Origin IGS: tcgatcctaattccctttatcccgaagccaaaaccgaaagttgctactattatttcggttttggctttttcttttctctacttctcaagaaaagggaaacaagcgctttgttccaaaagggaaaaagaggtccgtaattgaaaaaccttatatttggggcggttattattcatagaagtctaatataaacagaa .........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 ttctgtttatattagacttctatgaataataaccgccccaaatataaggtttttcaattacggacctctttttcccttttggaacaaagcgcttgtttcccttttcttgagaagtagagaaaagaaaaagccaaaaccgaaataatagtagcaactttcggttttggcttcgggataaagggaattaggatcga Mask Tandem Repeat Region ================================================ tcgatcctaattccctttatcccgaagccaaaaccgaaagttgctactattatttcggttttggctttttcttttctctacttctcaagaaaagggaaacaagcgctttgttccaaaagggaaaaagaggtccgtaattgaaaaaccttatatttggggcggttattattcatagaagtctaatataaacagaa Find is-nt database================================================ Query_seq: PG2105:PG2106|PG2105:PG2106:lipoprotein, putative:hypothetical protein:->->:2214640..2214833 194 tcgatcctaattccctttatcccgaagccaaaaccgaaagttgctactattatttcggttttggctttttcttttctctacttctcaagaaaagggaaacaagcgctttgttccaaaagggaaaaagaggtccgtaattgaaaaaccttatatttggggcggttattattcatagaagtctaatataaacagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2105:PG2106|PG2105:PG2106:lipoprotein, putative:hypothetical protein:->->:2214640..2214833 194 tcgatcctaattccctttatcccgaagccaaaaccgaaagttgctactattatttcggttttggctttttcttttctctacttctcaagaaaagggaaacaagcgctttgttccaaaagggaaaaagaggtccgtaattgaaaaaccttatatttggggcggttattattcatagaagtctaatataaacagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2105:PG2106|PG2105:PG2106:lipoprotein, putative:hypothetical protein:->->:2214640..2214833 194 tcgatcctaattccctttatcccgaagccaaaaccgaaagttgctactattatttcggttttggctttttcttttctctacttctcaagaaaagggaaacaagcgctttgttccaaaagggaaaaagaggtccgtaattgaaaaaccttatatttggggcggttattattcatagaagtctaatataaacagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcgatcctaattccctttatcccgaagccaaaaccgaaagttgctactattatttcggttttggctttttcttttctctacttctcaagaaaagggaaacaagcgctttgttccaaaagggaaaaagaggtccgtaattgaaaaaccttatatttggggcggttattattcatagaagtctaatataaacagaa Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 4 End: 138 ... M L I P F I P K P K P K V A T I I S V L A F S F L Y F S R K G K Q A L C S K R E K E V R N ........................................................ Protein_Len: 44 Strand: + Start: 41 End: 172 ........................................ M L L L F R F W L F L F S T S Q E K G N K R F V P K G K K R S V I E K P Y I W G G Y Y S ...................... Protein_Len: 31 Strand: - Start: 81 End: 173 ................................................................................ K E L F P F C A S Q E L L S F S T R L Q F V K Y K P R N N N M ..................... Protein_Len: 39 Strand: - Start: 53 End: 169 .................................................... K P K P K K K E R S R L F L S V L A K N W F P F L P G Y N F F R I N P A T I M ......................... tcgatcctaattccctttatcccgaagccaaaaccgaaagttgctactattatttcggttttggctttttcttttctctacttctcaagaaaagggaaacaagcgctttgttccaaaagggaaaaagaggtccgtaattgaaaaaccttatatttggggcggttattattcatagaagtctaatataaacagaa 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================================================ tcgatcctaattccctttatcccgaagccaaaaccgaaagttgctactattatttcggttttggctttttcttttctctacttctcaagaaaagggaaacaagcgctttgttccaaaagggaaaaagaggtccgtaattgaaaaaccttatatttggggcggttattattcatagaagtctaatataaacagaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.1 Tail_Score: -5.58522 Start: 27 End: 65 Full_Region: TCCCTTTATCCCGAA GCCAAAACCGAAA GTTGCTACTATTA TTTCGGTTTTGGC TTTTTCTTTTCTCTA ..........................GCCAAAACCGAAAGTTGCTACTATTATTTCGGTTTTGGC................................................................................................................................. TransTerm Strand: - Conf: 45 HP_score: -3.9 Tail_Score: -2.62244 Start: 96 End: 114 Full_Region: ctctttttccctttt ggaacaa agcgc ttgtttc ccttttcttgagaag ...............................................................................................ggaacaaagcgcttgtttc................................................................................ Find igs database================================================ Query_seq: PG2105:PG2106|PG2105:PG2106:lipoprotein, putative:hypothetical protein:->->:2214640..2214833 194 tcgatcctaattccctttatcccgaagccaaaaccgaaagttgctactattatttcggttttggctttttcttttctctacttctcaagaaaagggaaacaagcgctttgttccaaaagggaaaaagaggtccgtaattgaaaaaccttatatttggggcggttattattcatagaagtctaatataaacagaa Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: NC_002950_PG2105_PG2106|lipoprotein, putative:hypothetical protein|POSITIVE:POSITIVE|[2214640,2214833]|194 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 tcgatcctaattccctttatcccgaagccaaaaccgaaagttgctactattatttcggttttggctttttcttttctctacttctcaagaaaagggaaacaagcgctttgttccaaaagggaaaaagaggtccgtaattgaaaaaccttatatttggggcggttattattcatagaagtctaatataaacagaa tcgatcctaattccctttatcccgaagccaaaaccgaaagttgctactattatttcggttttggctttttcttttctctacttctcaagaaaagggaaacaagcgctttgttccaaaagggaaaaagaggtccgtaattgaaaaaccttatatttggggcggttattattcatagaagtctaatataaacagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGAUCCUAAUUCCCUUUAUCCCGAAGCCAAAACCGAAAGUUGCUACUAUUAUUUCGGUUUUGGCUUUUUCUUUUCUCUACUUCUCAAGAAAAGGGAAACAAGCGCUUUGUUCCAAAAGGGAAAAAGAGGUCCGUAAUUGAAAAACCUUAUAUUUGGGGCGGUUAUUAUUCAUAGAAGUCUAAUAUAAACAGAA ..((((((..((((((((.....((((((((((((((((.............))))))))))))))))..(((((((..........)))))))((((.((((...)))))))).))))))))..)).))))...............(((((((..((((..((((.....))))..)))))))))))...... (-50.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUGUUUAUAUUAGACUUCUAUGAAUAAUAACCGCCCCAAAUAUAAGGUUUUUCAAUUACGGACCUCUUUUUCCCUUUUGGAACAAAGCGCUUGUUUCCCUUUUCUUGAGAAGUAGAGAAAAGAAAAAGCCAAAACCGAAAUAAUAGUAGCAACUUUCGGUUUUGGCUUCGGGAUAAAGGGAAUUAGGAUCGA .((((.......))))......((((....((((.............)))).))))....(((.(((....((((((((.(((((((.....))))))).((((((((........))))))))...(((((((((((((((.............)))))))))))))))......))))))))..))).))). (-51.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 64 22 72 25 NC_002950:PG1561|5end_dTDP-4-dehydrorhamnose_reductase_1640995..1641225_NEGATIVE 354 45 1 60 2 NC_002950:PG1014|5end_TPR_domain_protein_1073763..1073993_POSITIVE 316 134 94 111 68 NC_002950:PG1487|5end_hypothetical_protein_1561468..1561698_POSITIVE 309 56 14 61 28 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 308 69 21 219 163 NC_002950:PG1462|5end_hypothetical_protein_1540860..1541090_POSITIVE 287 136 94 210 173 NC_002950:PG1633|5end_galactokinase_1713385..1713615_POSITIVE 286 30 6 54 34 NC_002950:PG0718|5end_hypothetical_protein_771573..771803_NEGATIVE 286 114 71 183 131 NC_002950:PG0011|5end_glycosyl_hydrolase,_family_3_11494..11724_POSITIVE 281 65 21 202 151 NC_002950:PG1596|5end_isoleucyl-tRNA_synthetase,_putative_1674543..1674773_POSITIVE 281 90 45 148 97 NC_002950:PG0466|5end_hypothetical_protein_510244..510474_NEGATIVE 279 89 43 199 154 NC_002950:PG0365|5end_3'-5'_exonuclease_domain_protein_400178..400408_NEGATIVE 278 60 18 52 1 NC_002950:PG0160|5end_hypothetical_protein_184085..184315_NEGATIVE 275 69 22 105 52 NC_002950:PG0149|5end_hypothetical_protein_172203..172433_NEGATIVE 274 69 23 161 113 NC_002950:PG0649|5end_hypothetical_protein_701820..702050_POSITIVE 273 157 112 202 160 NC_002950:PG1688|5end_transcription_elongation_factor_GreA_1774686..1774916_NEGATIVE 273 120 73 228 180 NC_002950:PG1682|5end_glycosyl_transferase,_group_1_family_protein_1768385..1768615_POSITIVE 271 69 21 139 82 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 270 96 55 214 166 NC_002950:PG1276|5end_DNA-binding_protein,_histone-like_family_1352945..1353175_POSITIVE 270 96 55 214 166 NC_002950:PG0566|5end_DNA-binding_protein,_histone-like_family_623441..623671_NEGATIVE 269 45 3 182 147 NC_002950:PG0017|5end_sensor_histidine_kinase_18307..18537_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 404 67 24 66 20 NC_002950:PG2105|3end_lipoprotein,_putative_2214579..2214729_POSITIVE 393 64 22 75 28 NC_002950:PG1562|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_1640992..1641142_NEGATIVE 279 89 43 122 77 NC_002950:PG0366|3end_hypothetical_protein_400255..400405_NEGATIVE 275 69 22 68 15 NC_002950:PG0150|3end_conserved_hypothetical_protein_TIGR01125_172240..172390_NEGATIVE 265 69 21 82 32 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 264 115 83 46 12 NC_002950:PG0935|3end_4-diphosphocytidyl-2C-methyl-D-erythritol_kinase_994297..994447_NEGATIVE 260 46 8 71 24 NC_002950:PG0767|3end_4-alpha-glucanotransferase_818557..818707_NEGATIVE 260 46 14 151 128 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 257 78 32 49 4 NC_002950:PG1640|3end_DNA-damage-inducible_protein_F_1719935..1720085_NEGATIVE 256 70 21 112 68 NC_002950:PG0870|3end_hypothetical_protein_932304..932454_NEGATIVE 255 136 92 127 66 NC_002950:PG2046|3end_hypothetical_protein_2145793..2145943_POSITIVE 255 65 23 65 31 NC_002950:PG0286|3end_hypothetical_protein_320454..320604_POSITIVE 252 64 21 87 36 NC_002950:PG1748|3end_transketolase_1832902..1833052_NEGATIVE 251 47 5 80 52 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 250 136 99 86 46 NC_002950:PG2029|3end_hypothetical_protein_2129202..2129352_POSITIVE 249 78 33 63 28 NC_002950:PG1949|3end_malate_dehydrogenase_2038184..2038334_NEGATIVE 248 136 93 124 78 NC_002950:PG0588|3end_3-methyl-2-oxobutanoate_hydroxymethyltransferase_645296..645446_NEGATIVE 248 69 21 59 2 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 247 75 34 52 12 NC_002950:PG1997|3end_hypothetical_protein_2087072..2087222_POSITIVE 245 59 13 102 34 NC_002950:PG1693|3end_HesA/MoeB/ThiF_family_protein_1777170..1777320_NEGATIVE