcttgatttagtatcaggctctgatttgtctatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcccctttttctccattctccttttttatatttgaagttatacaactttattatacagcattcccaccaccatgtaaatatgaattatcgcctcagtaacaagcttctaagcgattacaagaaaattaattagaacgaaaaagagcttgatttagtatcaggctctgatttgtctatt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 32 End: 130 ............................... M K L Y N F I I Q H S H H H V N M N Y R L S N K L L S D Y K K I N ................................................ tcccctttttctccattctccttttttatatttgaagttatacaactttattatacagcattcccaccaccatgtaaatatgaattatcgcctcagtaacaagcttctaagcgattacaagaaaattaattagaacgaaaaagagcttgatttagtatcaggctctgatttgtctatt 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: 50 End: 79 .................................................ATTTACATGGTGGTGGGAATGCTGTATAAT................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcccctttttctccattctccttttttatatttgaagttatacaactttattatacagcattcccaccaccatgtaaatatgaattatcgcctcagtaacaagcttctaagcgattacaagaaaattaattagaacgaaaaagagcttgatttagtatcaggctctgatttgtctatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2259:SSA_2260|SSA_2259:SSA_2260:hypothetical protein:DNA mismatch repair protein hexA, putative:<-<-:2255513..2255690 178 tcccctttttctccattctccttttttatatttgaagttatacaactttattatacagcattcccaccaccatgtaaatatgaattatcgcctcagtaacaagcttctaagcgattacaagaaaattaattagaacgaaaaagagcttgatttagtatcaggctctgatttgtctatt Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: NC_009009_SSA_2259_SSA_2260|hypothetical protein:DNA mismatch repair protein hexA, putative|NEGATIVE:NEGATIVE|[2255513,2255690]|178 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 tcccctttttctccattctccttttttatatttgaagttatacaactttattatacagcattcccaccaccatgtaaatatgaattatcgcctcagtaacaagcttctaagcgattacaagaaaattaattagaacgaaaaagagcttgatttagtatcaggctctgatttgtctatt tcccctttttctccattctccttttttatatttgaagttatacaactttattatacagcattcccaccaccatgtaaatatgaattatcgcctcagtaacaagcttctaagcgattacaagaaaattaattagaacgaaaaagagcttgatttagtatcaggctctgatttgtctatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCCUUUUUCUCCAUUCUCCUUUUUUAUAUUUGAAGUUAUACAACUUUAUUAUACAGCAUUCCCACCACCAUGUAAAUAUGAAUUAUCGCCUCAGUAACAAGCUUCUAAGCGAUUACAAGAAAAUUAAUUAGAACGAAAAAGAGCUUGAUUUAGUAUCAGGCUCUGAUUUGUCUAUU ......((((((............(((((((((((((((....))))))).......((((..........)))).))))))))..(((((...(((.....))).....)))))....)))))).....((((.((((..((((((((((.....))))))))))..)))))))).. (-33.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAGACAAAUCAGAGCCUGAUACUAAAUCAAGCUCUUUUUCGUUCUAAUUAAUUUUCUUGUAAUCGCUUAGAAGCUUGUUACUGAGGCGAUAAUUCAUAUUUACAUGGUGGUGGGAAUGCUGUAUAAUAAAGUUGUAUAACUUCAAAUAUAAAAAAGGAGAAUGGAGAAAAAGGGGA ............(((((.((((.....)))).)))))((((((((((..((....((((..(.(((((((...((.......)).)))))))...((((......))))..)..))))...((((((((...))))))))...............))..))))))))))......... (-33.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 860 110 61 201 152 NC_009009:SSA_2259|5end_hypothetical_protein_2255422..2255652_NEGATIVE 269 122 87 99 62 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 266 99 56 230 190 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 261 105 62 189 156 NC_009009:SSA_0538|5end_PduH_protein,_putative_533794..534024_POSITIVE 256 48 4 177 132 NC_009009:SSA_0034|5end_hypothetical_protein_39547..39777_POSITIVE 247 105 64 197 146 