Origin IGS: attattactattgaatttagaatgaatctctccaaatgtaacgacaatcgaggaggtaggatataaattttgaataaaaagcagctatagagtcacgcagtagcgtttgtggaaataaaaagagacgtacctccggaggggagatacgtctctgctttttcgtttttgtatctgctctgtatgagcaggggagtgaaatcaggga .........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 tccctgatttcactcccctgctcatacagagcagatacaaaaacgaaaaagcagagacgtatctcccctccggaggtacgtctctttttatttccacaaacgctactgcgtgactctatagctgctttttattcaaaatttatatcctacctcctcgattgtcgttacatttggagagattcattctaaattcaatagtaataat Mask Tandem Repeat Region ================================================ attattactattgaatttagaatgaatctctccaaatgtaacgacaatcgaggaggtaggatataaattttgaataaaaagcagctatagagtcacgcagtagcgtttgtggaaataaaaagagacgtacctccggaggggagatacgtctctgctttttcgtttttgtatctgctctgtatgagcaggggagtgaaatcaggga Find is-nt database================================================ Query_seq: PG1230:PG1232|PG1230:PG1232:hypothetical protein:glutamate dehydrogenase:<-<-:1308159..1308363 205 attattactattgaatttagaatgaatctctccaaatgtaacgacaatcgaggaggtaggatataaattttgaataaaaagcagctatagagtcacgcagtagcgtttgtggaaataaaaagagacgtacctccggaggggagatacgtctctgctttttcgtttttgtatctgctctgtatgagcaggggagtgaaatcaggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1230:PG1232|PG1230:PG1232:hypothetical protein:glutamate dehydrogenase:<-<-:1308159..1308363 205 attattactattgaatttagaatgaatctctccaaatgtaacgacaatcgaggaggtaggatataaattttgaataaaaagcagctatagagtcacgcagtagcgtttgtggaaataaaaagagacgtacctccggaggggagatacgtctctgctttttcgtttttgtatctgctctgtatgagcaggggagtgaaatcaggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1230:PG1232|PG1230:PG1232:hypothetical protein:glutamate dehydrogenase:<-<-:1308159..1308363 205 attattactattgaatttagaatgaatctctccaaatgtaacgacaatcgaggaggtaggatataaattttgaataaaaagcagctatagagtcacgcagtagcgtttgtggaaataaaaagagacgtacctccggaggggagatacgtctctgctttttcgtttttgtatctgctctgtatgagcaggggagtgaaatcaggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attattactattgaatttagaatgaatctctccaaatgtaacgacaatcgaggaggtaggatataaattttgaataaaaagcagctatagagtcacgcagtagcgtttgtggaaataaaaagagacgtacctccggaggggagatacgtctctgctttttcgtttttgtatctgctctgtatgagcaggggagtgaaatcaggga Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 87 End: 203 ...................................................................................... M E S R S S V C G N K K R R T S G G E I R L C F F V F V S A L Y E Q G S E I R .. Protein_Len: 32 Strand: + Start: 109 End: 204 ............................................................................................................ M E I K R D V P P E G R Y V S A F S F L Y L L C M S R G V K S G . Protein_Len: 31 Strand: - Start: 96 End: 188 ............................................................................................... A T A N T S I F L S T G G S P L Y T E A K E N K Y R S Q I L M ................. Protein_Len: 60 Strand: - Start: 20 End: 202 ................... S D R W I Y R C D L L Y S I F K S Y F A A I S D R L L T Q P F L F L R V E P P S I R R Q K K T K T D A R Y S C P L S I M ... attattactattgaatttagaatgaatctctccaaatgtaacgacaatcgaggaggtaggatataaattttgaataaaaagcagctatagagtcacgcagtagcgtttgtggaaataaaaagagacgtacctccggaggggagatacgtctctgctttttcgtttttgtatctgctctgtatgagcaggggagtgaaatcaggga 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================================================ attattactattgaatttagaatgaatctctccaaatgtaacgacaatcgaggaggtaggatataaattttgaataaaaagcagctatagagtcacgcagtagcgtttgtggaaataaaaagagacgtacctccggaggggagatacgtctctgctttttcgtttttgtatctgctctgtatgagcaggggagtgaaatcaggga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -8.0 Tail_Score: -5.2197 Start: 119 End: 155 Full_Region: CGTTTGTGGAAATAA AAAGAGACGTACCTCC GGAGG GGAGATACGTCTCTGC TTTTTCGTTTTTGTA ......................................................................................................................AAAGAGACGTACCTCCGGAGGGGAGATACGTCTCTGC.................................................. TransTerm Strand: + Conf: 85 HP_score: -11.5 Tail_Score: -3.70742 Start: 120 End: 154 Full_Region: GTTTGTGGAAATAAA AAGAGACGTACCTCC GGAGG GGAGATACGTCTCTG CTTTTTCGTTTTTGT .......................................................................................................................AAGAGACGTACCTCCGGAGGGGAGATACGTCTCTG................................................... TransTerm Strand: - Conf: 100 HP_score: -16.3 Tail_Score: -5.27335 Start: 122 End: 152 Full_Region: aaaaacgaaaaagca gagacgtatctcc cctcc ggaggtacgtctc tttttatttccacaa .........................................................................................................................gagacgtatctcccctccggaggtacgtctc..................................................... Find igs database================================================ Query_seq: PG1230:PG1232|PG1230:PG1232:hypothetical protein:glutamate dehydrogenase:<-<-:1308159..1308363 205 attattactattgaatttagaatgaatctctccaaatgtaacgacaatcgaggaggtaggatataaattttgaataaaaagcagctatagagtcacgcagtagcgtttgtggaaataaaaagagacgtacctccggaggggagatacgtctctgctttttcgtttttgtatctgctctgtatgagcaggggagtgaaatcaggga Intra-Species Hit: Count: 1 Min: 1 Max: 205 Len: 205 Subject: NC_002950_PG1230_PG1232|hypothetical protein:glutamate dehydrogenase|NEGATIVE:NEGATIVE|[1308159,1308363]|205 HSP 1 e-value: 1.0E-112 bit: 406.0 Len: 205 Query Start:1 Query End:205 Subject Strand: POSITIVE Subject Start: 1 Subject End: 205 attattactattgaatttagaatgaatctctccaaatgtaacgacaatcgaggaggtaggatataaattttgaataaaaagcagctatagagtcacgcagtagcgtttgtggaaataaaaagagacgtacctccggaggggagatacgtctctgctttttcgtttttgtatctgctctgtatgagcaggggagtgaaatcaggga attattactattgaatttagaatgaatctctccaaatgtaacgacaatcgaggaggtaggatataaattttgaataaaaagcagctatagagtcacgcagtagcgtttgtggaaataaaaagagacgtacctccggaggggagatacgtctctgctttttcgtttttgtatctgctctgtatgagcaggggagtgaaatcaggga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUACUAUUGAAUUUAGAAUGAAUCUCUCCAAAUGUAACGACAAUCGAGGAGGUAGGAUAUAAAUUUUGAAUAAAAAGCAGCUAUAGAGUCACGCAGUAGCGUUUGUGGAAAUAAAAAGAGACGUACCUCCGGAGGGGAGAUACGUCUCUGCUUUUUCGUUUUUGUAUCUGCUCUGUAUGAGCAGGGGAGUGAAAUCAGGGA .(((((.(((.......)))))))).((.((((..........((((.(((((((((.........(((((.(.....((((.(((((.(.......).))))))))).).)))))....(((((((((.((((.....)))).))))))))))))))))))...))))..((((((.....)))))).)))).))......... (-58.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCUGAUUUCACUCCCCUGCUCAUACAGAGCAGAUACAAAAACGAAAAAGCAGAGACGUAUCUCCCCUCCGGAGGUACGUCUCUUUUUAUUUCCACAAACGCUACUGCGUGACUCUAUAGCUGCUUUUUAUUCAAAAUUUAUAUCCUACCUCCUCGAUUGUCGUUACAUUUGGAGAGAUUCAUUCUAAAUUCAAUAGUAAUAAU .....(((.((......((((((.....))))))...........(((((((((((((((((((((.....)))))))))))))...............((((....))))...........))))))))..........................))..))).((((..(((((.(((.....)))...)))))..)))).... (-52.