Origin IGS: agaagagtttcccgtagtacgattcaagctctcctcgacaatggaaaagccgttgagaacctccgtcgagatgttcaacgcaagcattgccataaggacgacgtacatcaagttaatcatcttctggcgtggggaaacctttctctttatgattgccatgtaatatctttctattattacgccacccgtctgctgtgtttatatagtctgttcactatattcatatagcttgtttgctatgttttggggcagacgaacgcacgttagattta .........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 taaatctaacgtgcgttcgtctgccccaaaacatagcaaacaagctatatgaatatagtgaacagactatataaacacagcagacgggtggcgtaataatagaaagatattacatggcaatcataaagagaaaggtttccccacgccagaagatgattaacttgatgtacgtcgtccttatggcaatgcttgcgttgaacatctcgacggaggttctcaacggcttttccattgtcgaggagagcttgaatcgtactacgggaaactcttct Mask Tandem Repeat Region ================================================ agaagagtttcccgtagtacgattcaagctctcctcgacaatggaaaagccgttgagaacctccgtcgagatgttcaacgcaagcattgccataaggacgacgtacatcaagttaatcatcttctggcgtggggaaacctttctctttatgattgccatgtaatatctttctattattacgccacccgtctgctgtgtttatatagtctgttcactatattcatatagcttgtttgctatgttttggggcagacgaacgcacgttagattta Find is-nt database================================================ Query_seq: PI0315:PI0316|PI0315:PI0316:conserved hypothetical protein:conserved hypothetical protein:->->:298247..298518 272 agaagagtttcccgtagtacgattcaagctctcctcgacaatggaaaagccgttgagaacctccgtcgagatgttcaacgcaagcattgccataaggacgacgtacatcaagttaatcatcttctggcgtggggaaacctttctctttatgattgccatgtaatatctttctattattacgccacccgtctgctgtgtttatatagtctgttcactatattcatatagcttgtttgctatgttttggggcagacgaacgcacgttagattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0315:PI0316|PI0315:PI0316:conserved hypothetical protein:conserved hypothetical protein:->->:298247..298518 272 agaagagtttcccgtagtacgattcaagctctcctcgacaatggaaaagccgttgagaacctccgtcgagatgttcaacgcaagcattgccataaggacgacgtacatcaagttaatcatcttctggcgtggggaaacctttctctttatgattgccatgtaatatctttctattattacgccacccgtctgctgtgtttatatagtctgttcactatattcatatagcttgtttgctatgttttggggcagacgaacgcacgttagattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0315:PI0316|PI0315:PI0316:conserved hypothetical protein:conserved hypothetical protein:->->:298247..298518 272 agaagagtttcccgtagtacgattcaagctctcctcgacaatggaaaagccgttgagaacctccgtcgagatgttcaacgcaagcattgccataaggacgacgtacatcaagttaatcatcttctggcgtggggaaacctttctctttatgattgccatgtaatatctttctattattacgccacccgtctgctgtgtttatatagtctgttcactatattcatatagcttgtttgctatgttttggggcagacgaacgcacgttagattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaagagtttcccgtagtacgattcaagctctcctcgacaatggaaaagccgttgagaacctccgtcgagatgttcaacgcaagcattgccataaggacgacgtacatcaagttaatcatcttctggcgtggggaaacctttctctttatgattgccatgtaatatctttctattattacgccacccgtctgctgtgtttatatagtctgttcactatattcatatagcttgtttgctatgttttggggcagacgaacgcacgttagattta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 41 End: 160 ........................................ M E K P L R T S V E M F N A S I A I R T T Y I K L I I F W R G E T F L F M I A M ................................................................................................................ Protein_Len: 60 Strand: + Start: 22 End: 225 ..................... M Q A L L D N G K A V E N L R R D V Q R K H C H K D D V H Q V N H L L A W G N L S L Y D C H V I S F Y Y Y A T R L L C L ............................................... Protein_Len: 33 Strand: + Start: 173 End: 271 ............................................................................................................................................................................ M I T P P V C C V Y I V C S L Y S Y S L F A M F W G R R T H V R F . Protein_Len: 59 Strand: - Start: 1 End: 177 S S N G T T R N L S E E V I S F G N L V E T S I N L A L M A M L V V Y M L N I M K Q R P S V K R K I I A M Y Y R E I M ............................................................................................... agaagagtttcccgtagtacgattcaagctctcctcgacaatggaaaagccgttgagaacctccgtcgagatgttcaacgcaagcattgccataaggacgacgtacatcaagttaatcatcttctggcgtggggaaacctttctctttatgattgccatgtaatatctttctattattacgccacccgtctgctgtgtttatatagtctgttcactatattcatatagcttgtttgctatgttttggggcagacgaacgcacgttagattta 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================================================ agaagagtttcccgtagtacgattcaagctctcctcgacaatggaaaagccgttgagaacctccgtcgagatgttcaacgcaagcattgccataaggacgacgtacatcaagttaatcatcttctggcgtggggaaacctttctctttatgattgccatgtaatatctttctattattacgccacccgtctgctgtgtttatatagtctgttcactatattcatatagcttgtttgctatgttttggggcagacgaacgcacgttagattta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 46 HP_score: -2.8 Tail_Score: -3.30854 Start: 202 End: 219 Full_Region: CGTCTGCTGTGTTTA TATAGT CTGTTC ACTATA TTCATATAGCTTGTT .........................................................................................................................................................................................................TATAGTCTGTTCACTATA..................................................... TransTerm Strand: + Conf: 53 HP_score: -2.0 Tail_Score: -4.07568 Start: 224 End: 241 Full_Region: TGTTCACTATATTCA TATAGC TTGTTT GCTATG TTTTGGGGCAGACGA ...............................................................................................................................................................................................................................TATAGCTTGTTTGCTATG............................... Find igs database================================================ Query_seq: PI0315:PI0316|PI0315:PI0316:conserved hypothetical protein:conserved hypothetical protein:->->:298247..298518 272 agaagagtttcccgtagtacgattcaagctctcctcgacaatggaaaagccgttgagaacctccgtcgagatgttcaacgcaagcattgccataaggacgacgtacatcaagttaatcatcttctggcgtggggaaacctttctctttatgattgccatgtaatatctttctattattacgccacccgtctgctgtgtttatatagtctgttcactatattcatatagcttgtttgctatgttttggggcagacgaacgcacgttagattta Intra-Species Hit: Count: 1 Min: 1 Max: 272 Len: 272 Subject: pint_PI0315_PI0316|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[298247,298518]|272 HSP 1 e-value: 1.0E-152 bit: 539.0 Len: 272 Query Start:1 Query End:272 Subject Strand: POSITIVE Subject Start: 1 Subject End: 272 agaagagtttcccgtagtacgattcaagctctcctcgacaatggaaaagccgttgagaacctccgtcgagatgttcaacgcaagcattgccataaggacgacgtacatcaagttaatcatcttctggcgtggggaaacctttctctttatgattgccatgtaatatctttctattattacgccacccgtctgctgtgtttatatagtctgttcactatattcatatagcttgtttgctatgttttggggcagacgaacgcacgttagattta agaagagtttcccgtagtacgattcaagctctcctcgacaatggaaaagccgttgagaacctccgtcgagatgttcaacgcaagcattgccataaggacgacgtacatcaagttaatcatcttctggcgtggggaaacctttctctttatgattgccatgtaatatctttctattattacgccacccgtctgctgtgtttatatagtctgttcactatattcatatagcttgtttgctatgttttggggcagacgaacgcacgttagattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAGAGUUUCCCGUAGUACGAUUCAAGCUCUCCUCGACAAUGGAAAAGCCGUUGAGAACCUCCGUCGAGAUGUUCAACGCAAGCAUUGCCAUAAGGACGACGUACAUCAAGUUAAUCAUCUUCUGGCGUGGGGAAACCUUUCUCUUUAUGAUUGCCAUGUAAUAUCUUUCUAUUAUUACGCCACCCGUCUGCUGUGUUUAUAUAGUCUGUUCACUAUAUUCAUAUAGCUUGUUUGCUAUGUUUUGGGGCAGACGAACGCACGUUAGAUUUA (((((.(((((((..............(((.(((........)))...((.((((((...(((....)))...)))))))).)))...((((..((((.((...((.....))...)).)))).))))...))))))).))))).....(((((((...((((((.........))))))......((((((((.(....(((((((......)))))))..(((((((......)))))))...).))))))))...))).))))...... (-69.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCUAACGUGCGUUCGUCUGCCCCAAAACAUAGCAAACAAGCUAUAUGAAUAUAGUGAACAGACUAUAUAAACACAGCAGACGGGUGGCGUAAUAAUAGAAAGAUAUUACAUGGCAAUCAUAAAGAGAAAGGUUUCCCCACGCCAGAAGAUGAUUAACUUGAUGUACGUCGUCCUUAUGGCAAUGCUUGCGUUGAACAUCUCGACGGAGGUUCUCAACGGCUUUUCCAUUGUCGAGGAGAGCUUGAAUCGUACUACGGGAAACUCUUCU ....((((((((.((..(((((((........(((((......)))))....(((((((......))))))).......)))))))