Origin IGS: gaaaaagaaagcctgaattgatatagtctgtatctatgaagccataaaaacattcgatgattttttctttgccatgaaaaaagctgcacatatttttgcgaccggaataaaccaaacggcattaaatcactctttcataaaacgccccccaacggatgacaactattggtaggcaggtgagtgcactcaaataacgatataatttcctcagaccgtatatttttggatatatagggcggcaattctctacaattgtcgcccataatattt .........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 aaatattatgggcgacaattgtagagaattgccgccctatatatccaaaaatatacggtctgaggaaattatatcgttatttgagtgcactcacctgcctaccaatagttgtcatccgttggggggcgttttatgaaagagtgatttaatgccgtttggtttattccggtcgcaaaaatatgtgcagcttttttcatggcaaagaaaaaatcatcgaatgtttttatggcttcatagatacagactatatcaattcaggctttctttttc Mask Tandem Repeat Region ================================================ gaaaaagaaagcctgaattgatatagtctgtatctatgaagccataaaaacattcgatgattttttctttgccatgaaaaaagctgcacatatttttgcgaccggaataaaccaaacggcattaaatcactctttcataaaacgccccccaacggatgacaactattggtaggcaggtgagtgcactcaaataacgatataatttcctcagaccgtatatttttggatatatagggcggcaattctctacaattgtcgcccataatattt Find is-nt database================================================ Query_seq: PG1979:PG1980|PG1979:PG1980:hypothetical protein:hypothetical protein:-><-:2067580..2067849 270 gaaaaagaaagcctgaattgatatagtctgtatctatgaagccataaaaacattcgatgattttttctttgccatgaaaaaagctgcacatatttttgcgaccggaataaaccaaacggcattaaatcactctttcataaaacgccccccaacggatgacaactattggtaggcaggtgagtgcactcaaataacgatataatttcctcagaccgtatatttttggatatatagggcggcaattctctacaattgtcgcccataatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1979:PG1980|PG1979:PG1980:hypothetical protein:hypothetical protein:-><-:2067580..2067849 270 gaaaaagaaagcctgaattgatatagtctgtatctatgaagccataaaaacattcgatgattttttctttgccatgaaaaaagctgcacatatttttgcgaccggaataaaccaaacggcattaaatcactctttcataaaacgccccccaacggatgacaactattggtaggcaggtgagtgcactcaaataacgatataatttcctcagaccgtatatttttggatatatagggcggcaattctctacaattgtcgcccataatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1979:PG1980|PG1979:PG1980:hypothetical protein:hypothetical protein:-><-:2067580..2067849 270 gaaaaagaaagcctgaattgatatagtctgtatctatgaagccataaaaacattcgatgattttttctttgccatgaaaaaagctgcacatatttttgcgaccggaataaaccaaacggcattaaatcactctttcataaaacgccccccaacggatgacaactattggtaggcaggtgagtgcactcaaataacgatataatttcctcagaccgtatatttttggatatatagggcggcaattctctacaattgtcgcccataatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaaaagaaagcctgaattgatatagtctgtatctatgaagccataaaaacattcgatgattttttctttgccatgaaaaaagctgcacatatttttgcgaccggaataaaccaaacggcattaaatcactctttcataaaacgccccccaacggatgacaactattggtaggcaggtgagtgcactcaaataacgatataatttcctcagaccgtatatttttggatatatagggcggcaattctctacaattgtcgcccataatattt Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 17 End: 169 ................ M D I V C I Y E A I K T F D D F F F A M K K A A H I F A T G I N Q T A L N H S F I K R P P T D D N Y W ..................................................................................................... Protein_Len: 43 Strand: - Start: 138 End: 266 ......................................................................................................................................... L V G G L P H C S N T P L H T C E F L S I I E E S R I N K S I Y P P L E R C N D G M M .... Protein_Len: 48 Strand: - Start: 125 End: 268 ............................................................................................................................ I V R E Y F A G W R I V V I P L C T L A S L Y R Y L K R L G Y I K P Y I P R C N E V I T A W L M .. Protein_Len: 40 Strand: - Start: 3 End: 122 .. F S L R F Q Y L R Y R H L W L F M R H N K R Q W S F L Q V Y K Q S R F L G F P M .................................................................................................................................................... Protein_Len: 