Origin IGS: agtcagtccatcggatttaaggacaataaaaggcgacttatcgggaacttttccgaaagatagaaaccccaaatacaaagaggctgctctgcaaatcgtgcggagcagcctctttgctttttagccttagcatcttccgataggctttcttatagctgcaagggaaaaatagaggctcgtttctgcagtgaaacagcctctatttgttgtacggatttatacctgaa .........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 ttcaggtataaatccgtacaacaaatagaggctgtttcactgcagaaacgagcctctatttttcccttgcagctataagaaagcctatcggaagatgctaaggctaaaaagcaaagaggctgctccgcacgatttgcagagcagcctctttgtatttggggtttctatctttcggaaaagttcccgataagtcgccttttattgtccttaaatccgatggactgact Mask Tandem Repeat Region ================================================ agtcagtccatcggatttaaggacaataaaaggcgacttatcgggaacttttccgaaagatagaaaccccaaatacaaagaggctgctctgcaaatcgtgcggagcagcctctttgctttttagccttagcatcttccgataggctttcttatagctgcaagggaaaaatagaggctcgtttctgcagtgaaacagcctctatttgttgtacggatttatacctgaa Find is-nt database================================================ Query_seq: PG0278:PG0279|PG0278:PG0279:hypothetical protein:NADP-dependent malic enzyme:-><-:310538..310764 227 agtcagtccatcggatttaaggacaataaaaggcgacttatcgggaacttttccgaaagatagaaaccccaaatacaaagaggctgctctgcaaatcgtgcggagcagcctctttgctttttagccttagcatcttccgataggctttcttatagctgcaagggaaaaatagaggctcgtttctgcagtgaaacagcctctatttgttgtacggatttatacctgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0278:PG0279|PG0278:PG0279:hypothetical protein:NADP-dependent malic enzyme:-><-:310538..310764 227 agtcagtccatcggatttaaggacaataaaaggcgacttatcgggaacttttccgaaagatagaaaccccaaatacaaagaggctgctctgcaaatcgtgcggagcagcctctttgctttttagccttagcatcttccgataggctttcttatagctgcaagggaaaaatagaggctcgtttctgcagtgaaacagcctctatttgttgtacggatttatacctgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0278:PG0279|PG0278:PG0279:hypothetical protein:NADP-dependent malic enzyme:-><-:310538..310764 227 agtcagtccatcggatttaaggacaataaaaggcgacttatcgggaacttttccgaaagatagaaaccccaaatacaaagaggctgctctgcaaatcgtgcggagcagcctctttgctttttagccttagcatcttccgataggctttcttatagctgcaagggaaaaatagaggctcgtttctgcagtgaaacagcctctatttgttgtacggatttatacctgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtcagtccatcggatttaaggacaataaaaggcgacttatcgggaacttttccgaaagatagaaaccccaaatacaaagaggctgctctgcaaatcgtgcggagcagcctctttgctttttagccttagcatcttccgataggctttcttatagctgcaagggaaaaatagaggctcgtttctgcagtgaaacagcctctatttgttgtacggatttatacctgaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 26 End: 121 ......................... M K G D L S G T F P K D R N P K Y K E A A L Q I V R S S L F A F .......................................................................................................... Protein_Len: 51 Strand: + Start: 73 End: 225 ........................................................................ M Q R G C S A N R A E Q P L C F L A L A S S D R L S Y S C K G K I E A R F C S E T A S I C C T D L Y L .. Protein_Len: 52 Strand: - Start: 41 End: 196 ........................................ R S S K R F I S V G F V F L S S Q L D H P A A E K S K L R L M K R Y A K K Y S C P F F L P E N R C H F M ............................... Protein_Len: 36 Strand: - Start: 1 End: 108 T L G D S K L V I F P S K D P V K G F S L F G L Y L S A A R C I T R L M ....................................................................................................................... agtcagtccatcggatttaaggacaataaaaggcgacttatcgggaacttttccgaaagatagaaaccccaaatacaaagaggctgctctgcaaatcgtgcggagcagcctctttgctttttagccttagcatcttccgataggctttcttatagctgcaagggaaaaatagaggctcgtttctgcagtgaaacagcctctatttgttgtacggatttatacctgaa 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================================================ agtcagtccatcggatttaaggacaataaaaggcgacttatcgggaacttttccgaaagatagaaaccccaaatacaaagaggctgctctgcaaatcgtgcggagcagcctctttgctttttagccttagcatcttccgataggctttcttatagctgcaagggaaaaatagaggctcgtttctgcagtgaaacagcctctatttgttgtacggatttatacctgaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -18.0 Tail_Score: -3.75418 Start: 74 End: 118 Full_Region: atgctaaggctaaaa agcaaagaggctgctccgca cgatt tgcagagcagcctctttgta tttggggtttctatc .........................................................................agcaaagaggctgctccgcacgatttgcagagcagcctctttgta............................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -21.5 Tail_Score: -4.66833 Start: 75 End: 117 Full_Region: ATAGAAACCCCAAAT ACAAAGAGGCTGCTCTGCA AATCG TGCGGAGCAGCCTCTTTGC TTTTTAGCCTTAGCA ..........................................................................ACAAAGAGGCTGCTCTGCAAATCGTGCGGAGCAGCCTCTTTGC.............................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -25.0 Tail_Score: -3.39618 Start: 76 End: 116 Full_Region: TAGAAACCCCAAATA CAAAGAGGCTGCTCTGCA AATCG TGCGGAGCAGCCTCTTTG CTTTTTAGCCTTAGC ...........................................................................CAAAGAGGCTGCTCTGCAAATCGTGCGGAGCAGCCTCTTTG............................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -22.8 Tail_Score: -3.44991 Start: 76 End: 116 Full_Region: gctaaggctaaaaag caaagaggctgctccgca cgatt tgcagagcagcctctttg tatttggggtttcta ...........................................................................caaagaggctgctccgcacgatttgcagagcagcctctttg............................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -17.8 Tail_Score: -4.3453 Start: 80 End: 112 Full_Region: aggctaaaaagcaaa gaggctgctccgca cgatt tgcagagcagcctc tttgtatttggggtt ...............................................................................gaggctgctccgcacgatttgcagagcagcctc................................................................................................................... TransTerm Strand: + Conf: 87 HP_score: -10.1 Tail_Score: -4.31835 Start: 170 End: 202 Full_Region: GCTGCAAGGGAAAAA TAGAGGCTCGTTTC TGCAGT GAAACAGCCTCTA TTTGTTGTACGGATT .........................................................................................................................................................................TAGAGGCTCGTTTCTGCAGTGAAACAGCCTCTA......................... Find igs database================================================ Query_seq: PG0278:PG0279|PG0278:PG0279:hypothetical protein:NADP-dependent malic enzyme:-><-:310538..310764 227 agtcagtccatcggatttaaggacaataaaaggcgacttatcgggaacttttccgaaagatagaaaccccaaatacaaagaggctgctctgcaaatcgtgcggagcagcctctttgctttttagccttagcatcttccgataggctttcttatagctgcaagggaaaaatagaggctcgtttctgcagtgaaacagcctctatttgttgtacggatttatacctgaa Intra-Species Hit: Count: 1 Min: 1 Max: 227 Len: 227 Subject: NC_002950_PG0278_PG0279|hypothetical protein:NADP-dependent malic enzyme|POSITIVE:NEGATIVE|[310538,310764]|227 HSP 1 e-value: 1.0E-126 bit: 450.0 Len: 227 Query Start:1 Query End:227 Subject Strand: POSITIVE Subject Start: 1 Subject End: 227 agtcagtccatcggatttaaggacaataaaaggcgacttatcgggaacttttccgaaagatagaaaccccaaatacaaagaggctgctctgcaaatcgtgcggagcagcctctttgctttttagccttagcatcttccgataggctttcttatagctgcaagggaaaaatagaggctcgtttctgcagtgaaacagcctctatttgttgtacggatttatacctgaa agtcagtccatcggatttaaggacaataaaaggcgacttatcgggaacttttccgaaagatagaaaccccaaatacaaagaggctgctctgcaaatcgtgcggagcagcctctttgctttttagccttagcatcttccgataggctttcttatagctgcaagggaaaaatagaggctcgtttctgcagtgaaacagcctctatttgttgtacggatttatacctgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCAGUCCAUCGGAUUUAAGGACAAUAAAAGGCGACUUAUCGGGAACUUUUCCGAAAGAUAGAAACCCCAAAUACAAAGAGGCUGCUCUGCAAAUCGUGCGGAGCAGCCUCUUUGCUUUUUAGCCUUAGCAUCUUCCGAUAGGCUUUCUUAUAGCUGCAAGGGAAAAAUAGAGGCUCGUUUCUGCAGUGAAACAGCCUCUAUUUGUUGUACGGAUUUAUACCUGAA ..((((.((((((((.((((((....((((((((..(((.((((((....))))))))).................(((((((((((((((((.....))))))))))))))))))))))))).)))))).....)))))).))..(((.((((((..........(((((((((((.(((((......)))))))))))))))))))))).))).......)))). (-88.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAGGUAUAAAUCCGUACAACAAAUAGAGGCUGUUUCACUGCAGAAACGAGCCUCUAUUUUUCCCUUGCAGCUAUAAGAAAGCCUAUCGGAAGAUGCUAAGGCUAAAAAGCAAAGAGGCUGCUCCGCACGAUUUGCAGAGCAGCCUCUUUGUAUUUGGGGUUUCUAUCUUUCGGAAAAGUUCCCGAUAAGUCGCCUUUUAUUGUCCUUAAAUCCGAUGGACUGACU .....