Origin IGS: gtatttcttccgctttttttggaatactcattcgcatcgaaagctctacagagcctcaaggatgcggagaggattagtttgacacccgctcaaagctattttgctgagcgggtgttgcgctttctgcttgcagtccaataaacctgatgcccttaccggcgtctatctaagcataaacgacaaaaacacattagtcaaactttaagaaaacattgt .........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 acaatgttttcttaaagtttgactaatgtgtttttgtcgtttatgcttagatagacgccggtaagggcatcaggtttattggactgcaagcagaaagcgcaacacccgctcagcaaaatagctttgagcgggtgtcaaactaatcctctccgcatccttgaggctctgtagagctttcgatgcgaatgagtattccaaaaaaagcggaagaaatac Mask Tandem Repeat Region ================================================ gtatttcttccgctttttttggaatactcattcgcatcgaaagctctacagagcctcaaggatgcggagaggattagtttgacacccgctcaaagctattttgctgagcgggtgttgcgctttctgcttgcagtccaataaacctgatgcccttaccggcgtctatctaagcataaacgacaaaaacacattagtcaaactttaagaaaacattgt Find is-nt database================================================ Query_seq: PG0592:PG0593|PG0592:PG0593:50S ribosomal protein L31:htrA protein:->->:650286..650501 216 gtatttcttccgctttttttggaatactcattcgcatcgaaagctctacagagcctcaaggatgcggagaggattagtttgacacccgctcaaagctattttgctgagcgggtgttgcgctttctgcttgcagtccaataaacctgatgcccttaccggcgtctatctaagcataaacgacaaaaacacattagtcaaactttaagaaaacattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0592:PG0593|PG0592:PG0593:50S ribosomal protein L31:htrA protein:->->:650286..650501 216 gtatttcttccgctttttttggaatactcattcgcatcgaaagctctacagagcctcaaggatgcggagaggattagtttgacacccgctcaaagctattttgctgagcgggtgttgcgctttctgcttgcagtccaataaacctgatgcccttaccggcgtctatctaagcataaacgacaaaaacacattagtcaaactttaagaaaacattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0592:PG0593|PG0592:PG0593:50S ribosomal protein L31:htrA protein:->->:650286..650501 216 gtatttcttccgctttttttggaatactcattcgcatcgaaagctctacagagcctcaaggatgcggagaggattagtttgacacccgctcaaagctattttgctgagcgggtgttgcgctttctgcttgcagtccaataaacctgatgcccttaccggcgtctatctaagcataaacgacaaaaacacattagtcaaactttaagaaaacattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtatttcttccgctttttttggaatactcattcgcatcgaaagctctacagagcctcaaggatgcggagaggattagtttgacacccgctcaaagctattttgctgagcgggtgttgcgctttctgcttgcagtccaataaacctgatgcccttaccggcgtctatctaagcataaacgacaaaaacacattagtcaaactttaagaaaacattgt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 19 End: 138 .................. M E Y S F A S K A L Q S L K D A E R I S L T P A Q S Y F A E R V L R F L L A V Q .............................................................................. Protein_Len: 35 Strand: + Start: 98 End: 202 ................................................................................................. M L L S G C C A F C L Q S N K P D A L T G V Y L S I N D K N T L V K L .............. Protein_Len: 30 Strand: - Start: 77 End: 166 ............................................................................ N S V R E F S N Q Q A P T A S E A Q L G I F R I G K G A D M .................................................. Protein_Len: 30 Strand: - Start: 49 End: 138 ................................................ L A E L I R L P N T Q C G S L A I K S L P H Q A K Q K C D M .............................................................................. gtatttcttccgctttttttggaatactcattcgcatcgaaagctctacagagcctcaaggatgcggagaggattagtttgacacccgctcaaagctattttgctgagcgggtgttgcgctttctgcttgcagtccaataaacctgatgcccttaccggcgtctatctaagcataaacgacaaaaacacattagtcaaactttaagaaaacattgt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 170 End: 199 .........................................................................................................................................................................TTTGACTAATGTGTTTTTGTCGTTTATGCT................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtatttcttccgctttttttggaatactcattcgcatcgaaagctctacagagcctcaaggatgcggagaggattagtttgacacccgctcaaagctattttgctgagcgggtgttgcgctttctgcttgcagtccaataaacctgatgcccttaccggcgtctatctaagcataaacgacaaaaacacattagtcaaactttaagaaaacattgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 61 HP_score: -4.6 Tail_Score: -4.0616 Start: 77 End: 120 Full_Region: ATGCGGAGAGGATTA GTTTGACACCCGCTCA AAGCTATTTTGC TGAGCGGGTGTTGCGC TTTCTGCTTGCAGTC ............................................................................GTTTGACACCCGCTCAAAGCTATTTTGCTGAGCGGGTGTTGCGC................................................................................................ Find igs database================================================ Query_seq: PG0592:PG0593|PG0592:PG0593:50S ribosomal protein L31:htrA protein:->->:650286..650501 216 gtatttcttccgctttttttggaatactcattcgcatcgaaagctctacagagcctcaaggatgcggagaggattagtttgacacccgctcaaagctattttgctgagcgggtgttgcgctttctgcttgcagtccaataaacctgatgcccttaccggcgtctatctaagcataaacgacaaaaacacattagtcaaactttaagaaaacattgt Intra-Species Hit: Count: 1 Min: 21 Max: 216 Len: 196 Subject: NC_002950_PG0592_PG0593|50S ribosomal protein L31:htrA protein|POSITIVE:POSITIVE|[650286,650501]|216 HSP 1 e-value: 1.0E-107 bit: 389.0 Len: 196 Query Start:21 Query End:216 Subject Strand: POSITIVE Subject Start: 21 Subject End: 216 ....................ggaatactcattcgcatcgaaagctctacagagcctcaaggatgcggagaggattagtttgacacccgctcaaagctattttgctgagcgggtgttgcgctttctgcttgcagtccaataaacctgatgcccttaccggcgtctatctaagcataaacgacaaaaacacattagtcaaactttaagaaaacattgt ....................ggaatactcattcgcatcgaaagctctacagagcctcaaggatgcggagaggattagtttgacacccgctcaaagctattttgctgagcgggtgttgcgctttctgcttgcagtccaataaacctgatgcccttaccggcgtctatctaagcataaacgacaaaaacacattagtcaaactttaagaaaacattgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAUACUCAUUCGCAUCGAAAGCUCUACAGAGCCUCAAGGAUGCGGAGAGGAUUAGUUUGACACCCGCUCAAAGCUAUUUUGCUGAGCGGGUGUUGCGCUUUCUGCUUGCAGUCCAAUAAACCUGAUGCCCUUACCGGCGUCUAUCUAAGCAUAAACGACAAAAACACAUUAGUCAAACUUUAAGAAAACAUUGU ......(((.((((((((....((((....))))......)))))))))))....((((((((.((((((((..((......))))))))))..(((((.(((.((((((..((.......))..((((((......))))))....)))))).))))).)))..........))))))))............... (-60.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAUGUUUUCUUAAAGUUUGACUAAUGUGUUUUUGUCGUUUAUGCUUAGAUAGACGCCGGUAAGGGCAUCAGGUUUAUUGGACUGCAAGCAGAAAGCGCAACACCCGCUCAGCAAAAUAGCUUUGAGCGGGUGUCAAACUAAUCCUCUCCGCAUCCUUGAGGCUCUGUAGAGCUUUCGAUGCGAAUGAGUAUUCC ...............((((((((...(((((((((...(((..(((...((((((((((......))).....))))))).....)))))).)))))))))..(((((((((((......))..)))))))))))))))))....(((..((((((...(((((((....))))))).))))))...)))...... (-66.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 442 130 82 178 131 NC_002950:PG0700|5end_hypothetical_protein_756595..756825_NEGATIVE 401 114 73 159 118 NC_002950:PG1655|5end_hypothetical_protein_1737095..1737325_POSITIVE 375 140 92 124 66 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 374 140 91 114 69 NC_002950:PG0065|5end_efflux_transporter,_RND_family,_MFP_subunit_81187..81417_NEGATIVE 373 129 83 203 149 NC_002950:PG0660|5end_nitroreductase_family_protein_709695..709925_NEGATIVE 371 53 12 66 19 NC_002950:PG1304|5end_hypothetical_protein_1383474..1383704_NEGATIVE 369 108 66 77 33 NC_002950:PG1190|5end_glycerate_dehydrogenase_1272112..1272342_POSITIVE 363 110 63 97 42 NC_002950:PG1223|5end_hypothetical_protein_1299461..1299691_POSITIVE 363 69 23 193 151 NC_002950:PG0933|5end_translation_elongation_factor_G,_putative_989997..990227_POSITIVE 358 98 61 139 100 NC_002950:PG1695|5end_hypothetical_protein_1779440..1779670_POSITIVE 354 54 13 63 20 NC_002950:PG1701|5end_glutamine_amidotransferase,_class_II/dipeptidase_1787953..1788183_NEGATIVE 353 113 73 217 170 NC_002950:PG0694|5end_immunoreactive_42_kDa_antigen_PG33_750845..751075_NEGATIVE 346 108 65 137 87 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 346 110 63 204 153 NC_002950:PG0634|5end_ThiJ/PfpI_family_protein_686143..686373_POSITIVE 344 137 91 175 123 NC_002950:PG1922|5end_ribosomal_protein_L18_2017371..2017601_NEGATIVE 344 53 11 181 140 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 337 130 81 214 160 NC_002950:PG0412|5end_DNA_mismatch_repair_protein_MutL_451440..451670_NEGATIVE 336 107 66 193 147 NC_002950:PG2064|5end_hypothetical_protein_2160550..2160780_POSITIVE 336 70 25 203 156 NC_002950:PG0810|5end_hypothetical_protein_872567..872797_NEGATIVE 335 117 83 41 6 NC_002950:PG1365|5end_16S_rRNA-processing_protein_1446069..1446299_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 114 73 145 104 NC_002950:PG1654|3end_D-alanyl-D-alanine_dipeptidase_1737161..1737311_POSITIVE 363 116 74 85 35 NC_002950:PG0799|3end_hypothetical_protein_854599..854749_POSITIVE 362 110 63 65 15 NC_002950:PG1274|3end_elongation_factor_P_1352489..1352639_POSITIVE 357 129 87 144 96 NC_002950:PG0259|3end_hypothetical_protein_293701..293851_POSITIVE 354 54 13 70 27 NC_002950:PG1702|3end_DNA_gyrase,_B_subunit_1787946..1788096_NEGATIVE 350 140 91 139 78 NC_002950:PG0548|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_605759..605909_POSITIVE 347 104 61 145 102 NC_002950:PG0278|3end_hypothetical_protein_310477..310627_POSITIVE 345 48 7 60 20 NC_002950:PG0592|3end_50S_ribosomal_protein_L31_650225..650375_POSITIVE 335 110 63 65 15 NC_002950:PG0568|3end_elongation_factor_P_623999..624149_NEGATIVE 327 80 32 116 56 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 326 69 23 104 61 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 325 77 32 86 33 NC_002950:PG2102|3end_immunoreactive_61_kDa_antigen_PG91_2211424..2211574_NEGATIVE 325 49 9 51 1 NC_002950:PG2041|3end_hypothetical_protein_2139235..2139385_NEGATIVE 325 70 34 138 96 NC_002950:PG0127|3end_ferrochelatase_149667..149817_POSITIVE 323 90 41 145 72 NC_002950:PG0141|3end_spoOJ_protein_163878..164028_NEGATIVE 321 116 74 61 19 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 321 110 66 137 98 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 316 107 67 137 80 NC_002950:PG1977|3end_hypothetical_protein_2064687..2064837_NEGATIVE 316 116 74 83 35 NC_002950:PG1875|3end_hemolysin_1969647..1969797_NEGATIVE 314 140 94 50 7 NC_002950:PG1852|3end_exonuclease_1951194..1951344_NEGATIVE