Origin IGS: aagatgtgtaatgcaatcgacacaaacaatgataatctgtattatgtttacttatataaatgcttatcctttgaatgcacacttttgaaacagctaatccccgactaatgccttgccataagtcttggctctacagttatttttgcaactcccaaattggcactatctttggtgcgcaattatatcaaccgaaataagttgatacatacagatttgtcacgaaaagagaaggaaataaaattctcaacaaaataaaaaacagaaaaaacc .........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 ggttttttctgttttttattttgttgagaattttatttccttctcttttcgtgacaaatctgtatgtatcaacttatttcggttgatataattgcgcaccaaagatagtgccaatttgggagttgcaaaaataactgtagagccaagacttatggcaaggcattagtcggggattagctgtttcaaaagtgtgcattcaaaggataagcatttatataagtaaacataatacagattatcattgtttgtgtcgattgcattacacatctt Mask Tandem Repeat Region ================================================ aagatgtgtaatgcaatcgacacaaacaatgataatctgtattatgtttacttatataaatgcttatcctttgaatgcacacttttgaaacagctaatccccgactaatgccttgccataagtcttggctctacagttatttttgcaactcccaaattggcactatctttggtgcgcaattatatcaaccgaaataagttgatacatacagatttgtcacgaaaagagaaggaaataaaattctcaacaaaataaaaaacagaaaaaacc Find is-nt database================================================ Query_seq: PG1065:PG1066|PG1065:PG1066:dihydroorotate dehydrogenase:butyrate-acetoacetate CoA-transferase, subunit A:->->:1133391..1133660 270 aagatgtgtaatgcaatcgacacaaacaatgataatctgtattatgtttacttatataaatgcttatcctttgaatgcacacttttgaaacagctaatccccgactaatgccttgccataagtcttggctctacagttatttttgcaactcccaaattggcactatctttggtgcgcaattatatcaaccgaaataagttgatacatacagatttgtcacgaaaagagaaggaaataaaattctcaacaaaataaaaaacagaaaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1065:PG1066|PG1065:PG1066:dihydroorotate dehydrogenase:butyrate-acetoacetate CoA-transferase, subunit A:->->:1133391..1133660 270 aagatgtgtaatgcaatcgacacaaacaatgataatctgtattatgtttacttatataaatgcttatcctttgaatgcacacttttgaaacagctaatccccgactaatgccttgccataagtcttggctctacagttatttttgcaactcccaaattggcactatctttggtgcgcaattatatcaaccgaaataagttgatacatacagatttgtcacgaaaagagaaggaaataaaattctcaacaaaataaaaaacagaaaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1065:PG1066|PG1065:PG1066:dihydroorotate dehydrogenase:butyrate-acetoacetate CoA-transferase, subunit A:->->:1133391..1133660 270 aagatgtgtaatgcaatcgacacaaacaatgataatctgtattatgtttacttatataaatgcttatcctttgaatgcacacttttgaaacagctaatccccgactaatgccttgccataagtcttggctctacagttatttttgcaactcccaaattggcactatctttggtgcgcaattatatcaaccgaaataagttgatacatacagatttgtcacgaaaagagaaggaaataaaattctcaacaaaataaaaaacagaaaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagatgtgtaatgcaatcgacacaaacaatgataatctgtattatgtttacttatataaatgcttatcctttgaatgcacacttttgaaacagctaatccccgactaatgccttgccataagtcttggctctacagttatttttgcaactcccaaattggcactatctttggtgcgcaattatatcaaccgaaataagttgatacatacagatttgtcacgaaaagagaaggaaataaaattctcaacaaaataaaaaacagaaaaaacc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 4 End: 105 ... M C N A I D T N N D N L Y Y V Y L Y K C L S F E C T L L K Q L I P D ..................................................................................................................................................................... Protein_Len: 40 Strand: + Start: 75 End: 194 .......................................................................... M H T F E T A N P R L M P C H K S W L Y S Y F C N S Q I G T I F G A Q L Y Q P K ............................................................................ Protein_Len: 45 Strand: + Start: 118 End: 252 ..................................................................................................................... M S L G S T V I F A T P K L A L S L V R N Y I N R N K L I H T D L S R K E K E I K F S T K .................. Protein_Len: 36 Strand: - Start: 2 End: 109 . S T Y H L R C L C H Y D T N H K S I Y I S I R Q I C V K S V A L G R S M ................................................................................................................................................................. aagatgtgtaatgcaatcgacacaaacaatgataatctgtattatgtttacttatataaatgcttatcctttgaatgcacacttttgaaacagctaatccccgactaatgccttgccataagtcttggctctacagttatttttgcaactcccaaattggcactatctttggtgcgcaattatatcaaccgaaataagttgatacatacagatttgtcacgaaaagagaaggaaataaaattctcaacaaaataaaaaacagaaaaaacc 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: 16 End: 45 ...............ATCGACACAAACAATGATAATCTGTATTAT................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: + Score: 81 Start: 157 End: 173 ............................................................................................................................................................TTGGCACTATCTTTGGT................................................................................................. aagatgtgtaatgcaatcgacacaaacaatgataatctgtattatgtttacttatataaatgcttatcctttgaatgcacacttttgaaacagctaatccccgactaatgccttgccataagtcttggctctacagttatttttgcaactcccaaattggcactatctttggtgcgcaattatatcaaccgaaataagttgatacatacagatttgtcacgaaaagagaaggaaataaaattctcaacaaaataaaaaacagaaaaaacc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -3.0 Tail_Score: -3.13475 Start: 103 End: 124 Full_Region: AAACAGCTAATCCCC GACTAATG CCTTGC CATAAGTC TTGGCTCTACAGTTA ......................................................................................................GACTAATGCCTTGCCATAAGTC.................................................................................................................................................. TransTerm Strand: - Conf: 45 HP_score: -3.8 Tail_Score: -2.70932 Start: 183 End: 204 Full_Region: tgacaaatctgtatg tatcaact tatttc ggttgata taattgcgcaccaaa ......................................................................................................................................................................................tatcaacttatttcggttgata.................................................................. Find igs database================================================ Query_seq: PG1065:PG1066|PG1065:PG1066:dihydroorotate dehydrogenase:butyrate-acetoacetate CoA-transferase, subunit A:->->:1133391..1133660 270 aagatgtgtaatgcaatcgacacaaacaatgataatctgtattatgtttacttatataaatgcttatcctttgaatgcacacttttgaaacagctaatccccgactaatgccttgccataagtcttggctctacagttatttttgcaactcccaaattggcactatctttggtgcgcaattatatcaaccgaaataagttgatacatacagatttgtcacgaaaagagaaggaaataaaattctcaacaaaataaaaaacagaaaaaacc Intra-Species Hit: Count: 1 Min: 1 Max: 220 Len: 220 Subject: NC_002950_PG1065_PG1066|dihydroorotate dehydrogenase:butyrate-acetoacetate CoA-transferase, subunit A|POSITIVE:POSITIVE|[1133391,1133660]|270 HSP 1 e-value: 1.0E-121 bit: 436.0 Len: 220 Query Start:1 Query End:220 Subject Strand: POSITIVE Subject Start: 1 Subject End: 220 aagatgtgtaatgcaatcgacacaaacaatgataatctgtattatgtttacttatataaatgcttatcctttgaatgcacacttttgaaacagctaatccccgactaatgccttgccataagtcttggctctacagttatttttgcaactcccaaattggcactatctttggtgcgcaattatatcaaccgaaataagttgatacatacagatttgtcac.................................................. aagatgtgtaatgcaatcgacacaaacaatgataatctgtattatgtttacttatataaatgcttatcctttgaatgcacacttttgaaacagctaatccccgactaatgccttgccataagtcttggctctacagttatttttgcaactcccaaattggcactatctttggtgcgcaattatatcaaccgaaataagttgatacatacagatttgtcac.................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUGUGUAAUGCAAUCGACACAAACAAUGAUAAUCUGUAUUAUGUUUACUUAUAUAAAUGCUUAUCCUUUGAAUGCACACUUUUGAAACAGCUAAUCCCCGACUAAUGCCUUGCCAUAAGUCUUGGCUCUACAGUUAUUUUUGCAACUCCCAAAUUGGCACUAUCUUUGGUGCGCAAUUAUAUCAACCGAAAUAAGUUGAUACAUACAGAUUUGUCAC ....(((((..........))))).....(((((((((((((..((((.((((((.....(((......((..((........))..))..((((((.....((((.(((......))).))))))))))..............))).......(((((((((((....)))))).)))))............)))))).)))).))))))).)))))). (-44.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGACAAAUCUGUAUGUAUCAACUUAUUUCGGUUGAUAUAAUUGCGCACCAAAGAUAGUGCCAAUUUGGGAGUUGCAAAAAUAACUGUAGAGCCAAGACUUAUGGCAAGGCAUUAGUCGGGGAUUAGCUGUUUCAAAAGUGUGCAUUCAAAGGAUAAGCAUUUAUAUAAGUAAACAUAAUACAGAUUAUCAUUGUUUGUGUCGAUUGCAUUACACAUCUU (((....((((...((((((((((......))))))))))..(((((((....(((((((((......(.(((((......))))).)...((((.......))))..)))))).))).(..((.....))..)....)))))))......))))..(((.((((((((((((..(((((....)))))..)))))))))).)).)))....)))..... (-52.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 167 121 115 54 NC_002950:PG0465|5end_ferric_uptake_transcriptional_regulator_509403..509633_NEGATIVE 307 130 91 223 178 NC_002950:PG2179|5end_NADH-ubiquinone_oxidoreductase_2287806..2288036_NEGATIVE 307 134 91 203 165 NC_002950:PG1057|5end_hypothetical_protein_1123419..1123649_POSITIVE 307 130 81 140 99 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 302 138 91 117 56 NC_002950:PG1901|5end_ribosome_releasing_factor_2001352..2001582_NEGATIVE 298 138 92 153 102 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 298 150 101 58 9 NC_002950:PG0321|5end_arginine/ornithine_transport_system_ATPase_354648..354878_POSITIVE 296 134 92 198 146 NC_002950:PG1853|5end_DNA_polymerase_III,_beta_subunit_1953119..1953349_NEGATIVE 296 177 131 128 86 NC_002950:PG1185|5end_hypothetical_protein_1267752..1267982_NEGATIVE 294 130 81 149 96 NC_002950:PG0657|5end_Maf-like_protein_707782..708012_NEGATIVE 293 137 100 37 7 NC_002950:PG0347|5end_UDP-glucose_4-epimerase_381274..381504_POSITIVE 285 178 134 159 119 NC_002950:PG2202|5end_Holliday_junction_resolvase-like_protein_2309933..2310163_NEGATIVE 283 130 81 83 46 NC_002950:PG0571|5end_aspartate-semialdehyde_dehydrogenase_626399..626629_POSITIVE 282 200 152 77 21 NC_002950:PG1807|5end_v-type_ATPase,_subunit_K_1902069..1902299_POSITIVE 282 131 93 141 101 NC_002950:PG0517|5end_hypothetical_protein_562097..562327_NEGATIVE 281 129 92 37 5 NC_002950:PG1576|5end_L-aspartate_oxidase_1653016..1653246_POSITIVE 277 139 92 214 166 NC_002950:PG1395|5end_cell_shape-determining_protein_MreC,_putative_1477669..1477899_NEGATIVE 277 136 98 207 158 NC_002950:PG1065|5end_dihydroorotate_dehydrogenase_1132327..1132557_POSITIVE 276 136 91 49 4 NC_002950:PG1103|5end_ATPase,_AAA_family_1173605..1173835_POSITIVE 275 177 132 228 176 NC_002950:PG2074|5end_hypothetical_protein_2174661..2174891_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 130 81 133 80 NC_002950:PG0658|3end_phosphatase,_YrbI_family_707798..707948_NEGATIVE 279 174 131 137 91 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 278 179 135 43 1 NC_002950:PG0466|3end_hypothetical_protein_509489..509639_NEGATIVE 276 129 86 123 79 NC_002950:PG1232|3end_glutamate_dehydrogenase_1308274..1308424_NEGATIVE 275 138 93 120 79 NC_002950:PG1315|3end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_1395618..1395768_NEGATIVE 274 139 97 134 93 NC_002950:PG1043|3end_ferrous_iron_transport_protein_B_1110675..1110825_NEGATIVE 271 119 76 113 65 NC_002950:PG1633|3end_galactokinase_1714619..1714769_POSITIVE 266 133 93 82 42 NC_002950:PG1397|3end_bifunctional_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1478829..1478979_NEGATIVE 262 130 87 125 78 NC_002950:PG0161|3end_hypothetical_protein_184267..184417_NEGATIVE 261 177 152 137 114 NC_002950:PG0789|3end_hypothetical_protein_840702..840852_NEGATIVE 260 116 71 150 107 NC_002950:PG1396|3end_cell_shape-determining_protein_MreB_1477707..1477857_NEGATIVE 258 135 92 65 18 NC_002950:PG0715|3end_transporter_768676..768826_NEGATIVE 256 138 92 118 79 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 256 159 118 118 79 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 255 162 122 151 104 NC_002950:PG1353|3end_orotate_phosphoribosyltransferase_1433201..1433351_NEGATIVE 254 190 149 121 78 NC_002950:PG1565|3end_3-deoxy-D-manno-octulosonic-acid_transferase,_putative_1644621..1644771_NEGATIVE 253 192 151 85 43 NC_002950:PG1823|3end_hypothetical_protein_1918050..1918200_POSITIVE 252 199 151 42 2 NC_002950:PG1783|3end_glycosyl_transferase,_group_2_family_protein_1872658..1872808_POSITIVE 252 103 61 148 105 NC_002950:PG0807|3end_NusB_family_protein_863630..863780_NEGATIVE 252 129 89 95 56 NC_002950:PG0163|3end_diphosphate--fructose-6-phosphate_1-phosphotransferase_185236..185386_NEGATIVE