((((......))))...((((((((((((((((......))))).))))))))))).((((...............((((((((....)))....))))).....(((((((((((((((.(((.....))).)))))))))))))))....))))..((..(((.(((((........(((((((......)))))))........))))).)))..)).. (-82.19) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 432 140 91 56 2 NC_002950:PG1470|5end_hypothetical_protein_1548121..1548351_POSITIVE 419 126 83 73 27 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 397 114 78 152 118 NC_002950:PG2142|5end_GTP-binding_protein_Era_2247585..2247815_POSITIVE 387 149 101 213 160 NC_002950:PG1434|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_1519022..1519252_POSITIVE 378 118 75 184 125 NC_002950:PG0757|5end_hypothetical_protein_806370..806600_NEGATIVE 377 117 78 79 38 NC_002950:PG1268|5end_hypothetical_protein_1347371..1347601_POSITIVE 356 138 91 212 154 NC_002950:PG0227|5end_DNA_repair_protein_RadA_263978..264208_NEGATIVE 352 125 82 76 17 NC_002950:PG0135|5end_dimethyladenosine_transferase_157943..158173_NEGATIVE 347 125 82 74 8 NC_002950:PG2065|5end_conserved_hypothetical_protein_TIGR00048_2161000..2161230_POSITIVE 347 148 101 189 136 NC_002950:PG0307|5end_NADH-ubiquinone_oxidoreductase_342560..342790_POSITIVE 343 118 75 214 167 NC_002950:PG0221|5end_hypothetical_protein_255834..256064_NEGATIVE 342 116 76 58 16 NC_002950:PG0898|5end_hypothetical_protein_963350..963580_NEGATIVE 340 138 91 191 125 NC_002950:PG0559|5end_chlorohydrolase_family_protein_617496..617726_NEGATIVE 338 139 91 57 7 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 337 145 101 161 113 NC_002950:PG1542|5end_collagenase_1620788..1621018_POSITIVE 335 128 82 221 176 NC_002950:PG2100|5end_immunoreactive_63_kDa_antigen_PG102_2210191..2210421_NEGATIVE 333 126 81 199 145 NC_002950:PG1888|5end_hypothetical_protein_1985596..1985826_POSITIVE 332 146 101 204 141 NC_002950:PG1099|5end_hypothetical_protein_1168168..1168398_NEGATIVE 331 220 173 52 2 NC_002950:PG0997|5end_transcriptional_regulator,_putative_1056666..1056896_POSITIVE 330 150 101 164 120 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 434 113 79 61 28 NC_002950:PG1321|3end_formate--tetrahydrofolate_ligase_1399656..1399806_NEGATIVE 431 119 77 62 24 NC_002950:PG0933|3end_translation_elongation_factor_G,_putative_992236..992386_POSITIVE 413 118 78 66 28 NC_002950:PG1055|3end_thiol_protease_1121202..1121352_NEGATIVE 410 139 91 88 35 NC_002950:PG1004|3end_prolyl_oligopeptidase_family_protein_1060433..1060583_NEGATIVE 397 114 78 73 39 NC_002950:PG2141|3end_3-oxoacyl-(acyl_carrier_protein)_synthase_2247586..2247736_POSITIVE 378 118 75 87 28 NC_002950:PG0758|3end_peptidyl-dipeptidase_Dcp_806467..806617_NEGATIVE 371 120 71 52 11 NC_002950:PG0196|3end_peptidase,_M16_family_235808..235958_POSITIVE 369 115 77 66 21 NC_002950:PG0159|3end_endopeptidase_PepO_181095..181245_NEGATIVE 359 113 79 56 26 NC_002950:PG2177|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_2285266..2285416_NEGATIVE 352 112 79 61 31 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 344 116 79 124 80 NC_002950:PG0412|3end_DNA_mismatch_repair_protein_MutL_449584..449734_NEGATIVE 343 118 75 135 88 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 341 116 79 63 29 NC_002950:PG2106|3end_hypothetical_protein_2215457..2215607_POSITIVE 339 115 77 68 23 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 337 145 101 148 100 NC_002950:PG1541|3end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_1620855..1621005_POSITIVE 336 120 80 64 20 NC_002950:PG2170|3end_sugar_transporter_2276685..2276835_NEGATIVE 336 125 83 145 104 NC_002950:PG1743|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1827530..1827680_NEGATIVE 335 148 101 74 16 NC_002950:PG2172|3end_hypothetical_protein_2279191..2279341_NEGATIVE 335 128 82 134 89 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE 333 111 79 32 1 NC_002950:PG2107|3end_thiamine_biosynthesis_protein_ThiH_2215546..2215696_NEGATIVE