Origin IGS: gcacactgagattgttcctttttagcctgtcctccaatgcttggatggacatggataaaggaataacagctttgtcagcattcagaataaaacgatatgagagggtggaccaaaacgcatagttttggctcaccctcttcggttgtccgggacaatcgacaaatacaatctccggaacagaagaaaaggagcacgagaacgtgcctccctgctcatagctcaagcacctttttcttacttttgtagggactaacaaggaagcgcaacccgccaag .........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 cttggcgggttgcgcttccttgttagtccctacaaaagtaagaaaaaggtgcttgagctatgagcagggaggcacgttctcgtgctccttttcttctgttccggagattgtatttgtcgattgtcccggacaaccgaagagggtgagccaaaactatgcgttttggtccaccctctcatatcgttttattctgaatgctgacaaagctgttattcctttatccatgtccatccaagcattggaggacaggctaaaaaggaacaatctcagtgtgc Mask Tandem Repeat Region ================================================ gcacactgagattgttcctttttagcctgtcctccaatgcttggatggacatggataaaggaataacagctttgtcagcattcagaataaaacgatatgagagggtggaccaaaacgcatagttttggctcaccctcttcggttgtccgggacaatcgacaaatacaatctccggaacagaagaaaaggagcacgagaacgtgcctccctgctcatagctcaagcacctttttcttacttttgtagggactaacaaggaagcgcaacccgccaag Find is-nt database================================================ Query_seq: PG0597:PG0598|PG0597:PG0598:ribosomal protein L9:hypothetical protein:->->:654342..654616 275 gcacactgagattgttcctttttagcctgtcctccaatgcttggatggacatggataaaggaataacagctttgtcagcattcagaataaaacgatatgagagggtggaccaaaacgcatagttttggctcaccctcttcggttgtccgggacaatcgacaaatacaatctccggaacagaagaaaaggagcacgagaacgtgcctccctgctcatagctcaagcacctttttcttacttttgtagggactaacaaggaagcgcaacccgccaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0597:PG0598|PG0597:PG0598:ribosomal protein L9:hypothetical protein:->->:654342..654616 275 gcacactgagattgttcctttttagcctgtcctccaatgcttggatggacatggataaaggaataacagctttgtcagcattcagaataaaacgatatgagagggtggaccaaaacgcatagttttggctcaccctcttcggttgtccgggacaatcgacaaatacaatctccggaacagaagaaaaggagcacgagaacgtgcctccctgctcatagctcaagcacctttttcttacttttgtagggactaacaaggaagcgcaacccgccaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0597:PG0598|PG0597:PG0598:ribosomal protein L9:hypothetical protein:->->:654342..654616 275 gcacactgagattgttcctttttagcctgtcctccaatgcttggatggacatggataaaggaataacagctttgtcagcattcagaataaaacgatatgagagggtggaccaaaacgcatagttttggctcaccctcttcggttgtccgggacaatcgacaaatacaatctccggaacagaagaaaaggagcacgagaacgtgcctccctgctcatagctcaagcacctttttcttacttttgtagggactaacaaggaagcgcaacccgccaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcacactgagattgttcctttttagcctgtcctccaatgcttggatggacatggataaaggaataacagctttgtcagcattcagaataaaacgatatgagagggtggaccaaaacgcatagttttggctcaccctcttcggttgtccgggacaatcgacaaatacaatctccggaacagaagaaaaggagcacgagaacgtgcctccctgctcatagctcaagcacctttttcttacttttgtagggactaacaaggaagcgcaacccgccaag Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 6 End: 119 ..... M R L F L F S L S S N A W M D M D K G I T A L S A F R I K R Y E R V D Q N A ............................................................................................................................................................ Protein_Len: 49 Strand: + Start: 97 End: 243 ................................................................................................ M R G W T K T H S F G S P S S V V R D N R Q I Q S P E Q K K R S T R T C L P A H S S S T F F L L L ................................ Protein_Len: 44 Strand: + Start: 119 End: 250 ...................................................................................................................... M V L A H P L R L S G T I D K Y N L R N R R K G A R E R A S L L I A Q A P F S Y F C R D ......................... Protein_Len: 39 Strand: - Start: 78 End: 194 ............................................................................. C E S Y F S I L P H V L V C L K P E G E E T T R S L R C I C D G S C F F L L M ................................................................................. Protein_Len: 60 Strand: - Start: 2 End: 274 . Y S L T S W F A Y N Q S V R K P Q G P C D V F V I E P V S S F S C S F T G G Q E Y S L C R K R V K T P V L L S A C G A M . gcacactgagattgttcctttttagcctgtcctccaatgcttggatggacatggataaaggaataacagctttgtcagcattcagaataaaacgatatgagagggtggaccaaaacgcatagttttggctcaccctcttcggttgtccgggacaatcgacaaatacaatctccggaacagaagaaaaggagcacgagaacgtgcctccctgctcatagctcaagcacctttttcttacttttgtagggactaacaaggaagcgcaacccgccaag 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================================================ gcacactgagattgttcctttttagcctgtcctccaatgcttggatggacatggataaaggaataacagctttgtcagcattcagaataaaacgatatgagagggtggaccaaaacgcatagttttggctcaccctcttcggttgtccgggacaatcgacaaatacaatctccggaacagaagaaaaggagcacgagaacgtgcctccctgctcatagctcaagcacctttttcttacttttgtagggactaacaaggaagcgcaacccgccaag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 69 HP_score: -2.6 Tail_Score: -4.79352 Start: 93 End: 145 Full_Region: gtcgattgtcccgga caaccgaagagggtgagccaaaac tatgc gttttggtccaccctctcatatcg ttttattctgaatgc ............................................................................................caaccgaagagggtgagccaaaactatgcgttttggtccaccctctcatatcg.................................................................................................................................. TransTerm Strand: - Conf: 45 HP_score: -2.9 Tail_Score: -3.29584 Start: 96 End: 142 Full_Region: gattgtcccggacaa ccgaagagggtgagccaaaac tatgc gttttggtccaccctctcata tcgttttattctgaa ...............................................................................................ccgaagagggtgagccaaaactatgcgttttggtccaccctctcata..................................................................................................................................... TransTerm Strand: + Conf: 65 HP_score: -8.4 Tail_Score: -3.28924 Start: 97 End: 142 Full_Region: TCAGAATAAAACGAT ATGAGAGGGTGGACCAAAAC GCATA GTTTTGGCTCACCCTCTTCGG TTGTCCGGGACAATC ................................................................................................ATGAGAGGGTGGACCAAAACGCATAGTTTTGGCTCACCCTCTTCGG..................................................................................................................................... TransTerm Strand: - Conf: 71 HP_score: -9.9 Tail_Score: -3.2024 Start: 98 End: 140 Full_Region: ttgtcccggacaacc gaagagggtgagccaaaac tatgc gttttggtccaccctctca tatcgttttattctg .................................................................................................gaagagggtgagccaaaactatgcgttttggtccaccctctca....................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -16.0 Tail_Score: -3.23274 Start: 101 End: 137 Full_Region: AATAAAACGATATGA GAGGGTGGACCAAAAC GCATA GTTTTGGCTCACCCTC TTCGGTTGTCCGGGA ....................................................................................................GAGGGTGGACCAAAACGCATAGTTTTGGCTCACCCTC.......................................................................................................................................... TransTerm Strand: - Conf: 93 HP_score: -16.0 Tail_Score: -2.77512 Start: 101 End: 137 Full_Region: tcccggacaaccgaa gagggtgagccaaaac tatgc gttttggtccaccctc tcatatcgttttatt ....................................................................................................gagggtgagccaaaactatgcgttttggtccaccctc.......................................................................................................................................... TransTerm Strand: - Conf: 79 HP_score: -12.8 Tail_Score: -2.91796 Start: 103 End: 135 Full_Region: ccggacaaccgaaga gggtgagccaaaac tatgc gttttggtccaccc tctcatatcgtttta ......................................................................................................gggtgagccaaaactatgcgttttggtccaccc............................................................................................................................................ TransTerm Strand: - Conf: 84 HP_score: -7.6 Tail_Score: -4.90381 Start: 188 End: 208 Full_Region: ttgagctatgagcag ggaggcacg ttct cgtgctcc ttttcttctgttccg ...........................................................................................................................................................................................ggaggcacgttctcgtgctcc................................................................... Find igs database================================================ Query_seq: PG0597:PG0598|PG0597:PG0598:ribosomal protein L9:hypothetical protein:->->:654342..654616 275 gcacactgagattgttcctttttagcctgtcctccaatgcttggatggacatggataaaggaataacagctttgtcagcattcagaataaaacgatatgagagggtggaccaaaacgcatagttttggctcaccctcttcggttgtccgggacaatcgacaaatacaatctccggaacagaagaaaaggagcacgagaacgtgcctccctgctcatagctcaagcacctttttcttacttttgtagggactaacaaggaagcgcaacccgccaag Intra-Species Hit: Count: 1 Min: 1 Max: 275 Len: 275 Subject: NC_002950_PG0597_PG0598|ribosomal protein L9:hypothetical protein|POSITIVE:POSITIVE|[654342,654616]|275 HSP 1 e-value: 1.0E-154 bit: 545.0 Len: 275 Query Start:1 Query End:275 Subject Strand: POSITIVE Subject Start: 1 Subject End: 275 gcacactgagattgttcctttttagcctgtcctccaatgcttggatggacatggataaaggaataacagctttgtcagcattcagaataaaacgatatgagagggtggaccaaaacgcatagttttggctcaccctcttcggttgtccgggacaatcgacaaatacaatctccggaacagaagaaaaggagcacgagaacgtgcctccctgctcatagctcaagcacctttttcttacttttgtagggactaacaaggaagcgcaacccgccaag gcacactgagattgttcctttttagcctgtcctccaatgcttggatggacatggataaaggaataacagctttgtcagcattcagaataaaacgatatgagagggtggaccaaaacgcatagttttggctcaccctcttcggttgtccgggacaatcgacaaatacaatctccggaacagaagaaaaggagcacgagaacgtgcctccctgctcatagctcaagcacctttttcttacttttgtagggactaacaaggaagcgcaacccgccaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCACACUGAGAUUGUUCCUUUUUAGCCUGUCCUCCAAUGCUUGGAUGGACAUGGAUAAAGGAAUAACAGCUUUGUCAGCAUUCAGAAUAAAACGAUAUGAGAGGGUGGACCAAAACGCAUAGUUUUGGCUCACCCUCUUCGGUUGUCCGGGACAAUCGACAAAUACAAUCUCCGGAACAGAAGAAAAGGAGCACGAGAACGUGCCUCCCUGCUCAUAGCUCAAGCACCUUUUUCUUACUUUUGUAGGGACUAACAAGGAAGCGCAACCCGCCAAG .....(((((.((((((((((....(((((((((((.....)))).))))).))..))))))))))..(((.....))).)))))........(((...((((((((..(((((((.....)))))))..))))))))(((((((((...)))))))))........)))..(((............((((((((....)))).)))).(((.(...((....)).((((.(((((((....))))))).....))))..).)))..)))..... (-92.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGGCGGGUUGCGCUUCCUUGUUAGUCCCUACAAAAGUAAGAAAAAGGUGCUUGAGCUAUGAGCAGGGAGGCACGUUCUCGUGCUCCUUUUCUUCUGUUCCGGAGAUUGUAUUUGUCGAUUGUCCCGGACAACCGAAGAGGGUGAGCCAAAACUAUGCGUUUUGGUCCACCCUCUCAUAUCGUUUUAUUCUGAAUGCUGACAAAGCUGUUAUUCCUUUAUCCAUGUCCAUCCAAGCAUUGGAGGACAGGCUAAAAAGGAACAAUCUCAGUGUGC ..((((.....((((((..((.(((.(.........).))).))..))))))....)))).((((((((((.((((....)))))))).......))))))..((((((((.((((((..(((((...)))))..((.(((((((..(((((((.....)))))))..)))))))))....(((((......)))))..))))))........((((((..((.(((((.((((.....)))))))))))....))))))))))))))....... (-90.