Origin IGS: ggcaatcgcttttctcgcaaatgtatttatttaatccgaattatgcgaatcgaataacccgccccatttttcaaacttctataaggagggatatacactctcctgcgacaagcaaattttttcccgtacggcaaaattttcttgcagtgcaggccggttacagtttcacagccatggaactatagtttctcgactatgaaaataaagtttcacagctatgaaaccgcagtttcatagctgtgaaacttccatcggcctatagtcgatggttacgtactacccggaggat .........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 atcctccgggtagtacgtaaccatcgactataggccgatggaagtttcacagctatgaaactgcggtttcatagctgtgaaactttattttcatagtcgagaaactatagttccatggctgtgaaactgtaaccggcctgcactgcaagaaaattttgccgtacgggaaaaaatttgcttgtcgcaggagagtgtatatccctccttatagaagtttgaaaaatggggcgggttattcgattcgcataattcggattaaataaatacatttgcgagaaaagcgattgcc Mask Tandem Repeat Region ================================================ ggcaatcgcttttctcgcaaatgtatttatttaatccgaattatgcgaatcgaataacccgccccatttttcaaacttctataaggagggatatacactctcctgcgacaagcaaattttttcccgtacggcaaaattttcttgcagtgcaggccggttacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnccgcagtttcatagctgtgaaacttccatcggcctatagtcgatggttacgtactacccggaggat Find is-nt database================================================ Query_seq: PG2078:PG2079|PG2078:PG2079:hypothetical protein:hypothetical protein:<-<-:2178691..2178979 289 ggcaatcgcttttctcgcaaatgtatttatttaatccgaattatgcgaatcgaataacccgccccatttttcaaacttctataaggagggatatacactctcctgcgacaagcaaattttttcccgtacggcaaaattttcttgcagtgcaggccggttacagtttcacagccatggaactatagtttctcgactatgaaaataaagtttcacagctatgaaaccgcagtttcatagctgtgaaacttccatcggcctatagtcgatggttacgtactacccggaggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2078:PG2079|PG2078:PG2079:hypothetical protein:hypothetical protein:<-<-:2178691..2178979 289 ggcaatcgcttttctcgcaaatgtatttatttaatccgaattatgcgaatcgaataacccgccccatttttcaaacttctataaggagggatatacactctcctgcgacaagcaaattttttcccgtacggcaaaattttcttgcagtgcaggccggttacagtttcacagccatggaactatagtttctcgactatgaaaataaagtttcacagctatgaaaccgcagtttcatagctgtgaaacttccatcggcctatagtcgatggttacgtactacccggaggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2078:PG2079|PG2078:PG2079:hypothetical protein:hypothetical protein:<-<-:2178691..2178979 289 ggcaatcgcttttctcgcaaatgtatttatttaatccgaattatgcgaatcgaataacccgccccatttttcaaacttctataaggagggatatacactctcctgcgacaagcaaattttttcccgtacggcaaaattttcttgcagtgcaggccggttacagtttcacagccatggaactatagtttctcgactatgaaaataaagtttcacagctatgaaaccgcagtttcatagctgtgaaacttccatcggcctatagtcgatggttacgtactacccggaggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggcaatcgcttttctcgcaaatgtatttatttaatccgaattatgcgaatcgaataacccgccccatttttcaaacttctataaggagggatatacactctcctgcgacaagcaaattttttcccgtacggcaaaattttcttgcagtgcaggccggttacagtttcacagccatggaactatagtttctcgactatgaaaataaagtttcacagctatgaaaccgcagtttcatagctgtgaaacttccatcggcctatagtcgatggttacgtactacccggaggat Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 21 End: 182 .................... M Y L F N P N Y A N R I T R P I F Q T S I R R D I H S P A T S K F F P V R Q N F L A V Q A G Y S F T A M E L ........................................................................................................... Protein_Len: 48 Strand: + Start: 91 End: 234 .......................................................................................... M Y T L L R Q A N F F P Y G K I F L Q C R P V T V S Q P W N Y S F S T M K I K F H S Y E T A V S ....................................................... Protein_Len: 41 Strand: - Start: 30 End: 152 ............................. K I R I I R I S Y G A G N K L S R Y P P I Y V R R R C A F K K G Y P L I K K C H M ......................................................................................................................................... ggcaatcgcttttctcgcaaatgtatttatttaatccgaattatgcgaatcgaataacccgccccatttttcaaacttctataaggagggatatacactctcctgcgacaagcaaattttttcccgtacggcaaaattttcttgcagtgcaggccggttacagtttcacagccatggaactatagtttctcgactatgaaaataaagtttcacagctatgaaaccgcagtttcatagctgtgaaacttccatcggcctatagtcgatggttacgtactacccggaggat 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================================================ ggcaatcgcttttctcgcaaatgtatttatttaatccgaattatgcgaatcgaataacccgccccatttttcaaacttctataaggagggatatacactctcctgcgacaagcaaattttttcccgtacggcaaaattttcttgcagtgcaggccggttacagtttcacagccatggaactatagtttctcgactatgaaaataaagtttcacagctatgaaaccgcagtttcatagctgtgaaacttccatcggcctatagtcgatggttacgtactacccggaggat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -24.0 Tail_Score: -3.06501 Start: 207 End: 246 Full_Region: GACTATGAAAATAAA GTTTCACAGCTATGAAAC CGCA GTTTCATAGCTGTGAAAC TTCCATCGGCCTATA ..............................................................................................................................................................................................................GTTTCACAGCTATGAAACCGCAGTTTCATAGCTGTGAAAC........................................... TransTerm Strand: - Conf: 100 HP_score: -24.0 Tail_Score: -4.73614 Start: 207 End: 246 Full_Region: tataggccgatggaa gtttcacagctatgaaac tgcg gtttcatagctgtgaaac tttattttcatagtc ..............................................................................................................................................................................................................gtttcacagctatgaaactgcggtttcatagctgtgaaac........................................... TransTerm Strand: + Conf: 69 HP_score: -9.0 Tail_Score: -3.09516 Start: 249 End: 269 Full_Region: ATAGCTGTGAAACTT CCATCGGC CTATA GTCGATGG TTACGTACTACCCGG ........................................................................................................................................................................................................................................................CCATCGGCCTATAGTCGATGG.................... Find igs database================================================ Query_seq: PG2078:PG2079|PG2078:PG2079:hypothetical protein:hypothetical protein:<-<-:2178691..2178979 289 ggcaatcgcttttctcgcaaatgtatttatttaatccgaattatgcgaatcgaataacccgccccatttttcaaacttctataaggagggatatacactctcctgcgacaagcaaattttttcccgtacggcaaaattttcttgcagtgcaggccggttacagtttcacagccatggaactatagtttctcgactatgaaaataaagtttcacagctatgaaaccgcagtttcatagctgtgaaacttccatcggcctatagtcgatggttacgtactacccggaggat Intra-Species Hit: Count: 1 Min: 1 Max: 289 Len: 289 Subject: NC_002950_PG2078_PG2079|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2178691,2178979]|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 ggcaatcgcttttctcgcaaatgtatttatttaatccgaattatgcgaatcgaataacccgccccatttttcaaacttctataaggagggatatacactctcctgcgacaagcaaattttttcccgtacggcaaaattttcttgcagtgcaggccggttacagtttcacagccatggaactatagtttctcgactatgaaaataaagtttcacagctatgaaaccgcagtttcatagctgtgaaacttccatcggcctatagtcgatggttacgtactacccggaggat ggcaatcgcttttctcgcaaatgtatttatttaatccgaattatgcgaatcgaataacccgccccatttttcaaacttctataaggagggatatacactctcctgcgacaagcaaattttttcccgtacggcaaaattttcttgcagtgcaggccggttacagtttcacagccatggaactatagtttctcgactatgaaaataaagtttcacagctatgaaaccgcagtttcatagctgtgaaacttccatcggcctatagtcgatggttacgtactacccggaggat HSP 2 e-value: 1.0E-11 bit: 71.9 Len: 44 Query Start:205 Query End:248 Subject Strand: NEGATIVE Subject Start: 205 Subject End: 248 ............................................................................................................................................................................................................aagtttcacagctatgaaaccgcagtttcatagctgtgaaactt......................................... ............................................................................................................................................................................................................aagtttcacagctatgaaactgcggtttcatagctgtgaaactt......................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCAAUCGCUUUUCUCGCAAAUGUAUUUAUUUAAUCCGAAUUAUGCGAAUCGAAUAACCCGCCCCAUUUUUCAAACUUCUAUAAGGAGGGAUAUACACUCUCCUGCGACAAGCAAAUUUUUUCCCGUACGGCAAAAUUUUCUUGCAGUGCAGGCCGGUUACAGUUUCACAGCCAUGGAACUAUAGUUUCUCGACUAUGAAAAUAAAGUUUCACAGCUAUGAAACCGCAGUUUCAUAGCUGUGAAACUUCCAUCGGCCUAUAGUCGAUGGUUACGUACUACCCGGAGGAU (((..((((.....(((.(((((....)))))....))).....))))...((((((((.(((....................(((((((.......)))))))(((.((((.(((((((...((....)).))))))).))))...))).))).)))))....)))...)))..((...(((((((....)))))))......((((((((((((((((((((....))))))))))))))))))))((((((((.....))))))))...........))....... (-87.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCUCCGGGUAGUACGUAACCAUCGACUAUAGGCCGAUGGAAGUUUCACAGCUAUGAAACUGCGGUUUCAUAGCUGUGAAACUUUAUUUUCAUAGUCGAGAAACUAUAGUUCCAUGGCUGUGAAACUGUAACCGGCCUGCACUGCAAGAAAAUUUUGCCGUACGGGAAAAAAUUUGCUUGUCGCAGGAGAGUGUAUAUCCCUCCUUAUAGAAGUUUGAAAAAUGGGGCGGGUUAUUCGAUUCGCAUAAUUCGGAUUAAAUAAAUACAUUUGCGAGAAAAGCGAUUGCC .....((((....(((....((((((.(.....).)))))).(((((((((((((((.(((((..(((((.(..((((((((......))))))))..).)))))..))))).)))))))))))))))))).))))((((.((.((((((...)))))).)).)))).......((((((.((((((....((((((..(((.((((((.............)))))).))).((((..(((((.......)))))..)))).))))))))))))...))))))..... (-101.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 923 110 61 201 152 NC_002950:PG2078|5end_hypothetical_protein_2178600..2178830_NEGATIVE 421 247 206 179 138 NC_002950:PG1770|5end_hypothetical_protein_1857284..1857514_POSITIVE 385 157 111 203 146 NC_002950:PG1488|5end_hypothetical_protein_1561747..1561977_POSITIVE 359 164 125 73 20 NC_002950:PG1802|5end_hypothetical_protein_1895540..1895770_POSITIVE 356 176 141 227 189 NC_002950:PG0361|5end_hypothetical_protein_394094..394324_POSITIVE 353 170 124 65 18 NC_002950:PG1599|5end_hypothetical_protein_1679087..1679317_POSITIVE 344 189 141 58 10 NC_002950:PG1118|5end_clpB_protein_1194674..1194904_NEGATIVE 342 269 225 219 169 NC_002950:PG0963|5end_hypothetical_protein_1024332..1024562_NEGATIVE 337 189 142 88 39 NC_002950:PG2085|5end_tryptophanyl-tRNA_synthetase_2185532..2185762_POSITIVE 335 190 144 51 3 NC_002950:PG0909|5end_hypothetical_protein_973039..973269_NEGATIVE 329 130 88 79 29 NC_002950:PG1124|5end_ATP:cob(I)alamin_adenosyltransferase,_putative_1201036..1201266_NEGATIVE 328 185 141 100 36 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 325 177 131 228 163 NC_002950:PG2027|5end_hypothetical_protein_2125494..2125724_POSITIVE 325 277 238 220 182 NC_002950:PG1533|5end_Toprim_domain_protein_1613761..1613991_NEGATIVE 324 265 224 48 1 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 323 110 64 173 123 NC_002950:PG2073|5end_hypothetical_protein_2174374..2174604_NEGATIVE 323 110 64 173 123 NC_002950:PG1669|5end_hypothetical_protein_1755566..1755796_NEGATIVE 323 110 64 173 123 NC_002950:PG1264|5end_hypothetical_protein_1344895..1345125_NEGATIVE 323 110 64 173 123 NC_002950:PG0103|5end_hypothetical_protein_121290..121520_POSITIVE 322 175 141 91 48 NC_002950:PG0172|5end_exonuclease_193493..193723_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 164 125 69 16 NC_002950:PG1801|3end_v-type_ATPase,_subunit_E,_putative_1895616..1895766_POSITIVE 356 257 213 141 95 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 353 170 124 68 21 NC_002950:PG1598|3end_lipoprotein_signal_peptidase,_putative_1679170..1679320_POSITIVE 328 185 141 85 21 NC_002950:PG1246|3end_alanyl-tRNA_synthetase_1324509..1324659_POSITIVE 322 175 141 94 51 NC_002950:PG0171|3end_5'-nucleotidase_family_protein_193576..193726_POSITIVE 307 256 214 142 89 NC_002950:PG1943|3end_hypothetical_protein_2028974..2029124_NEGATIVE 307 189 141 86 30 NC_002950:PG1851|3end_phosphopantothenoylcysteine_decarboxylase/phosphopantothenate--cysteine_ligase_1949954..1950104_NEGATIVE 303 190 144 66 16 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 302 158 123 147 101 NC_002950:PG0758|3end_peptidyl-dipeptidase_Dcp_806467..806617_NEGATIVE 296 269 224 82 30 NC_002950:PG1733|3end_hypothetical_protein_1821186..1821336_NEGATIVE 296 190 141 62 11 NC_002950:PG1587|3end_PAP2_superfamily_protein_1665779..1665929_POSITIVE 293 131 98 45 5 NC_002950:PG1125|3end_hypothetical_protein_1201071..1201221_NEGATIVE 292 110 64 44 5 NC_002950:PG2074|3end_hypothetical_protein_2174503..2174653_NEGATIVE 292 260 215 150 90 NC_002950:PG2033|3end_glutamate_synthase,_small_subunit_2133415..2133565_NEGATIVE 292 168 128 118 85 NC_002950:PG1729|3end_thiol_peroxidase_1818342..1818492_NEGATIVE 292 110 64 44 5 NC_002950:PG1670|3end_hypothetical_protein_1755695..1755845_NEGATIVE 292 159 124 34 3 NC_002950:PG1663|3end_ABC_transporter,_ATP-binding_protein_1745868..1746018_POSITIVE 292 110 64 44 5 NC_002950:PG1265|3end_hypothetical_protein_1345024..1345174_NEGATIVE 292 110 64 44 5 NC_002950:PG0102|3end_hypothetical_protein_121241..121391_POSITIVE 291 162 123 49 5 NC_002950:PG1478|3end_conjugative_transposon_protein_TraK_1553493..1553643_NEGATIVE