Origin IGS: cgagtaaagaacaataaatagagagagggtatgcccatcgcggtgcataccctctcttgttttttattgtgacttagccgtatggaaaatcttcccgaactatctgccaaatctttttcgttcagttacgacagatgcgatcccgttctaaaagattgtaccgatccgaagagaaaaagacagaggcttggaggattacagacgaggctcga .........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 tcgagcctcgtctgtaatcctccaagcctctgtctttttctcttcggatcggtacaatcttttagaacgggatcgcatctgtcgtaactgaacgaaaaagatttggcagatagttcgggaagattttccatacggctaagtcacaataaaaaacaagagagggtatgcaccgcgatgggcataccctctctctatttattgttctttactcg Mask Tandem Repeat Region ================================================ cgagtaaagaacaataaatagagagagggtatgcccatcgcggtgcataccctctcttgttttttattgtgacttagccgtatggaaaatcttcccgaactatctgccaaatctttttcgttcagttacgacagatgcgatcccgttctaaaagattgtaccgatccgaagagaaaaagacagaggcttggaggattacagacgaggctcga Find is-nt database================================================ Query_seq: PG0308:PG0309|PG0308:PG0309:electron transport complex, RnfABCDGE type, A subunit:thiamine biosynthesis lipoprotein ApbE:-><-:343888..344099 212 cgagtaaagaacaataaatagagagagggtatgcccatcgcggtgcataccctctcttgttttttattgtgacttagccgtatggaaaatcttcccgaactatctgccaaatctttttcgttcagttacgacagatgcgatcccgttctaaaagattgtaccgatccgaagagaaaaagacagaggcttggaggattacagacgaggctcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0308:PG0309|PG0308:PG0309:electron transport complex, RnfABCDGE type, A subunit:thiamine biosynthesis lipoprotein ApbE:-><-:343888..344099 212 cgagtaaagaacaataaatagagagagggtatgcccatcgcggtgcataccctctcttgttttttattgtgacttagccgtatggaaaatcttcccgaactatctgccaaatctttttcgttcagttacgacagatgcgatcccgttctaaaagattgtaccgatccgaagagaaaaagacagaggcttggaggattacagacgaggctcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0308:PG0309|PG0308:PG0309:electron transport complex, RnfABCDGE type, A subunit:thiamine biosynthesis lipoprotein ApbE:-><-:343888..344099 212 cgagtaaagaacaataaatagagagagggtatgcccatcgcggtgcataccctctcttgttttttattgtgacttagccgtatggaaaatcttcccgaactatctgccaaatctttttcgttcagttacgacagatgcgatcccgttctaaaagattgtaccgatccgaagagaaaaagacagaggcttggaggattacagacgaggctcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgagtaaagaacaataaatagagagagggtatgcccatcgcggtgcataccctctcttgttttttattgtgacttagccgtatggaaaatcttcccgaactatctgccaaatctttttcgttcagttacgacagatgcgatcccgttctaaaagattgtaccgatccgaagagaaaaagacagaggcttggaggattacagacgaggctcga Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 14 End: 148 ............. M N R E R V C P S R C I P S L V F Y C D L A V W K I F P N Y L P N L F R S V T T D A I P F ................................................................ Protein_Len: 43 Strand: + Start: 82 End: 210 ................................................................................. M E N L P E L S A K S F S F S Y D R C D P V L K D C T D P K R K R Q R L G G L Q T R L .. Protein_Len: 37 Strand: + Start: 102 End: 212 ..................................................................................................... M C Q I F F V Q L R Q M R S R S K R L Y R S E E K K T E A W R I T D E A R Protein_Len: 41 Strand: - Start: 3 End: 125 .. T F F L L Y L S P I G M A T C V R E Q K K N H S L R I S F R G S S D A L D K E N M ....................................................................................... cgagtaaagaacaataaatagagagagggtatgcccatcgcggtgcataccctctcttgttttttattgtgacttagccgtatggaaaatcttcccgaactatctgccaaatctttttcgttcagttacgacagatgcgatcccgttctaaaagattgtaccgatccgaagagaaaaagacagaggcttggaggattacagacgaggctcga 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================================================ cgagtaaagaacaataaatagagagagggtatgcccatcgcggtgcataccctctcttgttttttattgtgacttagccgtatggaaaatcttcccgaactatctgccaaatctttttcgttcagttacgacagatgcgatcccgttctaaaagattgtaccgatccgaagagaaaaagacagaggcttggaggattacagacgaggctcga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -9.2 Tail_Score: -4.62803 Start: 19 End: 59 Full_Region: agtcacaataaaaaa caagagagggtatgcaccg cga tgggcataccctctctcta tttattgttctttac ..................caagagagggtatgcaccgcgatgggcataccctctctcta......................