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 377 159 116 201 151 NC_002950:PG0159|5end_endopeptidase_PepO_183164..183394_NEGATIVE 376 80 31 155 101 NC_002950:PG1936|5end_ribosomal_protein_L23_2023492..2023722_NEGATIVE 373 159 116 198 162 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 370 213 171 71 19 NC_002950:PG0309|5end_thiamine_biosynthesis_lipoprotein_ApbE_345023..345253_NEGATIVE 361 150 102 132 84 NC_002950:PG0724|5end_prolyl_oligopeptidase_family_protein_775229..775459_POSITIVE 359 150 101 222 163 NC_002950:PG2111|5end_thiS_protein_2221482..2221712_NEGATIVE 359 250 204 63 11 NC_002950:PG1212|5end_TPR_domain_protein_1291392..1291622_POSITIVE 349 220 173 171 120 NC_002950:PG1163|5end_cobyrinic_acid_a,c-diamide_synthase_1243381..1243611_NEGATIVE 346 219 174 183 138 NC_002950:PG1696|5end_type_II_DNA_modification_methyltransferase,_putative_1779973..1780203_POSITIVE 342 230 187 177 141 NC_002950:PG0882|5end_hypothetical_protein_944195..944425_POSITIVE 338 159 127 188 151 NC_002950:PG1285|5end_glucosamine-6-phosphate_deaminase_1362894..1363124_POSITIVE 337 175 132 194 153 NC_002950:PG1633|5end_galactokinase_1713385..1713615_POSITIVE 335 175 137 66 21 NC_002950:PG1562|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_1641582..1641812_NEGATIVE 335 219 174 67 27 NC_002950:PG1035|5end_hypothetical_protein_1096875..1097105_POSITIVE 334 139 94 176 123 NC_002950:PG1281|5end_hypothetical_protein_1358848..1359078_POSITIVE 328 214 171 112 72 NC_002950:PG1273|5end_hypothetical_protein_1351837..1352067_NEGATIVE 327 53 25 68 39 NC_002950:PG2225|5end_hypothetical_protein_2339440..2339670_POSITIVE 327 250 203 143 87 NC_002950:PG1899|5end_TonB-dependent_receptor,_putative_1999724..1999954_NEGATIVE 327 150 105 59 4 NC_002950:PG0446|5end_thiF_protein_486599..486829_POSITIVE 325 149 101 56 2 NC_002950:PG1851|5end_phosphopantothenoylcysteine_decarboxylase/phosphopantothenate--cysteine_ligase_1951168..1951398_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 442 149 101 64 21 NC_002950:PG1414|3end_hypothetical_protein_1499704..1499854_POSITIVE 400 220 173 74 24 NC_002950:PG1797|3end_DNA-binding_response_regulator/sensor_histidine_kinase_1892978..1893128_POSITIVE 398 228 181 85 43 NC_002950:PG0799|3end_hypothetical_protein_854599..854749_POSITIVE 390 150 101 82 30 NC_002950:PG1226|3end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1304048..1304198_POSITIVE 378 80 31 100 43 NC_002950:PG0597|3end_ribosomal_protein_L9_654281..654431_POSITIVE 376 80 31 140 86 NC_002950:PG1937|3end_50S_ribosomal_protein_L4_2023507..2023657_NEGATIVE 370 213 171 74 22 NC_002950:PG0310|3end_nitroreductase_family_protein_345020..345170_NEGATIVE 366 150 101 70 5 NC_002950:PG0537|3end_aminoacyl-histidine_dipeptidase_588394..588544_POSITIVE 365 139 91 48 2 NC_002950:PG0241|3end_lipoprotein,_putative_277360..277510_NEGATIVE 355 138 94 58 11 NC_002950:PG1910|3end_ribosomal_protein_L17_2010282..2010432_NEGATIVE 352 213 171 65 18 NC_002950:PG1630|3end_hypothetical_protein_1712142..1712292_POSITIVE 350 139 91 64 20 NC_002950:PG1004|3end_prolyl_oligopeptidase_family_protein_1060433..1060583_NEGATIVE 349 249 203 142 89 NC_002950:PG0198|3end_hypothetical_protein_237501..237651_POSITIVE 347 143 101 58 20 NC_002950:PG0553|3end_extracellular_protease,_putative_608367..608517_NEGATIVE 342 230 187 67 31 NC_002950:PG0881|3end_recombinase_A_944165..944315_POSITIVE 342 150 101 65 13 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 337 175 132 144 103 NC_002950:PG1632|3end_aldose_1-epimerase_1713415..1713565_POSITIVE 335 175 137 51 6 NC_002950:PG1563|3end_glucose-1-phosphate_thymidylyltransferase_1641597..1641747_NEGATIVE 335 219 174 89 49 NC_002950:PG1034|3end_ABC_transporter,_ATP-binding_protein_1096977..1097127_POSITIVE 332 150 101 57 10 NC_002950:PG0712|3end_hypothetical_protein_766784..766934_NEGATIVE