Origin IGS: tctttgatgtgcttatttcttgccgtgcaaagttagccattttttattcggcagctttccatttgtgtaggaaattactcccgaagcactccttatatacaatatttataatgtgaaaggcagcataatcggaaaaaaatgcgtaagtttgcagcacttataaacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgtttataagtgctgcaaacttacgcatttttttccgattatgctgcctttcacattataaatattgtatataaggagtgcttcgggagtaatttcctacacaaatggaaagctgccgaataaaaaatggctaactttgcacggcaagaaataagcacatcaaaga Mask Tandem Repeat Region ================================================ tctttgatgtgcttatttcttgccgtgcaaagttagccattttttattcggcagctttccatttgtgtaggaaattactcccgaagcactccttatatacaatatttataatgtgaaaggcagcataatcggaaaaaaatgcgtaagtttgcagcacttataaacg Find is-nt database================================================ Query_seq: PI0576:PI0577|PI0576:PI0577:helicase, UvrD/Rep:conserved hypothetical protein:->->:521785..521950 166 tctttgatgtgcttatttcttgccgtgcaaagttagccattttttattcggcagctttccatttgtgtaggaaattactcccgaagcactccttatatacaatatttataatgtgaaaggcagcataatcggaaaaaaatgcgtaagtttgcagcacttataaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0576:PI0577|PI0576:PI0577:helicase, UvrD/Rep:conserved hypothetical protein:->->:521785..521950 166 tctttgatgtgcttatttcttgccgtgcaaagttagccattttttattcggcagctttccatttgtgtaggaaattactcccgaagcactccttatatacaatatttataatgtgaaaggcagcataatcggaaaaaaatgcgtaagtttgcagcacttataaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0576:PI0577|PI0576:PI0577:helicase, UvrD/Rep:conserved hypothetical protein:->->:521785..521950 166 tctttgatgtgcttatttcttgccgtgcaaagttagccattttttattcggcagctttccatttgtgtaggaaattactcccgaagcactccttatatacaatatttataatgtgaaaggcagcataatcggaaaaaaatgcgtaagtttgcagcacttataaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttgatgtgcttatttcttgccgtgcaaagttagccattttttattcggcagctttccatttgtgtaggaaattactcccgaagcactccttatatacaatatttataatgtgaaaggcagcataatcggaaaaaaatgcgtaagtttgcagcacttataaacg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 9 End: 113 ........ M L I S C R A K L A I F Y S A A F H L C R K L L P K H S L Y T I F I M ..................................................... Protein_Len: 37 Strand: - Start: 47 End: 157 .............................................. E A A K W K H L F N S G F C E K Y V I N I I H F A A Y D S F F A Y T Q L M ......... Protein_Len: 30 Strand: - Start: 16 End: 105 ............... K K G H L T L W K K N P L K G N T Y S I V G S A S R I Y L M ............................................................. tctttgatgtgcttatttcttgccgtgcaaagttagccattttttattcggcagctttccatttgtgtaggaaattactcccgaagcactccttatatacaatatttataatgtgaaaggcagcataatcggaaaaaaatgcgtaagtttgcagcacttataaacg 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================================================ tctttgatgtgcttatttcttgccgtgcaaagttagccattttttattcggcagctttccatttgtgtaggaaattactcccgaagcactccttatatacaatatttataatgtgaaaggcagcataatcggaaaaaaatgcgtaagtttgcagcacttataaacg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0576:PI0577|PI0576:PI0577:helicase, UvrD/Rep:conserved hypothetical protein:->->:521785..521950 166 tctttgatgtgcttatttcttgccgtgcaaagttagccattttttattcggcagctttccatttgtgtaggaaattactcccgaagcactccttatatacaatatttataatgtgaaaggcagcataatcggaaaaaaatgcgtaagtttgcagcacttataaacg Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: pint_PI0576_PI0577|helicase, UvrD/Rep:conserved hypothetical protein|POSITIVE:POSITIVE|[521785,521950]|166 HSP 1 e-value: 6.0E-77 bit: 287.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 tctttgatgtgcttatttcttgccgtgcaaagttagccattttttattcggcagctttccatttgtgtaggaaattactcccgaagcactccttatatacaatatttataatgtgaaaggcagcataatcggnnnnnnntgcgtaagtttgcagcacttataaacg tctttgatgtgcttatttcttgccgtgcaaagttagccattttttattcggcagctttccatttgtgtaggaaattactcccgaagcactccttatatacaatatttataatgtgaaaggcagcataatcggaaaaaaatgcgtaagtttgcagcacttataaacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUGAUGUGCUUAUUUCUUGCCGUGCAAAGUUAGCCAUUUUUUAUUCGGCAGCUUUCCAUUUGUGUAGGAAAUUACUCCCGAAGCACUCCUUAUAUACAAUAUUUAUAAUGUGAAAGGCAGCAUAAUCGGAAAAAAAUGCGUAAGUUUGCAGCACUUAUAAACG .....((.(((((((((((((((((((.((((((.(((...........))))))))).)))..).)))))))))........)))))))).............(((((((.(((....((((.((...((.(......).))...))))))..)))))))))).. (-33.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUUAUAAGUGCUGCAAACUUACGCAUUUUUUUCCGAUUAUGCUGCCUUUCACAUUAUAAAUAUUGUAUAUAAGGAGUGCUUCGGGAGUAAUUUCCUACACAAAUGGAAAGCUGCCGAAUAAAAAAUGGCUAACUUUGCACGGCAAGAAAUAAGCACAUCAAAGA .((((((...(((((((((.((((.(((((((((((...(((((......................)))))...)))....(((((.(((..(((((.........)))))))).))))).))))))))).))).)))))..))))....)))))).......... (-37.75) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 70 21 73 22 pint:PI0035|5end_NAD-dependent_protein_deacetylase,_SIR2_family_37873..38103_POSITIVE 331 100 54 219 169 pint:PI0727|5end_integrase_659261..659491_POSITIVE 306 44 8 35 5 pint:PI1356|5end_hypothetical_protein_1273162..1273392_POSITIVE 302 44 8 77 47 pint:PI1567|5end_hypothetical_protein_1489229..1489459_POSITIVE 302 44 8 85 55 pint:PI1168|5end_hypothetical_protein_1089696..1089926_POSITIVE 302 44 8 77 47 pint:PI1167|5end_hypothetical_protein_1089688..1089918_POSITIVE 297 42 8 93 62 pint:PI1875|5end_hypothetical_protein_1818934..1819164_POSITIVE 286 156 113 89 41 pint:PI0597|5end_hypothetical_protein_546626..546856_POSITIVE 285 67 21 50 4 pint:PI1389|5end_transcriptional_regulator,_LuxR_family_1310039..1310269_POSITIVE 285 88 47 145 97 pint:PI0916|5end_hypothetical_protein_845617..845847_POSITIVE 284 87 47 225 179 pint:PI1894|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diamino_pimelate_ligase_1836947..1837177_POSITIVE 282 32 8 231 210 pint:PI1876|5end_possible_flagellar_motor_protein,_OmpA_family_1819082..1819312_POSITIVE 279 67 21 61 7 pint:PI1495|5end_conserved_hypothetical_protein_1414432..1414662_POSITIVE 279 44 3 146 105 pint:PI0356|5end_hypothetical_protein_326642..326872_POSITIVE 278 41 3 50 16 pint:PI0517|5end_apparent_PorT_homolog_476261..476491_POSITIVE 277 60 11 98 36 pint:PI0440|5end_transcription_antiterminator_410582..410812_POSITIVE 274 67 27 59 16 pint:PI0908|5end_conserved_hypothetical_protein_836870..837100_POSITIVE 269 155 111 178 137 pint:PI1610|5end_Na+/H+_anti-porter_1536942..1537172_POSITIVE 269 147 108 81 39 pint:PI1188|5end_hypothetical_protein_1108639..1108869_POSITIVE 266 55 11 74 24 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 100 54 131 81 pint:PI0726|3end_hypothetical_protein_659253..659403_POSITIVE 306 44 8 133 103 pint:PI1356|3end_hypothetical_protein_1273340..1273490_POSITIVE 305 50 8 125 89 pint:PI0759|3end_hypothetical_protein_693998..694148_POSITIVE 279 44 3 122 81 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 277 60 11 80 18 pint:PI0439|3end_conserved_hypothetical_protein;_possible_preprotein_translocase_subunit_SecE_410644..410794_POSITIVE 269 147 108 130 88 pint:PI1189|3end_conserved_hypothetical_protein_1108768..1108918_POSITIVE 263 70 26 128 80 pint:PI0487|3end_50S_ribosomal_protein_L17_446703..446853_POSITIVE 258 69 21 142 92 pint:PI1013|3end_probable_transcriptional_regulator_934368..934518_POSITIVE 256 38 2 120 85 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 256 49 8 80 18 pint:PI0632|3end_NusB_family_protein_(N_utilization_substance_protein_B)_579731..579881_POSITIVE 256 43 2 56 12 pint:PI0521|3end_hypothetical_protein_479061..479211_POSITIVE 255 39 3 151 108 pint:PI0163|3end_conserved_hypothetical_protein_158410..158560_POSITIVE 252 70 27 146 100 pint:PI0474|3end_30S_ribosomal_protein_S8_439515..439665_POSITIVE 250 155 111 145 91 pint:PI0860|3end_amidophosphoribosyltransferase_796276..796426_POSITIVE 249 59 11 64 10 pint:PI0333|3end_hypothetical_protein_313788..313938_POSITIVE 248 37 1 111 71 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 247 55 17 101 50 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 247 95 51 97 40 pint:PI0456|3end_30S_ribosomal_protein_S12_429219..429369_POSITIVE 247 54 18 108 63 pint:PI0343|3end_hypothetical_protein_317920..318070_POSITIVE 245 69 21 68 18 pint:PI0538|3end_transcriptional_regulator_492925..493075_POSITIVE