Origin IGS: agaattgttttcattgtatgttcagcttatcagctgtcgaaactatgcatattaatgtattcgtttctctctgcatgcaaaggtagtaaaaactttgtaacttcctataatactaaataaagcttcatggggtacaacgctgtttcaccacaccgaaagcaacaaaagaatgatgaaaagtcgcttagaaagtgaaaaagcacctgcttgttaaaaagaataaaaatatcaattgtaaaacataacatatcaacaacttgcagcgatctgatgtccgatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatcggacatcagatcgctgcaagttgttgatatgttatgttttacaattgatatttttattctttttaacaagcaggtgctttttcactttctaagcgacttttcatcattcttttgttgctttcggtgtggtgaaacagcgttgtaccccatgaagctttatttagtattataggaagttacaaagtttttactacctttgcatgcagagagaaacgaatacattaatatgcatagtttcgacagctgataagctgaacatacaatgaaaacaattct Mask Tandem Repeat Region ================================================ agaattgttttcattgtatgttcagcttatcagctgtcgaaactatgcatattaatgtattcgtttctctctgcatgcaaaggtagtaaaaactttgtaacttcctataatactaaataaagcttcatggggtacaacgctgtttcaccacaccgaaagcaacaaaagaatgatgaaaagtcgcttagaaagtgaaaaagcacctgcttgttaaaaagaataaaaatatcaattgtaaaacataacatatcaacaacttgcagcgatctgatgtccgatt Find is-nt database================================================ Query_seq: PI1224:PI1225|PI1224:PI1225:sensor histidine kinase and response regulator:hypothetical protein:->->:1147618..1147897 280 agaattgttttcattgtatgttcagcttatcagctgtcgaaactatgcatattaatgtattcgtttctctctgcatgcaaaggtagtaaaaactttgtaacttcctataatactaaataaagcttcatggggtacaacgctgtttcaccacaccgaaagcaacaaaagaatgatgaaaagtcgcttagaaagtgaaaaagcacctgcttgttaaaaagaataaaaatatcaattgtaaaacataacatatcaacaacttgcagcgatctgatgtccgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1224:PI1225|PI1224:PI1225:sensor histidine kinase and response regulator:hypothetical protein:->->:1147618..1147897 280 agaattgttttcattgtatgttcagcttatcagctgtcgaaactatgcatattaatgtattcgtttctctctgcatgcaaaggtagtaaaaactttgtaacttcctataatactaaataaagcttcatggggtacaacgctgtttcaccacaccgaaagcaacaaaagaatgatgaaaagtcgcttagaaagtgaaaaagcacctgcttgttaaaaagaataaaaatatcaattgtaaaacataacatatcaacaacttgcagcgatctgatgtccgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1224:PI1225|PI1224:PI1225:sensor histidine kinase and response regulator:hypothetical protein:->->:1147618..1147897 280 agaattgttttcattgtatgttcagcttatcagctgtcgaaactatgcatattaatgtattcgtttctctctgcatgcaaaggtagtaaaaactttgtaacttcctataatactaaataaagcttcatggggtacaacgctgtttcaccacaccgaaagcaacaaaagaatgatgaaaagtcgcttagaaagtgaaaaagcacctgcttgttaaaaagaataaaaatatcaattgtaaaacataacatatcaacaacttgcagcgatctgatgtccgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaattgttttcattgtatgttcagcttatcagctgtcgaaactatgcatattaatgtattcgtttctctctgcatgcaaaggtagtaaaaactttgtaacttcctataatactaaataaagcttcatggggtacaacgctgtttcaccacaccgaaagcaacaaaagaatgatgaaaagtcgcttagaaagtgaaaaagcacctgcttgttaaaaagaataaaaatatcaattgtaaaacataacatatcaacaacttgcagcgatctgatgtccgatt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 4 End: 117 ... M V F I V C S A Y Q L S K L C I L M Y S F L S A C K G S K N F V T S Y N T K ................................................................................................................................................................... Protein_Len: 35 Strand: + Start: 107 End: 211 .......................................................................................................... M I L N K A S W G T T L F H H T E S N K R M M K S R L E S E K A P A C ..................................................................... Protein_Len: 55 Strand: - Start: 108 End: 272 ........................................................................................................... L V L Y L K M P Y L A T E G C R F C C F F S S F D S L F H F L V Q K N F L I F I D I T F C L M D V V Q L S R M ........ agaattgttttcattgtatgttcagcttatcagctgtcgaaactatgcatattaatgtattcgtttctctctgcatgcaaaggtagtaaaaactttgtaacttcctataatactaaataaagcttcatggggtacaacgctgtttcaccacaccgaaagcaacaaaagaatgatgaaaagtcgcttagaaagtgaaaaagcacctgcttgttaaaaagaataaaaatatcaattgtaaaacataacatatcaacaacttgcagcgatctgatgtccgatt 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================================================ agaattgttttcattgtatgttcagcttatcagctgtcgaaactatgcatattaatgtattcgtttctctctgcatgcaaaggtagtaaaaactttgtaacttcctataatactaaataaagcttcatggggtacaacgctgtttcaccacaccgaaagcaacaaaagaatgatgaaaagtcgcttagaaagtgaaaaagcacctgcttgttaaaaagaataaaaatatcaattgtaaaacataacatatcaacaacttgcagcgatctgatgtccgatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1224:PI1225|PI1224:PI1225:sensor histidine kinase and response regulator:hypothetical protein:->->:1147618..1147897 280 agaattgttttcattgtatgttcagcttatcagctgtcgaaactatgcatattaatgtattcgtttctctctgcatgcaaaggtagtaaaaactttgtaacttcctataatactaaataaagcttcatggggtacaacgctgtttcaccacaccgaaagcaacaaaagaatgatgaaaagtcgcttagaaagtgaaaaagcacctgcttgttaaaaagaataaaaatatcaattgtaaaacataacatatcaacaacttgcagcgatctgatgtccgatt Intra-Species Hit: Count: 1 Min: 1 Max: 280 Len: 280 Subject: pint_PI1224_PI1225|sensor histidine kinase and response regulator:hypothetical protein|POSITIVE:POSITIVE|[1147618,1147897]|280 HSP 1 e-value: 2.0E-87 bit: 323.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 agaattgttttcattgtatgttcagcttatcagctgtcgaaactatgcatattaatgtattcgtttctctctgcatgcaaaggtagtaaaaactttgtaacttcctataatactaaataaagcttcatggggtacaacgctgtttcaccacaccgaaagcaac..................................................................................................................... agaattgttttcattgtatgttcagcttatcagctgtcgaaactatgcatattaatgtattcgtttctctctgcatgcaaaggtagtaaaaactttgtaacttcctataatactaaataaagcttcatggggtacaacgctgtttcaccacaccgaaagcaac..................................................................................................................... HSP 2 e-value: 2.0E-22 bit: 107.0 Len: 54 Query Start:227 Query End:280 Subject Strand: POSITIVE Subject Start: 227 Subject End: 280 ..................................................................................................................................................................................................................................tatcaattgtaaaacataacatatcaacaacttgcagcgatctgatgtccgatt ..................................................................................................................................................................................................................................tatcaattgtaaaacataacatatcaacaacttgcagcgatctgatgtccgatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUUGUUUUCAUUGUAUGUUCAGCUUAUCAGCUGUCGAAACUAUGCAUAUUAAUGUAUUCGUUUCUCUCUGCAUGCAAAGGUAGUAAAAACUUUGUAACUUCCUAUAAUACUAAAUAAAGCUUCAUGGGGUACAACGCUGUUUCACCACACCGAAAGCAACAAAAGAAUGAUGAAAAGUCGCUUAGAAAGUGAAAAAGCACCUGCUUGUUAAAAAGAAUAAAAAUAUCAAUUGUAAAACAUAACAUAUCAACAACUUGCAGCGAUCUGAUGUCCGAUU ....((((((((.((((((((.(((((....)))))..(((((.((((((....))))))..))))).....)))))))).(((.(...((((..(((....((((((.(..((......))..).))))))....)))..)))))))).....)))))))).........((((..(..(((((....((((....((((....))))........................(((........)))........))))..)))))..)..))))..... (-50.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCGGACAUCAGAUCGCUGCAAGUUGUUGAUAUGUUAUGUUUUACAAUUGAUAUUUUUAUUCUUUUUAACAAGCAGGUGCUUUUUCACUUUCUAAGCGACUUUUCAUCAUUCUUUUGUUGCUUUCGGUGUGGUGAAACAGCGUUGUACCCCAUGAAGCUUUAUUUAGUAUUAUAGGAAGUUACAAAGUUUUUACUACCUUUGCAUGCAGAGAGAAACGAAUACAUUAAUAUGCAUAGUUUCGACAGCUGAUAAGCUGAACAUACAAUGAAAACAAUUCU ............(.(((((...(((((((((....((((((........((.(((((...((((((((..((.(((((((((.(((((((..