Origin IGS: tacctgaataattaagttggttctgttttctctgttgcaagtctcgtccaatcgtccccgacaactacaaaaaacccgtctcgtaagacggaatcgggtgaccctcgagaccgagcaaagatatataaattcttcaggaaccaataacgccgtttccatccgggatcgataccgaaacgatgggattccgagggccgattaaaggggcaaagcaactactcttctatataaacttcgtatgtttgtccgcacaataaacgaacctctcccgtcaggggcaaaaacattcaataca .........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 tgtattgaatgtttttgcccctgacgggagaggttcgtttattgtgcggacaaacatacgaagtttatatagaagagtagttgctttgcccctttaatcggccctcggaatcccatcgtttcggtatcgatcccggatggaaacggcgttattggttcctgaagaatttatatatctttgctcggtctcgagggtcacccgattccgtcttacgagacgggttttttgtagttgtcggggacgattggacgagacttgcaacagagaaaacagaaccaacttaattattcaggta Mask Tandem Repeat Region ================================================ tacctgaataattaagttggttctgttttctctgttgcaagtctcgtccaatcgtccccgacaactacaaaaaacccgtctcgtaagacggaatcgggtgaccctcgagaccgagcaaagatatataaattcttcaggaaccaataacgccgtttccatccgggatcgataccgaaacgatgggattccgagggccgattaaaggggcaaagcaactactcttctatataaacttcgtatgtttgtccgcacaataaacgaacctctcccgtcaggggcaaaaacattcaataca Find is-nt database================================================ Query_seq: PG1676:PG1677|PG1676:PG1677:phosphoenolpyruvate carboxykinase:phosphoglycerate kinase:<-->:1762187..1762481 295 tacctgaataattaagttggttctgttttctctgttgcaagtctcgtccaatcgtccccgacaactacaaaaaacccgtctcgtaagacggaatcgggtgaccctcgagaccgagcaaagatatataaattcttcaggaaccaataacgccgtttccatccgggatcgataccgaaacgatgggattccgagggccgattaaaggggcaaagcaactactcttctatataaacttcgtatgtttgtccgcacaataaacgaacctctcccgtcaggggcaaaaacattcaataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1676:PG1677|PG1676:PG1677:phosphoenolpyruvate carboxykinase:phosphoglycerate kinase:<-->:1762187..1762481 295 tacctgaataattaagttggttctgttttctctgttgcaagtctcgtccaatcgtccccgacaactacaaaaaacccgtctcgtaagacggaatcgggtgaccctcgagaccgagcaaagatatataaattcttcaggaaccaataacgccgtttccatccgggatcgataccgaaacgatgggattccgagggccgattaaaggggcaaagcaactactcttctatataaacttcgtatgtttgtccgcacaataaacgaacctctcccgtcaggggcaaaaacattcaataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1676:PG1677|PG1676:PG1677:phosphoenolpyruvate carboxykinase:phosphoglycerate kinase:<-->:1762187..1762481 295 tacctgaataattaagttggttctgttttctctgttgcaagtctcgtccaatcgtccccgacaactacaaaaaacccgtctcgtaagacggaatcgggtgaccctcgagaccgagcaaagatatataaattcttcaggaaccaataacgccgtttccatccgggatcgataccgaaacgatgggattccgagggccgattaaaggggcaaagcaactactcttctatataaacttcgtatgtttgtccgcacaataaacgaacctctcccgtcaggggcaaaaacattcaataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacctgaataattaagttggttctgttttctctgttgcaagtctcgtccaatcgtccccgacaactacaaaaaacccgtctcgtaagacggaatcgggtgaccctcgagaccgagcaaagatatataaattcttcaggaaccaataacgccgtttccatccgggatcgataccgaaacgatgggattccgagggccgattaaaggggcaaagcaactactcttctatataaacttcgtatgtttgtccgcacaataaacgaacctctcccgtcaggggcaaaaacattcaataca Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 8 End: 199 ....... M I K L V L F S L L Q V S S N R P R Q L Q K T R L V R R N R V T L E T E Q R Y I N S S G T N N A V S I R D R Y R N D G I ................................................................................................ Protein_Len: 42 Strand: + Start: 129 End: 254 ................................................................................................................................ M L Q E P I T P F P S G I D T E T M G F R G P I K G A K Q L L F Y I N F V C L S A Q ......................................... Protein_Len: 30 Strand: - Start: 202 End: 291 ......................................................................................................................................................................................................... L P L A V V R R Y L S R I N T R V I F S G R G D P A F V N M .... Protein_Len: 60 Strand: - Start: 15 End: 215 .............. A L R T W D D G V V V F F G D R L V S D P S G R S R A F I Y L N K L F W Y R R K W G P D I G F R H S E S P R N F P C L M ................................................................................ Protein_Len: 60 Strand: - Start: 1 End: 186 I I L N T R N E R N C T E D L R G R C S C F V R R T L R F R T V R S V S C L Y I F E E P V L L A T E M R S R Y R F S P M ............................................................................................................. tacctgaataattaagttggttctgttttctctgttgcaagtctcgtccaatcgtccccgacaactacaaaaaacccgtctcgtaagacggaatcgggtgaccctcgagaccgagcaaagatatataaattcttcaggaaccaataacgccgtttccatccgggatcgataccgaaacgatgggattccgagggccgattaaaggggcaaagcaactactcttctatataaacttcgtatgtttgtccgcacaataaacgaacctctcccgtcaggggcaaaaacattcaataca 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================================================ tacctgaataattaagttggttctgttttctctgttgcaagtctcgtccaatcgtccccgacaactacaaaaaacccgtctcgtaagacggaatcgggtgaccctcgagaccgagcaaagatatataaattcttcaggaaccaataacgccgtttccatccgggatcgataccgaaacgatgggattccgagggccgattaaaggggcaaagcaactactcttctatataaacttcgtatgtttgtccgcacaataaacgaacctctcccgtcaggggcaaaaacattcaataca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -7.7 Tail_Score: -5.39755 Start: 75 End: 92 Full_Region: cgagggtcacccgat tccgtct tacg agacggg ttttttgtagttgtc ..........................................................................tccgtcttacgagacggg........................................................................................................................................................................................................... TransTerm Strand: - Conf: 76 HP_score: -9.0 Tail_Score: -3.82226 Start: 76 End: 91 Full_Region: gagggtcacccgatt ccgtct tacg agacgg gttttttgtagttgt ...........................................................................ccgtcttacgagacgg............................................................................................................................................................................................................ Find igs database================================================ Query_seq: PG1676:PG1677|PG1676:PG1677:phosphoenolpyruvate carboxykinase:phosphoglycerate kinase:<-->:1762187..1762481 295 