Origin IGS: tataaatctcttattaataggctatacgcgaaatcatccgtgaacttttagtgaactttctgaatgaaaactgctgcaaatctaagatatttcttggaataaacaaataatataacttatttattttcaagtatttaatattattttcaatttcatgaaatatacatcaaacagactcataatctggaggtccctggttcaagcccaggctggtccacaaatagattttcagatgacattggacagaatgtcattttaatctttaagacaaagacaagagggtgtatcataatttattttt .........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 aaaaataaattatgatacaccctcttgtctttgtcttaaagattaaaatgacattctgtccaatgtcatctgaaaatctatttgtggaccagcctgggcttgaaccagggacctccagattatgagtctgtttgatgtatatttcatgaaattgaaaataatattaaatacttgaaaataaataagttatattatttgtttattccaagaaatatcttagatttgcagcagttttcattcagaaagttcactaaaagttcacggatgatttcgcgtatagcctattaataagagatttata Mask Tandem Repeat Region ================================================ tataaatctcttattaataggctatacgcgaaatcatccgtgaacttttagtgaactttctgaatgaaaactgctgcaaatctaagatatttcttggaataaacaaataatataacttatttattttcaagtatttaatattattttcaatttcatgaaatatacatcaaacagactcataatctggaggtccctggttcaagcccaggctggtccacaaatagattttcagatgacattggacagaatgtcattttaatctttaagacaaagacaagagggtgtatcataatttattttt Find is-nt database================================================ Query_seq: PI2081:PI2082|PI2081:PI2082:conserved hypothetical protein; possible integrase:hypothetical protein:->->:2039717..2040017 301 tataaatctcttattaataggctatacgcgaaatcatccgtgaacttttagtgaactttctgaatgaaaactgctgcaaatctaagatatttcttggaataaacaaataatataacttatttattttcaagtatttaatattattttcaatttcatgaaatatacatcaaacagactcataatctggaggtccctggttcaagcccaggctggtccacaaatagattttcagatgacattggacagaatgtcattttaatctttaagacaaagacaagagggtgtatcataatttattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2081:PI2082|PI2081:PI2082:conserved hypothetical protein; possible integrase:hypothetical protein:->->:2039717..2040017 301 tataaatctcttattaataggctatacgcgaaatcatccgtgaacttttagtgaactttctgaatgaaaactgctgcaaatctaagatatttcttggaataaacaaataatataacttatttattttcaagtatttaatattattttcaatttcatgaaatatacatcaaacagactcataatctggaggtccctggttcaagcccaggctggtccacaaatagattttcagatgacattggacagaatgtcattttaatctttaagacaaagacaagagggtgtatcataatttattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2081:PI2082|PI2081:PI2082:conserved hypothetical protein; possible integrase:hypothetical protein:->->:2039717..2040017 301 tataaatctcttattaataggctatacgcgaaatcatccgtgaacttttagtgaactttctgaatgaaaactgctgcaaatctaagatatttcttggaataaacaaataatataacttatttattttcaagtatttaatattattttcaatttcatgaaatatacatcaaacagactcataatctggaggtccctggttcaagcccaggctggtccacaaatagattttcagatgacattggacagaatgtcattttaatctttaagacaaagacaagagggtgtatcataatttattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataaatctcttattaataggctatacgcgaaatcatccgtgaacttttagtgaactttctgaatgaaaactgctgcaaatctaagatatttcttggaataaacaaataatataacttatttattttcaagtatttaatattattttcaatttcatgaaatatacatcaaacagactcataatctggaggtccctggttcaagcccaggctggtccacaaatagattttcagatgacattggacagaatgtcattttaatctttaagacaaagacaagagggtgtatcataatttattttt Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 119 End: 256 ...................................................................................................................... M Y F Q V F N I I F N F M K Y T S N R L I I W R S L V Q A Q A G P Q I D F Q M T L D R M S F ............................................. Protein_Len: 47 Strand: + Start: 160 End: 300 ............................................................................................................................................................... M Y I K Q T H N L E V P G S S P G W S T N R F S D D I G Q N V I L I F K T K T R G C I I I Y F . Protein_Len: 38 Strand: - Start: 180 End: 293 ................................................................................................................................................................................... L R S T G P E L G P Q D V F L N E S S M P C F T M K I K L V F V L P H I M M ........ Protein_Len: 49 Strand: - Start: 17 End: 163 ................ Y A I R S I M R S S K T F K R F S F Q Q L D L I N R P I F L Y Y L K N I K L Y K I N N E I E H F M .......................................................................................................................................... tataaatctcttattaataggctatacgcgaaatcatccgtgaacttttagtgaactttctgaatgaaaactgctgcaaatctaagatatttcttggaataaacaaataatataacttatttattttcaagtatttaatattattttcaatttcatgaaatatacatcaaacagactcataatctggaggtccctggttcaagcccaggctggtccacaaatagattttcagatgacattggacagaatgtcattttaatctttaagacaaagacaagagggtgtatcataatttattttt 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================================================ tataaatctcttattaataggctatacgcgaaatcatccgtgaacttttagtgaactttctgaatgaaaactgctgcaaatctaagatatttcttggaataaacaaataatataacttatttattttcaagtatttaatattattttcaatttcatgaaatatacatcaaacagactcataatctggaggtccctggttcaagcccaggctggtccacaaatagattttcagatgacattggacagaatgtcattttaatctttaagacaaagacaagagggtgtatcataatttattttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 69 HP_score: -5.1 Tail_Score: -4.49756 Start: 234 End: 253 Full_Region: AAATAGATTTTCAGA TGACATT GGACAG AATGTCA TTTTAATCTTTAAGA .........................................................................................................................................................................................................................................TGACATTGGACAGAATGTCA................................................ Find igs database================================================ Query_seq: PI2081:PI2082|PI2081:PI2082:conserved hypothetical protein; possible integrase:hypothetical protein:->->:2039717..2040017 301 tataaatctcttattaataggctatacgcgaaatcatccgtgaacttttagtgaactttctgaatgaaaactgctgcaaatctaagatatttcttggaataaacaaataatataacttatttattttcaagtatttaatattattttcaatttcatgaaatatacatcaaacagactcataatctggaggtccctggttcaagcccaggctggtccacaaatagattttcagatgacattggacagaatgtcattttaatctttaagacaaagacaagagggtgtatcataatttattttt Intra-Species Hit: Count: 1 Min: 1 Max: 301 Len: 301 Subject: pint_PI2081_PI2082|conserved hypothetical protein; possible integrase:hypothetical protein|POSITIVE:POSITIVE|[2039717,2040017]|301 HSP 1 e-value: 1.0E-170 bit: 597.0 Len: 301 Query Start:1 Query End:301 Subject Strand: POSITIVE Subject Start: 1 Subject End: 301 tataaatctcttattaataggctatacgcgaaatcatccgtgaacttttagtgaactttctgaatgaaaactgctgcaaatctaagatatttcttggaataaacaaataatataacttatttattttcaagtatttaatattattttcaatttcatgaaatatacatcaaacagactcataatctggaggtccctggttcaagcccaggctggtccacaaatagattttcagatgacattggacagaatgtcattttaatctttaagacaaagacaagagggtgtatcataatttattttt tataaatctcttattaataggctatacgcgaaatcatccgtgaacttttagtgaactttctgaatgaaaactgctgcaaatctaagatatttcttggaataaacaaataatataacttatttattttcaagtatttaatattattttcaatttcatgaaatatacatcaaacagactcataatctggaggtccctggttcaagcccaggctggtccacaaatagattttcagatgacattggacagaatgtcattttaatctttaagacaaagacaagagggtgtatcataatttattttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAAUCUCUUAUUAAUAGGCUAUACGCGAAAUCAUCCGUGAACUUUUAGUGAACUUUCUGAAUGAAAACUGCUGCAAAUCUAAGAUAUUUCUUGGAAUAAACAAAUAAUAUAACUUAUUUAUUUUCAAGUAUUUAAUAUUAUUUUCAAUUUCAUGAAAUAUACAUCAAACAGACUCAUAAUCUGGAGGUCCCUGGUUCAAGCCCAGGCUGGUCCACAAAUAGAUUUUCAGAUGACAUUGGACAGAAUGUCAUUUUAAUCUUUAAGACAAAGACAAGAGGGUGUAUCAUAAUUUAUUUUU ..........(((((((.((....((((.((.....))))))..)).))))))).......(((((((..................(((((((.((((((....(((((((((....(((((......)))))....)))))))))...)))))).))))))).......(((..(((...(((((((((((..(((..((.((....))))..)))......)))))))))))((((((......)))))).......(((((.....)))))...)))..))).......))))))).. (-55.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUAAAUUAUGAUACACCCUCUUGUCUUUGUCUUAAAGAUUAAAAUGACAUUCUGUCCAAUGUCAUCUGAAAAUCUAUUUGUGGACCAGCCUGGGCUUGAACCAGGGACCUCCAGAUUAUGAGUCUGUUUGAUGUAUAUUUCAUGAAAUUGAAAAUAAUAUUAAAUACUUGAAAAUAAAUAAGUUAUAUUAUUUGUUUAUUCCAAGAAAUAUCUUAGAUUUGCAGCAGUUUUCAUUCAGAAAGUUCACUAAAAGUUCACGGAUGAUUUCGCGUAUAGCCUAUUAAUAAGAGAUUUAUA .....................(((((((...................