Origin IGS: aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt Mask Tandem Repeat Region ================================================ aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Find is-nt database================================================ Query_seq: PG0822:PG0823|PG0822:PG0823:hypothetical protein:hypothetical protein:<-->:880826..880957 132 aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0822:PG0823|PG0822:PG0823:hypothetical protein:hypothetical protein:<-->:880826..880957 132 aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0822:PG0823|PG0822:PG0823:hypothetical protein:hypothetical protein:<-->:880826..880957 132 aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 35 End: 130 .................................. M I P L H Y N T Q V H T K M Y D T H Y I V S F T E Y Q Q E K S S .. Protein_Len: 39 Strand: + Start: 15 End: 131 .............. M V E I T A K L Y L C T T I H K Y I Q K C M I H T I L L V L L N I N K K K V R . Protein_Len: 35 Strand: - Start: 14 End: 118 ............. I T S I V A F N Y R Q V V I C L Y M C F H I I C V I N N T K S F I L M .............. aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct 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: 83 Start: 87 End: 116 ......................................................................................GTTGATATTCAGTAAAACTAACAATATAGT................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0822:PG0823|PG0822:PG0823:hypothetical protein:hypothetical protein:<-->:880826..880957 132 aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Intra-Species Hit: Count: 2 Min: 1 Max: 132 Len: 132 Subject: NC_002950_PG1450_PG1451|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1534705,1534836]|132 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 132 aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Subject: NC_002950_PG0822_PG0823|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[880826,880957]|132 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Inter-species Hit: Count: 2 Min: 1 Max: 132 Len: 132 Subject: pint_PI0391_PI0392|conserved hypothetical protein:possible transcriptional regulator|POSITIVE:POSITIVE|[358277,358483]|207 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 76 Subject End: 207 aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Subject: tfor_TF0914_TF0915|conserved hypothetical protein; possible ketosteroid isomerase-related protein:possible transcriptional regulator|POSITIVE:POSITIVE|[955874,956006]|133 HSP 1 e-value: 2.0E-14 bit: 79.8 Len: 124 Query Start:5 Query End:128 Subject Strand: POSITIVE Subject Start: 6 Subject End: 129 ....tgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagtt.... ....tgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtt.... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUGUAUUUUAAAUUGUUGAAAUCACUGCAAAAUUAUACCUUUGCACUACAAUACACAAGUACAUACAAAAAUGUAUGAUACACACUAUAUUGUUAGUUUUACUGAAUAUCAACAAGAAAAAAGUUCGCU ........((((...(((((((..(((..(((((........))))).((((((((.....(((((((((....)))))).)))......))))).)))......)))...))))))).))))......... (-21.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGAACUUUUUUCUUGUUGAUAUUCAGUAAAACUAACAAUAUAGUGUGUAUCAUACAUUUUUGUAUGUACUUGUGUAUUGUAGUGCAAAGGUAUAAUUUUGCAGUGAUUUCAACAAUUUAAAAUACAUUUU ..............(((((((...(((.....((((.(((((((....(((.((((((....)))))))))...)))))))))))((((((......))))))..)))..)))))))............... (-29.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 784 90 41 181 132 NC_002950:PG1451|5end_hypothetical_protein_1534697..1534927_POSITIVE 784 90 41 181 132 NC_002950:PG0822|5end_hypothetical_protein_880735..880965_NEGATIVE 230 57 17 162 111 NC_002950:PG1019|5end_lipoprotein,_putative_1079215..1079445_POSITIVE 224 48 16 180 152 NC_002950:PG0047|5end_cell_division_protein_FtsH,_putative_59250..59480_NEGATIVE 209 83 42 181 133 NC_002950:PG1101|5end_sodium:solute_symporter_family_protein_1170469..1170699_NEGATIVE 206 70 30 90 50 NC_002950:PG1527|5end_hypothetical_protein_1605794..1606024_NEGATIVE 184 120 76 196 155 NC_002950:PG0043|5end_beta-hexosaminidase_51066..51296_POSITIVE 180 79 40 174 134 NC_002950:PG0035|5end_DNA_polymerase_III,_alpha_subunit_46284..46514_NEGATIVE 179 43 5 187 151 NC_002950:PG0780|5end_hypothetical_protein_833203..833433_NEGATIVE 175 48 6 49 4 NC_002950:PG1813|5end_ferredoxin,_4Fe-4S_1908374..1908604_NEGATIVE 174 60 17 82 32 NC_002950:PG1109|5end_mobilization_protein_1182792..1183022_NEGATIVE 172 44 26 102 84 NC_002950:PG1661|5end_hypothetical_protein_1744468..1744698_POSITIVE 171 56 24 184 150 NC_002950:PG1853|5end_DNA_polymerase_III,_beta_subunit_1953119..1953349_NEGATIVE 171 70 27 163 117 NC_002950:PG1777|5end_hypothetical_protein_1866708..1866938_POSITIVE 170 110 65 113 59 NC_002950:PG0698|5end_lipoprotein,_putative_753356..753586_NEGATIVE 168 109 68 215 167 NC_002950:PG0355|5end_hypothetical_protein_389644..389874_POSITIVE 167 70 25 173 121 NC_002950:PG1571|5end_metallo-beta-lactamase_superfamily_protein_1650353..1650583_NEGATIVE 164 64 21 94 36 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 163 100 59 190 150 NC_002950:PG1117|5end_MATE_efflux_family_protein_1190010..1190240_POSITIVE 163 56 28 221 190 NC_002950:PG0498|5end_S-ribosylhomocysteinase_537968..538198_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 64 23 54 18 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 230 57 17 149 98 NC_002950:PG1018|3end_hypothetical_protein_1079282..1079432_POSITIVE 188 68 23 138 89 NC_002950:PG1574|3end_hypothetical_protein_1652461..1652611_NEGATIVE 182 116 82 97 60 NC_002950:PG0274|3end_hypothetical_protein_306781..306931_POSITIVE 179 43 5 151 115 NC_002950:PG0781|3end_hypothetical_protein_833239..833389_NEGATIVE 176 121 81 40 3 NC_002950:PG0042|3end_serine_hydroxymethyltransferase_50989..51139_POSITIVE 171 70 27 77 31 NC_002950:PG1776|3end_dnaJ_protein_1866702..1866852_POSITIVE 170 110 65 81 27 NC_002950:PG0699|3end_maltodextrin_phosphorylase_753388..753538_NEGATIVE 167 70 25 80 28 NC_002950:PG1572|3end_hypothetical_protein_1650446..1650596_NEGATIVE 163 52 19 73 39 NC_002950:PG0319|3end_hypothetical_protein_353457..353607_POSITIVE 162 56 16 98 70 NC_002950:PG0815|3end_hypothetical_protein_876447..876597_POSITIVE 161 109 68 114 69 NC_002950:PG1447|3end_transcriptional_regulator,_AraC_family_1531363..1531513_NEGATIVE 161 109 68 114 69 NC_002950:PG0826|3end_transcriptional_regulator,_AraC_family_884149..884299_POSITIVE 158 97 72 37 8 NC_002950:PG1529|3end_hypothetical_protein_1609453..1609603_POSITIVE 154 50 24 116 90 NC_002950:PG1417|3end_fumarate_hydratase_class_I,_anaerobic_1503021..1503171_POSITIVE 152 53 16 39 2 NC_002950:PG1769|3end_hypothetical_protein_1857010..1857160_POSITIVE 151 120 76 60 11 NC_002950:PG1432|3end_sensor_histidine_kinase_1516734..1516884_NEGATIVE 151 69 29 71 23 NC_002950:PG1229|3end_hypothetical_protein_1305559..1305709_NEGATIVE 149 62 21 115 76 NC_002950:PG2214|3end_hypothetical_protein_2325301..2325451_NEGATIVE 148 69 25 147 102 NC_002950:PG0167|3end_ribosomal_protein_L25_188512..188662_NEGATIVE