Origin IGS: atatgtgtcgttttgattttttctgctgcaaaagtacggcaacaaacaggaataaaataaccccaataagcattacactgccccaaaacaacaatttgctcgcatataaacgcaacaggggtataagcgtggataatagggttatttatttgctcggcaggtaagtacctttgcacagaatctcacaaacaaatatgat .........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 atcatatttgtttgtgagattctgtgcaaaggtacttacctgccgagcaaataaataaccctattatccacgcttatacccctgttgcgtttatatgcgagcaaattgttgttttggggcagtgtaatgcttattggggttattttattcctgtttgttgccgtacttttgcagcagaaaaaatcaaaacgacacatat Mask Tandem Repeat Region ================================================ atatgtgtcgttttgattttttctgctgcaaaagtacggcaacaaacaggaataaaataaccccaataagcattacactgccccaaaacaacaatttgctcgcatataaacgcaacaggggtataagcgtggataatagggttatttatttgctcggcaggtaagtacctttgcacagaatctcacaaacaaatatgat Find is-nt database================================================ Query_seq: PI0227:PI0228|PI0227:PI0228:ABC transporter, ATP-binding/permease protein:outer membrane cobalamin receptor protein:->->:225693..225891 199 atatgtgtcgttttgattttttctgctgcaaaagtacggcaacaaacaggaataaaataaccccaataagcattacactgccccaaaacaacaatttgctcgcatataaacgcaacaggggtataagcgtggataatagggttatttatttgctcggcaggtaagtacctttgcacagaatctcacaaacaaatatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0227:PI0228|PI0227:PI0228:ABC transporter, ATP-binding/permease protein:outer membrane cobalamin receptor protein:->->:225693..225891 199 atatgtgtcgttttgattttttctgctgcaaaagtacggcaacaaacaggaataaaataaccccaataagcattacactgccccaaaacaacaatttgctcgcatataaacgcaacaggggtataagcgtggataatagggttatttatttgctcggcaggtaagtacctttgcacagaatctcacaaacaaatatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0227:PI0228|PI0227:PI0228:ABC transporter, ATP-binding/permease protein:outer membrane cobalamin receptor protein:->->:225693..225891 199 atatgtgtcgttttgattttttctgctgcaaaagtacggcaacaaacaggaataaaataaccccaataagcattacactgccccaaaacaacaatttgctcgcatataaacgcaacaggggtataagcgtggataatagggttatttatttgctcggcaggtaagtacctttgcacagaatctcacaaacaaatatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatgtgtcgttttgattttttctgctgcaaaagtacggcaacaaacaggaataaaataaccccaataagcattacactgccccaaaacaacaatttgctcgcatataaacgcaacaggggtataagcgtggataatagggttatttatttgctcggcaggtaagtacctttgcacagaatctcacaaacaaatatgat Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: + Start: 3 End: 161 .. M C R F D F F C C K S T A T N R N K I T P I S I T L P Q N N N L L A Y K R N R G I S V D N R V I Y L L G R ...................................... Protein_Len: 58 Strand: - Start: 3 End: 176 .. H T T K I K E A A F T R C C V P I F Y G W Y A N C Q G L V V I Q E C I F A V P T Y A H I I P N N I Q E A P L Y R Q M ....................... Protein_Len: 48 Strand: - Start: 2 End: 145 . I H R K S K K Q Q L L V A V F L F L I V G I L M V S G W F L L K S A Y L R L L P I L T S L L T M ...................................................... atatgtgtcgttttgattttttctgctgcaaaagtacggcaacaaacaggaataaaataaccccaataagcattacactgccccaaaacaacaatttgctcgcatataaacgcaacaggggtataagcgtggataatagggttatttatttgctcggcaggtaagtacctttgcacagaatctcacaaacaaatatgat 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================================================ atatgtgtcgttttgattttttctgctgcaaaagtacggcaacaaacaggaataaaataaccccaataagcattacactgccccaaaacaacaatttgctcgcatataaacgcaacaggggtataagcgtggataatagggttatttatttgctcggcaggtaagtacctttgcacagaatctcacaaacaaatatgat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0227:PI0228|PI0227:PI0228:ABC transporter, ATP-binding/permease protein:outer membrane cobalamin receptor protein:->->:225693..225891 199 atatgtgtcgttttgattttttctgctgcaaaagtacggcaacaaacaggaataaaataaccccaataagcattacactgccccaaaacaacaatttgctcgcatataaacgcaacaggggtataagcgtggataatagggttatttatttgctcggcaggtaagtacctttgcacagaatctcacaaacaaatatgat Intra-Species Hit: Count: 1 Min: 1 Max: 199 Len: 199 Subject: pint_PI0227_PI0228|ABC transporter, ATP-binding/permease protein:outer membrane cobalamin receptor protein|POSITIVE:POSITIVE|[225693,225891]|199 HSP 1 e-value: 1.0E-109 bit: 394.0 Len: 199 Query Start:1 Query End:199 Subject Strand: POSITIVE Subject Start: 1 Subject End: 199 atatgtgtcgttttgattttttctgctgcaaaagtacggcaacaaacaggaataaaataaccccaataagcattacactgccccaaaacaacaatttgctcgcatataaacgcaacaggggtataagcgtggataatagggttatttatttgctcggcaggtaagtacctttgcacagaatctcacaaacaaatatgat atatgtgtcgttttgattttttctgctgcaaaagtacggcaacaaacaggaataaaataaccccaataagcattacactgccccaaaacaacaatttgctcgcatataaacgcaacaggggtataagcgtggataatagggttatttatttgctcggcaggtaagtacctttgcacagaatctcacaaacaaatatgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUGUGUCGUUUUGAUUUUUUCUGCUGCAAAAGUACGGCAACAAACAGGAAUAAAAUAACCCCAAUAAGCAUUACACUGCCCCAAAACAACAAUUUGCUCGCAUAUAAACGCAACAGGGGUAUAAGCGUGGAUAAUAGGGUUAUUUAUUUGCUCGGCAGGUAAGUACCUUUGCACAGAAUCUCACAAACAAAUAUGAU .(((((...(((((((....(((((.((((((.((((..................((((((((.......(((.....((((((....(((....)))...((........))....)))))).....))).......))))))))(((((((...))))))).)))).)))))))))))..))).))))..))))).. (-46.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUAUUUGUUUGUGAGAUUCUGUGCAAAGGUACUUACCUGCCGAGCAAAUAAAUAACCCUAUUAUCCACGCUUAUACCCCUGUUGCGUUUAUAUGCGAGCAAAUUGUUGUUUUGGGGCAGUGUAAUGCUUAUUGGGGUUAUUUUAUUCCUGUUUGUUGCCGUACUUUUGCAGCAGAAAAAAUCAAAACGACACAUAU .......((((((.(((..((((((((((((((((......((((((((((((((((((((((.((..((((((....((((..((((((....))))))((((....))))...)))).)))))...)..)).)))))))).))))))..))))))..)).))))))))))).)))))....)))))))))....... (-55.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 130 81 170 109 pint:PI0734|5end_ABC_transporter,_ATP-binding_/_permease_667052..667282_POSITIVE 333 130 81 44 2 pint:PI1184|5end_conserved_hypothetical_protein_1105784..1106014_POSITIVE 314 133 91 176 121 pint:PI0930|5end_alpha-L-fucosidase_precursor_860977..861207_POSITIVE 314 158 111 83 36 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 298 159 111 62 2 pint:PI1774|5end_hypothetical_protein_1706184..1706414_POSITIVE 296 167 127 93 51 pint:PI1137|5end_hypothetical_protein_1062970..1063200_POSITIVE 296 50 4 192 141 pint:PI0395|5end_Na+-driven_multidrug_efflux_pump_360388..360618_POSITIVE 290 66 23 183 130 pint:PI0632|5end_NusB_family_protein_(N_utilization_substance_protein_B)_578476..578706_POSITIVE 286 129 83 167 125 pint:PI0683|5end_hypothetical_protein_619292..619522_POSITIVE 282 50 1 196 142 pint:PI1883|5end_conserved_hypothetical_protein;_possible_surface_protein_1824874..1825104_POSITIVE 280 60 21 94 42 pint:PI0598|5end_hypothetical_protein_547061..547291_POSITIVE 275 168 125 196 145 pint:PI2064|5end_conserved_hypothetical_protein;_possible_type_I_restriction-modification_system,_S_subunit_2025076..2025306_POSITIVE 274 180 138 158 103 pint:PI2031|5end_hypothetical_protein_1986053..1986283_POSITIVE 274 120 77 200 154 pint:PI2028|5end_shikimate_kinase_1982162..1982392_POSITIVE 274 49 6 67 20 pint:PI1278|5end_ribulose-phosphate_3-epimerase_(pentose-5-phosphate-3-epimerase)_1194567..1194797_POSITIVE 272 159 111 110 47 pint:PI1943|5end_hypothetical_protein_1901296..1901526_POSITIVE 272 130 92 91 40 pint:PI1430|5end_subtilisin-like_serine_proteinase_1349598..1349828_POSITIVE 271 50 2 71 5 pint:PI1708|5end_hypothetical_protein_1625087..1625317_POSITIVE 270 164 128 60 30 pint:PI1627|5end_hypothetical_protein_1550445..1550675_POSITIVE 269 142 101 75 31 pint:PI2166|5end_hypothetical_protein_2111394..2111624_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 158 111 87 40 pint:PI0354|3end_hypothetical_protein_326241..326391_POSITIVE 296 50 4 53 2 pint:PI0394|3end_transcriptional_regulator,_AraC_family_360329..360479_POSITIVE 292 160 111 88 44 pint:PI0189|3end_integrase_180437..180587_POSITIVE 286 129 83 51 9 pint:PI0681|3end_hypothetical_protein_619256..619406_POSITIVE 286 176 149 29 3 pint:PI0107|3end_2-methylthioadenine_synthetase_104652..104802_POSITIVE 285 159 114 44 1 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 281 174 139 42 5 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 274 120 77 88 42 pint:PI2027|3end_arginine_decarboxylase_1982130..1982280_POSITIVE 274 49 6 59 12 pint:PI1277|3end_hypothetical_protein_1194639..1194789_POSITIVE 270 164 128 57 27 pint:PI1626|3end_hypothetical_protein_1550522..1550672_POSITIVE 269 133 97 85 42 pint:PI0951|3end_hypothetical_protein_885448..885598_POSITIVE 268 169 128 41 3 pint:PI1924|3end_cytidine_deaminase_1866495..1866645_POSITIVE 266 142 101 138 94 pint:PI1398|3end_probable_imidazolonepropionase_1320672..1320822_POSITIVE 265 189 145 151 108 pint:PI2034|3end_conserved_hypothetical_protein_1988120..1988270_POSITIVE 265 179 138 151 97 pint:PI2030|3end_hypothetical_protein_1986127..1986277_POSITIVE 264 156 111 106 50 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 264 135 99 139 105 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 262 130 102 90 63 pint:PI2129|3end_octaprenyl-diphosphate_synthase_2077721..2077871_POSITIVE 262 112 77 151 128 pint:PI0682|3end_hypothetical_protein_619372..619522_POSITIVE 261 134 96 133 102 pint:PI0327|3end_hypothetical_protein_309107..309257_POSITIVE