Origin IGS: cctcgcttcttctttacctcgttgctgccatttggcagttctgctatcatatctgttcatataaaagtcctcttttctttgttttcaatcttgcttaatttccgaacgctgaccgatgagaacggagtgattacggtctaatctccccgataaccgaacgaggggagcaagcgcagtttgtgggtacaaactgacgtcttgcaatgtcagctaacgaaacgtttacgcataaagcgttttgtcgtccaaaaatgaatgctatgcattcagaagattaactgtgttcgtggcattcccaccgttcaatgtgttcagtaaaaatctattgttggtactaccctaaaacggtcgaggattttgagtgaaagggacatccttttactcgatagtccttgaccgtttttctgttgttta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaacaacagaaaaacggtcaaggactatcgagtaaaaggatgtccctttcactcaaaatcctcgaccgttttagggtagtaccaacaatagatttttactgaacacattgaacggtgggaatgccacgaacacagttaatcttctgaatgcatagcattcatttttggacgacaaaacgctttatgcgtaaacgtttcgttagctgacattgcaagacgtcagtttgtacccacaaactgcgcttgctcccctcgttcggttatcggggagattagaccgtaatcactccgttctcatcggtcagcgttcggaaattaagcaagattgaaaacaaagaaaagaggacttttatatgaacagatatgatagcagaactgccaaatggcagcaacgaggtaaagaagaagcgagg Mask Tandem Repeat Region ================================================ cctcgcttcttctttacctcgttgctgccatttggcagttctgctatcatatctgttcatataaaagtcctcttttctttgttttcaatcttgcttaatttccgaacgctgaccgatgagaacggagtgattacggtctaatctccccgataaccgaacgaggggagcaagcgcagtttgtgggtacaaactgacgtcttgcaatgtcagctaacgaaacgtttacgcataaagcgttttgtcgtccaaaaatgaatgctatgcattcagaagattaactgtgttcgtggcattcccaccgttcaatgtgttcagtaaaaatctattgttggtactaccctaaaacggtcgaggattttgagtgaaagggacatccttttactcgatagtccttgaccgtttttctgttgttta Find is-nt database================================================ Query_seq: PI0375:PI0376|PI0375:PI0376:hypothetical protein:conserved hypothetical protein:->->:346143..346556 414 cctcgcttcttctttacctcgttgctgccatttggcagttctgctatcatatctgttcatataaaagtcctcttttctttgttttcaatcttgcttaatttccgaacgctgaccgatgagaacggagtgattacggtctaatctccccgataaccgaacgaggggagcaagcgcagtttgtgggtacaaactgacgtcttgcaatgtcagctaacgaaacgtttacgcataaagcgttttgtcgtccaaaaatgaatgctatgcattcagaagattaactgtgttcgtggcattcccaccgttcaatgtgttcagtaaaaatctattgttggtactaccctaaaacggtcgaggattttgagtgaaagggacatccttttactcgatagtccttgaccgtttttctgttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0375:PI0376|PI0375:PI0376:hypothetical protein:conserved hypothetical protein:->->:346143..346556 414 cctcgcttcttctttacctcgttgctgccatttggcagttctgctatcatatctgttcatataaaagtcctcttttctttgttttcaatcttgcttaatttccgaacgctgaccgatgagaacggagtgattacggtctaatctccccgataaccgaacgaggggagcaagcgcagtttgtgggtacaaactgacgtcttgcaatgtcagctaacgaaacgtttacgcataaagcgttttgtcgtccaaaaatgaatgctatgcattcagaagattaactgtgttcgtggcattcccaccgttcaatgtgttcagtaaaaatctattgttggtactaccctaaaacggtcgaggattttgagtgaaagggacatccttttactcgatagtccttgaccgtttttctgttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0375:PI0376|PI0375:PI0376:hypothetical protein:conserved hypothetical protein:->->:346143..346556 414 cctcgcttcttctttacctcgttgctgccatttggcagttctgctatcatatctgttcatataaaagtcctcttttctttgttttcaatcttgcttaatttccgaacgctgaccgatgagaacggagtgattacggtctaatctccccgataaccgaacgaggggagcaagcgcagtttgtgggtacaaactgacgtcttgcaatgtcagctaacgaaacgtttacgcataaagcgttttgtcgtccaaaaatgaatgctatgcattcagaagattaactgtgttcgtggcattcccaccgttcaatgtgttcagtaaaaatctattgttggtactaccctaaaacggtcgaggattttgagtgaaagggacatccttttactcgatagtccttgaccgtttttctgttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctcgcttcttctttacctcgttgctgccatttggcagttctgctatcatatctgttcatataaaagtcctcttttctttgttttcaatcttgcttaatttccgaacgctgaccgatgagaacggagtgattacggtctaatctccccgataaccgaacgaggggagcaagcgcagtttgtgggtacaaactgacgtcttgcaatgtcagctaacgaaacgtttacgcataaagcgttttgtcgtccaaaaatgaatgctatgcattcagaagattaactgtgttcgtggcattcccaccgttcaatgtgttcagtaaaaatctattgttggtactaccctaaaacggtcgaggattttgagtgaaagggacatccttttactcgatagtccttgaccgtttttctgttgttta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 