Origin IGS: cagtgctaaacgtatttttaaattcatctcttagattttattgtttggcaacaaaagtacagattttatcacaaactaccaaaacaaagccgaatatttatgtaggaataagaacaaaaaaattgattgtctcgcgacaatcaatctttattaaccttaataatctaataccatgaaaaacacattgcaaagttaggcatacttacgcaaaattgcaaactttacaaatgctttcattttggtattaacacta .........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 tagtgttaataccaaaatgaaagcatttgtaaagtttgcaattttgcgtaagtatgcctaactttgcaatgtgtttttcatggtattagattattaaggttaataaagattgattgtcgcgagacaatcaatttttttgttcttattcctacataaatattcggctttgttttggtagtttgtgataaaatctgtacttttgttgccaaacaataaaatctaagagatgaatttaaaaatacgtttagcactg Mask Tandem Repeat Region ================================================ cagtgctaaacgtatttttaaattcatctcttagattttattgtttggcaacaaaagtacagattttatcacaaactaccaaaacaaagccgaatatttatgtaggaataagaacaaaaaaattgattgtctcgcgacaatcaatctttattaaccttaataatctaataccatgaaaaacacattgcaaagttaggcatacttacgcaaaattgcaaactttacaaatgctttcattttggtattaacacta Find is-nt database================================================ Query_seq: PI1322:PI1323|PI1322:PI1323:nucleoside permease:conserved hypothetical protein:->->:1241697..1241949 253 cagtgctaaacgtatttttaaattcatctcttagattttattgtttggcaacaaaagtacagattttatcacaaactaccaaaacaaagccgaatatttatgtaggaataagaacaaaaaaattgattgtctcgcgacaatcaatctttattaaccttaataatctaataccatgaaaaacacattgcaaagttaggcatacttacgcaaaattgcaaactttacaaatgctttcattttggtattaacacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1322:PI1323|PI1322:PI1323:nucleoside permease:conserved hypothetical protein:->->:1241697..1241949 253 cagtgctaaacgtatttttaaattcatctcttagattttattgtttggcaacaaaagtacagattttatcacaaactaccaaaacaaagccgaatatttatgtaggaataagaacaaaaaaattgattgtctcgcgacaatcaatctttattaaccttaataatctaataccatgaaaaacacattgcaaagttaggcatacttacgcaaaattgcaaactttacaaatgctttcattttggtattaacacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1322:PI1323|PI1322:PI1323:nucleoside permease:conserved hypothetical protein:->->:1241697..1241949 253 cagtgctaaacgtatttttaaattcatctcttagattttattgtttggcaacaaaagtacagattttatcacaaactaccaaaacaaagccgaatatttatgtaggaataagaacaaaaaaattgattgtctcgcgacaatcaatctttattaaccttaataatctaataccatgaaaaacacattgcaaagttaggcatacttacgcaaaattgcaaactttacaaatgctttcattttggtattaacacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagtgctaaacgtatttttaaattcatctcttagattttattgtttggcaacaaaagtacagattttatcacaaactaccaaaacaaagccgaatatttatgtaggaataagaacaaaaaaattgattgtctcgcgacaatcaatctttattaaccttaataatctaataccatgaaaaacacattgcaaagttaggcatacttacgcaaaattgcaaactttacaaatgctttcattttggtattaacacta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 35 End: 151 .................................. M L L F G N K S T D F I T N Y Q N K A E Y L C R N K N K K I D C L A T I N L Y ...................................................................................................... Protein_Len: 57 Strand: + Start: 3 End: 173 .. M L N V F L N S S L R F Y C L A T K V Q I L S Q T T K T K P N I Y V G I R T K K L I V S R Q S I F I N L N N L I P ................................................................................ Protein_Len: 30 Strand: - Start: 101 End: 190 .................................................................................................... T P I L V F F N I T E R C D I K I L R L L R I G H F V C Q M ............................................................... cagtgctaaacgtatttttaaattcatctcttagattttattgtttggcaacaaaagtacagattttatcacaaactaccaaaacaaagccgaatatttatgtaggaataagaacaaaaaaattgattgtctcgcgacaatcaatctttattaaccttaataatctaataccatgaaaaacacattgcaaagttaggcatacttacgcaaaattgcaaactttacaaatgctttcattttggtattaacacta 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================================================ cagtgctaaacgtatttttaaattcatctcttagattttattgtttggcaacaaaagtacagattttatcacaaactaccaaaacaaagccgaatatttatgtaggaataagaacaaaaaaattgattgtctcgcgacaatcaatctttattaaccttaataatctaataccatgaaaaacacattgcaaagttaggcatacttacgcaaaattgcaaactttacaaatgctttcattttggtattaacacta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 77 HP_score: -7.7 Tail_Score: -4.21319 Start: 121 End: 146 Full_Region: GAATAAGAACAAAAA AATTGATTGTC TCGC GACAATCAATC TTTATTAACCTTAAT ........................................................................................................................AATTGATTGTCTCGCGACAATCAATC........................................................................................................... TransTerm Strand: + Conf: 88 HP_score: -10.3 Tail_Score: -3.70139 Start: 123 End: 144 Full_Region: ATAAGAACAAAAAAA TTGATTGTC TCGC GACAATCAA TCTTTATTAACCTTA ..........................................................................................................................TTGATTGTCTCGCGACAATCAA............................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -10.3 Tail_Score: -5.97979 Start: 123 End: 144 Full_Region: taaggttaataaaga ttgattgtc gcga gacaatcaa tttttttgttcttat ..........................................................................................................................ttgattgtcgcgagacaatcaa............................................................................................................. Find igs database================================================ Query_seq: PI1322:PI1323|PI1322:PI1323:nucleoside permease:conserved hypothetical protein:->->:1241697..1241949 253 cagtgctaaacgtatttttaaattcatctcttagattttattgtttggcaacaaaagtacagattttatcacaaactaccaaaacaaagccgaatatttatgtaggaataagaacaaaaaaattgattgtctcgcgacaatcaatctttattaaccttaataatctaataccatgaaaaacacattgcaaagttaggcatacttacgcaaaattgcaaactttacaaatgctttcattttggtattaacacta Intra-Species Hit: Count: 1 Min: 1 Max: 253 Len: 253 Subject: pint_PI1322_PI1323|nucleoside permease:conserved hypothetical protein|POSITIVE:POSITIVE|[1241697,1241949]|253 HSP 1 e-value: 1.0E-128 bit: 460.0 Len: 253 Query Start:1 Query End:253 Subject Strand: POSITIVE Subject Start: 1 Subject End: 253 cagtgctaaacgtatttttaaattcatctcttagattttattgtttggcaacaaaagtacagattttatcacaaactaccaaaacaaagccgaatatttatgtaggaataagaacnnnnnnnttgattgtctcgcgacaatcaatctttattaaccttaataatctaataccatgaaaaacacattgcaaagttaggcatacttacgcaaaattgcaaactttacaaatgctttcattttggtattaacacta cagtgctaaacgtatttttaaattcatctcttagattttattgtttggcaacaaaagtacagattttatcacaaactaccaaaacaaagccgaatatttatgtaggaataagaacaaaaaaattgattgtctcgcgacaatcaatctttattaaccttaataatctaataccatgaaaaacacattgcaaagttaggcatacttacgcaaaattgcaaactttacaaatgctttcattttggtattaacacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUGCUAAACGUAUUUUUAAAUUCAUCUCUUAGAUUUUAUUGUUUGGCAACAAAAGUACAGAUUUUAUCACAAACUACCAAAACAAAGCCGAAUAUUUAUGUAGGAAUAAGAACAAAAAAAUUGAUUGUCUCGCGACAAUCAAUCUUUAUUAACCUUAAUAAUCUAAUACCAUGAAAAACACAUUGCAAAGUUAGGCAUACUUACGCAAAAUUGCAAACUUUACAAAUGCUUUCAUUUUGGUAUUAACACUA ...(((((((((......((((.((........)).)))).)))))))))..........................((((((((.(((((......((((((((((..((((.....(((.((((((((((....)))))))))).)))......))))....))))....)))))).......(((.((((((..(((..............))).)))))).)))..)))))..))))))))......... (-43.44) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUGUUAAUACCAAAAUGAAAGCAUUUGUAAAGUUUGCAAUUUUGCGUAAGUAUGCCUAACUUUGCAAUGUGUUUUUCAUGGUAUUAGAUUAUUAAGGUUAAUAAAGAUUGAUUGUCGCGAGACAAUCAAUUUUUUUGUUCUUAUUCCUACAUAAAUAUUCGGCUUUGUUUUGGUAGUUUGUGAUAAAAUCUGUACUUUUGUUGCCAAACAAUAAAAUCUAAGAGAUGAAUUUAAAAAUACGUUUAGCACUG ((((((((((((((....((((((((((((((((((.(((....(((....))))))..)))))))))).))))))))..))))))))......((((..(((.((((((((((((((....)))))))))))))))))..)))).............(((((.(((.((((((...(((((..((((((.......))))))..).))))..))))))..)))...)))))...............)))))) (-68.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 245 209 165 174 135 pint:PI0478|5end_50S_ribosomal_protein_L30_440923..441153_POSITIVE 230 228 181 215 169 pint:PI0920|5end_xanthan_lyase_849688..849918_POSITIVE 226 216 184 98 64 pint:PI0123|5end_outer_membrane_protein,_ompH_family_113906..114136_POSITIVE 223 48 2 196 141 pint:PI1183|5end_conserved_hypothetical_protein_1104442..1104672_POSITIVE 221 149 110 181 146 pint:PI0838|5end_DNA_replication_and_repair_protein_772699..772929_POSITIVE 220 240 193 228 176 pint:PI0635|5end_dephospho-CoA_kinase_580954..581184_POSITIVE 218 99 56 39 10 pint:PI0003|5end_pseudouridylate_synthase_4270..4500_POSITIVE 216 203 163 86 38 pint:PI0899|5end_methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase_828738..828968_POSITIVE 213 106 70 191 154 pint:PI0093|5end_riboflavin_biosynthesis_protein_90489..90719_POSITIVE 212 217 184 91 59 pint:PI0199|5end_phosphate_acetyltransferase_189890..190120_POSITIVE 211 240 198 94 44 pint:PI0798|5end_malonyl_CoA-acyl_carrier_protein_transacylase_736011..736241_POSITIVE 211 233 191 165 121 pint:PI0597|5end_hypothetical_protein_546626..546856_POSITIVE 210 160 113 165 114 pint:PI2060|5end_conserved_hypothetical_protein;_possible_metalloprotease_2017595..2017825_POSITIVE 210 84 41 171 125 pint:PI1874|5end_hypothetical_protein_1818437..1818667_POSITIVE 210 218 171 155 111 pint:PI0748|5end_possible_mobilization_protein_676616..676846_POSITIVE 206 203 168 218 179 pint:PI1835|5end_L-asparaginase_I_1776144..1776374_POSITIVE 206 116 71 111 66 pint:PI0280|5end_conserved_hypothetical_protein_266001..266231_POSITIVE 205 227 185 54 12 pint:PI1090|5end_tRNA_uracil_5-methyltransferase_1014366..1014596_POSITIVE 204 91 59 94 58 pint:PI1431|5end_conserved_hypothetical_protein_1352079..1352309_POSITIVE 203 209 183 159 135 pint:PI1157|5end_hypothetical_protein_1081704..1081934_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 219 173 67 23 pint:PI1909|3end_DNA_gyrase,_B_subunit_1855270..1855420_POSITIVE 269 80 36 92 48 pint:PI0451|3end_serine_proteases,__S51_group_425127..425277_POSITIVE 239 209 164 151 104 pint:PI0797|3end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735752..735902_POSITIVE 228 208 165 151 113 pint:PI0477|3end_30S_ribosomal_protein_S5_440981..441131_POSITIVE 221 149 110 83 48 pint:PI0837|3end_conserved_hypothetical_protein_772681..772831_POSITIVE 213 60 11 73 18 pint:PI0211|3end_hypothetical_protein_204278..204428_POSITIVE 213 106 70 133 96 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 211 233 191 67 23 pint:PI0596|3end_hypothetical_protein_546608..546758_POSITIVE 210 84 41 73 27 pint:PI1873|3end_hypothetical_protein_1818419..1818569_POSITIVE 210 228 181 72 26 pint:PI1003|3end_conserved_hypothetical_protein_925718..925868_POSITIVE 206 116 71 111 66 pint:PI0279|3end_hypothetical_protein_266081..266231_POSITIVE 204 119 72 137 92 pint:PI1723|3end_conserved_hypothetical_protein_1642133..1642283_POSITIVE 203 147 123 144 116 pint:PI1941|3end_outer_membrane_receptor;_ragA_protein_1900619..1900769_POSITIVE 202 218 171 54 8 pint:PI0328|3end_conserved_hypothetical_protein_309993..310143_POSITIVE 202 49 12 79 37 pint:PI0316|3end_conserved_hypothetical_protein_299082..299232_POSITIVE 201 90 42 94 46 pint:PI2012|3end_hypothetical_protein_1971555..1971705_POSITIVE 200 211 185 126 99 pint:PI1146|3end_translation_initiation_factor_IF3_1073503..1073653_POSITIVE 196 230 185 148 110 pint:PI0518|3end_5'-nucleotidase_precursor_477959..478109_POSITIVE 194 114 71 108 67 pint:PI0274|3end_conserved_hypothetical_protein_263187..263337_POSITIVE 193 107 74 80 54 pint:PI1712|3end_hypothetical_protein_1627774..1627924_POSITIVE