Origin IGS: tgaataagtctatttattttttgcaaaagtacttatttatatcgaacaaagcgatttttgcgatataaaaaatgccttcataaagcataaatagcaatatgaaggcacttaattacagttttgtttctatttattatcttgttttttgtgttggcatattgttttcttgaaatag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctatttcaagaaaacaatatgccaacacaaaaaacaagataataaatagaaacaaaactgtaattaagtgccttcatattgctatttatgctttatgaaggcattttttatatcgcaaaaatcgctttgttcgatataaataagtacttttgcaaaaaataaatagacttattca Mask Tandem Repeat Region ================================================ tgaataagtctatttattttttgcaaaagtacttatttatatcgaacaaagcgatttttgcgatataaaaaatgccttcataaagcataaatagcaatatgaaggcacttaattacagttttgtttctatttattatcttgttttttgtgttggcatattgttttcttgaaatag Find is-nt database================================================ Query_seq: PI2040:PI2041|PI2040:PI2041:conserved hypothetical protein; possible transporter:conserved hypothetical protein:->->:1994126..1994300 175 tgaataagtctatttattttttgcaaaagtacttatttatatcgaacaaagcgatttttgcgatataaaaaatgccttcataaagcataaatagcaatatgaaggcacttaattacagttttgtttctatttattatcttgttttttgtgttggcatattgttttcttgaaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2040:PI2041|PI2040:PI2041:conserved hypothetical protein; possible transporter:conserved hypothetical protein:->->:1994126..1994300 175 tgaataagtctatttattttttgcaaaagtacttatttatatcgaacaaagcgatttttgcgatataaaaaatgccttcataaagcataaatagcaatatgaaggcacttaattacagttttgtttctatttattatcttgttttttgtgttggcatattgttttcttgaaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2040:PI2041|PI2040:PI2041:conserved hypothetical protein; possible transporter:conserved hypothetical protein:->->:1994126..1994300 175 tgaataagtctatttattttttgcaaaagtacttatttatatcgaacaaagcgatttttgcgatataaaaaatgccttcataaagcataaatagcaatatgaaggcacttaattacagttttgtttctatttattatcttgttttttgtgttggcatattgttttcttgaaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaataagtctatttattttttgcaaaagtacttatttatatcgaacaaagcgatttttgcgatataaaaaatgccttcataaagcataaatagcaatatgaaggcacttaattacagttttgtttctatttattatcttgttttttgtgttggcatattgttttcttgaaatag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 81 End: 173 ................................................................................ L A Y I A I H L C K I V T K N R N I I K N K T N A Y Q K R S M .. tgaataagtctatttattttttgcaaaagtacttatttatatcgaacaaagcgatttttgcgatataaaaaatgccttcataaagcataaatagcaatatgaaggcacttaattacagttttgtttctatttattatcttgttttttgtgttggcatattgttttcttgaaatag 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================================================ tgaataagtctatttattttttgcaaaagtacttatttatatcgaacaaagcgatttttgcgatataaaaaatgccttcataaagcataaatagcaatatgaaggcacttaattacagttttgtttctatttattatcttgttttttgtgttggcatattgttttcttgaaatag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -3.7 Tail_Score: -3.40141 Start: 72 End: 108 Full_Region: TTTGCGATATAAAAA ATGCCTTCATAAAGC ATAAATA GCAATATGAAGGCAC TTAATTACAGTTTTG .......................................................................ATGCCTTCATAAAGCATAAATAGCAATATGAAGGCAC................................................................... TransTerm Strand: - Conf: 90 HP_score: -7.2 Tail_Score: -5.36441 Start: 73 End: 107 Full_Region: aaaactgtaattaag tgccttcatattgc tatttat gctttatgaaggca ttttttatatcgcaa ........................................................................tgccttcatattgctatttatgctttatgaaggca.................................................................... Find igs database================================================ Query_seq: PI2040:PI2041|PI2040:PI2041:conserved hypothetical protein; possible transporter:conserved hypothetical protein:->->:1994126..1994300 175 tgaataagtctatttattttttgcaaaagtacttatttatatcgaacaaagcgatttttgcgatataaaaaatgccttcataaagcataaatagcaatatgaaggcacttaattacagttttgtttctatttattatcttgttttttgtgttggcatattgttttcttgaaatag Intra-Species Hit: Count: 1 Min: 1 Max: 175 Len: 175 Subject: pint_PI2040_PI2041|conserved hypothetical protein; possible transporter:conserved hypothetical protein|POSITIVE:POSITIVE|[1994126,1994300]|175 HSP 1 e-value: 8.0E-95 bit: 347.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 tgaataagtctatttattttttgcaaaagtacttatttatatcgaacaaagcgatttttgcgatataaaaaatgccttcataaagcataaatagcaatatgaaggcacttaattacagttttgtttctatttattatcttgttttttgtgttggcatattgttttcttgaaatag tgaataagtctatttattttttgcaaaagtacttatttatatcgaacaaagcgatttttgcgatataaaaaatgccttcataaagcataaatagcaatatgaaggcacttaattacagttttgtttctatttattatcttgttttttgtgttggcatattgttttcttgaaatag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUAAGUCUAUUUAUUUUUUGCAAAAGUACUUAUUUAUAUCGAACAAAGCGAUUUUUGCGAUAUAAAAAAUGCCUUCAUAAAGCAUAAAUAGCAAUAUGAAGGCACUUAAUUACAGUUUUGUUUCUAUUUAUUAUCUUGUUUUUUGUGUUGGCAUAUUGUUUUCUUGAAAUAG (((((((((((................)).)))))))))