38 Strand: - Start: 2 End: 115 . F L F G S N I Y D T D I F G Y F C E I I K E K G H F F S C M N K R G S Y V M ........................................................................................................................................................... gaaaaagaaagcctgaattgatatagtctgtatctatgaagccataaaaacattcgatgattttttctttgccatgaaaaaagctgcacatatttttgcgaccggaataaaccaaacggcattaaatcactctttcataaaacgccccccaacggatgacaactattggtaggcaggtgagtgcactcaaataacgatataatttcctcagaccgtatatttttggatatatagggcggcaattctctacaattgtcgcccataatattt 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================================================ gaaaaagaaagcctgaattgatatagtctgtatctatgaagccataaaaacattcgatgattttttctttgccatgaaaaaagctgcacatatttttgcgaccggaataaaccaaacggcattaaatcactctttcataaaacgccccccaacggatgacaactattggtaggcaggtgagtgcactcaaataacgatataatttcctcagaccgtatatttttggatatatagggcggcaattctctacaattgtcgcccataatattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1979:PG1980|PG1979:PG1980:hypothetical protein:hypothetical protein:-><-:2067580..2067849 270 gaaaaagaaagcctgaattgatatagtctgtatctatgaagccataaaaacattcgatgattttttctttgccatgaaaaaagctgcacatatttttgcgaccggaataaaccaaacggcattaaatcactctttcataaaacgccccccaacggatgacaactattggtaggcaggtgagtgcactcaaataacgatataatttcctcagaccgtatatttttggatatatagggcggcaattctctacaattgtcgcccataatattt Intra-Species Hit: Count: 1 Min: 1 Max: 270 Len: 270 Subject: NC_002950_PG1979_PG1980|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[2067580,2067849]|270 HSP 1 e-value: 1.0E-151 bit: 535.0 Len: 270 Query Start:1 Query End:270 Subject Strand: POSITIVE Subject Start: 1 Subject End: 270 gaaaaagaaagcctgaattgatatagtctgtatctatgaagccataaaaacattcgatgattttttctttgccatgaaaaaagctgcacatatttttgcgaccggaataaaccaaacggcattaaatcactctttcataaaacgccccccaacggatgacaactattggtaggcaggtgagtgcactcaaataacgatataatttcctcagaccgtatatttttggatatatagggcggcaattctctacaattgtcgcccataatattt gaaaaagaaagcctgaattgatatagtctgtatctatgaagccataaaaacattcgatgattttttctttgccatgaaaaaagctgcacatatttttgcgaccggaataaaccaaacggcattaaatcactctttcataaaacgccccccaacggatgacaactattggtaggcaggtgagtgcactcaaataacgatataatttcctcagaccgtatatttttggatatatagggcggcaattctctacaattgtcgcccataatattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAAGAAAGCCUGAAUUGAUAUAGUCUGUAUCUAUGAAGCCAUAAAAACAUUCGAUGAUUUUUUCUUUGCCAUGAAAAAAGCUGCACAUAUUUUUGCGACCGGAAUAAACCAAACGGCAUUAAAUCACUCUUUCAUAAAACGCCCCCCAACGGAUGACAACUAUUGGUAGGCAGGUGAGUGCACUCAAAUAACGAUAUAAUUUCCUCAGACCGUAUAUUUUUGGAUAUAUAGGGCGGCAAUUCUCUACAAUUGUCGCCCAUAAUAUUU ............(..((...(((..(((((((((......(((............((((((((......((((...........((((........))))...((......))....))))..)))))).))...........(((..((((..(.......)..))))..))).)))(((....))).......)))).........)))))..)))...))..).......(((((((((((......)))))))))))......... (-60.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAUUAUGGGCGACAAUUGUAGAGAAUUGCCGCCCUAUAUAUCCAAAAAUAUACGGUCUGAGGAAAUUAUAUCGUUAUUUGAGUGCACUCACCUGCCUACCAAUAGUUGUCAUCCGUUGGGGGGCGUUUUAUGAAAGAGUGAUUUAAUGCCGUUUGGUUUAUUCCGGUCGCAAAAAUAUGUGCAGCUUUUUUCAUGGCAAAGAAAAAAUCAUCGAAUGUUUUUAUGGCUUCAUAGAUACAGACUAUAUCAAUUCAGGCUUUCUUUUUC ..((((...(((((.(((((......))))).)))))...))))............((((((((...........((...((((((.(((((....(((..((((..(.......)..))))..))).((....))..))))))))))).)).(((((((((((...(((((.((((((((.......(((((((........))))))).......)))))))).)))))..)))))).)))))........))))))))