Origin IGS: tctgatcacttacttctaaagcaacaaccccaacgacacaaagtggagtgtcattggggttgcttctttttctgaaaatacaataagaaaatgcagcacaagttattgtgtgcagagtgcgagtct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agactcgcactctgcacacaataacttgtgctgcattttcttattgtattttcagaaaaagaagcaaccccaatgacactccactttgtgtcgttggggttgttgctttagaagtaagtgatcaga Mask Tandem Repeat Region ================================================ tctgatcacttacttctaaagcaacaaccccaacgacacaaagtggagtgtcattggggttgcttctttttctgaaaatacaataagaaaatgcagcacaagttattgtgtgcagagtgcgagtct Find is-nt database================================================ Query_seq: PG1762:PG1763|PG1762:PG1763:protein-export membrane protein SecD/protein-export membrane protein SecF:ribonuclease III:-><-:1850963..1851088 126 tctgatcacttacttctaaagcaacaaccccaacgacacaaagtggagtgtcattggggttgcttctttttctgaaaatacaataagaaaatgcagcacaagttattgtgtgcagagtgcgagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1762:PG1763|PG1762:PG1763:protein-export membrane protein SecD/protein-export membrane protein SecF:ribonuclease III:-><-:1850963..1851088 126 tctgatcacttacttctaaagcaacaaccccaacgacacaaagtggagtgtcattggggttgcttctttttctgaaaatacaataagaaaatgcagcacaagttattgtgtgcagagtgcgagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1762:PG1763|PG1762:PG1763:protein-export membrane protein SecD/protein-export membrane protein SecF:ribonuclease III:-><-:1850963..1851088 126 tctgatcacttacttctaaagcaacaaccccaacgacacaaagtggagtgtcattggggttgcttctttttctgaaaatacaataagaaaatgcagcacaagttattgtgtgcagagtgcgagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctgatcacttacttctaaagcaacaaccccaacgacacaaagtggagtgtcattggggttgcttctttttctgaaaatacaataagaaaatgcagcacaagttattgtgtgcagagtgcgagtct Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 2 End: 115 . Q D S V E L A V V G V V C L P T D N P N S R K R F I C Y S F A A C T I T H M ........... tctgatcacttacttctaaagcaacaaccccaacgacacaaagtggagtgtcattggggttgcttctttttctgaaaatacaataagaaaatgcagcacaagttattgtgtgcagagtgcgagtct 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================================================ tctgatcacttacttctaaagcaacaaccccaacgacacaaagtggagtgtcattggggttgcttctttttctgaaaatacaataagaaaatgcagcacaagttattgtgtgcagagtgcgagtct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 91 HP_score: -10.5 Tail_Score: -4.84359 Start: 21 End: 66 Full_Region: TCACTTACTTCTAAA GCAACAACCCCAACGACAC AAAGTGGA GTGTCATTGGGGTTGCTTC TTTTTCTGAAAATAC ....................GCAACAACCCCAACGACACAAAGTGGAGTGTCATTGGGGTTGCTTC............................................................ TransTerm Strand: - Conf: 100 HP_score: -14.9 Tail_Score: -3.57792 Start: 21 End: 66 Full_Region: gtattttcagaaaaa gaagcaaccccaatgacac tccacttt gtgtcgttggggttgttgc tttagaagtaagtga ....................gaagcaaccccaatgacactccactttgtgtcgttggggttgttgc............................................................ TransTerm Strand: + Conf: 90 HP_score: -10.8 Tail_Score: -4.52873 Start: 24 End: 63 Full_Region: CTTACTTCTAAAGCA ACAACCCCAACGACAC AAAGTGGA GTGTCATTGGGGTTGC TTCTTTTTCTGAAAA .......................ACAACCCCAACGACACAAAGTGGAGTGTCATTGGGGTTGC............................................................... TransTerm Strand: - Conf: 100 HP_score: -16.5 Tail_Score: -3.52204 Start: 25 End: 62 Full_Region: tttcagaaaaagaag caaccccaatgacac tccacttt gtgtcgttggggttg ttgctttagaagtaa ........................caaccccaatgacactccactttgtgtcgttggggttg................................................................ TransTerm Strand: - Conf: 95 HP_score: -12.4 Tail_Score: -3.89354 Start: 28 End: 59 Full_Region: cagaaaaagaagcaa ccccaatgacac tccacttt gtgtcgttgggg ttgttgctttagaag ...........................ccccaatgacactccactttgtgtcgttgggg................................................................... Find igs database================================================ Query_seq: PG1762:PG1763|PG1762:PG1763:protein-export membrane protein SecD/protein-export membrane protein SecF:ribonuclease III:-><-:1850963..1851088 126 tctgatcacttacttctaaagcaacaaccccaacgacacaaagtggagtgtcattggggttgcttctttttctgaaaatacaataagaaaatgcagcacaagttattgtgtgcagagtgcgagtct Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_002950_PG1762_PG1763|protein-export membrane protein SecD/protein-export membrane protein SecF:ribonuclease III|POSITIVE:NEGATIVE|[1850963,1851088]|126 HSP 1 e-value: 9.0E-66 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 tctgatcacttacttctaaagcaacaaccccaacgacacaaagtggagtgtcattggggttgcttctttttctgaaaatacaataagaaaatgcagcacaagttattgtgtgcagagtgcgagtct tctgatcacttacttctaaagcaacaaccccaacgacacaaagtggagtgtcattggggttgcttctttttctgaaaatacaataagaaaatgcagcacaagttattgtgtgcagagtgcgagtct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUGAUCACUUACUUCUAAAGCAACAACCCCAACGACACAAAGUGGAGUGUCAUUGGGGUUGCUUCUUUUUCUGAAAAUACAAUAAGAAAAUGCAGCACAAGUUAUUGUGUGCAGAGUGCGAGUCU ...((((((((.........((..(((((((((.(((((........))))).))))))))).....((((((............)))))).)).(((((........))))).)))))...))). (-38.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGACUCGCACUCUGCACACAAUAACUUGUGCUGCAUUUUCUUAUUGUAUUUUCAGAAAAAGAAGCAACCCCAAUGACACUCCACUUUGUGUCGUUGGGGUUGUUGCUUUAGAAGUAAGUGAUCAGA .((.((((....(((((((((....))))).))))......................((((.(((((((((((((((((........))))))))))))))))).))))........))))))... (-46.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 69 21 115 61 NC_002950:PG0246|5end_hypothetical_protein_281241..281471_NEGATIVE 284 72 34 191 162 NC_002950:PG0192|5end_cationic_outer_membrane_protein_OmpH_229590..229820_POSITIVE 276 66 25 61 26 NC_002950:PG0228|5end_DdaH_family_protein_264950..265180_NEGATIVE 273 90 41 209 152 NC_002950:PG1027|5end_hypothetical_protein_1089439..1089669_NEGATIVE 265 69 21 77 25 NC_002950:PG2037|5end_hypothetical_protein_2137812..2138042_NEGATIVE 260 68 22 194 144 NC_002950:PG2112|5end_hypothetical_protein_2221471..2221701_POSITIVE 259 66 21 59 6 NC_002950:PG1734|5end_transporter,_putative_1822561..1822791_NEGATIVE 257 79 40 166 118 NC_002950:PG1509|5end_HAD-superfamily_hydrolase,_subfamily_IA,_variant_1_family_protein_1586691..1586921_POSITIVE 256 66 28 108 63 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 256 76 37 70 29 NC_002950:PG0120|5end_UDP-N-acetylglucosamine_2-epimerase_143004..143234_POSITIVE 255 76 49 115 86 NC_002950:PG1940|5end_elongation_factor_EF-2_2027220..2027450_NEGATIVE 254 110 63 149 102 NC_002950:PG1786|5end_hypothetical_protein_1874358..1874588_POSITIVE 254 56 14 124 91 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 250 63 30 129 88 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 248 72 31 49 7 NC_002950:PG1338|5end_umuC_protein_1418246..1418476_POSITIVE 248 75 34 69 16 NC_002950:PG0221|5end_hypothetical_protein_255834..256064_NEGATIVE 247 63 21 194 162 NC_002950:PG0962|5end_prolyl-tRNA_synthetase_1023808..1024038_NEGATIVE 246 77 34 225 181 NC_002950:PG0877|5end_hypothetical_protein_941545..941775_NEGATIVE 245 73 31 106 67 NC_002950:PG1593|5end_shikimate_kinase_1671503..1671733_POSITIVE 245 69 33 193 168 NC_002950:PG0375|5end_50S_ribosomal_protein_L13_405934..406164_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 65 25 72 29 NC_002950:PG1762|3end_protein-export_membrane_protein_SecD/protein-export_membrane_protein_SecF_1850902..1851052_POSITIVE 304 63 41 137 110 NC_002950:PG0163|3end_diphosphate--fructose-6-phosphate_1-phosphotransferase_185236..185386_NEGATIVE 297 67 21 151 96 NC_002950:PG1684|3end_hypothetical_protein_1771483..1771633_POSITIVE 284 72 34 134 105 NC_002950:PG0191|3end_outer_membrane_protein,_putative_229613..229763_POSITIVE 265 69 21 80 28 NC_002950:PG2038|3end_N-acetylmuramoyl-L-alanine_amidase,_putative_2137809..2137959_NEGATIVE 264 60 18 81 33 NC_002950:PG2147|3end_xanthine_phosphoribosyltransferase_2254819..2254969_NEGATIVE 264 66 24 112 79 NC_002950:PG1559|3end_aminomethyltransferase_1637904..1638054_NEGATIVE 261 74 32 68 15 NC_002950:PG0409|3end_hypothetical_protein_442350..442500_POSITIVE 259 66 21 92 39 NC_002950:PG1735|3end_MutT/nudix_family_protein_1822528..1822678_NEGATIVE 257 79 40 83 35 NC_002950:PG1508|3end_hypothetical_protein_1586688..1586838_POSITIVE 256 66 28 127 82 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 256 76 37 64 23 NC_002950:PG0119|3end_glycosyl_transferase,_WecB/TagA/CpsF_family_143078..143228_POSITIVE 255 76 49 102 73 NC_002950:PG1941|3end_30S_ribosomal_protein_S7_2027233..2027383_NEGATIVE 245 73 31 58 19 NC_002950:PG1592|3end_HDIG_domain_protein_1671535..1671685_POSITIVE 243 68 21 74 18 NC_002950:PG1409|3end_hypothetical_protein_1492873..1493023_NEGATIVE 243 64 40 40 19 NC_002950:PG0138|3end_malonyl_CoA-acyl_carrier_protein_transacylase_161634..161784_POSITIVE 242 68 30 55 7 NC_002950:PG0306|3end_electron_transport_complex,_RnfABCDGE_type,_G_subunit_342643..342793_POSITIVE 240 60 18 62 18 NC_002950:PG0005|3end_hypothetical_protein_3797..3947_NEGATIVE 238 60 13 73 32 NC_002950:PG1898|3end_transporter,_putative_1996727..1996877_NEGATIVE 238 73 31 70 19 NC_002950:PG0624|3end_hypothetical_protein_678664..678814_POSITIVE