..((((..((((((((...((((((((((((((((((((((((..((.......))..)))))))))..........((........))............)))))))))))).))).)))))))).))))..... (-37.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUUUCAAGAAAACAAUAUGCCAACACAAAAAACAAGAUAAUAAAUAGAAACAAAACUGUAAUUAAGUGCCUUCAUAUUGCUAUUUAUGCUUUAUGAAGGCAUUUUUUAUAUCGCAAAAAUCGCUUUGUUCGAUAUAAAUAAGUACUUUUGCAAAAAAUAAAUAGACUUAUUCA (((((((((((..((..............................((((........))))....(((((((((((((..((.......))..)))))))))))))(((((((((((((......))))..)))))))))...))..)))))........))))))......... (-32.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 107 73 208 174 pint:PI2042|5end_cation-transporting_ATPase_1994175..1994405_POSITIVE 249 164 124 54 12 pint:PI0220|5end_conserved_hypothetical_protein_211980..212210_POSITIVE 248 86 43 58 19 pint:PI0482|5end_50S_ribosomal_protein_L36_443346..443576_POSITIVE 248 96 51 209 162 pint:PI0188|5end_phosphomethylpyrimidine_kinase_178433..178663_POSITIVE 243 88 44 187 143 pint:PI1048|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_966277..966507_POSITIVE 242 118 83 44 5 pint:PI1546|5end_mobilizable_transposon,_excision_protein_1464060..1464290_POSITIVE 237 62 22 134 96 pint:PI1883|5end_conserved_hypothetical_protein;_possible_surface_protein_1824874..1825104_POSITIVE 235 169 146 198 169 pint:PI0106|5end_ABC_transport_system,_ATP-binding/permease_101381..101611_POSITIVE 234 167 121 71 15 pint:PI1300|5end_probable_glycosyltransferase_1213190..1213420_POSITIVE 230 151 118 151 114 pint:PI1444|5end_protease_ClpB_1365472..1365702_POSITIVE 228 169 122 125 83 pint:PI1872|5end_glycosyl_transferase,_group_2_family_protein_1817057..1817287_POSITIVE 228 145 104 139 98 pint:PI0660|5end_conserved_hypothetical_protein_603438..603668_POSITIVE 226 155 115 168 129 pint:PI0699|5end_conserved_hypothetical_protein_636647..636877_POSITIVE 223 170 144 121 91 pint:PI1770|5end_4-alpha-glucanotransferase_1697336..1697566_POSITIVE 222 157 111 222 163 pint:PI0435|5end_30S_ribosomal_protein_S21_406997..407227_POSITIVE 221 88 41 220 174 pint:PI1531|5end_biotin--acetyl-CoA-carboxylase_ligase_1450839..1451069_POSITIVE 219 105 61 108 64 pint:PI1857|5end_guanylate_kinase_1803816..1804046_POSITIVE 217 98 51 102 61 pint:PI0606|5end_naphthoate_synthase_552956..553186_POSITIVE 214 105 70 180 144 pint:PI1253|5end_hypothetical_protein_1175516..1175746_POSITIVE 213 165 124 187 143 pint:PI0801|5end_hypothetical_protein_739365..739595_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 86 43 41 2 pint:PI0481|3end_translation_initiation_factor_IF-1_443409..443559_POSITIVE 235 124 84 60 15 pint:PI1922|3end_hypothetical_protein_1865454..1865604_POSITIVE 235 63 43 151 132 pint:PI0482|3end_50S_ribosomal_protein_L36_443539..443689_POSITIVE 233 156 112 142 87 pint:PI0019|3end_conserved_hypothetical_protein_24454..24604_POSITIVE 232 64 21 136 91 pint:PI1512|3end_hypothetical_protein_1429893..1430043_POSITIVE 228 169 122 121 79 pint:PI1871|3end_glycosyl_transferase,_group_1_family_protein_1817133..1817283_POSITIVE 224 167 138 52 17 pint:PI1299|3end_glycosyltransferase_1213251..1213401_POSITIVE 224 159 116 148 109 pint:PI0645|3end_hypothetical_protein_586807..586957_POSITIVE 223 105 71 143 112 pint:PI1400|3end_hypothetical_protein_1321908..1322058_POSITIVE 219 105 61 97 53 pint:PI1856|3end_nicotinate-nucleotide_adenylyltransferase_1803885..1804035_POSITIVE 217 98 51 92 51 pint:PI0605|3end_chloromuconate_cycloisomerase_553026..553176_POSITIVE 216 162 122 141 103 pint:PI0363|3end_hypothetical_protein_333760..333910_POSITIVE 214 118 85 38 1 pint:PI1545|3end_conserved_hypothetical_protein_1464134..1464284_POSITIVE 213 165 124 73 29 pint:PI0800|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_739331..739481_POSITIVE 209 128 81 137 89 pint:PI1386|3end_sugar_phosphate_isomerase_1308031..1308181_POSITIVE 209 164 141 121 96 pint:PI1133|3end_GrpE_protein_1060404..1060554_POSITIVE 208 153 113 121 88 pint:PI2004|3end_1-deoxy-D-xylulose_5-phosphate_synthase_1963004..1963154_POSITIVE 205 156 113 127 88 pint:PI1214|3end_peptide_chain_release_factor_1_1133820..1133970_POSITIVE 204 145 101 145 101 pint:PI0698|3end_conserved_hypothetical_protein_636711..636861_POSITIVE 203 161 121 133 81 pint:PI1773|3end_alpha-amylase_(neopullulanase)_1706107..1706257_POSITIVE