......... (-63.24) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 183 144 218 170 NC_002950:PG0414|5end_hypothetical_protein_453652..453882_NEGATIVE 332 180 142 218 187 NC_002950:PG0526|5end_putative_inner_membrane_protein_translocase_component_YidC_570746..570976_POSITIVE 326 185 143 56 16 NC_002950:PG0028|5end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_33863..34093_POSITIVE 325 185 143 55 7 NC_002950:PG0423|5end_hypothetical_protein_462251..462481_POSITIVE 314 189 145 81 26 NC_002950:PG1233|5end_hypothetical_protein_1309885..1310115_POSITIVE 301 184 143 184 130 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 298 120 72 57 11 NC_002950:PG1703|5end_MazG_family_protein_1790753..1790983_NEGATIVE 297 250 203 192 151 NC_002950:PG0738|5end_cytidine/deoxycytidylate_deaminase_family_protein_786463..786693_POSITIVE 296 180 143 144 109 NC_002950:PG0471|5end_hypothetical_protein_512288..512518_POSITIVE 292 185 143 59 15 NC_002950:PG1794|5end_DNA_polymerase_type_I_1885978..1886208_POSITIVE 291 190 143 98 43 NC_002950:PG0723|5end_hypothetical_protein_774949..775179_POSITIVE 289 187 144 185 144 NC_002950:PG2205|5end_2-dehydropantoate_2-reductase_2316121..2316351_POSITIVE 288 185 142 227 171 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 287 158 112 194 121 NC_002950:PG0767|5end_4-alpha-glucanotransferase_820533..820763_NEGATIVE 287 77 41 93 50 NC_002950:PG0417|5end_ATP-dependent_protease_ATP-binding_subunit_458624..458854_NEGATIVE 286 179 144 186 154 NC_002950:PG0312|5end_hypothetical_protein_347048..347278_NEGATIVE 285 122 85 156 119 NC_002950:PG1897|5end_thiamin_pyrophosphokinase_catalytic_domain_protein_1996730..1996960_NEGATIVE 284 124 84 53 3 NC_002950:PG0529|5end_carbamoyl-phosphate_synthase_small_subunit_574637..574867_POSITIVE 283 184 143 72 34 NC_002950:PG1163|5end_cobyrinic_acid_a,c-diamide_synthase_1243381..1243611_NEGATIVE 283 188 142 67 9 NC_002950:PG0153|5end_aspartyl-tRNA_synthetase_177430..177660_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 188 142 53 12 NC_002950:PG1247|3end_3-dehydroquinate_synthase_1325585..1325735_POSITIVE 332 180 142 90 59 NC_002950:PG0525|3end_CTP_synthetase_570698..570848_POSITIVE 326 185 143 49 9 NC_002950:PG0027|3end_hypothetical_protein_33936..34086_POSITIVE 320 178 144 148 108 NC_002950:PG0415|3end_peptidyl-prolyl_cis-trans_isomerase,_PPIC-type_453714..453864_NEGATIVE 310 124 84 39 1 NC_002950:PG0230|3end_transaldolase_266114..266264_POSITIVE 300 188 143 68 1 NC_002950:PG1875|3end_hemolysin_1969647..1969797_NEGATIVE 287 77 41 56 13 NC_002950:PG0418|3end_ATP-dependent_Clp_protease,_proteolytic_subunit_458661..458811_NEGATIVE 285 184 143 134 102 NC_002950:PG0816|3end_hypothetical_protein_876386..876536_NEGATIVE 280 185 143 81 29 NC_002950:PG1152|3end_hypothetical_protein_1234674..1234824_NEGATIVE 279 99 55 105 52 NC_002950:PG2043|3end_conserved_hypothetical_protein_TIGR00486_2143392..2143542_POSITIVE 278 187 145 110 61 NC_002950:PG0927|3end_conserved_hypothetical_protein_TIGR00150_984634..984784_NEGATIVE 276 186 144 64 19 NC_002950:PG0715|3end_transporter_768676..768826_NEGATIVE 265 190 142 94 54 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 264 183 143 39 1 NC_002950:PG1303|3end_helicase,_putative_1382147..1382297_POSITIVE 263 216 171 64 3 NC_002950:PG1711|3end_alpha-1,2-mannosidase_family_protein_1796652..1796802_NEGATIVE 263 190 146 52 5 NC_002950:PG1038|3end_ATP-dependent_DNA_helicase_UvrD/PcrA/Rep_Family_1105121..1105271_POSITIVE 261 199 152 71 27 NC_002950:PG2200|3end_TPR_domain_protein_2306720..2306870_NEGATIVE 261 261 236 136 111 NC_002950:PG2067|3end_pyridoxal_phosphate_biosynthetic_protein_PdxA_2164392..2164542_POSITIVE 261 248 202 99 57 NC_002950:PG1731|3end_3-dehydroquinate_dehydratase_1819678..1819828_NEGATIVE 261 183 142 52 16 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE