Origin IGS: atcttttttcgatctacaaagaaagactcaaataacatctttagccaatctgttttacagacgctattacgcaaagttaattaaaaactgtgctacctttgtatatatgtacgcttaacccacaattata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tataattgtgggttaagcgtacatatatacaaaggtagcacagtttttaattaactttgcgtaatagcgtctgtaaaacagattggctaaagatgttatttgagtctttctttgtagatcgaaaaaagat Mask Tandem Repeat Region ================================================ atcttttttcgatctacaaagaaagactcaaataacatctttagccaatctgttttacagacgctattacgcaaagttaattaaaaactgtgctacctttgtatatatgtacgcttaacccacaattata Find is-nt database================================================ Query_seq: PG1877:PG1878|PG1877:PG1878:Na+/H+ antiporter:cysteinyl-tRNA synthetase:<-->:1972938..1973067 130 atcttttttcgatctacaaagaaagactcaaataacatctttagccaatctgttttacagacgctattacgcaaagttaattaaaaactgtgctacctttgtatatatgtacgcttaacccacaattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1877:PG1878|PG1877:PG1878:Na+/H+ antiporter:cysteinyl-tRNA synthetase:<-->:1972938..1973067 130 atcttttttcgatctacaaagaaagactcaaataacatctttagccaatctgttttacagacgctattacgcaaagttaattaaaaactgtgctacctttgtatatatgtacgcttaacccacaattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1877:PG1878|PG1877:PG1878:Na+/H+ antiporter:cysteinyl-tRNA synthetase:<-->:1972938..1973067 130 atcttttttcgatctacaaagaaagactcaaataacatctttagccaatctgttttacagacgctattacgcaaagttaattaaaaactgtgctacctttgtatatatgtacgcttaacccacaattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcttttttcgatctacaaagaaagactcaaataacatctttagccaatctgttttacagacgctattacgcaaagttaattaaaaactgtgctacctttgtatatatgtacgcttaacccacaattata Predict ORF larger than 30AA ================================================ atcttttttcgatctacaaagaaagactcaaataacatctttagccaatctgttttacagacgctattacgcaaagttaattaaaaactgtgctacctttgtatatatgtacgcttaacccacaattata 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================================================ atcttttttcgatctacaaagaaagactcaaataacatctttagccaatctgttttacagacgctattacgcaaagttaattaaaaactgtgctacctttgtatatatgtacgcttaacccacaattata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 40 HP_score: -2.0 Tail_Score: -2.75389 Start: 71 End: 93 Full_Region: TACAGACGCTATTAC GCAAAGTT AATTAAA AACTGTGC TACCTTTGTATATAT ......................................................................GCAAAGTTAATTAAAAACTGTGC..................................... Find igs database================================================ Query_seq: PG1877:PG1878|PG1877:PG1878:Na+/H+ antiporter:cysteinyl-tRNA synthetase:<-->:1972938..1973067 130 atcttttttcgatctacaaagaaagactcaaataacatctttagccaatctgttttacagacgctattacgcaaagttaattaaaaactgtgctacctttgtatatatgtacgcttaacccacaattata Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_002950_PG1877_PG1878|Na+/H+ antiporter:cysteinyl-tRNA synthetase|NEGATIVE:POSITIVE|[1972938,1973067]|130 HSP 1 e-value: 4.0E-68 bit: 258.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 atcttttttcgatctacaaagaaagactcaaataacatctttagccaatctgttttacagacgctattacgcaaagttaattaaaaactgtgctacctttgtatatatgtacgcttaacccacaattata atcttttttcgatctacaaagaaagactcaaataacatctttagccaatctgttttacagacgctattacgcaaagttaattaaaaactgtgctacctttgtatatatgtacgcttaacccacaattata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUUUUUCGAUCUACAAAGAAAGACUCAAAUAACAUCUUUAGCCAAUCUGUUUUACAGACGCUAUUACGCAAAGUUAAUUAAAAACUGUGCUACCUUUGUAUAUAUGUACGCUUAACCCACAAUUAUA ..............(((((((....................((((...((((.....)))).))))....(((.((((.......)))).)))...)))))))........................... (-18.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAUUGUGGGUUAAGCGUACAUAUAUACAAAGGUAGCACAGUUUUUAAUUAACUUUGCGUAAUAGCGUCUGUAAAACAGAUUGGCUAAAGAUGUUAUUUGAGUCUUUCUUUGUAGAUCGAAAAAAGAU ......((((.(.....).))))....((((((((..(((.((((.......)))).)))....(((((((((.....)))))..))))...................)))))))).............. (-24.