Origin IGS: taaagtcgctacaccttattatattatatatagaaacgagaaactccattggtattgtaaaagagcaataccgatggagtttctttgcgtaatgtatatttctgtgcttgcaataagttgtcggaacagacaagggagagactgccacagtagaaaaacagcagagaaattatctatttgctgcttgatgacgaaggtgaaaaaatgcccctattttgtaaagatagttttcttaaaaa .........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 tttttaagaaaactatctttacaaaataggggcattttttcaccttcgtcatcaagcagcaaatagataatttctctgctgtttttctactgtggcagtctctcccttgtctgttccgacaacttattgcaagcacagaaatatacattacgcaaagaaactccatcggtattgctcttttacaataccaatggagtttctcgtttctatatataatataataaggtgtagcgacttta Mask Tandem Repeat Region ================================================ taaagtcgctacaccttattatattatatatagaaacgagaaactccattggtattgtaaaagagcaataccgatggagtttctttgcgtaatgtatatttctgtgcttgcaataagttgtcggaacagacaagggagagactgccacagtagaaaaacagcagagaaattatctatttgctgcttgatgacgaaggtgaaaaaatgcccctattttgtaaagatagttttcttaaaaa Find is-nt database================================================ Query_seq: PI0658:PI0659|PI0658:PI0659:conserved hypothetical protein:hypothetical protein:->->:603104..603342 239 taaagtcgctacaccttattatattatatatagaaacgagaaactccattggtattgtaaaagagcaataccgatggagtttctttgcgtaatgtatatttctgtgcttgcaataagttgtcggaacagacaagggagagactgccacagtagaaaaacagcagagaaattatctatttgctgcttgatgacgaaggtgaaaaaatgcccctattttgtaaagatagttttcttaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0658:PI0659|PI0658:PI0659:conserved hypothetical protein:hypothetical protein:->->:603104..603342 239 taaagtcgctacaccttattatattatatatagaaacgagaaactccattggtattgtaaaagagcaataccgatggagtttctttgcgtaatgtatatttctgtgcttgcaataagttgtcggaacagacaagggagagactgccacagtagaaaaacagcagagaaattatctatttgctgcttgatgacgaaggtgaaaaaatgcccctattttgtaaagatagttttcttaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0658:PI0659|PI0658:PI0659:conserved hypothetical protein:hypothetical protein:->->:603104..603342 239 taaagtcgctacaccttattatattatatatagaaacgagaaactccattggtattgtaaaagagcaataccgatggagtttctttgcgtaatgtatatttctgtgcttgcaataagttgtcggaacagacaagggagagactgccacagtagaaaaacagcagagaaattatctatttgctgcttgatgacgaaggtgaaaaaatgcccctattttgtaaagatagttttcttaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaagtcgctacaccttattatattatatatagaaacgagaaactccattggtattgtaaaagagcaataccgatggagtttctttgcgtaatgtatatttctgtgcttgcaataagttgtcggaacagacaagggagagactgccacagtagaaaaacagcagagaaattatctatttgctgcttgatgacgaaggtgaaaaaatgcccctattttgtaaagatagttttcttaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 23 End: 238 ...................... M I Y R N E K L H W Y C K R A I P M E F L C V M Y I S V L A I S C R N R Q G R D C H S R K T A E K L S I C C L M T K V K . Protein_Len: 49 Strand: - Start: 27 End: 173 .......................... I Y F R S V G N T N Y F L L V S P T E K R L T Y K Q A Q L L N D S C V L S L S G C Y F F L L S I M .................................................................. Protein_Len: 56 Strand: - Start: 22 End: 189 ..................... I I Y L F S F S W Q Y Q L L A I G I S N R Q T I Y I E T S A I L Q R F L C P L S Q W L L F V A S F N D I Q Q K M .................................................. Protein_Len: 49 Strand: - Start: 2 End: 148 . F D S C R I I N Y I S V L F E M P I T F S C Y R H L K K A Y H I N R H K C Y T T P V S L P S V A M ........................................................................................... taaagtcgctacaccttattatattatatatagaaacgagaaactccattggtattgtaaaagagcaataccgatggagtttctttgcgtaatgtatatttctgtgcttgcaataagttgtcggaacagacaagggagagactgccacagtagaaaaacagcagagaaattatctatttgctgcttgatgacgaaggtgaaaaaatgcccctattttgtaaagatagttttcttaaaaa 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================================================ taaagtcgctacaccttattatattatatatagaaacgagaaactccattggtattgtaaaagagcaataccgatggagtttctttgcgtaatgtatatttctgtgcttgcaataagttgtcggaacagacaagggagagactgccacagtagaaaaacagcagagaaattatctatttgctgcttgatgacgaaggtgaaaaaatgcccctattttgtaaagatagttttcttaaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 88 HP_score: -13.0 Tail_Score: -3.10297 Start: 38 End: 85 Full_Region: aatatacattacgca aagaaactccatcggtattg ctctttta caataccaatggagtttctc gtttctatatataat .....................................aagaaactccatcggtattgctcttttacaataccaatggagtttctc.......................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -18.5 Tail_Score: -3.70863 Start: 40 End: 83 Full_Region: TATATATAGAAACGA GAAACTCCATTGGTATTGT AAAAGA GCAATACCGATGGAGTTTC TTTGCGTAATGTATA .......................................GAAACTCCATTGGTATTGTAAAAGAGCAATACCGATGGAGTTTC............................................................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -15.6 Tail_Score: -3.10187 Start: 40 End: 83 Full_Region: tatacattacgcaaa gaaactccatcggtattg ctctttta caataccaatggagtttc tcgtttctatatata .......................................gaaactccatcggtattgctcttttacaataccaatggagtttc............................................................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -13.5 Tail_Score: -4.47183 Start: 44 End: 79 Full_Region: TATAGAAACGAGAAA CTCCATTGGTATTGT AAAAGA GCAATACCGATGGAG TTTCTTTGCGTAATG ...........................................CTCCATTGGTATTGTAAAAGAGCAATACCGATGGAG................................................................................................................................................................ TransTerm Strand: - Conf: 90 HP_score: -10.6 Tail_Score: -4.19307 Start: 44 End: 79 Full_Region: cattacgcaaagaaa ctccatcggtattg ctctttta caataccaatggag tttctcgtttctata ...........................................ctccatcggtattgctcttttacaataccaatggag................................................................................................................................................................ Find igs database================================================ Query_seq: PI0658:PI0659|PI0658:PI0659:conserved hypothetical protein:hypothetical protein:->->:603104..603342 239 taaagtcgctacaccttattatattatatatagaaacgagaaactccattggtattgtaaaagagcaataccgatggagtttctttgcgtaatgtatatttctgtgcttgcaataagttgtcggaacagacaagggagagactgccacagtagaaaaacagcagagaaattatctatttgctgcttgatgacgaaggtgaaaaaatgcccctattttgtaaagatagttttcttaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 239 Len: 239 Subject: pint_PI0658_PI0659|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[603104,603342]|239 HSP 1 e-value: 1.0E-133 bit: 474.0 Len: 239 Query Start:1 Query End:239 Subject Strand: POSITIVE Subject Start: 1 Subject End: 239 taaagtcgctacaccttattatattatatatagaaacgagaaactccattggtattgtaaaagagcaataccgatggagtttctttgcgtaatgtatatttctgtgcttgcaataagttgtcggaacagacaagggagagactgccacagtagaaaaacagcagagaaattatctatttgctgcttgatgacgaaggtgaaaaaatgcccctattttgtaaagatagttttcttaaaaa taaagtcgctacaccttattatattatatatagaaacgagaaactccattggtattgtaaaagagcaataccgatggagtttctttgcgtaatgtatatttctgtgcttgcaataagttgtcggaacagacaagggagagactgccacagtagaaaaacagcagagaaattatctatttgctgcttgatgacgaaggtgaaaaaatgcccctattttgtaaagatagttttcttaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGUCGCUACACCUUAUUAUAUUAUAUAUAGAAACGAGAAACUCCAUUGGUAUUGUAAAAGAGCAAUACCGAUGGAGUUUCUUUGCGUAAUGUAUAUUUCUGUGCUUGCAAUAAGUUGUCGGAACAGACAAGGGAGAGACUGCCACAGUAGAAAAACAGCAGAGAAAUUAUCUAUUUGCUGCUUGAUGACGAAGGUGAAAAAAUGCCCCUAUUUUGUAAAGAUAGUUUUCUUAAAAA ...((((.((...((((........(((((((...(((((((((((((((((((((((......))))))))))))))))))))...)))..))))))).(((((.((.((((....)))).)).))))).)))).)).))))..((.(((((.....(((((((...........))))))).....(.((....)).)..........))))).))..((((......))))..... (-68.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAAGAAAACUAUCUUUACAAAAUAGGGGCAUUUUUUCACCUUCGUCAUCAAGCAGCAAAUAGAUAAUUUCUCUGCUGUUUUUCUACUGUGGCAGUCUCUCCCUUGUCUGUUCCGACAACUUAUUGCAAGCACAGAAAUAUACAUUACGCAAAGAAACUCCAUCGGUAUUGCUCUUUUACAAUACCAAUGGAGUUUCUCGUUUCUAUAUAUAAUAUAAUAAGGUGUAGCGACUUUA .......(((((...((((((.....))))))....)))))....((((((((.(((((((...(((.....))).)))))))......((((((((((.......(((((......)))))...)))))...)))))..(((((....(((...(((((((((((.(((((((........))))))).))))))))))))))...)))))............))))..))))..... (-57.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 229 181 185 137 pint:PI0056|5end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_54967..55197_POSITIVE 348 148 103 88 42 pint:PI1609|5end_Na+/H+_anti-porter_1536058..1536288_POSITIVE 332 147 101 60 22 pint:PI1772|5end_pullulanase_1702257..1702487_POSITIVE 330 138 101 35 1 pint:PI0936|5end_conserved_hypothetical_protein_868329..868559_POSITIVE 328 150 107 185 133 pint:PI0164|5end_conserved_hypothetical_protein_158478..158708_POSITIVE 320 156 116 40 3 pint:PI0228|5end_outer_membrane_cobalamin_receptor_protein_225752..225982_POSITIVE 314 149 103 51 7 pint:PI1993|5end_thiol_protease/hemagglutinin,_PrtT_precursor_1946615..1946845_POSITIVE 314 125 81 202 141 pint:PI1592|5end_conserved_hypothetical_protein;_possible_permease_1519897..1520127_POSITIVE 310 155 115 121 78 pint:PI1890|5end_cell_division_protein_FtsW_1832886..1833116_POSITIVE 309 145 103 63 24 pint:PI0585|5end_conserved_hypothetical_protein_532660..532890_POSITIVE 305 165 123 106 58 pint:PI1858|5end_conserved_hypothetical_protein_1804400..1804630_POSITIVE 304 136 101 72 31 pint:PI0527|5end_outer_membrane_efflux_protein_482375..482605_POSITIVE 302 150 102 217 159 pint:PI0733|5end_membrane_protein;_predicted_exporter_664389..664619_POSITIVE 302 145 101 79 42 pint:PI0045|5end_thiamine_biosynthesis_protein_43768..43998_POSITIVE 301 147 102 86 40 pint:PI1834|5end_anaerobic_C4-dicarboxylate_membrane_transporter_1774861..1775091_POSITIVE 300 144 103 82 34 pint:PI0736|5end_transcriptional_regulator,_TetR_family_670580..670810_POSITIVE 299 229 184 164 121 pint:PI0202|5end_DNA_helicase_191753..191983_POSITIVE 298 166 122 208 165 pint:PI0032|5end_hypothetical_protein_36085..36315_POSITIVE 295 154 122 46 14 pint:PI0652|5end_conserved_hypothetical_protein_592878..593108_POSITIVE 291 147 102 64 22 pint:PI1032|5end_methylmalonyl-CoA_decarboxylase,_alpha_subunit_948463..948693_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 480 90 41 55 9 pint:PI0658|3end_conserved_hypothetical_protein_603043..603193_POSITIVE 333 225 182 128 86 pint:PI1679|3end_hypothetical_protein_1594964..1595114_POSITIVE 304 136 101 56 15 pint:PI0526|3end_hypothetical_protein_482439..482589_POSITIVE 302 150 102 115 57 pint:PI0732|3end_conserved_hypothetical_protein_664367..664517_POSITIVE 302 145 101 88 51 pint:PI0044|3end_thiamine_biosynthetic_enzyme_43857..44007_POSITIVE 299 229 184 66 23 pint:PI0200|3end_hypothetical_protein_191735..191885_POSITIVE 287 146 101 77 29 pint:PI1960|3end_hypothetical_protein_1918983..1919133_POSITIVE 287 120 71 143 86 pint:PI1732|3end_hypothetical_protein_1652098..1652248_POSITIVE 287 95 51 75 34 pint:PI1466|3end_GTP-binding_protein,_possible_GTP1/OBG_family_1393133..1393283_POSITIVE 287 112 75 145 108 pint:PI0657|3end_conserved_hypothetical_protein_602167..602317_POSITIVE 283 147 102 146 89 pint:PI0348|3end_conserved_hypothetical_protein_323211..323361_POSITIVE 280 130 84 56 2 pint:PI0322|3end_hypothetical_protein_303812..303962_POSITIVE 277 162 122 130 84 pint:PI1387|3end_cardiolipin_synthetase_1309417..1309567_POSITIVE 277 145 101 88 40 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 275 95 53 58 23 pint:PI2002|3end_hypothetical_protein_1960915..1961065_POSITIVE 272 146 103 150 102 pint:PI0914|3end_ATPase,_AAA_family_844992..845142_POSITIVE 271 199 151 136 80 pint:PI1067|3end_thymidylate_synthase_984811..984961_POSITIVE 270 229 182 118 73 pint:PI1129|3end_hypothetical_protein_1055603..1055753_POSITIVE 270 138 92 79 22 pint:PI0512|3end_conserved_hypothetical_protein_471440..471590_POSITIVE 270 167 123 61 21 pint:PI0087|3end_conserved_hypothetical_protein_86733..86883_POSITIVE