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 983 140 91 231 182 NC_002950:PG1230|5end_hypothetical_protein_1308068..1308298_NEGATIVE 378 176 131 81 35 NC_002950:PG1738|5end_hypothetical_protein_1825131..1825361_NEGATIVE 366 176 134 47 2 NC_002950:PG0325|5end_hypothetical_protein_359714..359944_NEGATIVE 351 156 119 178 125 NC_002950:PG1654|5end_D-alanyl-D-alanine_dipeptidase_1736458..1736688_POSITIVE 344 179 131 142 83 NC_002950:PG1831|5end_ATP-dependent_DNA_helicase_RecQ_1925422..1925652_NEGATIVE 344 176 134 140 91 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 340 189 141 169 121 NC_002950:PG0583|5end_cell_division_protein_FtsA_640425..640655_POSITIVE 339 178 134 219 168 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 333 168 121 175 126 NC_002950:PG0327|5end_hypothetical_protein_362061..362291_NEGATIVE 332 193 154 181 134 NC_002950:PG1888|5end_hypothetical_protein_1985596..1985826_POSITIVE 332 180 131 194 144 NC_002950:PG0704|5end_phosphoglycerate_mutase_family_protein_758928..759158_POSITIVE 331 168 121 205 151 NC_002950:PG1899|5end_TonB-dependent_receptor,_putative_1999724..1999954_NEGATIVE 330 190 149 186 135 NC_002950:PG0431|5end_hypothetical_protein_468978..469208_POSITIVE 329 166 128 55 13 NC_002950:PG1017|5end_pyruvate_phosphate_dikinase_1076138..1076368_POSITIVE 328 174 132 223 177 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 325 200 152 137 79 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 322 199 152 217 162 NC_002950:PG0829|5end_hypothetical_protein_886746..886976_NEGATIVE 321 182 141 80 38 NC_002950:PG1195|5end_8-amino-7-oxononanoate_synthase_1273979..1274209_POSITIVE 317 195 151 208 167 NC_002950:PG1458|5end_hypothetical_protein_1539144..1539374_POSITIVE 316 167 121 157 106 NC_002950:PG1035|5end_hypothetical_protein_1096875..1097105_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 176 131 84 38 NC_002950:PG1739|3end_hypothetical_protein_1825128..1825278_NEGATIVE 352 176 131 106 60 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE 351 156 119 98 45 NC_002950:PG1653|3end_hypothetical_protein_1736458..1736608_POSITIVE 348 162 122 147 103 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 344 176 134 125 76 NC_002950:PG1246|3end_alanyl-tRNA_synthetase_1324509..1324659_POSITIVE 340 189 141 120 72 NC_002950:PG0582|3end_cell_division_protein_FtsQ,_putative_640456..640606_POSITIVE 340 180 135 70 18 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE 339 178 134 130 79 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 333 168 121 81 32 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 331 168 121 130 76 NC_002950:PG1900|3end_ribosome-associated_GTPase_1999799..1999949_NEGATIVE 328 174 132 122 76 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 328 179 131 89 47 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 328 180 132 51 4 NC_002950:PG0261|3end_ISPg3,_transposase_293862..294012_NEGATIVE 325 200 152 132 74 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 323 197 151 147 97 NC_002950:PG1874|3end_hypothetical_protein_1969253..1969403_NEGATIVE 323 180 133 56 9 NC_002950:PG0053|3end_hypothetical_protein_64967..65117_NEGATIVE 322 180 133 75 26 NC_002950:PG2010|3end_phosphomannomutase,_putative_2100952..2101102_POSITIVE 316 179 134 138 76 NC_002950:PG1722|3end_hypothetical_protein_1812633..1812783_NEGATIVE 316 128 81 72 28 NC_002950:PG0217|3end_hypothetical_protein_253463..253613_POSITIVE 315 194 152 88 49 NC_002950:PG1345|3end_glycosyl_transferase,_group_1_family_protein_1426791..1426941_POSITIVE