tacctgaataattaagttggttctgttttctctgttgcaagtctcgtccaatcgtccccgacaactacaaaaaacccgtctcgtaagacggaatcgggtgaccctcgagaccgagcaaagatatataaattcttcaggaaccaataacgccgtttccatccgggatcgataccgaaacgatgggattccgagggccgattaaaggggcaaagcaactactcttctatataaacttcgtatgtttgtccgcacaataaacgaacctctcccgtcaggggcaaaaacattcaataca Intra-Species Hit: Count: 1 Min: 1 Max: 295 Len: 295 Subject: NC_002950_PG1676_PG1677|phosphoenolpyruvate carboxykinase:phosphoglycerate kinase|NEGATIVE:POSITIVE|[1762187,1762481]|295 HSP 1 e-value: 1.0E-166 bit: 585.0 Len: 295 Query Start:1 Query End:295 Subject Strand: POSITIVE Subject Start: 1 Subject End: 295 tacctgaataattaagttggttctgttttctctgttgcaagtctcgtccaatcgtccccgacaactacaaaaaacccgtctcgtaagacggaatcgggtgaccctcgagaccgagcaaagatatataaattcttcaggaaccaataacgccgtttccatccgggatcgataccgaaacgatgggattccgagggccgattaaaggggcaaagcaactactcttctatataaacttcgtatgtttgtccgcacaataaacgaacctctcccgtcaggggcaaaaacattcaataca tacctgaataattaagttggttctgttttctctgttgcaagtctcgtccaatcgtccccgacaactacaaaaaacccgtctcgtaagacggaatcgggtgaccctcgagaccgagcaaagatatataaattcttcaggaaccaataacgccgtttccatccgggatcgataccgaaacgatgggattccgagggccgattaaaggggcaaagcaactactcttctatataaacttcgtatgtttgtccgcacaataaacgaacctctcccgtcaggggcaaaaacattcaataca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACCUGAAUAAUUAAGUUGGUUCUGUUUUCUCUGUUGCAAGUCUCGUCCAAUCGUCCCCGACAACUACAAAAAACCCGUCUCGUAAGACGGAAUCGGGUGACCCUCGAGACCGAGCAAAGAUAUAUAAAUUCUUCAGGAACCAAUAACGCCGUUUCCAUCCGGGAUCGAUACCGAAACGAUGGGAUUCCGAGGGCCGAUUAAAGGGGCAAAGCAACUACUCUUCUAUAUAAACUUCGUAUGUUUGUCCGCACAAUAAACGAACCUCUCCCGUCAGGGGCAAAAACAUUCAAUACA ....(((((......(((((((((((((..(((.((((..((((((.......((((((((..............((((((....))))))..))))).)))...))))))...))))))).....))))......)))))))))...(((.........(((........)))....(((((((....((((..((.(((..((((((((.((..(((.................)))))))))))).)....))).))..)))))))))))...)))......)))))..... (-76.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAUUGAAUGUUUUUGCCCCUGACGGGAGAGGUUCGUUUAUUGUGCGGACAAACAUACGAAGUUUAUAUAGAAGAGUAGUUGCUUUGCCCCUUUAAUCGGCCCUCGGAAUCCCAUCGUUUCGGUAUCGAUCCCGGAUGGAAACGGCGUUAUUGGUUCCUGAAGAAUUUAUAUAUCUUUGCUCGGUCUCGAGGGUCACCCGAUUCCGUCUUACGAGACGGGUUUUUUGUAGUUGUCGGGGACGAUUGGACGAGACUUGCAACAGAGAAAACAGAACCAACUUAAUUAUUCAGGUA ....(((((((.......(((....)))...(((((((((.(((((..(((...........)))..))))).......(((((....(.(.(((((((((((((((..(((..........((.((((((..((..((....)).))..)))))).)).(((((.........)))))....)))..)))))))).(((((((((((((....)))))))............))))))...))))))).).)....))))).....)))).)))))........)))))))... (-81.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1047 120 71 211 162 NC_002950:PG1676|5end_phosphoenolpyruvate_carboxykinase_1762096..1762326_NEGATIVE 391 200 151 226 168 NC_002950:PG2003|5end_deoxyguanosinetriphosphate_triphosphohydrolase_2092991..2093221_NEGATIVE 373 115 76 65 10 NC_002950:PG2032|5end_primosomal_protein_N'_2133381..2133611_NEGATIVE 371 199 151 226 178 NC_002950:PG1604|5end_immunoreactive_84_kDa_antigen_PG93_1682737..1682967_POSITIVE 369 119 74 165 123 NC_002950:PG0068|5end_hypothetical_protein_81748..81978_POSITIVE 367 203 161 62 4 NC_002950:PG1572|5end_hypothetical_protein_1651252..1651482_NEGATIVE 363 209 161 194 143 NC_002950:PG1829|5end_long-chain-fatty-acid--CoA_ligase,_putative_1922980..1923210_NEGATIVE 