Origin IGS: ttagttcatagaagctcaccccagtagaggtagcgagttttgctggggtgagtgtctatctgttattgtttagtcattacgacccaatagatgggtattatcaaaactccatattagat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atctaatatggagttttgataatacccatctattgggtcgtaatgactaaacaataacagatagacactcaccccagcaaaactcgctacctctactggggtgagcttctatgaactaa Mask Tandem Repeat Region ================================================ ttagttcatagaagctcaccccagtagaggtagcgagttttgctggggtgagtgtctatctgttattgtttagtcattacgacccaatagatgggtattatcaaaactccatattagat Find is-nt database================================================ Query_seq: PG0114:PG0115|PG0114:PG0115:hypothetical protein:hexapeptide transferase family protein:->->:138059..138177 119 ttagttcatagaagctcaccccagtagaggtagcgagttttgctggggtgagtgtctatctgttattgtttagtcattacgacccaatagatgggtattatcaaaactccatattagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0114:PG0115|PG0114:PG0115:hypothetical protein:hexapeptide transferase family protein:->->:138059..138177 119 ttagttcatagaagctcaccccagtagaggtagcgagttttgctggggtgagtgtctatctgttattgtttagtcattacgacccaatagatgggtattatcaaaactccatattagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0114:PG0115|PG0114:PG0115:hypothetical protein:hexapeptide transferase family protein:->->:138059..138177 119 ttagttcatagaagctcaccccagtagaggtagcgagttttgctggggtgagtgtctatctgttattgtttagtcattacgacccaatagatgggtattatcaaaactccatattagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttagttcatagaagctcaccccagtagaggtagcgagttttgctggggtgagtgtctatctgttattgtttagtcattacgacccaatagatgggtattatcaaaactccatattagat Predict ORF larger than 30AA ================================================ ttagttcatagaagctcaccccagtagaggtagcgagttttgctggggtgagtgtctatctgttattgtttagtcattacgacccaatagatgggtattatcaaaactccatattagat 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================================================ ttagttcatagaagctcaccccagtagaggtagcgagttttgctggggtgagtgtctatctgttattgtttagtcattacgacccaatagatgggtattatcaaaactccatattagat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -2.2 Tail_Score: -3.30243 Start: 81 End: 97 Full_Region: TTGTTTAGTCATTAC GACCCA ATAGA TGGGTA TTATCAAAACTCCAT ................................................................................GACCCAATAGATGGGTA...................... Find igs database================================================ Query_seq: PG0114:PG0115|PG0114:PG0115:hypothetical protein:hexapeptide transferase family protein:->->:138059..138177 119 ttagttcatagaagctcaccccagtagaggtagcgagttttgctggggtgagtgtctatctgttattgtttagtcattacgacccaatagatgggtattatcaaaactccatattagat Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_002950_PG0114_PG0115|hypothetical protein:hexapeptide transferase family protein|POSITIVE:POSITIVE|[138059,138177]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 ttagttcatagaagctcaccccagtagaggtagcgagttttgctggggtgagtgtctatctgttattgtttagtcattacgacccaatagatgggtattatcaaaactccatattagat ttagttcatagaagctcaccccagtagaggtagcgagttttgctggggtgagtgtctatctgttattgtttagtcattacgacccaatagatgggtattatcaaaactccatattagat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGUUCAUAGAAGCUCACCCCAGUAGAGGUAGCGAGUUUUGCUGGGGUGAGUGUCUAUCUGUUAUUGUUUAGUCAUUACGACCCAAUAGAUGGGUAUUAUCAAAACUCCAUAUUAGAU ........((((.((((((((((((((((.(....).)))))))))))))))).))))((((.(((.((((.(........(((((.....))))).....).))))...))).)))). (-39.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUAAUAUGGAGUUUUGAUAAUACCCAUCUAUUGGGUCGUAAUGACUAAACAAUAACAGAUAGACACUCACCCCAGCAAAACUCGCUACCUCUACUGGGGUGAGCUUCUAUGAACUAA ........((.((((...((...(((((.....))))).))...))))...)).......(((((..((((((((((..................))))))))))..)))))