Origin IGS: tgaaccggagcagctggtgatagaagccggctgtgacagcttggagttggtgtgtgtcagatactccaaaaccatcagttcgctgaaacggcagctgaaagaggtgaataagtctaacagtgagcttaaggaggcagaacaggaaaaaaccaagaataccttctttatgagactcaagtatttttttaccggacttttatccggtattgcagcaacagtattaacaaggttcgttattgcttacattcggaaaaagaaactggtttgacagttctcatctaaacagtaacccaccattataaatatcaagaaaatgagtaaaaacaagaatttcatctacggcatagcagcc .........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 ggctgctatgccgtagatgaaattcttgtttttactcattttcttgatatttataatggtgggttactgtttagatgagaactgtcaaaccagtttctttttccgaatgtaagcaataacgaaccttgttaatactgttgctgcaataccggataaaagtccggtaaaaaaatacttgagtctcataaagaaggtattcttggttttttcctgttctgcctccttaagctcactgttagacttattcacctctttcagctgccgtttcagcgaactgatggttttggagtatctgacacacaccaactccaagctgtcacagccggcttctatcaccagctgctccggttca Mask Tandem Repeat Region ================================================ tgaaccggagcagctggtgatagaagccggctgtgacagcttggagttggtgtgtgtcagatactccaaaaccatcagttcgctgaaacggcagctgaaagaggtgaataagtctaacagtgagcttaaggaggcagaacaggaaaaaaccaagaataccttctttatgagactcaagtatttttttaccggacttttatccggtattgcagcaacagtattaacaaggttcgttattgcttacattcggaaaaagaaactggtttgacagttctcatctaaacagtaacccaccattataaatatcaagaaaatgagtaaaaacaagaatttcatctacggcatagcagcc Find is-nt database================================================ Query_seq: PI0356:PI0358|PI0356:PI0358:hypothetical protein:hypothetical protein:->->:327349..327700 352 tgaaccggagcagctggtgatagaagccggctgtgacagcttggagttggtgtgtgtcagatactccaaaaccatcagttcgctgaaacggcagctgaaagaggtgaataagtctaacagtgagcttaaggaggcagaacaggaaaaaaccaagaataccttctttatgagactcaagtatttttttaccggacttttatccggtattgcagcaacagtattaacaaggttcgttattgcttacattcggaaaaagaaactggtttgacagttctcatctaaacagtaacccaccattataaatatcaagaaaatgagtaaaaacaagaatttcatctacggcatagcagcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0356:PI0358|PI0356:PI0358:hypothetical protein:hypothetical protein:->->:327349..327700 352 tgaaccggagcagctggtgatagaagccggctgtgacagcttggagttggtgtgtgtcagatactccaaaaccatcagttcgctgaaacggcagctgaaagaggtgaataagtctaacagtgagcttaaggaggcagaacaggaaaaaaccaagaataccttctttatgagactcaagtatttttttaccggacttttatccggtattgcagcaacagtattaacaaggttcgttattgcttacattcggaaaaagaaactggtttgacagttctcatctaaacagtaacccaccattataaatatcaagaaaatgagtaaaaacaagaatttcatctacggcatagcagcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0356:PI0358|PI0356:PI0358:hypothetical protein:hypothetical protein:->->:327349..327700 352 tgaaccggagcagctggtgatagaagccggctgtgacagcttggagttggtgtgtgtcagatactccaaaaccatcagttcgctgaaacggcagctgaaagaggtgaataagtctaacagtgagcttaaggaggcagaacaggaaaaaaccaagaataccttctttatgagactcaagtatttttttaccggacttttatccggtattgcagcaacagtattaacaaggttcgttattgcttacattcggaaaaagaaactggtttgacagttctcatctaaacagtaacccaccattataaatatcaagaaaatgagtaaaaacaagaatttcatctacggcatagcagcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaccggagcagctggtgatagaagccggctgtgacagcttggagttggtgtgtgtcagatactccaaaaccatcagttcgctgaaacggcagctgaaagaggtgaataagtctaacagtgagcttaaggaggcagaacaggaaaaaaccaagaataccttctttatgagactcaagtatttttttaccggacttttatccggtattgcagcaacagtattaacaaggttcgttattgcttacattcggaaaaagaaactggtttgacagttctcatctaaacagtaacccaccattataaatatcaagaaaatgagtaaaaacaagaatttcatctacggcatagcagcc Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 14 End: 265 ............. M V I E A G C D S L E L V C V R Y S K T I S S L K R Q L K E V N K S N S E L K E A E Q E K T K N T F F M R L K Y F F T G ....................................................................................... Protein_Len: 31 Strand: - Start: 244 End: 336 ................................................................................................................................................................................................................................................... M R F F F S T Q C N E D L C Y G V M I F I L F I L L F L F K M ................ Protein_Len: 60 Strand: - Start: 2 End: 181 . F R L L Q H Y F G A T V A Q L Q H T D S V G F G D T R Q F P L Q F L H I L R V T L K L L C F L F F G L I G E K H S E L M ........................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 1 End: 237 L Y E L V M L E S F R C S F S T F L D L L S S L S A S C S F V L F V K K I L S L Y K K V P S K D P I A A V T N V L N T M ................................................................................................................... tgaaccggagcagctggtgatagaagccggctgtgacagcttggagttggtgtgtgtcagatactccaaaaccatcagttcgctgaaacggcagctgaaagaggtgaataagtctaacagtgagcttaaggaggcagaacaggaaaaaaccaagaataccttctttatgagactcaagtatttttttaccggacttttatccggtattgcagcaacagtattaacaaggttcgttattgcttacattcggaaaaagaaactggtttgacagttctcatctaaacagtaacccaccattataaatatcaagaaaatgagtaaaaacaagaatttcatctacggcatagcagcc 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: 82 Start: 296 End: 325 .......................................................................................................................................................................................................................................................................................................GTTTTTACTCATTTTCTTGATATTTATAAT........................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgaaccggagcagctggtgatagaagccggctgtgacagcttggagttggtgtgtgtcagatactccaaaaccatcagttcgctgaaacggcagctgaaagaggtgaataagtctaacagtgagcttaaggaggcagaacaggaaaaaaccaagaataccttctttatgagactcaagtatttttttaccggacttttatccggtattgcagcaacagtattaacaaggttcgttattgcttacattcggaaaaagaaactggtttgacagttctcatctaaacagtaacccaccattataaatatcaagaaaatgagtaaaaacaagaatttcatctacggcatagcagcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0356:PI0358|PI0356:PI0358:hypothetical protein:hypothetical protein:->->:327349..327700 352 tgaaccggagcagctggtgatagaagccggctgtgacagcttggagttggtgtgtgtcagatactccaaaaccatcagttcgctgaaacggcagctgaaagaggtgaataagtctaacagtgagcttaaggaggcagaacaggaaaaaaccaagaataccttctttatgagactcaagtatttttttaccggacttttatccggtattgcagcaacagtattaacaaggttcgttattgcttacattcggaaaaagaaactggtttgacagttctcatctaaacagtaacccaccattataaatatcaagaaaatgagtaaaaacaagaatttcatctacggcatagcagcc Intra-Species Hit: Count: 1 Min: 1 Max: 352 Len: 352 Subject: pint_PI0356_PI0358|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[327349,327700]|352 HSP 1 e-value: 0.0 bit: 656.0 Len: 352 Query Start:1 Query End:352 Subject Strand: POSITIVE Subject Start: 1 Subject End: 352 tgaaccggagcagctggtgatagaagccggctgtgacagcttggagttggtgtgtgtcagatactccaaaaccatcagttcgctgaaacggcagctgaaagaggtgaataagtctaacagtgagcttaaggaggcagaacaggaaaaaaccaagaataccttctttatgagactcaagtannnnnnnaccggacttttatccggtattgcagcaacagtattaacaaggttcgttattgcttacattcggaaaaagaaactggtttgacagttctcatctaaacagtaacccaccattataaatatcaagaaaatgagtaaaaacaagaatttcatctacggcatagcagcc tgaaccggagcagctggtgatagaagccggctgtgacagcttggagttggtgtgtgtcagatactccaaaaccatcagttcgctgaaacggcagctgaaagaggtgaataagtctaacagtgagcttaaggaggcagaacaggaaaaaaccaagaataccttctttatgagactcaagtatttttttaccggacttttatccggtattgcagcaacagtattaacaaggttcgttattgcttacattcggaaaaagaaactggtttgacagttctcatctaaacagtaacccaccattataaatatcaagaaaatgagtaaaaacaagaatttcatctacggcatagcagcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAACCGGAGCAGCUGGUGAUAGAAGCCGGCUGUGACAGCUUGGAGUUGGUGUGUGUCAGAUACUCCAAAACCAUCAGUUCGCUGAAACGGCAGCUGAAAGAGGUGAAUAAGUCUAACAGUGAGCUUAAGGAGGCAGAACAGGAAAAAACCAAGAAUACCUUCUUUAUGAGACUCAAGUAUUUUUUUACCGGACUUUUAUCCGGUAUUGCAGCAACAGUAUUAACAAGGUUCGUUAUUGCUUACAUUCGGAAAAAGAAACUGGUUUGACAGUUCUCAUCUAAACAGUAACCCACCAUUAUAAAUAUCAAGAAAAUGAGUAAAAACAAGAAUUUCAUCUACGGCAUAGCAGCC ......(..(((((((((.......)))))))))..)....(((..((((.((((.....)))).))))..)))((((((.((((...))))))))))...(((((((....(((.....((((((((((((((.......((......)).......))))))...)))).))))..(((((((((((((((......))))))).....................(((..(((((((......((..((...((((.(((......)))))))..))..)))))))))..))).............))))))))..........)))..)))))))..(((......))) (-89.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCUGCUAUGCCGUAGAUGAAAUUCUUGUUUUUACUCAUUUUCUUGAUAUUUAUAAUGGUGGGUUACUGUUUAGAUGAGAACUGUCAAACCAGUUUCUUUUUCCGAAUGUAAGCAAUAACGAACCUUGUUAAUACUGUUGCUGCAAUACCGGAUAAAAGUCCGGUAAAAAAAUACUUGAGUCUCAUAAAGAAGGUAUUCUUGGUUUUUUCCUGUUCUGCCUCCUUAAGCUCACUGUUAGACUUAUUCACCUCUUUCAGCUGCCGUUUCAGCGAACUGAUGGUUUUGGAGUAUCUGACACACACCAACUCCAAGCUGUCACAGCCGGCUUCUAUCACCAGCUGCUCCGGUUCA .((((....((.((((.(((((.............(((......)))......((((((((((((.........((((((....((((...................((((.((((((...(((...))).....)))))))))).((((((((....)))))))).........)))).)))))).(((.(((((.....((......)).....))))).))).))))))))))))..............))))).)))).))..))))(((((((((((((.(((((...((.....))...))))))))))))).((((.((.........)).))))....))))). (-84.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 444 56 11 230 181 pint:PI1828|5end_peptidase,_M23/M37_family,_C-terminal_1768419..1768649_POSITIVE 363 50 2 229 185 pint:PI1641|5end_hypothetical_protein_1558495..1558725_POSITIVE 363 50 2 229 185 pint:PI0347|5end_hypothetical_protein_321267..321497_POSITIVE 358 57 13 192 144 pint:PI2177|5end_phosphoribosylaminoimidazole_carboxylase_2117127..2117357_POSITIVE 358 59 11 167 117 pint:PI2094|5end_hypothetical_protein_2049540..2049770_POSITIVE 358 49 2 56 5 pint:PI1677|5end_cell_division_protein_FtsH_1591766..1591996_POSITIVE 353 57 11 190 139 pint:PI1321|5end_conserved_hypothetical_protein_1239764..1239994_POSITIVE 353 45 8 77 32 pint:PI0495|5end_conserved_hypothetical_protein_454872..455102_POSITIVE 353 45 8 68 23 pint:PI0494|5end_hypothetical_protein_454863..455093_POSITIVE 349 49 8 49 5 pint:PI0323|5end_hypothetical_protein_305349..305579_POSITIVE 347 67 27 133 88 pint:PI1517|5end_AcrB/AcrD_family_multidrug_resistance_protein_1435831..1436061_POSITIVE 345 63 28 73 34 pint:PI1319|5end_possible_OmpA_,_outer_membrane_protein-related_protein_1235655..1235885_POSITIVE 341 46 6 106 51 pint:PI2028|5end_shikimate_kinase_1982162..1982392_POSITIVE 340 49 4 89 45 pint:PI0155|5end_conserved_hypothetical_protein_148290..148520_POSITIVE 337 65 22 211 163 pint:PI1197|5end_pseudouridylate_synthetase_1113558..1113788_POSITIVE 337 65 22 54 6 pint:PI1196|5end_hypothetical_protein_1113401..1113631_POSITIVE 337 58 15 201 154 pint:PI0667|5end_hypothetical_protein_610113..610343_POSITIVE 334 50 9 231 190 pint:PI1165|5end_hypothetical_protein_1089389..1089619_POSITIVE 334 50 9 147 106 pint:PI1166|5end_hypothetical_protein_1089305..1089535_POSITIVE 329 50 1 64 15 pint:PI1477|5end_TonB-dependent_outer_membrane_receptor_1399734..1399964_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 386 49 7 63 27 pint:PI0324|3end_conserved_hypothetical_protein_305680..305830_POSITIVE 353 57 11 107 56 pint:PI1320|3end_conserved_hypothetical_protein_1239761..1239911_POSITIVE 352 60 11 146 86 pint:PI0189|3end_integrase_180437..180587_POSITIVE 351 48 8 151 101 pint:PI1380|3end_conserved_hypothetical_protein_1303242..1303392_POSITIVE 349 59 15 142 89 pint:PI0860|3end_amidophosphoribosyltransferase_796276..796426_POSITIVE 349 49 2 118 44 pint:PI0779|3end_predicted_TPR-repeat-containing_protein_715800..715950_POSITIVE 337 108 63 95 42 pint:PI1954|3end_translation_initiation_factor_IF-2_1911647..1911797_POSITIVE 332 60 11 54 1 pint:PI1740|3end_DedA_family_protein_1662316..1662466_POSITIVE 328 60 13 100 48 pint:PI1794|3end_conserved_hypothetical_protein_1726696..1726846_POSITIVE 326 58 15 84 34 pint:PI2122|3end_conserved_hypothetical_protein_2070480..2070630_POSITIVE 321 50 5 69 21 pint:PI1832|3end_conserved_hypothetical_protein_1774023..1774173_POSITIVE 321 67 25 144 98 pint:PI1364|3end_dipeptidyl_peptidase_IV_1283993..1284143_POSITIVE 317 45 4 107 46 pint:PI1924|3end_cytidine_deaminase_1866495..1866645_POSITIVE 311 139 91 114 68 pint:PI1149|3end_30S_ribosomal_protein_S18_1075757..1075907_POSITIVE 310 66 25 137 86 pint:PI0135|3end_internalin-related_protein_127257..127407_POSITIVE 309 114 72 59 10 pint:PI0040|3end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41872..42022_POSITIVE 308 58 11 49 14 pint:PI0245|3end_possible_mobilization_protein_244258..244408_POSITIVE 307 250 202 43 2 pint:PI0175|3end_succinyl-CoA_synthetase_beta_subunit_168233..168383_POSITIVE 306 50 5 99 60 pint:PI0904|3end_conserved_hypothetical_protein_834295..834445_POSITIVE 306 60 13 83 36 pint:PI0584|3end_hypothetical_protein_527656..527806_POSITIVE