Origin IGS: tttttaatcctcttgttcttgtcttctgcttatatttattatatagtgggagctggatggcatacaagcatcaattttagatagactgttgcattttgaggtgaatggc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gccattcacctcaaaatgcaacagtctatctaaaattgatgcttgtatgccatccagctcccactatataataaatataagcagaagacaagaacaagaggattaaaaa Mask Tandem Repeat Region ================================================ tttttaatcctcttgttcttgtcttctgcttatatttattatatagtgggagctggatggcatacaagcatcaattttagatagactgttgcattttgaggtgaatggc Find is-nt database================================================ Query_seq: SSA_0922:SSA_0923|SSA_0922:SSA_0923:hypothetical protein:Transcriptional regulator, TetR/AcrR family, putative:<-->:933041..933149 109 tttttaatcctcttgttcttgtcttctgcttatatttattatatagtgggagctggatggcatacaagcatcaattttagatagactgttgcattttgaggtgaatggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0922:SSA_0923|SSA_0922:SSA_0923:hypothetical protein:Transcriptional regulator, TetR/AcrR family, putative:<-->:933041..933149 109 tttttaatcctcttgttcttgtcttctgcttatatttattatatagtgggagctggatggcatacaagcatcaattttagatagactgttgcattttgaggtgaatggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0922:SSA_0923|SSA_0922:SSA_0923:hypothetical protein:Transcriptional regulator, TetR/AcrR family, putative:<-->:933041..933149 109 tttttaatcctcttgttcttgtcttctgcttatatttattatatagtgggagctggatggcatacaagcatcaattttagatagactgttgcattttgaggtgaatggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttaatcctcttgttcttgtcttctgcttatatttattatatagtgggagctggatggcatacaagcatcaattttagatagactgttgcattttgaggtgaatggc Predict ORF larger than 30AA ================================================ tttttaatcctcttgttcttgtcttctgcttatatttattatatagtgggagctggatggcatacaagcatcaattttagatagactgttgcattttgaggtgaatggc 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: 18 End: 47 .................CTTGTCTTCTGCTTATATTTATTATATAGT.............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttaatcctcttgttcttgtcttctgcttatatttattatatagtgggagctggatggcatacaagcatcaattttagatagactgttgcattttgaggtgaatggc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0922:SSA_0923|SSA_0922:SSA_0923:hypothetical protein:Transcriptional regulator, TetR/AcrR family, putative:<-->:933041..933149 109 tttttaatcctcttgttcttgtcttctgcttatatttattatatagtgggagctggatggcatacaagcatcaattttagatagactgttgcattttgaggtgaatggc Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_009009_SSA_0922_SSA_0923|hypothetical protein:Transcriptional regulator, TetR/AcrR family, putative|NEGATIVE:POSITIVE|[933041,933149]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 tttttaatcctcttgttcttgtcttctgcttatatttattatatagtgggagctggatggcatacaagcatcaattttagatagactgttgcattttgaggtgaatggc tttttaatcctcttgttcttgtcttctgcttatatttattatatagtgggagctggatggcatacaagcatcaattttagatagactgttgcattttgaggtgaatggc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAAUCCUCUUGUUCUUGUCUUCUGCUUAUAUUUAUUAUAUAGUGGGAGCUGGAUGGCAUACAAGCAUCAAUUUUAGAUAGACUGUUGCAUUUUGAGGUGAAUGGC ........((((....(((.(.((((..((((((.....)))).))..))))).)))..(((.(((..((((.......))).)..)))))).....))))........ (-21.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCAUUCACCUCAAAAUGCAACAGUCUAUCUAAAAUUGAUGCUUGUAUGCCAUCCAGCUCCCACUAUAUAAUAAAUAUAAGCAGAAGACAAGAACAAGAGGAUUAAAAA ........((((.....(((((((..((((.......)))).)))).)))......(((.....(((((.....))))))))...............))))........ (-14.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 875 90 41 181 132 NC_009009:SSA_0922|5end_hypothetical_protein_932950..933180_NEGATIVE 319 89 46 208 168 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 302 93 51 177 127 NC_009009:SSA_1676|5end_Transcriptional_regulator,_LytTr_family,_putative_1671313..1671543_NEGATIVE 280 91 51 131 81 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 278 100 51 153 105 NC_009009:SSA_1957|5end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1954670..1954900_NEGATIVE 275 68 23 141 98 NC_009009:SSA_1501|5end_Cytidylate_kinase,_putative_1505772..1506002_NEGATIVE 273 61 21 121 81 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 271 82 43 212 163 NC_009009:SSA_2333|5end_Integral_membrane_protein,_putative_2336460..2336690_NEGATIVE 268 98 52 102 49 NC_009009:SSA_1655|5end_hypothetical_protein_1651816..1652046_NEGATIVE 266 56 11 217 173 NC_009009:SSA_0103|5end_Integral_membrane_protein,_putative_105490..105720_NEGATIVE 254 94 53 187 151 NC_009009:SSA_1668|5end_NrdI_protein,_putative_1668091..1668321_NEGATIVE 253 55 12 71 32 NC_009009:SSA_0576|5end_Conserved_GTPase,_putative_570039..570269_POSITIVE 252 58 16 76 37 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 251 99 53 126 81 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 248 57 11 145 93 NC_009009:SSA_0966|5end_Uridine_kinase,_putative_975063..975293_POSITIVE 247 89 42 161 108 NC_009009:SSA_0666|5end_hypothetical_protein_649788..650018_NEGATIVE 243 60 12 204 150 NC_009009:SSA_2046|5end_Uridine_phosphorylase,_putative_2049721..2049951_NEGATIVE 239 92 52 62 19 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 239 55 18 192 160 NC_009009:SSA_1041|5end_Sugar_ABC_transporter,_permease_protein,_putative_1056398..1056628_POSITIVE 237 60 15 60 10 NC_009009:SSA_1823|5end_hypothetical_protein_1812513..1812743_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 68 23 131 88 NC_009009:SSA_1502|3end_Conserved_uncharacterized_protein_(contains_LysM,_Lysin_motif)_1505782..1505932_NEGATIVE 273 61 21 118 78 NC_009009:SSA_2278|3end_Ukp_protein,_putative_2280410..2280560_NEGATIVE 268 89 49 144 104 NC_009009:SSA_2258|3end_hypothetical_protein_2253389..2253539_NEGATIVE 253 55 12 68 29 NC_009009:SSA_0575|3end_Hydrolase,_HAD_superfamily,_putative_570116..570266_POSITIVE 251 85 43 55 3 NC_009009:SSA_2191|3end_Conserved_uncharacterized_protein_2193082..2193232_POSITIVE 251 69 23 149 107 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 251 99 53 80 35 NC_009009:SSA_0912|3end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_924229..924379_POSITIVE 246 53 14 71 21 NC_009009:SSA_1100|3end_Hemolysin_exporter,_ATPase_component,_putative_1122088..1122238_POSITIVE 241 90 44 151 97 NC_009009:SSA_1678|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1671336..1671486_NEGATIVE 237 60 15 57 7 NC_009009:SSA_1824|3end_hypothetical_protein_1812516..1812666_NEGATIVE 235 59 11 49 5 NC_009009:SSA_1903|3end_hypothetical_protein_1897388..1897538_NEGATIVE 234 34 1 123 88 NC_009009:SSA_2226|3end_Organic_radical_activating_chaperone,_putative_2227151..2227301_NEGATIVE 234 88 45 54 9 NC_009009:SSA_1984|3end_Cell_surface_SD_repeat_antigen_precursor,_putative_1976048..1976198_NEGATIVE 231 60 11 88 25 NC_009009:SSA_0627|3end_hypothetical_protein_617975..618125_POSITIVE 229 90 41 89 48 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 229 68 33 34 4 NC_009009:SSA_1349|3end_Transcriptional_regulator,_biotin_repressor_family,_putative_1366513..1366663_POSITIVE 229 97 54 92 46 NC_009009:SSA_1324|3end_Ceramide_glucosyltransferase,_putative_1340428..1340578_NEGATIVE 227 61 21 144 103 NC_009009:SSA_1269|3end_hypothetical_protein_1291970..1292120_NEGATIVE 226 29 1 87 57 NC_009009:SSA_1455|3end_Conserved_hypothetical_cytosolic_protein_1461134..1461284_NEGATIVE 226 100 57 149 110 NC_009009:SSA_1419|3end_hypothetical_protein_1428995..1429145_NEGATIVE