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 798 70 21 161 112 NC_002950:PG1877|5end_Na+/H+_antiporter_1972847..1973077_NEGATIVE 246 103 63 164 128 NC_002950:PG1595|5end_ribulose-phosphate_3-epimerase_1674250..1674480_NEGATIVE 240 90 45 136 88 NC_002950:PG2190|5end_cell-division_ATP-binding_protein_2297909..2298139_NEGATIVE 238 101 61 171 133 NC_002950:PG0242|5end_conserved_hypothetical_protein_TIGR00096_278960..279190_NEGATIVE 231 76 43 48 11 NC_002950:PG0179|5end_hypothetical_protein_201783..202013_POSITIVE 229 72 36 179 140 NC_002950:PG2055|5end_dihydroorotate_dehydrogenase_2153060..2153290_NEGATIVE 224 72 36 152 109 NC_002950:PG0979|5end_hypothetical_protein_1040752..1040982_POSITIVE 222 78 37 210 162 NC_002950:PG2126|5end_conserved_hypothetical_protein_TIGR00044_2233112..2233342_NEGATIVE 222 123 91 166 141 NC_002950:PG0113|5end_hypothetical_protein_135925..136155_POSITIVE 219 103 62 214 170 NC_002950:PG1578|5end_quinolinate_synthetase_1655466..1655696_POSITIVE 217 130 86 184 146 NC_002950:PG1592|5end_HDIG_domain_protein_1669383..1669613_POSITIVE 216 80 37 147 98 NC_002950:PG0412|5end_DNA_mismatch_repair_protein_MutL_451440..451670_NEGATIVE 211 122 88 167 125 NC_002950:PG1028|5end_TPR_domain_protein_1089670..1089900_POSITIVE 211 70 27 91 48 NC_002950:PG0746|5end_sensor_histidine_kinase_793903..794133_NEGATIVE 210 122 88 90 52 NC_002950:PG1937|5end_50S_ribosomal_protein_L4_2024136..2024366_NEGATIVE 202 110 69 97 49 NC_002950:PG1325|5end_hypothetical_protein_1403878..1404108_NEGATIVE 200 114 92 222 202 NC_002950:PG0629|5end_inorganic_polyphosphate/ATP-NAD_kinase_683364..683594_NEGATIVE 198 71 34 226 185 NC_002950:PG0025|5end_fumarylacetoacetate_hydrolase_family_protein_28457..28687_POSITIVE 197 68 21 133 98 NC_002950:PG1355|5end_acyltransferase,_putative_1435292..1435522_NEGATIVE 197 123 82 194 150 NC_002950:PG0709|5end_peptidyl-prolyl_cis-trans_isomerase_FkpA,_FKBP-type_765417..765647_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 225 76 44 111 77 NC_002950:PG1811|3end_hypothetical_protein_1906975..1907125_POSITIVE 216 80 37 150 101 NC_002950:PG0413|3end_hypothetical_protein_451437..451587_NEGATIVE 211 70 27 94 51 NC_002950:PG0747|3end_sigma-54_dependent_DNA-binding_response_regulator_793900..794050_NEGATIVE 210 122 88 90 52 NC_002950:PG1938|3end_50S_ribosomal_protein_L3_2024136..2024286_NEGATIVE 207 90 60 146 116 NC_002950:PG0243|3end_hypothetical_protein_278976..279126_NEGATIVE 197 68 21 64 29 NC_002950:PG1356|3end_hypothetical_protein_1435361..1435511_NEGATIVE 194 69 27 93 44 NC_002950:PG2176|3end_ISPg2,_transposase_2283215..2283365_NEGATIVE 193 65 34 101 71 NC_002950:PG1701|3end_glutamine_amidotransferase,_class_II/dipeptidase_1786145..1786295_NEGATIVE 193 122 87 110 67 NC_002950:PG1225|3end_ABC_transporter,_ATP-binding_protein_1303336..1303486_POSITIVE 192 116 85 140 110 NC_002950:PG1321|3end_formate--tetrahydrofolate_ligase_1399656..1399806_NEGATIVE 192 71 36 141 114 NC_002950:PG1160|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_1238981..1239131_NEGATIVE 191 120 86 64 26 NC_002950:PG2073|3end_hypothetical_protein_2174219..2174369_NEGATIVE 191 120 86 64 26 NC_002950:PG1669|3end_hypothetical_protein_1755411..1755561_NEGATIVE 191 120 86 64 26 NC_002950:PG1264|3end_hypothetical_protein_1344740..1344890_NEGATIVE 191 120 86 64 26 NC_002950:PG0103|3end_hypothetical_protein_121525..121675_POSITIVE 190 54 11 129 88 NC_002950:PG1442|3end_hypothetical_protein_1527602..1527752_NEGATIVE 190 128 88 124 86 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 188 78 41 60 30 NC_002950:PG2190|3end_cell-division_ATP-binding_protein_2297169..2297319_NEGATIVE 188 78 36 88 57 NC_002950:PG1404|3end_rhomboid_family_protein_1487071..1487221_NEGATIVE 187 77 34 112 74 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE