Origin IGS: ttatgttttatcaacttacatctatataacacattatcgtggctttttcaaacttcaattaactctttttaacaataaaacacttatataccgcttttcatttctattttttatacctttgtggtgcagtataaaacgaacagttacattttgttattatcattaatttattattataacactttaaattagaaca .........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 tgttctaatttaaagtgttataataataaattaatgataataacaaaatgtaactgttcgttttatactgcaccacaaaggtataaaaaatagaaatgaaaagcggtatataagtgttttattgttaaaaagagttaattgaagtttgaaaaagccacgataatgtgttatatagatgtaagttgataaaacataa Mask Tandem Repeat Region ================================================ ttatgttttatcaacttacatctatataacacattatcgtggctttttcaaacttcaattaactctttttaacaataaaacacttatataccgcttttcatttctattttttatacctttgtggtgcagtataaaacgaacagttacattttgttattatcattaatttattattataacactttaaattagaaca Find is-nt database================================================ Query_seq: PI1755:PI1756|PI1755:PI1756:RNA polymerase sigma-70 factor, ECF subfamily:conserved hypothetical protein:->->:1682571..1682766 196 ttatgttttatcaacttacatctatataacacattatcgtggctttttcaaacttcaattaactctttttaacaataaaacacttatataccgcttttcatttctattttttatacctttgtggtgcagtataaaacgaacagttacattttgttattatcattaatttattattataacactttaaattagaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1755:PI1756|PI1755:PI1756:RNA polymerase sigma-70 factor, ECF subfamily:conserved hypothetical protein:->->:1682571..1682766 196 ttatgttttatcaacttacatctatataacacattatcgtggctttttcaaacttcaattaactctttttaacaataaaacacttatataccgcttttcatttctattttttatacctttgtggtgcagtataaaacgaacagttacattttgttattatcattaatttattattataacactttaaattagaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1755:PI1756|PI1755:PI1756:RNA polymerase sigma-70 factor, ECF subfamily:conserved hypothetical protein:->->:1682571..1682766 196 ttatgttttatcaacttacatctatataacacattatcgtggctttttcaaacttcaattaactctttttaacaataaaacacttatataccgcttttcatttctattttttatacctttgtggtgcagtataaaacgaacagttacattttgttattatcattaatttattattataacactttaaattagaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttatgttttatcaacttacatctatataacacattatcgtggctttttcaaacttcaattaactctttttaacaataaaacacttatataccgcttttcatttctattttttatacctttgtggtgcagtataaaacgaacagttacattttgttattatcattaatttattattataacactttaaattagaaca Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 20 End: 163 ................... M Y I T H Y R G F F K L Q L T L F N N K T L I Y R F S F L F F I P L W C S I K R T V T F C Y Y H ................................. Protein_Len: 34 Strand: + Start: 88 End: 189 ....................................................................................... M P L F I S I F Y T F V V Q Y K T N S Y I L L L S L I Y Y Y N T L N ....... ttatgttttatcaacttacatctatataacacattatcgtggctttttcaaacttcaattaactctttttaacaataaaacacttatataccgcttttcatttctattttttatacctttgtggtgcagtataaaacgaacagttacattttgttattatcattaatttattattataacactttaaattagaaca 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================================================ ttatgttttatcaacttacatctatataacacattatcgtggctttttcaaacttcaattaactctttttaacaataaaacacttatataccgcttttcatttctattttttatacctttgtggtgcagtataaaacgaacagttacattttgttattatcattaatttattattataacactttaaattagaaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1755:PI1756|PI1755:PI1756:RNA polymerase sigma-70 factor, ECF subfamily:conserved hypothetical protein:->->:1682571..1682766 196 ttatgttttatcaacttacatctatataacacattatcgtggctttttcaaacttcaattaactctttttaacaataaaacacttatataccgcttttcatttctattttttatacctttgtggtgcagtataaaacgaacagttacattttgttattatcattaatttattattataacactttaaattagaaca Intra-Species Hit: Count: 1 Min: 1 Max: 196 Len: 196 Subject: pint_PI1755_PI1756|RNA polymerase sigma-70 factor, ECF subfamily:conserved hypothetical protein|POSITIVE:POSITIVE|[1682571,1682766]|196 HSP 1 e-value: 1.0E-107 bit: 389.0 Len: 196 Query Start:1 Query End:196 Subject Strand: POSITIVE Subject Start: 1 Subject End: 196 ttatgttttatcaacttacatctatataacacattatcgtggctttttcaaacttcaattaactctttttaacaataaaacacttatataccgcttttcatttctattttttatacctttgtggtgcagtataaaacgaacagttacattttgttattatcattaatttattattataacactttaaattagaaca ttatgttttatcaacttacatctatataacacattatcgtggctttttcaaacttcaattaactctttttaacaataaaacacttatataccgcttttcatttctattttttatacctttgtggtgcagtataaaacgaacagttacattttgttattatcattaatttattattataacactttaaattagaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUGUUUUAUCAACUUACAUCUAUAUAACACAUUAUCGUGGCUUUUUCAAACUUCAAUUAACUCUUUUUAACAAUAAAACACUUAUAUACCGCUUUUCAUUUCUAUUUUUUAUACCUUUGUGGUGCAGUAUAAAACGAACAGUUACAUUUUGUUAUUAUCAUUAAUUUAUUAUUAUAACACUUUAAAUUAGAACA ...(((((((............................((((((..(((.................(((((....)))))......(((((.((...((((...................)))).)).)))))....))).))))))....((((((.((.((......)).)).))))))........))))))) (-18.11) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUCUAAUUUAAAGUGUUAUAAUAAUAAAUUAAUGAUAAUAACAAAAUGUAACUGUUCGUUUUAUACUGCACCACAAAGGUAUAAAAAAUAGAAAUGAAAAGCGGUAUAUAAGUGUUUUAUUGUUAAAAAGAGUUAAUUGAAGUUUGAAAAAGCCACGAUAAUGUGUUAUAUAGAUGUAAGUUGAUAAAACAUAA ((((.(((((((......(((((((.....((((..((((.((((..(((((.(((((..(((((((((..........)))))))))..((....))...))))))))))...))))))))..)))).........((((..((((....))))..))))....)))))))......)))))))....))))... (-30.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 140 92 63 7 pint:PI1431|5end_conserved_hypothetical_protein_1352079..1352309_POSITIVE 273 129 84 219 177 pint:PI0127|5end_conserved_hypothetical_protein_118683..118913_POSITIVE 260 143 102 220 174 pint:PI1792|5end_hypothetical_protein_1724641..1724871_POSITIVE 247 138 100 171 127 pint:PI0614|5end_glucose-6-phosphate_isomerase_563170..563400_POSITIVE 237 130 81 196 151 pint:PI1279|5end_RNA_polymerase_sigma_factor/ECF_subfamily_(sigma-70)_1195215..1195445_POSITIVE 234 155 121 147 107 pint:PI1186|5end_conserved_hypothetical_protein_1106480..1106710_POSITIVE 234 128 84 178 124 pint:PI0801|5end_hypothetical_protein_739365..739595_POSITIVE 224 159 121 72 39 pint:PI0382|5end_conserved_hypothetical_protein_351510..351740_POSITIVE 223 150 104 154 107 pint:PI0684|5end_coproporphyrinogen_III_oxidase_619357..619587_POSITIVE 223 150 104 89 42 pint:PI0683|5end_hypothetical_protein_619292..619522_POSITIVE 219 133 93 184 139 pint:PI1690|5end_transcription_regulator;_possible_Fe2+/Zn2+_uptake_regulation_proteins_1604984..1605214_POSITIVE 215 159 115 226 181 pint:PI0466|5end_30S_ribosomal_protein_S3_435725..435955_POSITIVE 214 107 90 124 107 pint:PI1954|5end_translation_initiation_factor_IF-2_1908784..1909014_POSITIVE 214 127 91 197 153 pint:PI0313|5end_conserved_hypothetical_protein_294833..295063_POSITIVE 214 127 91 85 41 pint:PI0311|5end_hypothetical_protein_294721..294951_POSITIVE 213 44 1 230 179 pint:PI1769|5end_hypothetical_protein_1696507..1696737_POSITIVE 213 130 91 51 21 pint:PI1767|5end_fructokinase,_pfkB_family_1694285..1694515_POSITIVE 211 128 81 122 72 pint:PI1605|5end_conserved_hypothetical_protein_1534244..1534474_POSITIVE 211 160 111 131 63 pint:PI0133|5end_hypothetical_protein_124334..124564_POSITIVE 210 129 91 69 28 pint:PI1848|5end_hypothetical_protein_1793799..1794029_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 129 84 45 3 pint:PI0126|3end_conserved_hypothetical_protein_118589..118739_POSITIVE 241 129 96 147 113 pint:PI0777|3end_predicted_TPR-repeat-containing_protein_714474..714624_POSITIVE 238 132 100 150 116 pint:PI0613|3end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_563239..563389_POSITIVE 234 50 1 134 88 pint:PI1730|3end_hypothetical_protein_1650367..1650517_POSITIVE 234 155 121 144 104 pint:PI1185|3end_hypothetical_protein_1106557..1106707_POSITIVE 234 128 84 64 10 pint:PI0800|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_739331..739481_POSITIVE 224 159 121 36 3 pint:PI0381|3end_probable_transcriptional_regulator,_AraC_family_351554..351704_POSITIVE 223 150 104 89 42 pint:PI0682|3end_hypothetical_protein_619372..619522_POSITIVE 221 138 92 59 12 pint:PI1609|3end_Na+/H+_anti-porter_1537100..1537250_POSITIVE 214 129 81 141 94 pint:PI1441|3end_hypothetical_protein_1363673..1363823_POSITIVE 214 140 93 113 71 pint:PI0036|3end_glutathione_peroxidase_39289..39439_POSITIVE 213 130 91 36 6 pint:PI1766|3end_sugar_transporter,_possible_glucose/galactose_transporter_1694350..1694500_POSITIVE 209 139 94 91 46 pint:PI1548|3end_conserved_hypothetical_protein_1466886..1467036_POSITIVE 205 129 82 135 99 pint:PI0813|3end_conserved_hypothetical_protein_752938..753088_POSITIVE 202 150 114 37 6 pint:PI1224|3end_sensor_histidine_kinase_and_response_regulator_1147557..1147707_POSITIVE 201 44 3 123 83 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 201 131 93 118 79 pint:PI0967|3end_conserved_hypothetical_protein_896559..896709_POSITIVE 200 137 91 101 51 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 199 129 99 39 11 pint:PI1847|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_1793849..1793999_POSITIVE 198 146 113 41 9 pint:PI1948|3end_hypothetical_protein_1903256..1903406_POSITIVE