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -14.3 Tail_Score: -3.90009 Start: 21 End: 58 Full_Region: gtcacaataaaaaac aagagagggtatgcaccg cga tgggcataccctctctc tatttattgttcttt ....................aagagagggtatgcaccgcgatgggcataccctctctc.......................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -16.9 Tail_Score: -3.49969 Start: 23 End: 56 Full_Region: cacaataaaaaacaa gagagggtatgcaccg cga tgggcataccctctc tctatttattgttct ......................gagagggtatgcaccgcgatgggcataccctctc............................................................................................................................................................ Find igs database================================================ Query_seq: PG0308:PG0309|PG0308:PG0309:electron transport complex, RnfABCDGE type, A subunit:thiamine biosynthesis lipoprotein ApbE:-><-:343888..344099 212 cgagtaaagaacaataaatagagagagggtatgcccatcgcggtgcataccctctcttgttttttattgtgacttagccgtatggaaaatcttcccgaactatctgccaaatctttttcgttcagttacgacagatgcgatcccgttctaaaagattgtaccgatccgaagagaaaaagacagaggcttggaggattacagacgaggctcga Intra-Species Hit: Count: 1 Min: 1 Max: 212 Len: 212 Subject: NC_002950_PG0308_PG0309|electron transport complex, RnfABCDGE type, A subunit:thiamine biosynthesis lipoprotein ApbE|POSITIVE:NEGATIVE|[343888,344099]|212 HSP 1 e-value: 1.0E-117 bit: 420.0 Len: 212 Query Start:1 Query End:212 Subject Strand: POSITIVE Subject Start: 1 Subject End: 212 cgagtaaagaacaataaatagagagagggtatgcccatcgcggtgcataccctctcttgttttttattgtgacttagccgtatggaaaatcttcccgaactatctgccaaatctttttcgttcagttacgacagatgcgatcccgttctaaaagattgtaccgatccgaagagaaaaagacagaggcttggaggattacagacgaggctcga cgagtaaagaacaataaatagagagagggtatgcccatcgcggtgcataccctctcttgttttttattgtgacttagccgtatggaaaatcttcccgaactatctgccaaatctttttcgttcagttacgacagatgcgatcccgttctaaaagattgtaccgatccgaagagaaaaagacagaggcttggaggattacagacgaggctcga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAGUAAAGAACAAUAAAUAGAGAGAGGGUAUGCCCAUCGCGGUGCAUACCCUCUCUUGUUUUUUAUUGUGACUUAGCCGUAUGGAAAAUCUUCCCGAACUAUCUGCCAAAUCUUUUUCGUUCAGUUACGACAGAUGCGAUCCCGUUCUAAAAGAUUGUACCGAUCCGAAGAGAAAAAGACAGAGGCUUGGAGGAUUACAGACGAGGCUCGA (((((.(((.((((((((..((((((((((((((((.....)).))))))))))))))....))))))))..)))...(((.((...((((((((.((....)).(((...((((((((.(((.........(((.(((....))))))....(((((...))))).)))..))))))))....)))..)))))))).)).)))..))))). (-71.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGAGCCUCGUCUGUAAUCCUCCAAGCCUCUGUCUUUUUCUCUUCGGAUCGGUACAAUCUUUUAGAACGGGAUCGCAUCUGUCGUAACUGAACGAAAAAGAUUUGGCAGAUAGUUCGGGAAGAUUUUCCAUACGGCUAAGUCACAAUAAAAAACAAGAGAGGGUAUGCACCGCGAUGGGCAUACCCUCUCUCUAUUUAUUGUUCUUUACUCG .((((...................((((............((....))..((...(((((((..((((...(((((((((.((((......))))...))))...)).))).))))..)))))))..))....)))).....((((((((.....(((((((((((((.((.....)))))))))))))))...))))))))......)))) (-65.