22 End: 138 ..................... M L P F G S S A I I S V H I K V L F S L F S I L L N F R T L T D E N G V I T V .................................................................................................................................................................................................................................................................................... Protein_Len: 34 Strand: + Start: 239 End: 340 .............................................................................................................................................................................................................................................. M S S K N E C Y A F R R L T V F V A F P P F N V F S K N L L L V L P .......................................................................... Protein_Len: 43 Strand: - Start: 134 End: 262 ..................................................................................................................................... P R I E G I V S R P S C A C N T P V F Q R R A I D A L S V N V C L A N Q R G F I F A M ........................................................................................................................................................ Protein_Len: 41 Strand: - Start: 88 End: 210 ....................................................................................... D Q K I E S R Q G I L V S H N R D L R G S L R V L P A L A T Q P Y L S V D Q L T M ............................................................................................................................................................................................................ cctcgcttcttctttacctcgttgctgccatttggcagttctgctatcatatctgttcatataaaagtcctcttttctttgttttcaatcttgcttaatttccgaacgctgaccgatgagaacggagtgattacggtctaatctccccgataaccgaacgaggggagcaagcgcagtttgtgggtacaaactgacgtcttgcaatgtcagctaacgaaacgtttacgcataaagcgttttgtcgtccaaaaatgaatgctatgcattcagaagattaactgtgttcgtggcattcccaccgttcaatgtgttcagtaaaaatctattgttggtactaccctaaaacggtcgaggattttgagtgaaagggacatccttttactcgatagtccttgaccgtttttctgttgttta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 21 End: 50 ....................GTTGCTGCCATTTGGCAGTTCTGCTATCAT............................................................................................................................................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cctcgcttcttctttacctcgttgctgccatttggcagttctgctatcatatctgttcatataaaagtcctcttttctttgttttcaatcttgcttaatttccgaacgctgaccgatgagaacggagtgattacggtctaatctccccgataaccgaacgaggggagcaagcgcagtttgtgggtacaaactgacgtcttgcaatgtcagctaacgaaacgtttacgcataaagcgttttgtcgtccaaaaatgaatgctatgcattcagaagattaactgtgttcgtggcattcccaccgttcaatgtgttcagtaaaaatctattgttggtactaccctaaaacggtcgaggattttgagtgaaagggacatccttttactcgatagtccttgaccgtttttctgttgttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 66 HP_score: -7.3 Tail_Score: -3.4252 Start: 123 End: 149 Full_Region: ccctcgttcggttat cggggagatta gaccg taatcactccg ttctcatcggtcagc ..........................................................................................................................cggggagattagaccgtaatcactccg......................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 95 HP_score: -9.5 Tail_Score: -4.56597 Start: 253 End: 269 Full_Region: acacagttaatcttc tgaatgc ata gcattca tttttggacgacaaa ............................................................................................................................................................................................................................................................tgaatgcatagcattca................................................................................................................................................. TransTerm Strand: - Conf: 83 HP_score: -9.0 Tail_Score: -4.15565 Start: 346 End: 399 Full_Region: taaacaacagaaaaa cggtcaaggactatcgagtaaaagg atgtc cctttcactcaaaatcctcgaccg ttttagggtagtacc .........................................................................................................................................................................................................................................................................................................................................................cggtcaaggactatcgagtaaaaggatgtccctttcactcaaaatcctcgaccg............... TransTerm Strand: + Conf: 100 HP_score: -16.2 Tail_Score: -3.71819 Start: 347 End: 398 Full_Region: GTACTACCCTAAAAC GGTCGAGGATTTTGAGTGAAAGGG ACA TCCTTTTACTCGATAGTCCTTGACC GTTTTTCTGTTGTTT ..........................................................................................................................................................................................................................................................................................................................................................GGTCGAGGATTTTGAGTGAAAGGGACATCCTTTTACTCGATAGTCCTTGACC................ Find igs database================================================ Query_seq: PI0375:PI0376|PI0375:PI0376:hypothetical protein:conserved hypothetical protein:->->:346143..346556 414 cctcgcttcttctttacctcgttgctgccatttggcagttctgctatcatatctgttcatataaaagtcctcttttctttgttttcaatcttgcttaatttccgaacgctgaccgatgagaacggagtgattacggtctaatctccccgataaccgaacgaggggagcaagcgcagtttgtgggtacaaactgacgtcttgcaatgtcagctaacgaaacgtttacgcataaagcgttttgtcgtccaaaaatgaatgctatgcattcagaagattaactgtgttcgtggcattcccaccgttcaatgtgttcagtaaaaatctattgttggtactaccctaaaacggtcgaggattttgagtgaaagggacatccttttactcgatagtccttgaccgtttttctgttgttta Intra-Species Hit: Count: 2 Min: 1 Max: 414 Len: 414 Subject: pint_PI0375_PI0376|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[346143,346556]|414 HSP 1 e-value: 0.0 bit: 821.0 Len: 414 Query Start:1 Query End:414 Subject Strand: POSITIVE Subject Start: 1 Subject End: 414 cctcgcttcttctttacctcgttgctgccatttggcagttctgctatcatatctgttcatataaaagtcctcttttctttgttttcaatcttgcttaatttccgaacgctgaccgatgagaacggagtgattacggtctaatctccccgataaccgaacgaggggagcaagcgcagtttgtgggtacaaactgacgtcttgcaatgtcagctaacgaaacgtttacgcataaagcgttttgtcgtccaaaaatgaatgctatgcattcagaagattaactgtgttcgtggcattcccaccgttcaatgtgttcagtaaaaatctattgttggtactaccctaaaacggtcgaggattttgagtgaaagggacatccttttactcgatagtccttgaccgtttttctgttgttta cctcgcttcttctttacctcgttgctgccatttggcagttctgctatcatatctgttcatataaaagtcctcttttctttgttttcaatcttgcttaatttccgaacgctgaccgatgagaacggagtgattacggtctaatctccccgataaccgaacgaggggagcaagcgcagtttgtgggtacaaactgacgtcttgcaatgtcagctaacgaaacgtttacgcataaagcgttttgtcgtccaaaaatgaatgctatgcattcagaagattaactgtgttcgtggcattcccaccgttcaatgtgttcagtaaaaatctattgttggtactaccctaaaacggtcgaggattttgagtgaaagggacatccttttactcgatagtccttgaccgtttttctgttgttta Subject: pint_PI0745_PI0746|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[675731,676110]|380 HSP 1 e-value: 9.0E-35 bit: 149.0 Len: 155 Query Start:52 Query End:206 Subject Strand: NEGATIVE Subject Start: 185 Subject End: 329 ...................................................tctgttcatataaaagtcctcttttctttgttttcaatcttgcttaatttccgaacgctgaccgatgagaacggagtgattacggtctaatctccccgataaccgaacgaggggagcaagcgcagtttgtgggtacaaactgacgtcttgcaatg................................................................................................................................................................................................................ ...................................................tctgttcatataaaagtcctcttttcgttattt---------cttaatttctgatggctgaccgatgagaacggagtgattacggtctaacctccc-gataattaaacgaggagagcaagcgcagtttgtgggtacaaactgacgtcttgcaatg................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUCGCUUCUUCUUUACCUCGUUGCUGCCAUUUGGCAGUUCUGCUAUCAUAUCUGUUCAUAUAAAAGUCCUCUUUUCUUUGUUUUCAAUCUUGCUUAAUUUCCGAACGCUGACCGAUGAGAACGGAGUGAUUACGGUCUAAUCUCCCCGAUAACCGAACGAGGGGAGCAAGCGCAGUUUGUGGGUACAAACUGACGUCUUGCAAUGUCAGCUAACGAAACGUUUACGCAUAAAGCGUUUUGUCGUCCAAAAAUGAAUGCUAUGCAUUCAGAAGAUUAACUGUGUUCGUGGCAUUCCCACCGUUCAAUGUGUUCAGUAAAAAUCUAUUGUUGGUACUACCCUAAAACGGUCGAGGAUUUUGAGUGAAAGGGACAUCCUUUUACUCGAUAGUCCUUGACCGUUUUUCUGUUGUUUA ..............((((..((.((((((....))))))...))........(((..(((((...((.((...((.(((((((((((.((..((.............)).....))))))))))))).))....)).))................(((((..(((((((((((((((((((....)))))))).)).))))).((((((....(((((((((((.......)))))))))))..........(((((((...)))))))(((.((.....)).))).))))))))))..))))).)))))..)))...............))))..((...((((((((((((((((((((((((((((.....)))))))))))).))))))))))))))))...))...... (-129.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACAACAGAAAAACGGUCAAGGACUAUCGAGUAAAAGGAUGUCCCUUUCACUCAAAAUCCUCGACCGUUUUAGGGUAGUACCAACAAUAGAUUUUUACUGAACACAUUGAACGGUGGGAAUGCCACGAACACAGUUAAUCUUCUGAAUGCAUAGCAUUCAUUUUUGGACGACAAAACGCUUUAUGCGUAAACGUUUCGUUAGCUGACAUUGCAAGACGUCAGUUUGUACCCACAAACUGCGCUUGCUCCCCUCGUUCGGUUAUCGGGGAGAUUAGACCGUAAUCACUCCGUUCUCAUCGGUCAGCGUUCGGAAAUUAAGCAAGAUUGAAAACAAAGAAAAGAGGACUUUUAUAUGAACAGAUAUGAUAGCAGAACUGCCAAAUGGCAGCAACGAGGUAAAGAAGAAGCGAGG ......((...(((((((((.((((.....((((.(((((.....))))).))))....)))).)))))))))...))..((((...............((((((...((((.(((((((((.....(((((.((((((((....(((((((...))))))).....(((((.....((((.....))))...))))).)))))))).....(((((.((.((((((((....))))))))))))))).......))))).....(((((.(((((.....))))).)))))))))))))).)))).)))))).......((...........((...(((((....)))))...))..((....))...))....(((((....)))))......)))).............. (-119.