Origin IGS: taaaaagtgaattgtttttaaagttataatgcgtagtaaagggtgtgccgaaaattcatttcgacatgcccttttttcttttgcagcgcattgtttttccctctttttctctcttatctttataggaacgtgatgaatcacgcccttgcatatgtgtttcaaaaacaagtctgccaaattatttacgtgtaaataaatatttttctacacgtaagtaataatttatttacacgtaagtaaatatttcttta .........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 taaagaaatatttacttacgtgtaaataaattattacttacgtgtagaaaaatatttatttacacgtaaataatttggcagacttgtttttgaaacacatatgcaagggcgtgattcatcacgttcctataaagataagagagaaaaagagggaaaaacaatgcgctgcaaaagaaaaaagggcatgtcgaaatgaattttcggcacaccctttactacgcattataactttaaaaacaattcacttttta Mask Tandem Repeat Region ================================================ taaaaagtgaattgtttttaaagttataatgcgtagtaaagggtgtgccgaaaattcatttcgacatgcccttttttcttttgcagcgcattgtttttccctctttttctctcttatctttataggaacgtgatgaatcacgcccttgcatatgtgtttcaaaaacaagtctgccaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Find is-nt database================================================ Query_seq: PI0647:PI0648|PI0647:PI0648:potassium uptake protein:hypothetical protein:->->:589337..589587 251 taaaaagtgaattgtttttaaagttataatgcgtagtaaagggtgtgccgaaaattcatttcgacatgcccttttttcttttgcagcgcattgtttttccctctttttctctcttatctttataggaacgtgatgaatcacgcccttgcatatgtgtttcaaaaacaagtctgccaaattatttacgtgtaaataaatatttttctacacgtaagtaataatttatttacacgtaagtaaatatttcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0647:PI0648|PI0647:PI0648:potassium uptake protein:hypothetical protein:->->:589337..589587 251 taaaaagtgaattgtttttaaagttataatgcgtagtaaagggtgtgccgaaaattcatttcgacatgcccttttttcttttgcagcgcattgtttttccctctttttctctcttatctttataggaacgtgatgaatcacgcccttgcatatgtgtttcaaaaacaagtctgccaaattatttacgtgtaaataaatatttttctacacgtaagtaataatttatttacacgtaagtaaatatttcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0647:PI0648|PI0647:PI0648:potassium uptake protein:hypothetical protein:->->:589337..589587 251 taaaaagtgaattgtttttaaagttataatgcgtagtaaagggtgtgccgaaaattcatttcgacatgcccttttttcttttgcagcgcattgtttttccctctttttctctcttatctttataggaacgtgatgaatcacgcccttgcatatgtgtttcaaaaacaagtctgccaaattatttacgtgtaaataaatatttttctacacgtaagtaataatttatttacacgtaagtaaatatttcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaagtgaattgtttttaaagttataatgcgtagtaaagggtgtgccgaaaattcatttcgacatgcccttttttcttttgcagcgcattgtttttccctctttttctctcttatctttataggaacgtgatgaatcacgcccttgcatatgtgtttcaaaaacaagtctgccaaattatttacgtgtaaataaatatttttctacacgtaagtaataatttatttacacgtaagtaaatatttcttta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 11 End: 130 .......... M V F K V I M R S K G C A E N S F R H A L F S F A A H C F S L F F S L I F I G T ......................................................................................................................... Protein_Len: 49 Strand: + Start: 43 End: 189 .......................................... M C R K F I S T C P F F F C S A L F F P L F L S Y L Y R N V M N H A L A Y V F Q K Q V C Q I I Y V .............................................................. Protein_Len: 31 Strand: - Start: 59 End: 151 .......................................................... K S M G K K R K C R M T K G E K E R K D K Y S R S S D R G Q M .................................................................................................... Protein_Len: 60 Strand: - Start: 1 End: 198 L T I I R L L P H A S F E N R C A R K E K A A C Q K E R K K E R I K I P V H H I V G K C I H K L F L D A L N N V H L Y M ..................................................... taaaaagtgaattgtttttaaagttataatgcgtagtaaagggtgtgccgaaaattcatttcgacatgcccttttttcttttgcagcgcattgtttttccctctttttctctcttatctttataggaacgtgatgaatcacgcccttgcatatgtgtttcaaaaacaagtctgccaaattatttacgtgtaaataaatatttttctacacgtaagtaataatttatttacacgtaagtaaatatttcttta 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================================================ taaaaagtgaattgtttttaaagttataatgcgtagtaaagggtgtgccgaaaattcatttcgacatgcccttttttcttttgcagcgcattgtttttccctctttttctctcttatctttataggaacgtgatgaatcacgcccttgcatatgtgtttcaaaaacaagtctgccaaattatttacgtgtaaataaatatttttctacacgtaagtaataatttatttacacgtaagtaaatatttcttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -8.3 Tail_Score: -5.79595 Start: 41 End: 71 Full_Region: ATAATGCGTAGTAAA GGGTGTGCCGAAA ATTCA TTTCGACATGCCC TTTTTTCTTTTGCAG ........................................GGGTGTGCCGAAAATTCATTTCGACATGCCC.................................................................................................................................................................................... TransTerm Strand: - Conf: 64 HP_score: -6.1 Tail_Score: -3.75015 Start: 41 End: 71 Full_Region: ctgcaaaagaaaaaa gggcatgtcgaaa tgaat tttcggcacaccc tttactacgcattat ........................................gggcatgtcgaaatgaattttcggcacaccc.................................................................................................................................................................................... Find igs database================================================ Query_seq: PI0647:PI0648|PI0647:PI0648:potassium uptake protein:hypothetical protein:->->:589337..589587 251 taaaaagtgaattgtttttaaagttataatgcgtagtaaagggtgtgccgaaaattcatttcgacatgcccttttttcttttgcagcgcattgtttttccctctttttctctcttatctttataggaacgtgatgaatcacgcccttgcatatgtgtttcaaaaacaagtctgccaaattatttacgtgtaaataaatatttttctacacgtaagtaataatttatttacacgtaagtaaatatttcttta Intra-Species Hit: Count: 1 Min: 1 Max: 251 Len: 251 Subject: pint_PI0647_PI0648|potassium uptake protein:hypothetical protein|POSITIVE:POSITIVE|[589337,589587]|251 HSP 1 e-value: 8.0E-68 bit: 258.0 Len: 130 Query Start:122 Query End:251 Subject Strand: POSITIVE Subject Start: 122 Subject End: 251 .........................................................................................................................ataggaacgtgatgaatcacgcccttgcatatgtgtttcaaaaacaagtctgccaaattatttacgtgtaaataaatatttttctacacgtaagtaataatttatttacacgtaagtaaatatttcttta .........................................................................................................................ataggaacgtgatgaatcacgcccttgcatatgtgtttcaaaaacaagtctgccaaattatttacgtgtaaataaatatttttctacacgtaagtaataatttatttacacgtaagtaaatatttcttta HSP 2 e-value: 5.0E-32 bit: 139.0 Len: 70 Query Start:1 Query End:70 Subject Strand: POSITIVE Subject Start: 1 Subject End: 70 taaaaagtgaattgtttttaaagttataatgcgtagtaaagggtgtgccgaaaattcatttcgacatgcc..................................................................................................................................................................................... taaaaagtgaattgtttttaaagttataatgcgtagtaaagggtgtgccgaaaattcatttcgacatgcc..................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAGUGAAUUGUUUUUAAAGUUAUAAUGCGUAGUAAAGGGUGUGCCGAAAAUUCAUUUCGACAUGCCCUUUUUUCUUUUGCAGCGCAUUGUUUUUCCCUCUUUUUCUCUCUUAUCUUUAUAGGAACGUGAUGAAUCACGCCCUUGCAUAUGUGUUUCAAAAACAAGUCUGCCAAAUUAUUUACGUGUAAAUAAAUAUUUUUCUACACGUAAGUAAUAAUUUAUUUACACGUAAGUAAAUAUUUCUUUA ...((((.((.((((((((......(((((((((.((((((((((((.(((((.....))))).))))))))........)))).)))))))))............................((((..(((((....)))))..))))............)))))))).)).......(((((((((((((((((((((((.......((....))))).))))))))))))))))))))......)))). (-62.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGAAAUAUUUACUUACGUGUAAAUAAAUUAUUACUUACGUGUAGAAAAAUAUUUAUUUACACGUAAAUAAUUUGGCAGACUUGUUUUUGAAACACAUAUGCAAGGGCGUGAUUCAUCACGUUCCUAUAAAGAUAAGAGAGAAAAAGAGGGAAAAACAAUGCGCUGCAAAAGAAAAAAGGGCAUGUCGAAAUGAAUUUUCGGCACACCCUUUACUACGCAUUAUAACUUUAAAAACAAUUCACUUUUUA ((((((.....(((.((((((((((((((((..((((......))))......)))))))))))))))).))).......((.(((((((((((......((((.(((((((((....))))).))))...................((((((.......((((.((............)).))))(((((((.....)))))))...)))))).....))))......))))))))))).))..)))))) (-64.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 552 218 171 215 166 pint:PI0173|5end_hypothetical_protein_165305..165535_POSITIVE 540 250 201 152 103 pint:PI0130|5end_hypothetical_protein_122032..122262_POSITIVE 532 218 171 165 118 pint:PI0115|5end_hypothetical_protein_108062..108292_POSITIVE 532 218 171 151 104 pint:PI0111|5end_hypothetical_protein_108048..108278_POSITIVE 532 218 171 116 69 pint:PI0112|5end_hypothetical_protein_108013..108243_POSITIVE 520 219 178 143 102 pint:PI1462|5end_hypothetical_protein_1385094..1385324_POSITIVE 515 169 123 196 143 pint:PI0902|5end_hypothetical_protein_832291..832521_POSITIVE 509 216 175 231 190 pint:PI0599|5end_hypothetical_protein_547376..547606_POSITIVE 488 156 111 184 138 pint:PI0866|5end_hypothetical_protein_803776..804006_POSITIVE 483 159 123 200 163 pint:PI1041|5end_hypothetical_protein_960443..960673_POSITIVE 478 230 182 144 96 pint:PI0619|5end_hypothetical_protein_569364..569594_POSITIVE 427 236 195 116 75 pint:PI1450|5end_hypothetical_protein_1372683..1372913_POSITIVE 414 230 182 128 80 pint:PI0312|5end_hypothetical_protein_294591..294821_POSITIVE 397 89 41 195 144 pint:PI0537|5end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_489756..489986_POSITIVE 393 155 124 168 138 pint:PI0933|5end_hypothetical_protein_865700..865930_POSITIVE 392 207 169 231 193 pint:PI0114|5end_hypothetical_protein_108139..108369_POSITIVE 383 88 41 171 124 pint:PI1086|5end_pyruvate:ferredoxin_oxidoreductase_1006602..1006832_POSITIVE 375 149 104 144 101 pint:PI0069|5end_hypothetical_protein_67072..67302_POSITIVE 373 214 172 227 181 pint:PI1674|5end_hypothetical_protein_1587829..1588059_POSITIVE 373 214 172 116 70 pint:PI1673|5end_hypothetical_protein_1587718..1587948_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 552 218 171 68 19 pint:PI0172|3end_ISPg3-related_transposase_165238..165388_POSITIVE 520 219 178 42 1 pint:PI1461|3end_conserved_hypothetical_protein_1385073..1385223_POSITIVE 449 156 111 78 36 pint:PI1440|3end_conserved_hypothetical_protein_1363009..1363159_POSITIVE 401 157 112 53 2 pint:PI0962|3end_phosphoglycerate_mutase_892702..892852_POSITIVE 397 89 41 138 87 pint:PI0535|3end_hypothetical_protein_489779..489929_POSITIVE 392 250 209 42 1 pint:PI0598|3end_hypothetical_protein_547233..547383_POSITIVE 376 159 111 66 17 pint:PI2088|3end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_2045815..2045965_POSITIVE 372 156 118 49 2 pint:PI0117|3end_ribonuclease_HI_111314..111464_POSITIVE 344 218 176 101 59 pint:PI2105|3end_hypothetical_protein_2059586..2059736_POSITIVE 320 157 124 95 66 pint:PI1820|3end_hypothetical_protein_1760377..1760527_POSITIVE 315 219 178 73 32 pint:PI0533|3end_ABC_transporter,_permease_protein_488421..488571_POSITIVE 301 218 178 50 10 pint:PI0797|3end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735752..735902_POSITIVE 300 205 162 151 106 pint:PI2082|3end_hypothetical_protein_2040263..2040413_POSITIVE 295 90 41 97 25 pint:PI0605|3end_chloromuconate_cycloisomerase_553026..553176_POSITIVE 293 189 141 151 85 pint:PI2039|3end_hypothetical_protein_1992991..1993141_POSITIVE 289 77 40 122 86 pint:PI0173|3end_hypothetical_protein_165558..165708_POSITIVE 284 90 41 67 18 pint:PI0915|3end_hypothetical_protein_845997..846147_POSITIVE 279 240 195 72 27 pint:PI0701|3end_hypothetical_protein_638537..638687_POSITIVE 278 120 71 135 81 pint:PI1743|3end_stationary-phase_survival_protein_1664930..1665080_POSITIVE 275 110 61 146 98 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE