Origin IGS: ctttaaataggtgtaattaattatattacctgtcggtaagattaaagtttgaaatactcaatacgtaagaacatagtaagcatagccatataatagtttgctgcaaagttccgaaattttctcggaatgagcaaattattcgcagtaaatcaggcaagctggctcgtttgcgggagcaagaataggagtagaactgacaagatggcacactggttgcggtatggcatagttggcatatcgtttgtaattaatgaagcgaatacatctgaaaaggcagtagcataacagaaattgataataataaaaacaaaaaaatatacatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgtatatttttttgtttttattattatcaatttctgttatgctactgccttttcagatgtattcgcttcattaattacaaacgatatgccaactatgccataccgcaaccagtgtgccatcttgtcagttctactcctattcttgctcccgcaaacgagccagcttgcctgatttactgcgaataatttgctcattccgagaaaatttcggaactttgcagcaaactattatatggctatgcttactatgttcttacgtattgagtatttcaaactttaatcttaccgacaggtaatataattaattacacctatttaaag Mask Tandem Repeat Region ================================================ ctttaaataggtgtaattaattatattacctgtcggtaagattaaagtttgaaatactcaatacgtaagaacatagtaagcatagccatataatagtttgctgcaaagttccgaaattttctcggaatgagcaaattattcgcagtaaatcaggcaagctggctcgtttgcgggagcaagaataggagtagaactgacaagatggcacactggttgcggtatggcatagttggcatatcgtttgtaattaatgaagcgaatacatctgaaaaggcagtagcataacagaaattgataataataaaaacaaaaaaatatacatt Find is-nt database================================================ Query_seq: PI0495:PI0496|PI0495:PI0496:conserved hypothetical protein:heat shock protein hsp70 (chaperone protein dnaK):->->:456449..456771 323 ctttaaataggtgtaattaattatattacctgtcggtaagattaaagtttgaaatactcaatacgtaagaacatagtaagcatagccatataatagtttgctgcaaagttccgaaattttctcggaatgagcaaattattcgcagtaaatcaggcaagctggctcgtttgcgggagcaagaataggagtagaactgacaagatggcacactggttgcggtatggcatagttggcatatcgtttgtaattaatgaagcgaatacatctgaaaaggcagtagcataacagaaattgataataataaaaacaaaaaaatatacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0495:PI0496|PI0495:PI0496:conserved hypothetical protein:heat shock protein hsp70 (chaperone protein dnaK):->->:456449..456771 323 ctttaaataggtgtaattaattatattacctgtcggtaagattaaagtttgaaatactcaatacgtaagaacatagtaagcatagccatataatagtttgctgcaaagttccgaaattttctcggaatgagcaaattattcgcagtaaatcaggcaagctggctcgtttgcgggagcaagaataggagtagaactgacaagatggcacactggttgcggtatggcatagttggcatatcgtttgtaattaatgaagcgaatacatctgaaaaggcagtagcataacagaaattgataataataaaaacaaaaaaatatacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0495:PI0496|PI0495:PI0496:conserved hypothetical protein:heat shock protein hsp70 (chaperone protein dnaK):->->:456449..456771 323 ctttaaataggtgtaattaattatattacctgtcggtaagattaaagtttgaaatactcaatacgtaagaacatagtaagcatagccatataatagtttgctgcaaagttccgaaattttctcggaatgagcaaattattcgcagtaaatcaggcaagctggctcgtttgcgggagcaagaataggagtagaactgacaagatggcacactggttgcggtatggcatagttggcatatcgtttgtaattaatgaagcgaatacatctgaaaaggcagtagcataacagaaattgataataataaaaacaaaaaaatatacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttaaataggtgtaattaattatattacctgtcggtaagattaaagtttgaaatactcaatacgtaagaacatagtaagcatagccatataatagtttgctgcaaagttccgaaattttctcggaatgagcaaattattcgcagtaaatcaggcaagctggctcgtttgcgggagcaagaataggagtagaactgacaagatggcacactggttgcggtatggcatagttggcatatcgtttgtaattaatgaagcgaatacatctgaaaaggcagtagcataacagaaattgataataataaaaacaaaaaaatatacatt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 90 End: 182 ......................................................................................... M I V C C K V P K F S R N E Q I I R S K S G K L A R L R E Q E ............................................................................................................................................. Protein_Len: 52 Strand: + Start: 127 End: 282 .............................................................................................................................. M S K L F A V N Q A S W L V C G S K N R S R T D K M A H W L R Y G I V G I S F V I N E A N T S E K A V A ......................................... Protein_Len: 50 Strand: - Start: 153 End: 302 ........................................................................................................................................................ A L Q S T Q P L L F L L L V S L I A C Q N R Y P M T P M D N T I L S A F V D S F A T A Y C F N I I M ..................... Protein_Len: 60 Strand: - Start: 139 End: 318 .......................................................................................................................................... E C Y I L C A P E N A P A L I P T S S V L H C V P Q P I A Y N A Y R K Y N I F R I C R F L C Y C L L F Q Y Y Y F C F F M ..... Protein_Len: 30 Strand: - Start: 45 End: 134 ............................................ L K F Y E I R L F M T L M A M Y Y N A A F N R F K R P I L M ............................................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 29 End: 238 ............................ L V Y S C L L C L W I I T Q Q L T G F N E R F S C I I R L L D P L S A R K R S C S Y S Y F Q C S P V S T A T H C L Q C M ..................................................................................... ctttaaataggtgtaattaattatattacctgtcggtaagattaaagtttgaaatactcaatacgtaagaacatagtaagcatagccatataatagtttgctgcaaagttccgaaattttctcggaatgagcaaattattcgcagtaaatcaggcaagctggctcgtttgcgggagcaagaataggagtagaactgacaagatggcacactggttgcggtatggcatagttggcatatcgtttgtaattaatgaagcgaatacatctgaaaaggcagtagcataacagaaattgataataataaaaacaaaaaaatatacatt 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================================================ PromScan Matrix: RpoN Strand: + Score: 89 Start: 202 End: 218 .........................................................................................................................................................................................................ATGGCACACTGGTTGCG......................................................................................................... ctttaaataggtgtaattaattatattacctgtcggtaagattaaagtttgaaatactcaatacgtaagaacatagtaagcatagccatataatagtttgctgcaaagttccgaaattttctcggaatgagcaaattattcgcagtaaatcaggcaagctggctcgtttgcgggagcaagaataggagtagaactgacaagatggcacactggttgcggtatggcatagttggcatatcgtttgtaattaatgaagcgaatacatctgaaaaggcagtagcataacagaaattgataataataaaaacaaaaaaatatacatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0495:PI0496|PI0495:PI0496:conserved hypothetical protein:heat shock protein hsp70 (chaperone protein dnaK):->->:456449..456771 323 ctttaaataggtgtaattaattatattacctgtcggtaagattaaagtttgaaatactcaatacgtaagaacatagtaagcatagccatataatagtttgctgcaaagttccgaaattttctcggaatgagcaaattattcgcagtaaatcaggcaagctggctcgtttgcgggagcaagaataggagtagaactgacaagatggcacactggttgcggtatggcatagttggcatatcgtttgtaattaatgaagcgaatacatctgaaaaggcagtagcataacagaaattgataataataaaaacaaaaaaatatacatt Intra-Species Hit: Count: 1 Min: 1 Max: 302 Len: 302 Subject: pint_PI0495_PI0496|conserved hypothetical protein:heat shock protein hsp70 (chaperone protein dnaK)|POSITIVE:POSITIVE|[456449,456771]|323 HSP 1 e-value: 1.0E-170 bit: 599.0 Len: 302 Query Start:1 Query End:302 Subject Strand: POSITIVE Subject Start: 1 Subject End: 302 ctttaaataggtgtaattaattatattacctgtcggtaagattaaagtttgaaatactcaatacgtaagaacatagtaagcatagccatataatagtttgctgcaaagttccgaaattttctcggaatgagcaaattattcgcagtaaatcaggcaagctggctcgtttgcgggagcaagaataggagtagaactgacaagatggcacactggttgcggtatggcatagttggcatatcgtttgtaattaatgaagcgaatacatctgaaaaggcagtagcataacagaaattgataataat..................... ctttaaataggtgtaattaattatattacctgtcggtaagattaaagtttgaaatactcaatacgtaagaacatagtaagcatagccatataatagtttgctgcaaagttccgaaattttctcggaatgagcaaattattcgcagtaaatcaggcaagctggctcgtttgcgggagcaagaataggagtagaactgacaagatggcacactggttgcggtatggcatagttggcatatcgtttgtaattaatgaagcgaatacatctgaaaaggcagtagcataacagaaattgataataat..................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAAAUAGGUGUAAUUAAUUAUAUUACCUGUCGGUAAGAUUAAAGUUUGAAAUACUCAAUACGUAAGAACAUAGUAAGCAUAGCCAUAUAAUAGUUUGCUGCAAAGUUCCGAAAUUUUCUCGGAAUGAGCAAAUUAUUCGCAGUAAAUCAGGCAAGCUGGCUCGUUUGCGGGAGCAAGAAUAGGAGUAGAACUGACAAGAUGGCACACUGGUUGCGGUAUGGCAUAGUUGGCAUAUCGUUUGUAAUUAAUGAAGCGAAUACAUCUGAAAAGGCAGUAGCAUAACAGAAAUUGAUAAUAAU ..........((...((((((((((...(.(((((((.........((((((..(((((....(....)......................(((((((((((.....(((((((.......))))))).))))))))))).).))))..))))))......((((.(((((....))))).....))))...))))))).)..............((((((((.((....)).)))))))).))))))))))...)).......((((.....((....))....))))............. (-69.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUAUCAAUUUCUGUUAUGCUACUGCCUUUUCAGAUGUAUUCGCUUCAUUAAUUACAAACGAUAUGCCAACUAUGCCAUACCGCAACCAGUGUGCCAUCUUGUCAGUUCUACUCCUAUUCUUGCUCCCGCAAACGAGCCAGCUUGCCUGAUUUACUGCGAAUAAUUUGCUCAUUCCGAGAAAAUUUCGGAACUUUGCAGCAAACUAUUAUAUGGCUAUGCUUACUAUGUUCUUACGUAUUGAGUAUUUCAAACUUUAAUCUUACCGACAGGUAAUAUAAUUAAUUACACCUAUUUAAAG .............((((....((....)).....))))............((((((((.....(((...........((((((.......(((((....(((..((.((((...(((......((((....))))..)))..)))).))..))).)))))..((((.((((((((((((((((...))))))))...)).)))))).)))).)))))).(((((((.(((((....))))).)))))))...........))).((((....))))...))))))))............... (-55.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 381 235 198 52 16 pint:PI2013|5end_hypothetical_protein_1972329..1972559_POSITIVE 373 234 191 78 17 pint:PI0029|5end_glutamine_amidotransferase_(GMP_synthase_(glutamine-hydrolyzing))_32593..32823_POSITIVE 355 185 142 217 174 pint:PI0787|5end_glycosyltransferase_724136..724366_POSITIVE 341 219 171 208 164 pint:PI0274|5end_conserved_hypothetical_protein_262856..263086_POSITIVE 340 210 161 69 13 pint:PI0698|5end_conserved_hypothetical_protein_635372..635602_POSITIVE 339 235 198 101 53 pint:PI1790|5end_hypothetical_protein_1722179..1722409_POSITIVE 337 217 176 139 103 pint:PI1640|5end_hypothetical_protein_1558062..1558292_POSITIVE 337 209 161 197 133 pint:PI0790|5end_hypothetical_protein_728953..729183_POSITIVE 331 190 141 169 104 pint:PI0606|5end_naphthoate_synthase_552956..553186_POSITIVE 331 198 156 146 99 pint:PI0415|5end_malate_dehydrogenase_385358..385588_POSITIVE 329 219 171 63 9 pint:PI1572|5end_hypothetical_protein_1497782..1498012_POSITIVE 325 198 152 183 111 pint:PI1755|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1681930..1682160_POSITIVE 325 198 151 213 165 pint:PI0277|5end_hypothetical_protein_264980..265210_POSITIVE 324 187 142 128 64 pint:PI0250|5end_hypothetical_protein_246946..247176_POSITIVE 321 190 141 201 145 pint:PI1831|5end_conserved_hypothetical_protein_1770298..1770528_POSITIVE 320 199 151 79 32 pint:PI1887|5end_cell_division_protein_1829115..1829345_POSITIVE 320 198 154 60 12 pint:PI0324|5end_conserved_hypothetical_protein_303735..303965_POSITIVE 319 205 161 188 153 pint:PI1989|5end_conserved_hypothetical_protein;_possible_thioredoxin_1944018..1944248_POSITIVE 319 220 171 107 39 pint:PI0635|5end_dephospho-CoA_kinase_580954..581184_POSITIVE 319 246 203 217 177 pint:PI0351|5end_hypothetical_protein_324317..324547_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 234 191 132 71 pint:PI0028|3end_aminopeptidase_32727..32877_POSITIVE 355 185 142 139 96 pint:PI0785|3end_hypothetical_protein_724138..724288_POSITIVE 355 185 142 136 93 pint:PI0786|3end_conserved_hypothetical_protein;_possible_glycosyltransferase_724135..724285_POSITIVE 337 217 176 130 94 pint:PI1639|3end_conserved_hypothetical_protein_1558133..1558283_POSITIVE 337 208 165 104 59 pint:PI1306|3end_dipeptidyl_peptidase_IV_1222452..1222602_POSITIVE 334 235 203 112 79 pint:PI0043|3end_thiamine_phosphate_pyrophosphorylase_43156..43306_POSITIVE 324 187 142 128 64 pint:PI0249|3end_conserved_hypothetical_protein_247026..247176_POSITIVE 320 198 154 57 9 pint:PI0322|3end_hypothetical_protein_303812..303962_POSITIVE 318 246 201 75 34 pint:PI1927|3end_hypothetical_protein_1872046..1872196_POSITIVE 318 208 162 144 93 pint:PI1343|3end_conserved_hypothetical_protein_1258539..1258689_POSITIVE 316 235 194 51 5 pint:PI1053|3end_conserved_hypothetical_protein_973638..973788_POSITIVE 309 220 171 138 96 pint:PI2025|3end_conserved_hypothetical_protein_1979452..1979602_POSITIVE 306 240 195 128 67 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 305 195 152 112 63 pint:PI0553|3end_recombination_protein_504383..504533_POSITIVE 302 180 134 144 104 pint:PI0142|3end_DNA-binding_protein_134191..134341_POSITIVE 301 204 162 145 93 pint:PI1867|3end_helicase_related_protein_1814668..1814818_POSITIVE 301 190 141 50 1 pint:PI0106|3end_ABC_transport_system,_ATP-binding/permease_103317..103467_POSITIVE 300 244 203 114 72 pint:PI0644|3end_dnaJ_protein_586569..586719_POSITIVE 300 227 188 84 41 pint:PI0300|3end_transposase_285761..285911_POSITIVE 299 208 162 140 94 pint:PI0873|3end_conserved_hypothetical_protein;_possible_permease_808956..809106_POSITIVE