Origin IGS: agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Mask Tandem Repeat Region ================================================ agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt Find is-nt database================================================ Query_seq: PG1450:PG1451|PG1450:PG1451:hypothetical protein:hypothetical protein:<-->:1534705..1534836 132 agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1450:PG1451|PG1450:PG1451:hypothetical protein:hypothetical protein:<-->:1534705..1534836 132 agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1450:PG1451|PG1450:PG1451:hypothetical protein:hypothetical protein:<-->:1534705..1534836 132 agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 15 End: 119 .............. M L I F S K T N N I V C I I H F C M Y L C I V V Q R Y N F A V I S T I ............. Protein_Len: 32 Strand: - Start: 3 End: 98 .. S S K E Q Q Y E T F S V I Y H T D Y M K T H V Q T N Y H L P I M .................................. Protein_Len: 39 Strand: - Start: 2 End: 118 . R V K K K N I N L L V L L I T H I M C K Q I Y K H I T T C L Y L K A T I E V M .............. agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt 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: 17 End: 46 ................GTTGATATTCAGTAAAACTAACAATATAGT...................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1450:PG1451|PG1450:PG1451:hypothetical protein:hypothetical protein:<-->:1534705..1534836 132 agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt 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: POSITIVE Subject Start: 1 Subject End: 132 agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt 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: NEGATIVE Subject Start: 1 Subject End: 132 agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt 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: NEGATIVE Subject Start: 76 Subject End: 207 agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacatttt 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: NEGATIVE Subject Start: 6 Subject End: 129 ....aacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaataca.... ....aacttttttattcttgataatcaataaatctaataatacggtatgtatcctacaatattgtaggtacttgcagattgtagtgcaaaggtataactttgcagtggttctaacaattaaaaataca.... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGAACUUUUUUCUUGUUGAUAUUCAGUAAAACUAACAAUAUAGUGUGUAUCAUACAUUUUUGUAUGUACUUGUGUAUUGUAGUGCAAAGGUAUAAUUUUGCAGUGAUUUCAACAAUUUAAAAUACAUUUU ..............(((((((...(((.....((((.(((((((....(((.((((((....)))))))))...)))))))))))((((((......))))))..)))..)))))))............... (-29.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUGUAUUUUAAAUUGUUGAAAUCACUGCAAAAUUAUACCUUUGCACUACAAUACACAAGUACAUACAAAAAUGUAUGAUACACACUAUAUUGUUAGUUUUACUGAAUAUCAACAAGAAAAAAGUUCGCU ........((((...(((((((..(((..(((((........))))).((((((((.....(((((((((....)))))).)))......))))).)))......)))...))))))).))))......... (-21.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 765 110 61 201 152 NC_002950:PG1450|5end_hypothetical_protein_1534614..1534844_NEGATIVE 765 110 61 201 152 NC_002950:PG0823|5end_hypothetical_protein_880818..881048_POSITIVE 309 110 75 161 113 NC_002950:PG0589|5end_bifunctional_GMP_synthase/glutamine_amidotransferase_protein_647708..647938_NEGATIVE 281 94 59 140 103 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 266 109 64 151 99 NC_002950:PG0927|5end_conserved_hypothetical_protein_TIGR00150_985050..985280_NEGATIVE 258 103 63 171 131 NC_002950:PG1528|5end_hypothetical_protein_1605783..1606013_POSITIVE 230 98 52 181 138 NC_002950:PG2172|5end_hypothetical_protein_2279937..2280167_NEGATIVE 229 106 61 105 54 NC_002950:PG1661|5end_hypothetical_protein_1744468..1744698_POSITIVE 222 89 41 51 17 NC_002950:PG0695|5end_immunoreactive_43_kDa_antigen_PG32_752067..752297_NEGATIVE 215 93 51 118 65 NC_002950:PG0664|5end_oxidoreductase,_Gfo/Idh/MocA_family_710293..710523_POSITIVE 214 120 76 98 46 NC_002950:PG1446|5end_MATE_efflux_family_protein_1531227..1531457_NEGATIVE 214 120 76 59 7 NC_002950:PG0827|5end_MATE_efflux_family_protein_884166..884396_POSITIVE 212 103 66 203 168 NC_002950:PG1624|5end_ISPg1,_transposase_1707273..1707503_NEGATIVE 211 103 62 54 2 NC_002950:PG0437|5end_polysaccharide_export_protein,_BexD/CtrA/VexA_family_476877..477107_NEGATIVE 207 94 62 186 149 NC_002950:PG1278|5end_phosphoserine_aminotransferase_1355352..1355582_POSITIVE 206 94 71 90 68 NC_002950:PG1546|5end_hypothetical_protein_1624087..1624317_POSITIVE 205 94 59 119 81 NC_002950:PG0188|5end_lipoprotein,_putative_223934..224164_POSITIVE 203 113 71 132 82 NC_002950:PG0713|5end_anthranilate_synthase_component_II_767749..767979_NEGATIVE 202 86 45 74 31 NC_002950:PG1373|5end_hypothetical_protein_1454750..1454980_POSITIVE 199 87 47 225 186 NC_002950:PG1814|5end_DNA_primase_1910627..1910857_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 109 64 139 87 NC_002950:PG0928|3end_response_regulator_985062..985212_NEGATIVE 243 96 51 55 11 NC_002950:PG1591|3end_hypothetical_protein_1669094..1669244_POSITIVE 210 112 74 150 113 NC_002950:PG0876|3end_tRNA_modification_GTPase_939250..939400_NEGATIVE 206 94 71 78 56 NC_002950:PG1545|3end_superoxide_dismutase,_Fe-Mn_1624155..1624305_POSITIVE 199 77 34 102 63 NC_002950:PG0338|3end_hypothetical_protein_375137..375287_POSITIVE 194 97 58 124 83 NC_002950:PG0582|3end_cell_division_protein_FtsQ,_putative_640456..640606_POSITIVE 191 94 52 149 104 NC_002950:PG0181|3end_immunoreactive_32_kDa_antigen_PG49_205485..205635_POSITIVE 190 107 61 104 64 NC_002950:PG1226|3end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1304048..1304198_POSITIVE 188 93 73 40 20 NC_002950:PG1594|3end_ComEC/Rec2-related_protein_1672052..1672202_NEGATIVE 187 108 72 131 100 NC_002950:PG0613|3end_hypothetical_protein_665955..666105_POSITIVE 186 110 61 92 33 NC_002950:PG0021|3end_TIM-barrel_protein,_putative,_NifR3_family_24122..24272_NEGATIVE 185 106 64 65 16 NC_002950:PG2023|3end_methionyl-tRNA_formyltransferase_2117565..2117715_NEGATIVE 184 87 46 74 26 NC_002950:PG1353|3end_orotate_phosphoribosyltransferase_1433201..1433351_NEGATIVE 183 46 3 86 49 NC_002950:PG0736|3end_ribonuclease_HII_786293..786443_POSITIVE 183 46 1 86 45 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 182 110 71 51 13 NC_002950:PG1960|3end_ribosomal_protein_L28_2048424..2048574_NEGATIVE 180 93 65 53 27 NC_002950:PG1767|3end_lipoprotein,_putative_1855115..1855265_POSITIVE 180 117 74 144 111 NC_002950:PG1582|3end_batA_protein_1660384..1660534_POSITIVE 180 116 79 124 88 NC_002950:PG0936|3end_xanthine/uracil_permease_family_protein_995150..995300_NEGATIVE 177 35 3 142 108 NC_002950:PG1450|3end_hypothetical_protein_1534300..1534450_NEGATIVE