....... (-31.97) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 405 56 14 190 143 NC_002950:PG1162|5end_ATP:cob(I)alamin_adenosyltransferase,_putative_1242039..1242269_NEGATIVE 397 64 21 187 131 NC_002950:PG1242|5end_replicative_DNA_helicase_1317435..1317665_POSITIVE 385 60 14 92 32 NC_002950:PG0638|5end_tetraacyldisaccharide_4'-kinase_691183..691413_NEGATIVE 363 57 14 66 24 NC_002950:PG0680|5end_efflux_transporter,_MFP_component,_RND_family_730968..731198_POSITIVE 363 49 4 200 150 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 356 57 14 182 139 NC_002950:PG1069|5end_alcohol_dehydrogenase,_zinc-containing,_putative_1135499..1135729_POSITIVE 354 70 21 88 38 NC_002950:PG2187|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_2294643..2294873_NEGATIVE 344 48 3 125 86 NC_002950:PG0606|5end_hypothetical_protein_662558..662788_NEGATIVE 343 54 13 54 9 NC_002950:PG1169|5end_hypothetical_protein_1249181..1249411_NEGATIVE 336 56 14 216 175 NC_002950:PG1913|5end_30S_ribosomal_protein_S11_2012926..2013156_NEGATIVE 328 57 23 206 175 NC_002950:PG0486|5end_methylated-DNA--protein-cysteine_S-methyltransferase_525934..526164_NEGATIVE 325 55 14 50 8 NC_002950:PG0459|5end_ISPg5,_transposase_Orf1_501894..502124_NEGATIVE 321 48 10 201 150 NC_002950:PG0048|5end_conserved_hypothetical_protein_TIGR00092_60557..60787_NEGATIVE 317 87 42 138 96 NC_002950:PG2134|5end_lipoprotein,_putative_2239927..2240157_POSITIVE 315 59 26 145 107 NC_002950:PG1365|5end_16S_rRNA-processing_protein_1446069..1446299_NEGATIVE 314 48 8 133 88 NC_002950:PG1029|5end_hypothetical_protein_1091080..1091310_POSITIVE 313 68 21 103 51 NC_002950:PG0326|5end_hypothetical_protein_360974..361204_NEGATIVE 308 69 21 84 22 NC_002950:PG0980|5end_hypothetical_protein_1040897..1041127_POSITIVE 308 79 35 105 67 NC_002950:PG0170|5end_methionyl-tRNA_synthetase_189652..189882_POSITIVE 306 57 14 190 143 NC_002950:PG0861|5end_helicase,_SNF2/RAD54_family_919247..919477_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 474 59 13 83 34 NC_002950:PG0114|3end_hypothetical_protein_137998..138148_POSITIVE 390 46 6 149 116 NC_002950:PG1163|3end_cobyrinic_acid_a,c-diamide_synthase_1242062..1242212_NEGATIVE 385 60 14 62 2 NC_002950:PG0639|3end_signal_peptide_peptidase_SppA,_67K_type_691213..691363_NEGATIVE 375 62 21 150 96 NC_002950:PG1241|3end_GTP-binding_protein_LepA_1317480..1317630_POSITIVE 356 57 14 140 97 NC_002950:PG1068|3end_hypothetical_protein_1135537..1135687_POSITIVE 354 70 21 98 48 NC_002950:PG2188|3end_diaminopimelate_decarboxylase_2294633..2294783_NEGATIVE 339 49 5 146 97 NC_002950:PG1169|3end_hypothetical_protein_1249083..1249233_NEGATIVE 321 59 22 141 100 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 317 87 42 124 82 NC_002950:PG2133|3end_lipoprotein,_putative_2239993..2240143_POSITIVE 315 59 26 138 100 NC_002950:PG1366|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1446076..1446226_NEGATIVE 314 48 8 69 24 NC_002950:PG1028|3end_TPR_domain_protein_1091096..1091246_POSITIVE 308 69 21 97 35 NC_002950:PG0979|3end_hypothetical_protein_1040990..1041140_POSITIVE 306 57 14 136 89 NC_002950:PG0860|3end_transcriptional_regulator,_putative_919273..919423_POSITIVE 301 59 16 144 105 NC_002950:PG1949|3end_malate_dehydrogenase_2038184..2038334_NEGATIVE 300 69 27 82 31 NC_002950:PG2063|3end_hypothetical_protein_2160390..2160540_NEGATIVE 300 68 26 145 96 NC_002950:PG0365|3end_3'-5'_exonuclease_domain_protein_399612..399762_NEGATIVE 299 55 13 82 26 NC_002950:PG1236|3end_hypothetical_protein_1312312..1312462_POSITIVE 296 56 13 129 77 NC_002950:PG0896|3end_beta-galactosidase_960382..960532_POSITIVE 296 59 14 82 27 NC_002950:PG0564|3end_hypothetical_protein_621416..621566_NEGATIVE 294 60 14 61 8 NC_002950:PG0928|3end_response_regulator_985062..985212_NEGATIVE