..)))))).....)))).........................((((..(((((((...((((...((((((..((.....))..))))))....))))..(((...((((((.....)))))).((((((((..((((.........))))..)))))))).....)))....)))))))..)))) (-81.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 59 12 187 142 pint:PI0651|5end_HD_superfamily_hydrolase_592270..592500_POSITIVE 331 106 63 166 127 pint:PI0222|5end_conserved_hypothetical_protein_217808..218038_POSITIVE 329 98 51 105 44 pint:PI1009|5end_cytochrome_c_nitrite_reductase,_large_subunit_929342..929572_POSITIVE 324 158 121 229 190 pint:PI2176|5end_conserved_hypothetical_protein_2116484..2116714_POSITIVE 323 56 11 231 185 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 321 90 43 81 31 pint:PI1248|5end_conserved_hypothetical_protein_1173214..1173444_POSITIVE 321 81 42 148 97 pint:PI0857|5end_hypothetical_protein_790697..790927_POSITIVE 320 88 42 173 126 pint:PI1623|5end_hypothetical_protein_1547163..1547393_POSITIVE 319 130 81 229 173 pint:PI0981|5end_outer_membrane_protein,_TonB_dependent_receptor_906968..907198_POSITIVE 317 130 83 80 33 pint:PI0889|5end_pyruvate_kinase_818758..818988_POSITIVE 315 105 63 104 55 pint:PI1892|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_1834217..1834447_POSITIVE 313 216 179 155 123 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 306 103 61 88 23 pint:PI1271|5end_transcriptional_regulator,__AraC/XylS_family_1190755..1190985_POSITIVE 305 227 181 94 39 pint:PI1715|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1631639..1631869_POSITIVE 304 100 51 107 49 pint:PI0564|5end_hypothetical_protein_511537..511767_POSITIVE 303 90 41 224 176 pint:PI1644|5end_hypothetical_protein_1560372..1560602_POSITIVE 299 263 223 229 185 pint:PI0136|5end_surface_antigen_BspA_127105..127335_POSITIVE 298 106 61 156 85 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 297 89 41 168 109 pint:PI1620|5end__two-component_system_sensor_protein_1543956..1544186_POSITIVE 297 98 51 70 20 pint:PI0839|5end_conserved_hypothetical_protein_773843..774073_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 106 63 74 35 pint:PI0221|3end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_217796..217946_POSITIVE 320 108 64 150 104 pint:PI0857|3end_hypothetical_protein_790986..791136_POSITIVE 306 60 11 64 14 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 306 103 61 82 17 pint:PI1270|3end_probable_dipeptidyl_peptidase_1190829..1190979_POSITIVE 304 100 51 147 89 pint:PI0565|3end_hypothetical_protein_511657..511807_POSITIVE 303 77 49 126 98 pint:PI1705|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_1622706..1622856_POSITIVE 299 85 48 97 56 pint:PI2068|3end_hypothetical_protein_2028800..2028950_POSITIVE 297 89 41 150 91 pint:PI1619|3end_two-component_system_response_regulator_1544018..1544168_POSITIVE 297 98 51 74 24 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 294 107 63 62 20 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 292 98 53 121 67 pint:PI0140|3end_conserved_hypothetical_protein_132106..132256_POSITIVE 285 100 51 59 19 pint:PI1136|3end_conserved_hypothetical_protein_1062541..1062691_POSITIVE 284 266 228 118 79 pint:PI1868|3end_hypothetical_protein_1814915..1815065_POSITIVE 284 93 51 138 94 pint:PI0560|3end_hypothetical_protein_508910..509060_POSITIVE 283 79 32 73 26 pint:PI1795|3end_conserved_hypothetical_protein_1730486..1730636_POSITIVE 283 269 221 135 73 pint:PI0139|3end_pyridoxine_biosynthesis_protein_132724..132874_POSITIVE 278 42 2 53 16 pint:PI1151|3end_hypothetical_protein_1076382..1076532_POSITIVE 277 136 94 147 103 pint:PI0736|3end_transcriptional_regulator,_TetR_family_671271..671421_POSITIVE 276 101 63 107 65 pint:PI0365|3end_hypothetical_protein_336118..336268_POSITIVE 274 215 180 76 47 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE