Origin IGS: gccatacaaagggacgtaagaccttattgtatttcttgctttcagccctgttccctttcgggagcggggcttttttgctttatgaaggggcgaagaggaggctaagcggtatgattcctcggcgaaaaaattcatgcctccgcctcccggctccgaatcatccgaacgagcaatcgaaggatgctgtcgctcccaatttacacagattagtatccggctttaggcttggccatgcagtagcataagggatttatatacctttggaaataataaaattggatcactcgct .........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 agcgagtgatccaattttattatttccaaaggtatataaatcccttatgctactgcatggccaagcctaaagccggatactaatctgtgtaaattgggagcgacagcatccttcgattgctcgttcggatgattcggagccgggaggcggaggcatgaattttttcgccgaggaatcataccgcttagcctcctcttcgccccttcataaagcaaaaaagccccgctcccgaaagggaacagggctgaaagcaagaaatacaataaggtcttacgtccctttgtatggc Mask Tandem Repeat Region ================================================ gccatacaaagggacgtaagaccttattgtatttcttgctttcagccctgttccctttcgggagcggggcttttttgctttatgaaggggcgaagaggaggctaagcggtatgattcctcggcgaaaaaattcatgcctccgcctcccggctccgaatcatccgaacgagcaatcgaaggatgctgtcgctcccaatttacacagattagtatccggctttaggcttggccatgcagtagcataagggatttatatacctttggaaataataaaattggatcactcgct Find is-nt database================================================ Query_seq: PG0452:PG0453|PG0452:PG0453:hypothetical protein:hypothetical protein:->->:495167..495455 289 gccatacaaagggacgtaagaccttattgtatttcttgctttcagccctgttccctttcgggagcggggcttttttgctttatgaaggggcgaagaggaggctaagcggtatgattcctcggcgaaaaaattcatgcctccgcctcccggctccgaatcatccgaacgagcaatcgaaggatgctgtcgctcccaatttacacagattagtatccggctttaggcttggccatgcagtagcataagggatttatatacctttggaaataataaaattggatcactcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0452:PG0453|PG0452:PG0453:hypothetical protein:hypothetical protein:->->:495167..495455 289 gccatacaaagggacgtaagaccttattgtatttcttgctttcagccctgttccctttcgggagcggggcttttttgctttatgaaggggcgaagaggaggctaagcggtatgattcctcggcgaaaaaattcatgcctccgcctcccggctccgaatcatccgaacgagcaatcgaaggatgctgtcgctcccaatttacacagattagtatccggctttaggcttggccatgcagtagcataagggatttatatacctttggaaataataaaattggatcactcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0452:PG0453|PG0452:PG0453:hypothetical protein:hypothetical protein:->->:495167..495455 289 gccatacaaagggacgtaagaccttattgtatttcttgctttcagccctgttccctttcgggagcggggcttttttgctttatgaaggggcgaagaggaggctaagcggtatgattcctcggcgaaaaaattcatgcctccgcctcccggctccgaatcatccgaacgagcaatcgaaggatgctgtcgctcccaatttacacagattagtatccggctttaggcttggccatgcagtagcataagggatttatatacctttggaaataataaaattggatcactcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gccatacaaagggacgtaagaccttattgtatttcttgctttcagccctgttccctttcgggagcggggcttttttgctttatgaaggggcgaagaggaggctaagcggtatgattcctcggcgaaaaaattcatgcctccgcctcccggctccgaatcatccgaacgagcaatcgaaggatgctgtcgctcccaatttacacagattagtatccggctttaggcttggccatgcagtagcataagggatttatatacctttggaaataataaaattggatcactcgct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 4 End: 102 ... M Q R D V R P Y C I S C F Q P C S L S G A G L F C F M K G R R G G ........................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 27 End: 242 .......................... M Y F L L S A L F P F G S G A F L L Y E G A K R R L S G M I P R R K N S C L R L P A P N H P N E Q S K D A V A P N L H R ............................................... Protein_Len: 30 Strand: - Start: 161 End: 250 ................................................................................................................................................................ G F S C D F S A T A G L K C L N T D P K L S P W A T A Y P M ....................................... Protein_Len: 60 Strand: - Start: 1 End: 213 R A K L G T G K R S R P K K A K H L P S S S A L R Y S E E A F F N M G G G G P E S D D S R A I S P H Q R E W N V C I L M ............................................................................ gccatacaaagggacgtaagaccttattgtatttcttgctttcagccctgttccctttcgggagcggggcttttttgctttatgaaggggcgaagaggaggctaagcggtatgattcctcggcgaaaaaattcatgcctccgcctcccggctccgaatcatccgaacgagcaatcgaaggatgctgtcgctcccaatttacacagattagtatccggctttaggcttggccatgcagtagcataagggatttatatacctttggaaataataaaattggatcactcgct 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================================================ gccatacaaagggacgtaagaccttattgtatttcttgctttcagccctgttccctttcgggagcggggcttttttgctttatgaaggggcgaagaggaggctaagcggtatgattcctcggcgaaaaaattcatgcctccgcctcccggctccgaatcatccgaacgagcaatcgaaggatgctgtcgctcccaatttacacagattagtatccggctttaggcttggccatgcagtagcataagggatttatatacctttggaaataataaaattggatcactcgct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.7 Tail_Score: -5.42514 Start: 45 End: 70 Full_Region: TATTTCTTGCTTTCA GCCCTGTTCCC TTTC GGGAGCGGGGC TTTTTTGCTTTATGA ............................................GCCCTGTTCCCTTTCGGGAGCGGGGC........................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PG0452:PG0453|PG0452:PG0453:hypothetical protein:hypothetical protein:->->:495167..495455 289 gccatacaaagggacgtaagaccttattgtatttcttgctttcagccctgttccctttcgggagcggggcttttttgctttatgaaggggcgaagaggaggctaagcggtatgattcctcggcgaaaaaattcatgcctccgcctcccggctccgaatcatccgaacgagcaatcgaaggatgctgtcgctcccaatttacacagattagtatccggctttaggcttggccatgcagtagcataagggatttatatacctttggaaataataaaattggatcactcgct Intra-Species Hit: Count: 1 Min: 1 Max: 289 Len: 289 Subject: NC_002950_PG0452_PG0453|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[495167,495455]|289 HSP 1 e-value: 1.0E-162 bit: 573.0 Len: 289 Query Start:1 Query End:289 Subject Strand: POSITIVE Subject Start: 1 Subject End: 289 gccatacaaagggacgtaagaccttattgtatttcttgctttcagccctgttccctttcgggagcggggcttttttgctttatgaaggggcgaagaggaggctaagcggtatgattcctcggcgaaaaaattcatgcctccgcctcccggctccgaatcatccgaacgagcaatcgaaggatgctgtcgctcccaatttacacagattagtatccggctttaggcttggccatgcagtagcataagggatttatatacctttggaaataataaaattggatcactcgct gccatacaaagggacgtaagaccttattgtatttcttgctttcagccctgttccctttcgggagcggggcttttttgctttatgaaggggcgaagaggaggctaagcggtatgattcctcggcgaaaaaattcatgcctccgcctcccggctccgaatcatccgaacgagcaatcgaaggatgctgtcgctcccaatttacacagattagtatccggctttaggcttggccatgcagtagcataagggatttatatacctttggaaataataaaattggatcactcgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCAUACAAAGGGACGUAAGACCUUAUUGUAUUUCUUGCUUUCAGCCCUGUUCCCUUUCGGGAGCGGGGCUUUUUUGCUUUAUGAAGGGGCGAAGAGGAGGCUAAGCGGUAUGAUUCCUCGGCGAAAAAAUUCAUGCCUCCGCCUCCCGGCUCCGAAUCAUCCGAACGAGCAAUCGAAGGAUGCUGUCGCUCCCAAUUUACACAGAUUAGUAUCCGGCUUUAGGCUUGGCCAUGCAGUAGCAUAAGGGAUUUAUAUACCUUUGGAAAUAAUAAAAUUGGAUCACUCGCU .(((..((((((...(((((.((((((.((.....((((....((((((((((((....))))))))))))((((((((((.....))))))))))...((((((((((.(((((((...((((((....)))..)))...(((....)))...)))))))))...(((....)))..((((((((((................)).))))))))........))))))))..))))..))))))))..)))))...)))))).............))).......... (-93.65) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGAGUGAUCCAAUUUUAUUAUUUCCAAAGGUAUAUAAAUCCCUUAUGCUACUGCAUGGCCAAGCCUAAAGCCGGAUACUAAUCUGUGUAAAUUGGGAGCGACAGCAUCCUUCGAUUGCUCGUUCGGAUGAUUCGGAGCCGGGAGGCGGAGGCAUGAAUUUUUUCGCCGAGGAAUCAUACCGCUUAGCCUCCUCUUCGCCCCUUCAUAAAGCAAAAAAGCCCCGCUCCCGAAAGGGAACAGGGCUGAAAGCAAGAAAUACAAUAAGGUCUUACGUCCCUUUGUAUGGC ((((((..(((............((((((.(((.............((((....))))(((...)))....)))..((((......))))...))))))((....)).......)))..))))))...((((..(((((..(((((((..((((((((.(((((.....))))).))))...)))).)))))))))))).....))))...((.....(((((.(.((((....)))).).)))))....)).....((((((...((.(....).))..))))))... (-84.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 469 154 119 195 160 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 440 176 131 147 98 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 439 109 61 51 3 NC_002950:PG0476|5end_yngK_protein_518762..518992_NEGATIVE 425 77 36 80 31 NC_002950:PG2227|5end_hypothetical_protein_2342008..2342238_POSITIVE 420 110 61 180 127 NC_002950:PG1695|5end_hypothetical_protein_1779440..1779670_POSITIVE 414 89 44 187 138 NC_002950:PG1342|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_1422585..1422815_POSITIVE 407 177 140 60 6 NC_002950:PG1787|5end_hypothetical_protein_1875908..1876138_NEGATIVE 404 123 84 193 151 NC_002950:PG0240|5end_hydrolase,_haloacid_dehalogenase-like_family_277093..277323_NEGATIVE 403 125 84 46 2 NC_002950:PG2000|5end_signal_peptidase-related_protein_2089468..2089698_NEGATIVE 396 78 31 157 102 NC_002950:PG0068|5end_hypothetical_protein_81748..81978_POSITIVE 386 180 138 117 62 NC_002950:PG1006|5end_hypothetical_protein_1066478..1066708_NEGATIVE 385 169 121 219 164 NC_002950:PG1842|5end_acetyltransferase,_GNAT_family_1938241..1938471_POSITIVE 384 155 112 74 21 NC_002950:PG2218|5end_potassium_uptake_protein_TrkA_2331580..2331810_POSITIVE 384 190 141 65 2 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 381 176 135 53 4 NC_002950:PG0584|5end_cell_division_protein_FtsZ_641867..642097_POSITIVE 379 98 52 212 171 NC_002950:PG0738|5end_cytidine/deoxycytidylate_deaminase_family_protein_786463..786693_POSITIVE 375 90 45 103 41 NC_002950:PG1223|5end_hypothetical_protein_1299461..1299691_POSITIVE 375 190 141 66 7 NC_002950:PG0007|5end_hypothetical_protein_6913..7143_NEGATIVE 373 170 140 231 199 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 368 172 135 48 4 NC_002950:PG1900|5end_ribosome-associated_GTPase_2000746..2000976_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 439 109 61 61 13 NC_002950:PG0477|3end_pantoate--beta-alanine_ligase_518752..518902_NEGATIVE 436 71 44 47 20 NC_002950:PG0452|3end_hypothetical_protein_495106..495256_POSITIVE 425 77 36 83 34 NC_002950:PG2226|3end_hypothetical_protein_2342091..2342241_POSITIVE 412 109 61 97 36 NC_002950:PG0020|3end_transcriptional_regulator,_MarR_family_24166..24316_POSITIVE 403 125 84 56 12 NC_002950:PG2001|3end_signal_peptidase_I_2089458..2089608_NEGATIVE 402 180 140 141 98 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 393 190 141 97 38 NC_002950:PG2032|3end_primosomal_protein_N'_2130868..2131018_NEGATIVE 386 100 54 71 24 NC_002950:PG2036|3end_ion_transporter_2137552..2137702_POSITIVE 386 180 138 77 22 NC_002950:PG1007|3end_transcriptional_regulator,_GntR_family_1066518..1066668_NEGATIVE 386 110 64 130 82 NC_002950:PG0767|3end_4-alpha-glucanotransferase_818557..818707_NEGATIVE 381 176 135 50 1 NC_002950:PG0583|3end_cell_division_protein_FtsA_641944..642094_POSITIVE 377 109 61 142 75 NC_002950:PG0932|3end_DNA_polymerase_III,_delta_prime_subunit,_putative_989833..989983_POSITIVE 374 174 135 76 31 NC_002950:PG0915|3end_hypothetical_protein_977057..977207_POSITIVE 374 190 142 149 97 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 373 70 24 137 84 NC_002950:PG1866|3end_hypothetical_protein_1964736..1964886_POSITIVE 371 189 141 151 99 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 366 99 54 143 90 NC_002950:PG1836|3end_nucleoside_permease_NupG_1929858..1930008_POSITIVE 364 96 53 67 21 NC_002950:PG0569|3end_hypothetical_protein_624697..624847_NEGATIVE 361 190 142 68 15 NC_002950:PG0459|3end_ISPg5,_transposase_Orf1_501517..501667_NEGATIVE 358 79 31 142 79 NC_002950:PG0597|3end_ribosomal_protein_L9_654281..654431_POSITIVE