((((((((......))))))))....(((((.((((((((((...(((((.......)))))...((.((((((.((((..((((((((((...(((((......)))))...))))))))))((((..(((((((((((......))))))))))).))))......)))))))))).))...(((((.....)))))..........))))))))))))))).((.....))......)))))))....... (-59.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 219 185 87 45 pint:PI1494|5end_conserved_hypothetical_protein_1413046..1413276_POSITIVE 288 220 181 229 174 pint:PI0546|5end_hypothetical_protein_497799..498029_POSITIVE 280 219 183 180 134 pint:PI0264|5end_transfer_region-related_protein,_TraN_256494..256724_POSITIVE 278 212 176 173 131 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 277 239 194 96 54 pint:PI1364|5end_dipeptidyl_peptidase_IV_1281862..1282092_POSITIVE 276 220 171 218 174 pint:PI0447|5end_DNA-directed_RNA_polymerase,_beta'_subunit_417314..417544_POSITIVE 275 213 174 213 179 pint:PI1540|5end_hypothetical_protein_1461362..1461592_POSITIVE 274 213 179 73 36 pint:PI1059|5end_conserved_hypothetical_protein_978114..978344_POSITIVE 273 216 177 213 174 pint:PI1697|5end_conserved_hypothetical_protein_1612217..1612447_POSITIVE 272 230 185 100 57 pint:PI0127|5end_conserved_hypothetical_protein_118683..118913_POSITIVE 265 225 184 221 163 pint:PI0250|5end_hypothetical_protein_246946..247176_POSITIVE 264 219 176 216 167 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 261 215 174 160 123 pint:PI1877|5end_hypothetical_protein_1819910..1820140_POSITIVE 261 236 193 222 173 pint:PI0708|5end_conserved_hypothetical_protein_644475..644705_POSITIVE 260 224 182 58 9 pint:PI1778|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1710009..1710239_POSITIVE 258 253 230 32 10 pint:PI0724|5end_DNA_polymerase_III,_delta_subunit_657403..657633_POSITIVE 256 226 185 63 12 pint:PI1428|5end_quinolinate_synthetase_A_1346626..1346856_POSITIVE 252 219 172 75 21 pint:PI0718|5end_hypothetical_protein_653725..653955_POSITIVE 250 300 272 137 109 pint:PI1463|5end_fumarate_hydratase,_class_I_1385349..1385579_POSITIVE 249 213 181 80 39 pint:PI1235|5end_60_kDa_chaperonin,_groEL,_cpn60_1157186..1157416_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 277 208 163 118 72 pint:PI2161|3end_hypothetical_protein_2108751..2108901_POSITIVE 277 239 194 76 34 pint:PI1363|3end_hypothetical_protein_1281922..1282072_POSITIVE 274 213 179 63 26 pint:PI1058|3end_possible_FHA_domain_protein_978184..978334_POSITIVE 261 215 174 138 101 pint:PI1876|3end_possible_flagellar_motor_protein,_OmpA_family_1819968..1820118_POSITIVE 260 224 182 50 1 pint:PI1777|3end_conserved_hypothetical_protein_1710081..1710231_POSITIVE 250 300 272 91 63 pint:PI1462|3end_hypothetical_protein_1385383..1385533_POSITIVE 247 235 194 68 5 pint:PI0159|3end_hypothetical_protein_152120..152270_POSITIVE 246 218 175 149 90 pint:PI0587|3end_conserved_hypothetical_protein_535347..535497_POSITIVE 242 220 174 82 21 pint:PI0057|3end_conserved_hypothetical_protein_56512..56662_POSITIVE 241 78 31 151 111 pint:PI1824|3end_ThiJ/PfpI_family_protein_1765005..1765155_POSITIVE 241 215 171 145 84 pint:PI0828|3end_GMP_synthase_(glutamine_amidotransferase)_765695..765845_POSITIVE 240 98 53 120 76 pint:PI0026|3end_two-component_system_response_regulator_30537..30687_POSITIVE 236 224 185 42 6 pint:PI0999|3end_hypothetical_protein_922812..922962_POSITIVE 235 213 172 106 56 pint:PI0809|3end_hypothetical_protein_747108..747258_POSITIVE 235 212 171 148 100 pint:PI0142|3end_DNA-binding_protein_134191..134341_POSITIVE 234 216 186 47 16 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 234 241 202 59 17 pint:PI1650|3end_N-acetylmuramoyl-L-alanine_amidase_1563901..1564051_POSITIVE 234 246 202 135 94 pint:PI1568|3end_OmpA_family_protein_1491043..1491193_POSITIVE 233 216 171 58 11 pint:PI0256|3end_conjugative_transposon_protein,_TraE_249420..249570_POSITIVE 232 218 177 64 20 pint:PI0740|3end_hypothetical_protein_672365..672515_POSITIVE