Origin IGS: ttccttttggggttaaaagtgtaattaatgttctataacggcgcaaatatacagtttcttttggtaccaccaaaaaaaacgaccaaatgctgtttgcattgagcccttttatccggaagccttacgcatggctattccttttacagacgggggcacccgatcttgcgcaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgcgcaagatcgggtgcccccgtctgtaaaaggaatagccatgcgtaaggcttccggataaaagggctcaatgcaaacagcatttggtcgttttttttggtggtaccaaaagaaactgtatatttgcgccgttatagaacattaattacacttttaaccccaaaaggaa Mask Tandem Repeat Region ================================================ ttccttttggggttaaaagtgtaattaatgttctataacggcgcaaatatacagtttcttttggtaccaccaaaaaaaacgaccaaatgctgtttgcattgagcccttttatccggaagccttacgcatggctattccttttacagacgggggcacccgatcttgcgcaa Find is-nt database================================================ Query_seq: PG1828:PG1829|PG1828:PG1829:lipoprotein, putative:long-chain-fatty-acid--CoA ligase, putative:<-<-:1921227..1921396 170 ttccttttggggttaaaagtgtaattaatgttctataacggcgcaaatatacagtttcttttggtaccaccaaaaaaaacgaccaaatgctgtttgcattgagcccttttatccggaagccttacgcatggctattccttttacagacgggggcacccgatcttgcgcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1828:PG1829|PG1828:PG1829:lipoprotein, putative:long-chain-fatty-acid--CoA ligase, putative:<-<-:1921227..1921396 170 ttccttttggggttaaaagtgtaattaatgttctataacggcgcaaatatacagtttcttttggtaccaccaaaaaaaacgaccaaatgctgtttgcattgagcccttttatccggaagccttacgcatggctattccttttacagacgggggcacccgatcttgcgcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1828:PG1829|PG1828:PG1829:lipoprotein, putative:long-chain-fatty-acid--CoA ligase, putative:<-<-:1921227..1921396 170 ttccttttggggttaaaagtgtaattaatgttctataacggcgcaaatatacagtttcttttggtaccaccaaaaaaaacgaccaaatgctgtttgcattgagcccttttatccggaagccttacgcatggctattccttttacagacgggggcacccgatcttgcgcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttccttttggggttaaaagtgtaattaatgttctataacggcgcaaatatacagtttcttttggtaccaccaaaaaaaacgaccaaatgctgtttgcattgagcccttttatccggaagccttacgcatggctattccttttacagacgggggcacccgatcttgcgcaa Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 35 End: 169 .................................. M T A Q I Y S F F W Y H Q K K R P N A V C I E P F Y P E A L R M A I P F T D G G T R S C A . Protein_Len: 37 Strand: - Start: 2 End: 112 . G K P T L L T I L T R Y R R L Y V T E K P V V L F F S W I S N A N L G K M .......................................................... ttccttttggggttaaaagtgtaattaatgttctataacggcgcaaatatacagtttcttttggtaccaccaaaaaaaacgaccaaatgctgtttgcattgagcccttttatccggaagccttacgcatggctattccttttacagacgggggcacccgatcttgcgcaa 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================================================ ttccttttggggttaaaagtgtaattaatgttctataacggcgcaaatatacagtttcttttggtaccaccaaaaaaaacgaccaaatgctgtttgcattgagcccttttatccggaagccttacgcatggctattccttttacagacgggggcacccgatcttgcgcaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -8.1 Tail_Score: -3.24976 Start: 52 End: 81 Full_Region: caaacagcatttggt cgttttttttggt ggt accaaaagaaactg tatatttgcgccgtt ...................................................cgttttttttggtggtaccaaaagaaactg......................................................................................... TransTerm Strand: - Conf: 83 HP_score: -11.8 Tail_Score: -3.18571 Start: 54 End: 80 Full_Region: aaacagcatttggtc gttttttttggt ggt accaaaagaaac tgtatatttgcgccg .....................................................gttttttttggtggtaccaaaagaaac.......................................................................................... TransTerm Strand: - Conf: 55 HP_score: -2.8 Tail_Score: -4.11456 Start: 81 End: 105 Full_Region: gcttccggataaaag ggctcaatgc aaaca gcatttggtc gttttttttggtggt ................................................................................ggctcaatgcaaacagcatttggtc................................................................. Find igs database================================================ Query_seq: PG1828:PG1829|PG1828:PG1829:lipoprotein, putative:long-chain-fatty-acid--CoA ligase, putative:<-<-:1921227..1921396 170 ttccttttggggttaaaagtgtaattaatgttctataacggcgcaaatatacagtttcttttggtaccaccaaaaaaaacgaccaaatgctgtttgcattgagcccttttatccggaagccttacgcatggctattccttttacagacgggggcacccgatcttgcgcaa Intra-Species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: NC_002950_PG1828_PG1829|lipoprotein, putative:long-chain-fatty-acid--CoA ligase, putative|NEGATIVE:NEGATIVE|[1921227,1921396]|170 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 ttccttttggggttaaaagtgtaattaatgttctataacggcgcaaatatacagtttcttttggtaccaccnnnnnnnncgaccaaatgctgtttgcattgagcccttttatccggaagccttacgcatggctattccttttacagacgggggcacccgatcttgcgcaa ttccttttggggttaaaagtgtaattaatgttctataacggcgcaaatatacagtttcttttggtaccaccaaaaaaaacgaccaaatgctgtttgcattgagcccttttatccggaagccttacgcatggctattccttttacagacgggggcacccgatcttgcgcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUUUUGGGGUUAAAAGUGUAAUUAAUGUUCUAUAACGGCGCAAAUAUACAGUUUCUUUUGGUACCACCAAAAAAAACGACCAAAUGCUGUUUGCAUUGAGCCCUUUUAUCCGGAAGCCUUACGCAUGGCUAUUCCUUUUACAGACGGGGGCACCCGAUCUUGCGCAA ...((((((((..((((((.((..(((((((.....(((((((..........((((.((((((.....)))))).)))).......))))))).))))))))).)))))))))))))).....((((.((.....))......(((((((....)))).)))))))... (-43.23) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCGCAAGAUCGGGUGCCCCCGUCUGUAAAAGGAAUAGCCAUGCGUAAGGCUUCCGGAUAAAAGGGCUCAAUGCAAACAGCAUUUGGUCGUUUUUUUUGGUGGUACCAAAAGAAACUGUAUAUUUGCGCCGUUAUAGAACAUUAAUUACACUUUUAACCCCAAAAGGAA .(((((.(((.((((....)))))))......((.....))..))))).(((...((((((....((((.(((((.....))))).))))(((((((((((.....)))))))))))....)))))).)))....................(((((......)))))... (-43.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 961 130 81 221 172 NC_002950:PG1828|5end_lipoprotein,_putative_1921136..1921366_NEGATIVE 382 167 125 179 139 NC_002950:PG1760|5end_ABC_transporter,_ATP-binding_protein_1846507..1846737_POSITIVE 376 167 121 67 8 NC_002950:PG1692|5end_ABC_transporter,_ATP-binding_protein_1777173..1777403_NEGATIVE 364 155 112 68 24 NC_002950:PG0699|5end_maltodextrin_phosphorylase_755958..756188_NEGATIVE 356 159 111 58 2 NC_002950:PG0658|5end_phosphatase,_YrbI_family_708319..708549_NEGATIVE 349 160 111 79 23 NC_002950:PG0425|5end_esterase,_putative_463989..464219_NEGATIVE 348 166 126 75 21 NC_002950:PG0506|5end_arginine-specific_cysteine_proteinase_545335..545565_POSITIVE 345 160 113 206 157 NC_002950:PG0678|5end_pyrazinamidase/nicotinamidase,_putative_728879..729109_POSITIVE 343 167 126 180 134 NC_002950:PG1342|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_1422585..1422815_POSITIVE 340 128 83 200 147 NC_002950:PG0271|5end_single-stranded_binding_protein_303842..304072_POSITIVE 331 139 106 68 36 NC_002950:PG1781|5end_uridine_kinase_1870023..1870253_POSITIVE 330 169 125 183 132 NC_002950:PG0172|5end_exonuclease_193493..193723_POSITIVE 329 157 112 65 10 NC_002950:PG0777|5end_electron_transfer_flavoprotein,_beta_subunit_831059..831289_NEGATIVE 328 160 111 72 19 NC_002950:PG0791|5end_adenylate_kinase_843177..843407_NEGATIVE 326 159 113 228 177 NC_002950:PG2101|5end_hypothetical_protein_2211273..2211503_NEGATIVE 325 169 125 174 129 NC_002950:PG0899|5end_cytochrome_d_ubiquinol_oxidase,_subunit_II_964660..964890_NEGATIVE 321 160 118 216 165 NC_002950:PG1159|5end_cobalamin_biosynthesis_protein_CbiB_1238967..1239197_NEGATIVE 321 135 91 180 134 NC_002950:PG1069|5end_alcohol_dehydrogenase,_zinc-containing,_putative_1135499..1135729_POSITIVE 319 167 121 170 119 NC_002950:PG1024|5end_hypothetical_protein_1086698..1086928_POSITIVE 317 168 121 52 2 NC_002950:PG0120|5end_UDP-N-acetylglucosamine_2-epimerase_143004..143234_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 167 121 70 11 NC_002950:PG1693|3end_HesA/MoeB/ThiF_family_protein_1777170..1777320_NEGATIVE 348 166 126 57 3 NC_002950:PG0505|3end_hypothetical_protein_545397..545547_POSITIVE 344 139 92 139 96 NC_002950:PG0926|3end_hypothetical_protein_984407..984557_NEGATIVE 340 128 83 149 96 NC_002950:PG0270|3end_redox-sensitive_transcriptional_activator_OxyR_303871..304021_POSITIVE 337 168 126 48 1 NC_002950:PG1681|3end_glycogen_debranching_enzyme,_archaeal_type,_putative_1768468..1768618_POSITIVE 336 159 114 107 37 NC_002950:PG1472|3end_hypothetical_protein_1549760..1549910_POSITIVE 335 155 112 108 57 NC_002950:PG1811|3end_hypothetical_protein_1906975..1907125_POSITIVE 328 159 111 64 8 NC_002950:PG1416|3end_enoyl-(acyl-carrier-protein)_reductase_II_1501078..1501228_POSITIVE 328 160 111 71 18 NC_002950:PG0792|3end_hypoxanthine_phosphoribosyltransferase_843178..843328_NEGATIVE 326 159 113 77 26 NC_002950:PG2102|3end_immunoreactive_61_kDa_antigen_PG91_2211424..2211574_NEGATIVE 325 169 125 128 83 NC_002950:PG0900|3end_cytochrome_d_ubiquinol_oxidase,_subunit_I_964706..964856_NEGATIVE 321 135 91 138 92 NC_002950:PG1068|3end_hypothetical_protein_1135537..1135687_POSITIVE 315 154 115 114 67 NC_002950:PG0814|3end_hypothetical_protein_875904..876054_NEGATIVE 311 159 112 148 98 NC_002950:PG1657|3end_methylmalonyl-CoA_mutase_1741571..1741721_POSITIVE 308 154 113 89 45 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 298 157 113 130 73 NC_002950:PG1375|3end_hypothetical_protein_1456743..1456893_POSITIVE 297 160 116 38 1 NC_002950:PG1217|3end_hypothetical_protein_1295987..1296137_POSITIVE 297 157 112 119 68 NC_002950:PG0404|3end_hypothetical_protein_439768..439918_NEGATIVE 297 168 124 145 98 NC_002950:PG0200|3end_hypothetical_protein_238121..238271_NEGATIVE 296 153 113 73 21 NC_002950:PG1597|3end_DnaK_suppressor_protein,_putative_1678486..1678636_POSITIVE