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 67 26 87 42 NC_002950:PG0448|5end_hypothetical_protein_488089..488319_POSITIVE 380 55 18 119 76 NC_002950:PG1130|5end_TPR_domain_protein_1208053..1208283_POSITIVE 375 196 162 188 158 NC_002950:PG1688|5end_transcription_elongation_factor_GreA_1774686..1774916_NEGATIVE 352 71 32 164 129 NC_002950:PG2142|5end_GTP-binding_protein_Era_2247585..2247815_POSITIVE 349 140 92 221 169 NC_002950:PG1003|5end_hypothetical_protein_1059232..1059462_POSITIVE 339 210 162 196 147 NC_002950:PG0952|5end_4-hydroxy-3-methylbut-2-en-1-yl_diphosphate_synthase_1010922..1011152_POSITIVE 327 210 161 74 28 NC_002950:PG0140|5end_hypothetical_protein_163858..164088_NEGATIVE 325 57 17 70 14 NC_002950:PG0452|5end_hypothetical_protein_492879..493109_POSITIVE 322 149 103 170 130 NC_002950:PG1978|5end_hypothetical_protein_2067337..2067567_NEGATIVE 321 60 21 155 100 NC_002950:PG0086|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_102359..102589_NEGATIVE 320 53 16 180 148 NC_002950:PG1727|5end_yitL_protein_1816709..1816939_POSITIVE 319 140 91 114 57 NC_002950:PG1799|5end_hypothetical_protein_1894499..1894729_POSITIVE 319 57 12 154 114 NC_002950:PG1509|5end_HAD-superfamily_hydrolase,_subfamily_IA,_variant_1_family_protein_1586691..1586921_POSITIVE 319 70 25 55 14 NC_002950:PG0685|5end_ABC_transporter,_ATP-binding_protein_740116..740346_POSITIVE 315 80 34 230 195 NC_002950:PG1034|5end_ABC_transporter,_ATP-binding_protein_1096163..1096393_POSITIVE 315 49 12 220 176 NC_002950:PG0172|5end_exonuclease_193493..193723_POSITIVE 314 60 18 213 167 NC_002950:PG1709|5end_ISPg5,_transposase_Orf1_1794914..1795144_POSITIVE 313 138 95 187 143 NC_002950:PG0312|5end_hypothetical_protein_347048..347278_NEGATIVE 311 65 21 187 139 NC_002950:PG0735|5end_aminotransferase,_class_V_784383..784613_POSITIVE 309 60 25 101 68 NC_002950:PG0608|5end_hypothetical_protein_662945..663175_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 623 57 11 69 21 NC_002950:PG0308|3end_electron_transport_complex,_RnfABCDGE_type,_A_subunit_343827..343977_POSITIVE 396 67 26 94 49 NC_002950:PG0447|3end_hypothetical_protein_488176..488326_POSITIVE 374 69 21 89 24 NC_002950:PG0618|3end_alkyl_hydroperoxide_reductase,_C_subunit_671018..671168_POSITIVE 361 58 18 54 1 NC_002950:PG1633|3end_galactokinase_1714619..1714769_POSITIVE 355 68 25 58 1 NC_002950:PG1634|3end_hypothetical_protein_1714723..1714873_NEGATIVE 352 71 32 85 50 NC_002950:PG2141|3end_3-oxoacyl-(acyl_carrier_protein)_synthase_2247586..2247736_POSITIVE 349 140 92 146 94 NC_002950:PG1002|3end_hypothetical_protein_1059237..1059387_POSITIVE 349 60 11 75 33 NC_002950:PG0232|3end_zinc_carboxypeptidase,_putative_267458..267608_NEGATIVE 338 59 11 63 14 NC_002950:PG0933|3end_translation_elongation_factor_G,_putative_992236..992386_POSITIVE 329 60 18 45 1 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 327 210 161 54 8 NC_002950:PG0141|3end_spoOJ_protein_163878..164028_NEGATIVE 319 57 12 71 31 NC_002950:PG1508|3end_hypothetical_protein_1586688..1586838_POSITIVE 311 65 21 128 80 NC_002950:PG0734|3end_nitroreductase_family_protein_784404..784554_POSITIVE 310 80 38 114 73 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE 309 60 25 70 37 NC_002950:PG0607|3end_hypothetical_protein_662994..663144_POSITIVE 308 69 22 59 17 NC_002950:PG0196|3end_peptidase,_M16_family_235808..235958_POSITIVE 305 57 13 62 9 NC_002950:PG1949|3end_malate_dehydrogenase_2038184..2038334_NEGATIVE 305 80 32 148 88 NC_002950:PG0412|3end_DNA_mismatch_repair_protein_MutL_449584..449734_NEGATIVE 305 60 20 51 6 NC_002950:PG0241|3end_lipoprotein,_putative_277360..277510_NEGATIVE 305 207 162 139 94 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE