Origin IGS: gacatttcctcgtacagtagtgaccctattttaccataaatcagcacttttttcgacagaaaaagagtagggcaaagcgcgactcctacacaattgtcaatgcattcttcttgacactaagttatgatataatagaacagaacatttatcaaaaggagtcttaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattaagactccttttgataaatgttctgttctattatatcataacttagtgtcaagaagaatgcattgacaattgtgtaggagtcgcgctttgccctactctttttctgtcgaaaaaagtgctgatttatggtaaaatagggtcactactgtacgaggaaatgtc Mask Tandem Repeat Region ================================================ gacatttcctcgtacagtagtgaccctattttaccataaatcagcacttttttcgacagaaaaagagtagggcaaagcgcgactcctacacaattgtcaatgcattcttcttgacactaagttatgatataatagaacagaacatttatcaaaaggagtcttaatt Find is-nt database================================================ Query_seq: SSA_2066:SSA_2067|SSA_2066:SSA_2067:DNA polymerase III polC-type, putative:hypothetical protein:<-->:2070228..2070393 166 gacatttcctcgtacagtagtgaccctattttaccataaatcagcacttttttcgacagaaaaagagtagggcaaagcgcgactcctacacaattgtcaatgcattcttcttgacactaagttatgatataatagaacagaacatttatcaaaaggagtcttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2066:SSA_2067|SSA_2066:SSA_2067:DNA polymerase III polC-type, putative:hypothetical protein:<-->:2070228..2070393 166 gacatttcctcgtacagtagtgaccctattttaccataaatcagcacttttttcgacagaaaaagagtagggcaaagcgcgactcctacacaattgtcaatgcattcttcttgacactaagttatgatataatagaacagaacatttatcaaaaggagtcttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2066:SSA_2067|SSA_2066:SSA_2067:DNA polymerase III polC-type, putative:hypothetical protein:<-->:2070228..2070393 166 gacatttcctcgtacagtagtgaccctattttaccataaatcagcacttttttcgacagaaaaagagtagggcaaagcgcgactcctacacaattgtcaatgcattcttcttgacactaagttatgatataatagaacagaacatttatcaaaaggagtcttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacatttcctcgtacagtagtgaccctattttaccataaatcagcacttttttcgacagaaaaagagtagggcaaagcgcgactcctacacaattgtcaatgcattcttcttgacactaagttatgatataatagaacagaacatttatcaaaaggagtcttaatt Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 36 End: 161 ................................... M N Q H F F R Q K K S R A K R D S Y T I V N A F F L T L S Y D I I E Q N I Y Q K E S * ..... Protein_Len: 33 Strand: - Start: 3 End: 101 .. M E E Y L L S G I K G Y I L V K K S L F L T P C L A V G V C N D M ................................................................. gacatttcctcgtacagtagtgaccctattttaccataaatcagcacttttttcgacagaaaaagagtagggcaaagcgcgactcctacacaattgtcaatgcattcttcttgacactaagttatgatataatagaacagaacatttatcaaaaggagtcttaatt 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: 87 Start: 124 End: 153 ...........................................................................................................................TTTGATAAATGTTCTGTTCTATTATATCAT............. PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 28 End: 57 ...........................GTCGAAAAAAGTGCTGATTTATGGTAAAAT............................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacatttcctcgtacagtagtgaccctattttaccataaatcagcacttttttcgacagaaaaagagtagggcaaagcgcgactcctacacaattgtcaatgcattcttcttgacactaagttatgatataatagaacagaacatttatcaaaaggagtcttaatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 76 HP_score: -5.3 Tail_Score: -4.96848 Start: 65 End: 85 Full_Region: ttgacaattgtgtag gagtcgcgc ttt gccctactc tttttctgtcgaaaa ................................................................gagtcgcgctttgccctactc................................................................................. Find igs database================================================ Query_seq: SSA_2066:SSA_2067|SSA_2066:SSA_2067:DNA polymerase III polC-type, putative:hypothetical protein:<-->:2070228..2070393 166 gacatttcctcgtacagtagtgaccctattttaccataaatcagcacttttttcgacagaaaaagagtagggcaaagcgcgactcctacacaattgtcaatgcattcttcttgacactaagttatgatataatagaacagaacatttatcaaaaggagtcttaatt Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: NC_009009_SSA_2066_SSA_2067|DNA polymerase III polC-type, putative:hypothetical protein|NEGATIVE:POSITIVE|[2070228,2070393]|166 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 gacatttcctcgtacagtagtgaccctattttaccataaatcagcacttttttcgacagaaaaagagtagggcaaagcgcgactcctacacaattgtcaatgcattcttcttgacactaagttatgatataatagaacagaacatttatcaaaaggagtcttaatt gacatttcctcgtacagtagtgaccctattttaccataaatcagcacttttttcgacagaaaaagagtagggcaaagcgcgactcctacacaattgtcaatgcattcttcttgacactaagttatgatataatagaacagaacatttatcaaaaggagtcttaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAUUUCCUCGUACAGUAGUGACCCUAUUUUACCAUAAAUCAGCACUUUUUUCGACAGAAAAAGAGUAGGGCAAAGCGCGACUCCUACACAAUUGUCAAUGCAUUCUUCUUGACACUAAGUUAUGAUAUAAUAGAACAGAACAUUUAUCAAAAGGAGUCUUAAUU ................