NC_009009:SSA_1179|5end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1207806..1208036_NEGATIVE 247 99 56 109 64 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 238 35 3 215 179 NC_009009:SSA_1119|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1144491..1144721_POSITIVE 235 112 85 64 27 NC_009009:SSA_0457|5end_Fructokinase,_putative_460663..460893_POSITIVE 233 168 122 214 178 NC_009009:SSA_1435|5end_hypothetical_protein_1442212..1442442_NEGATIVE 232 120 71 57 9 NC_009009:SSA_1489|5end_hypothetical_protein_1495788..1496018_NEGATIVE 230 113 71 61 7 NC_009009:SSA_0670|5end_Conserved_uncharacterized_protein_653920..654150_POSITIVE 227 44 4 192 147 NC_009009:SSA_0168|5end_hypothetical_protein_166457..166687_POSITIVE 226 122 90 57 14 NC_009009:SSA_0753|5end_Foldase_protein_prsA_precursor,_putative_734968..735198_POSITIVE 225 118 79 78 32 NC_009009:SSA_0075|5end_ABC_sugar_transporter,_permease_protein,_putative_78963..79193_POSITIVE 224 170 128 205 170 NC_009009:SSA_1988|5end_ABC-type_transport_system_(uncharacterized),_permease_component,_putative_1984188..1984418_NEGATIVE 223 98 55 201 165 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 221 78 34 178 140 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 221 123 81 163 119 NC_009009:SSA_0127|5end_Multispanning_membrane_protein,_translocator_of_proteins,_putative_117720..117950_POSITIVE 220 48 6 129 78 NC_009009:SSA_0613|5end_Glucosyltransferase,_putative_601847..602077_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 150 103 64 23 NC_009009:SSA_2135|3end_Transcriptional_repressor,_DeoR_family_(possibly_truncated),_putative_2137474..2137624_POSITIVE 256 48 4 150 105 NC_009009:SSA_0033|3end_Phosphoribosylglycinamide_(GAR)_formyltransferase,_putative_39600..39750_POSITIVE 247 99 56 112 67 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 244 167 124 75 32 NC_009009:SSA_0871|3end_Cell_division_protein_FtsX,_putative_864627..864777_POSITIVE 242 113 87 132 104 NC_009009:SSA_1270|3end_Flavodoxin_1293476..1293626_NEGATIVE 229 112 73 133 83 NC_009009:SSA_1740|3end_hypothetical_protein_1727081..1727231_NEGATIVE 228 25 3 142 119 NC_009009:SSA_1118|3end_Peptide_methionine_sulfoxide_reductase,_putative_1144511..1144661_POSITIVE 223 98 55 143 107 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 221 124 81 68 24 NC_009009:SSA_1723|3end_hypothetical_protein_1709893..1710043_POSITIVE 221 78 34 113 75 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 221 123 81 150 106 NC_009009:SSA_0126|3end_50S_ribosomal_protein_L15,_putative_117787..117937_POSITIVE 220 140 92 61 17 NC_009009:SSA_2191|3end_Conserved_uncharacterized_protein_2193082..2193232_POSITIVE 220 48 6 59 8 NC_009009:SSA_0612|3end_Rgg_protein,_putative_601857..602007_POSITIVE 218 86 45 48 3 NC_009009:SSA_2277|3end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2275983..2276133_NEGATIVE 218 166 131 84 57 NC_009009:SSA_0457|3end_Fructokinase,_putative_461642..461792_POSITIVE 217 92 57 151 107 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 216 78 34 113 75 NC_009009:SSA_1369|3end_FmtA-like_protein,_putative_1384142..1384292_NEGATIVE 216 165 133 92 62 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 216 114 88 28 4 NC_009009:SSA_1054|3end_CBS_domain_protein,_putative_1070973..1071123_POSITIVE 211 50 4 73 23 NC_009009:SSA_1849|3end_Primosomal_protein_N',_putative_1843262..1843412_NEGATIVE