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 792 150 108 231 190 pint:PI0746|5end_hypothetical_protein_675971..676201_POSITIVE 449 196 153 126 73 pint:PI0300|5end_transposase_285163..285393_POSITIVE 371 46 4 201 161 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 361 200 153 185 136 pint:PI1157|5end_hypothetical_protein_1081704..1081934_POSITIVE 358 47 4 58 5 pint:PI1498|5end_probable_membrane_associated_lipoprotein_1418427..1418657_POSITIVE 351 184 141 175 125 pint:PI0280|5end_conserved_hypothetical_protein_266001..266231_POSITIVE 345 164 122 91 30 pint:PI0223|5end_topoisomerase_IA_218377..218607_POSITIVE 342 43 2 178 130 pint:PI1985|5end_hypothetical_protein_1940291..1940521_POSITIVE 342 43 2 71 23 pint:PI1984|5end_MutT/nudix_family_protein_1940184..1940414_POSITIVE 334 160 115 127 65 pint:PI0566|5end_enoyl-[acyl-carrier-protein]_reductase_511832..512062_POSITIVE 333 198 155 109 70 pint:PI1381|5end_conserved_hypothetical_protein_1303060..1303290_POSITIVE 331 265 221 111 62 pint:PI1008|5end_cytochrome_c_nitrite_reductase,_small_subunit_928784..929014_POSITIVE 327 45 4 113 56 pint:PI0141|5end_glutamine_amidotransferase_involved_in_pyridoxine_biosynthesis_132710..132940_POSITIVE 326 70 22 72 24 pint:PI1364|5end_dipeptidyl_peptidase_IV_1281862..1282092_POSITIVE 324 58 20 197 137 pint:PI0693|5end_periplasmic_iron_binding_protein,_ABC_transporter_628387..628617_POSITIVE 323 160 114 120 70 pint:PI1491|5end_conserved_hypothetical_protein_1409410..1409640_POSITIVE 323 130 92 89 43 pint:PI1271|5end_transcriptional_regulator,__AraC/XylS_family_1190755..1190985_POSITIVE 322 237 191 126 73 pint:PI0005|5end_hypothetical_protein_6984..7214_POSITIVE 321 209 162 174 134 pint:PI0601|5end_hypothetical_protein_548758..548988_POSITIVE 321 44 7 217 170 pint:PI0147|5end_HIT_family_protein_140833..141063_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 164 122 76 15 pint:PI0222|3end_conserved_hypothetical_protein_218442..218592_POSITIVE 343 44 2 131 97 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 328 180 134 144 108 pint:PI0227|3end_ABC_transporter,_ATP-binding/permease_protein_225632..225782_POSITIVE 326 70 22 52 4 pint:PI1363|3end_hypothetical_protein_1281922..1282072_POSITIVE 324 58 20 99 39 pint:PI0691|3end_hypothetical_protein_628369..628519_POSITIVE 323 130 92 83 37 pint:PI1270|3end_probable_dipeptidyl_peptidase_1190829..1190979_POSITIVE 321 209 162 133 93 pint:PI0600|3end_bifunctional_purine_biosynthesis_protein,_5-aminoimidazole-4-carboxamide_ribonucleotide(AICAR)_transformylase/IMP_cyclohydrolase_548797..548947_POSITIVE 319 210 161 88 37 pint:PI0553|3end_recombination_protein_504383..504533_POSITIVE 317 170 121 106 44 pint:PI0279|3end_hypothetical_protein_266081..266231_POSITIVE 315 150 102 44 2 pint:PI1639|3end_conserved_hypothetical_protein_1558133..1558283_POSITIVE 313 177 134 86 38 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 309 186 146 150 105 pint:PI0091|3end_hypothetical_protein_89774..89924_POSITIVE 308 375 331 65 20 pint:PI1496|3end_nucleoside_phosphorylase_1417816..1417966_POSITIVE 305 209 161 143 80 pint:PI0666|3end_chorismate_synthase_610171..610321_POSITIVE 304 200 153 117 49 pint:PI0058|3end_conserved_hypothetical_protein_57044..57194_POSITIVE 303 188 143 74 29 pint:PI0047|3end_phosphomethylpyrimidine_kinase_46781..46931_POSITIVE 302 190 141 70 11 pint:PI2158|3end_glycosyl_transferase,_group_2_family_protein_2105347..2105497_POSITIVE 302 250 210 133 87 pint:PI1666|3end_conserved_hypothetical_protein_1579418..1579568_POSITIVE 300 200 154 82 27 pint:PI2157|3end_xanthosine_triphosphate_pyrophosphatase,_HAM1_family_2104457..2104607_POSITIVE 299 184 145 63 29 pint:PI1223|3end_conserved_hypothetical_protein_1144459..1144609_POSITIVE