((..((.((((((((.................((((((....))))))))))))))))..))..(((((((.......((((((..........))))))........(((((.................)))))..)))))))...... (-31.15) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAAGACUCCUUUUGAUAAAUGUUCUGUUCUAUUAUAUCAUAACUUAGUGUCAAGAAGAAUGCAUUGACAAUUGUGUAGGAGUCGCGCUUUGCCCUACUCUUUUUCUGUCGAAAAAAGUGCUGAUUUAUGGUAAAAUAGGGUCACUACUGUACGAGGAAAUGUC ......((((((((.((......((..(((((((((.((((((((.((((((((((..........)))))......(((((.((........)))))))..((((((....))))))...))))).)))))))).))))))).))..))..)).)))))...))) (-35.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 944 90 41 181 132 NC_009009:SSA_2066|5end_DNA_polymerase_III_polC-type,_putative_2070137..2070367_NEGATIVE 334 114 71 57 9 NC_009009:SSA_1165|5end_Transcriptional_regulator,_GntR_family,_putative_1191087..1191317_POSITIVE 334 90 47 230 184 NC_009009:SSA_1080|5end_Transcriptional_repressor_of_the_fructose_operon,_DeoR_family,_putative_1097538..1097768_POSITIVE 307 105 64 209 164 NC_009009:SSA_0765|5end_hypothetical_protein_745519..745749_POSITIVE 292 114 72 48 12 NC_009009:SSA_0876|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870233..870463_POSITIVE 291 89 47 162 112 NC_009009:SSA_0903|5end_NAD(P)H_dehydrogenase_(quinone),_putative_893242..893472_POSITIVE 290 99 52 229 185 NC_009009:SSA_2102|5end_Conserved_uncharacterized_protein_2106410..2106640_NEGATIVE 288 98 59 226 190 NC_009009:SSA_1419|5end_hypothetical_protein_1429675..1429905_NEGATIVE 286 45 3 132 77 NC_009009:SSA_0689|5end_Penicillin-binding_protein_2B,_putative_672262..672492_POSITIVE 273 78 31 156 113 NC_009009:SSA_1802|5end_Snf2_family_protein,_putative_1786470..1786700_NEGATIVE 271 108 64 223 186 NC_009009:SSA_1903|5end_hypothetical_protein_1898182..1898412_NEGATIVE 270 50 5 142 99 NC_009009:SSA_1543|5end_hypothetical_protein_1547835..1548065_POSITIVE 268 89 41 151 112 NC_009009:SSA_2098|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2103617..2103847_NEGATIVE 268 97 55 55 11 NC_009009:SSA_1750|5end_Extracellular_nuclease,_putative_1737922..1738152_NEGATIVE 265 87 41 128 88 NC_009009:SSA_0393|5end_Bacteriocin_ABC-type_exporter,_ATP_binding/permease_protein,_putative_388766..388996_POSITIVE 263 99 64 208 172 NC_009009:SSA_0666|5end_hypothetical_protein_649788..650018_NEGATIVE 262 110 64 80 25 NC_009009:SSA_1653|5end_hypothetical_protein_1651371..1651601_NEGATIVE 262 87 62 26 1 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 257 99 52 226 176 NC_009009:SSA_0040|5end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_46308..46538_POSITIVE 256 118 72 222 176 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 90 47 60 14 NC_009009:SSA_1079|3end_hypothetical_protein_1097448..1097598_POSITIVE 291 89 47 86 36 NC_009009:SSA_0901|3end_Alpha-acetolactate_decarboxylase,_putative_893246..893396_POSITIVE 290 99 52 139 95 NC_009009:SSA_2103|3end_hypothetical_protein_2106500..2106650_NEGATIVE 272 78 43 147 118 NC_009009:SSA_0492|3end_NADH-dependent_flavin_oxidoreductase,_putative_492771..492921_POSITIVE 268 89 41 147 108 NC_009009:SSA_2099|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2103621..2103771_NEGATIVE 268 90 43 49 3 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 265 59 14 121 71 NC_009009:SSA_0507|3end_hypothetical_protein_506442..506592_POSITIVE 262 110 64 60 5 NC_009009:SSA_1655|3end_hypothetical_protein_1651391..1651541_NEGATIVE 255 115 77 147 98 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 249 80 34 87 28 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 243 114 71 81 40 NC_009009:SSA_0636|3end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625809..625959_POSITIVE 237 62 25 57 22 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE 236 49 6 142 94 NC_009009:SSA_2154|3end_Conserved_uncharacterized_protein_2154762..2154912_NEGATIVE 235 60 14 90 33 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 232 117 75 52 9 NC_009009:SSA_2308|3end_hypothetical_protein_2309893..2310043_NEGATIVE 232 89 41 70 27 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 232 87 45 81 37 NC_009009:SSA_0307|3end_Glutamine_synthetase_type_1,_putative_304413..304563_POSITIVE 231 111 76 52 17 NC_009009:SSA_2113|3end_hypothetical_protein_2116228..2116378_NEGATIVE 231 58 15 148 102 NC_009009:SSA_1818|3end_Very_short_patch_repair_endonuclease,_putative_1805655..1805805_NEGATIVE 229 110 62 120 57 NC_009009:SSA_2140|3end_Ribonuclease_P_protein_component,_putative_2140308..2140458_NEGATIVE