362 118 75 100 50 NC_002950:PG2052|5end_dihydrodipicolinate_synthase_2149636..2149866_POSITIVE 359 228 181 62 12 NC_002950:PG2215|5end_mannose-1-phosphate_guanylyltransferase_2327695..2327925_NEGATIVE 359 213 176 177 143 NC_002950:PG1857|5end_hypothetical_protein_1956373..1956603_NEGATIVE 358 198 151 221 165 NC_002950:PG1478|5end_conjugative_transposon_protein_TraK_1554116..1554346_NEGATIVE 358 195 151 153 107 NC_002950:PG0858|5end_hypothetical_protein_917540..917770_POSITIVE 355 100 54 131 84 NC_002950:PG1695|5end_hypothetical_protein_1779440..1779670_POSITIVE 353 190 141 68 22 NC_002950:PG0282|5end_ABC_transporter,_ATP-binding_protein_316915..317145_NEGATIVE 351 217 173 226 174 NC_002950:PG2064|5end_hypothetical_protein_2160550..2160780_POSITIVE 349 217 172 179 128 NC_002950:PG1102|5end_hypothetical_protein_1173637..1173867_NEGATIVE 349 198 160 70 25 NC_002950:PG0350|5end_internalin-related_protein_386810..387040_NEGATIVE 347 79 32 179 128 NC_002950:PG1057|5end_hypothetical_protein_1123419..1123649_POSITIVE 347 199 160 76 24 NC_002950:PG0322|5end_serine/threonine_transporter_355708..355938_POSITIVE 346 200 151 162 114 NC_002950:PG2097|5end_ribose-phosphate_pyrophosphokinase_2206462..2206692_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 391 200 151 82 24 NC_002950:PG2004|3end_hypothetical_protein_2093135..2093285_NEGATIVE 383 120 74 56 2 NC_002950:PG1889|3end_hypothetical_protein_1987090..1987240_POSITIVE 376 198 151 74 24 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 370 100 53 150 98 NC_002950:PG1625|3end_hypothetical_protein_1708718..1708868_POSITIVE 368 198 156 150 102 NC_002950:PG1807|3end_v-type_ATPase,_subunit_K_1902625..1902775_POSITIVE 353 194 152 66 21 NC_002950:PG1409|3end_hypothetical_protein_1492873..1493023_NEGATIVE 348 198 155 55 9 NC_002950:PG1186|3end_hypothetical_protein_1267703..1267853_NEGATIVE 347 198 151 103 49 NC_002950:PG1649|3end_hypothetical_protein_1730030..1730180_NEGATIVE 344 209 161 127 86 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE 343 78 37 100 62 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 341 190 143 134 76 NC_002950:PG2202|3end_Holliday_junction_resolvase-like_protein_2309517..2309667_NEGATIVE 337 185 148 144 105 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 336 197 151 82 25 NC_002950:PG1007|3end_transcriptional_regulator,_GntR_family_1066518..1066668_NEGATIVE 335 99 52 139 95 NC_002950:PG0033|3end_RmuC_domain_protein_40242..40392_NEGATIVE 331 215 172 137 104 NC_002950:PG2119|3end_oxidoreductase,_Gfo/Idh/MocA_family_2227598..2227748_POSITIVE 327 207 162 145 97 NC_002950:PG2095|3end_lipoprotein,_putative_2198290..2198440_NEGATIVE 327 210 161 137 69 NC_002950:PG2026|3end_phosphoglycerate_mutase_family_protein_2125545..2125695_POSITIVE 327 65 32 140 108 NC_002950:PG1056|3end_hypothetical_protein_1123479..1123629_POSITIVE 324 58 16 54 11 NC_002950:PG1694|3end_hypothetical_protein_1777916..1778066_NEGATIVE 324 280 235 55 2 NC_002950:PG1416|3end_enoyl-(acyl-carrier-protein)_reductase_II_1501078..1501228_POSITIVE