(((((((((................)))))))..))...))))))).))).(((((.((.((((.(((......))).)))).))....)))))..........)))..))).)).))))))))..))))))).......))))))..)))))))))....))).)).)................... (-57.55) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 165 122 189 145 pint:PI1026|5end_uridine_phosphorylase_942300..942530_POSITIVE 306 68 24 107 58 pint:PI0530|5end_possible_membrane-fusion_protein_483772..484002_POSITIVE 296 176 138 78 36 pint:PI0993|5end_probable_TPR-repeat-containing_protein_917175..917405_POSITIVE 291 103 76 97 70 pint:PI0114|5end_hypothetical_protein_108139..108369_POSITIVE 279 140 93 138 97 pint:PI0566|5end_enoyl-[acyl-carrier-protein]_reductase_511832..512062_POSITIVE 272 76 31 179 125 pint:PI1735|5end_conserved_hypothetical_protein_1653428..1653658_POSITIVE 271 164 121 45 1 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 271 278 233 200 141 pint:PI0093|5end_riboflavin_biosynthesis_protein_90489..90719_POSITIVE 267 144 101 156 113 pint:PI0690|5end_uracil_permease_626025..626255_POSITIVE 266 170 128 55 10 pint:PI0285|5end_succinyltransferase_protein_270097..270327_POSITIVE 264 78 56 51 28 pint:PI0650|5end_conserved_hypothetical_protein_591617..591847_POSITIVE 264 48 5 51 10 pint:PI0356|5end_hypothetical_protein_326642..326872_POSITIVE 262 83 55 101 66 pint:PI1854|5end_possible_glycosyl_transferase_1800925..1801155_POSITIVE 260 62 24 166 135 pint:PI1630|5end_hypothetical_protein_1552127..1552357_POSITIVE 260 160 120 74 26 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 258 160 112 218 159 pint:PI1873|5end_hypothetical_protein_1817878..1818108_POSITIVE 256 110 62 209 159 pint:PI1638|5end_conserved_hypothetical_protein_1555337..1555567_POSITIVE 255 43 1 196 152 pint:PI0656|5end_peptidase_T_(tripeptide_aminopeptidase)_599833..600063_POSITIVE 254 161 124 147 105 pint:PI1516|5end_multidrug_resistance_protein;_HlyD_family_secretion_protein_1434381..1434611_POSITIVE 254 78 33 141 107 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 159 122 123 89 pint:PI2008|3end__ABC_transporter,_ATP-binding_protein_1967961..1968111_POSITIVE 305 106 61 81 42 pint:PI0809|3end_hypothetical_protein_747108..747258_POSITIVE 296 176 138 45 3 pint:PI0992|3end_RNA_polymerase_sigma-70_factor_917222..917372_POSITIVE 291 103 76 143 116 pint:PI0111|3end_hypothetical_protein_108265..108415_POSITIVE 291 103 76 90 63 pint:PI0112|3end_hypothetical_protein_108212..108362_POSITIVE 284 165 125 41 3 pint:PI1025|3end_tRNA_modification_GTPase_942232..942382_POSITIVE 280 163 138 132 108 pint:PI1554|3end_hypothetical_protein_1470483..1470633_POSITIVE 278 157 113 123 79 pint:PI0581|3end_conserved_hypothetical_protein_532589..532739_POSITIVE 271 164 121 55 11 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 271 278 233 142 83 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 260 159 115 89 34 pint:PI1918|3end_uracil-DNA_glycosylase_1862224..1862374_POSITIVE 256 110 62 76 26 pint:PI1637|3end_hypothetical_protein_1555284..1555434_POSITIVE 252 190 146 55 6 pint:PI0284|3end_flavoprotein_A_270157..270307_POSITIVE 252 84 60 131 103 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 247 83 57 86 61 pint:PI1730|3end_hypothetical_protein_1650367..1650517_POSITIVE 245 148 122 54 30 pint:PI0469|3end_30S_ribosomal_protein_S17_437445..437595_POSITIVE 242 220 171 72 13 pint:PI1446|3end_conserved_hypothetical_protein_1369832..1369982_POSITIVE 242 48 4 106 53 pint:PI0999|3end_hypothetical_protein_922812..922962_POSITIVE 236 160 120 71 22 pint:PI0166|3end_hypothetical_protein_161258..161408_POSITIVE 233 157 112 122 78 pint:PI1822|3end_ABC_transporter,_ATP-binding_/_permease_1763265..1763415_POSITIVE