Origin IGS: taaggaaaaagaaaaattgtttgtttgtagcgaaaatcaaagggctacaataccttaaataggctgttagaaatctaaaaccgccaagctttctacgagtttggcggtttttattttgcttgtcggtatctttttgcggattgctcggtatctttttgtagattactcgatatctttttgcggattactcggtatctttttgcggattactcggtatctttttgtagattgctcggtatctttttgtagattgctcgatatctttttatagaatgctcggtatcttttgaagaggtgttcgtgtaagttcatttaaaacaaaaaagtctataaaaaagatgttatatcgttcagatataacatcttttaaatagaaccgcaaagttcttacattatcttaaacaaataagtgttgttta .........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 taaacaacacttatttgtttaagataatgtaagaactttgcggttctatttaaaagatgttatatctgaacgatataacatcttttttatagacttttttgttttaaatgaacttacacgaacacctcttcaaaagataccgagcattctataaaaagatatcgagcaatctacaaaaagataccgagcaatctacaaaaagataccgagtaatccgcaaaaagataccgagtaatccgcaaaaagatatcgagtaatctacaaaaagataccgagcaatccgcaaaaagataccgacaagcaaaataaaaaccgccaaactcgtagaaagcttggcggttttagatttctaacagcctatttaaggtattgtagccctttgattttcgctacaaacaaacaatttttctttttcctta Mask Tandem Repeat Region ================================================ taaggaaaaagaaaaattgtttgtttgtagcgaaaatcaaagggctacaataccttaaataggctgttagaaatctaaaaccgccaagctttctacgagtttggcggtttttattttgcttgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaagaggtgttcgtgtaagttcatttaaaacaaaaaagtctataaaaaagatgttatatcgttcagatataacatcttttaaatagaaccgcaaagttcttacattatcttaaacaaataagtgttgttta Find is-nt database================================================ Query_seq: PI0939:PI0940|PI0939:PI0940:TonB-dependent outer membrane protein:ribonuclease G:->->:872502..872920 419 taaggaaaaagaaaaattgtttgtttgtagcgaaaatcaaagggctacaataccttaaataggctgttagaaatctaaaaccgccaagctttctacgagtttggcggtttttattttgcttgtcggtatctttttgcggattgctcggtatctttttgtagattactcgatatctttttgcggattactcggtatctttttgcggattactcggtatctttttgtagattgctcggtatctttttgtagattgctcgatatctttttatagaatgctcggtatcttttgaagaggtgttcgtgtaagttcatttaaaacaaaaaagtctataaaaaagatgttatatcgttcagatataacatcttttaaatagaaccgcaaagttcttacattatcttaaacaaataagtgttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0939:PI0940|PI0939:PI0940:TonB-dependent outer membrane protein:ribonuclease G:->->:872502..872920 419 taaggaaaaagaaaaattgtttgtttgtagcgaaaatcaaagggctacaataccttaaataggctgttagaaatctaaaaccgccaagctttctacgagtttggcggtttttattttgcttgtcggtatctttttgcggattgctcggtatctttttgtagattactcgatatctttttgcggattactcggtatctttttgcggattactcggtatctttttgtagattgctcggtatctttttgtagattgctcgatatctttttatagaatgctcggtatcttttgaagaggtgttcgtgtaagttcatttaaaacaaaaaagtctataaaaaagatgttatatcgttcagatataacatcttttaaatagaaccgcaaagttcttacattatcttaaacaaataagtgttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0939:PI0940|PI0939:PI0940:TonB-dependent outer membrane protein:ribonuclease G:->->:872502..872920 419 taaggaaaaagaaaaattgtttgtttgtagcgaaaatcaaagggctacaataccttaaataggctgttagaaatctaaaaccgccaagctttctacgagtttggcggtttttattttgcttgtcggtatctttttgcggattgctcggtatctttttgtagattactcgatatctttttgcggattactcggtatctttttgcggattactcggtatctttttgtagattgctcggtatctttttgtagattgctcgatatctttttatagaatgctcggtatcttttgaagaggtgttcgtgtaagttcatttaaaacaaaaaagtctataaaaaagatgttatatcgttcagatataacatcttttaaatagaaccgcaaagttcttacattatcttaaacaaataagtgttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaggaaaaagaaaaattgtttgtttgtagcgaaaatcaaagggctacaataccttaaataggctgttagaaatctaaaaccgccaagctttctacgagtttggcggtttttattttgcttgtcggtatctttttgcggattgctcggtatctttttgtagattactcgatatctttttgcggattactcggtatctttttgcggattactcggtatctttttgtagattgctcggtatctttttgtagattgctcgatatctttttatagaatgctcggtatcttttgaagaggtgttcgtgtaagttcatttaaaacaaaaaagtctataaaaaagatgttatatcgttcagatataacatcttttaaatagaaccgcaaagttcttacattatcttaaacaaataagtgttgttta Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: + Start: 101 End: 268 .................................................................................................... M A V F I L L V G I F L R I A R Y L F V D Y S I S F C G L L G I F L R I T R Y L F V D C S V S F C R L L D I F L ....................................................................................................................................................... Protein_Len: 38 Strand: - Start: 269 End: 382 ............................................................................................................................................................................................................................................................................ L I S P I K Q L P T R T L E N L V F F D I F F I N Y R E S I V D K L Y F R M ..................................... Protein_Len: 49 Strand: - Start: 166 End: 312 ..................................................................................................................................................................... E I D K Q P N S P I K K R I V R Y R K T S Q E T D K Q L N S S I K K Y F A R Y R K F L H E H L N M ........................................................................................................... Protein_Len: 54 Strand: - Start: 2 End: 163 . L F F F F Q K N T A F I L P S C Y R L Y A T L F R F G G L K R R T Q R N K N Q K D T D K Q P N S P I K K Y M ................................................................................................................................................................................................................................................................ taaggaaaaagaaaaattgtttgtttgtagcgaaaatcaaagggctacaataccttaaataggctgttagaaatctaaaaccgccaagctttctacgagtttggcggtttttattttgcttgtcggtatctttttgcggattgctcggtatctttttgtagattactcgatatctttttgcggattactcggtatctttttgcggattactcggtatctttttgtagattgctcggtatctttttgtagattgctcgatatctttttatagaatgctcggtatcttttgaagaggtgttcgtgtaagttcatttaaaacaaaaaagtctataaaaaagatgttatatcgttcagatataacatcttttaaatagaaccgcaaagttcttacattatcttaaacaaataagtgttgttta 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================================================ taaggaaaaagaaaaattgtttgtttgtagcgaaaatcaaagggctacaataccttaaataggctgttagaaatctaaaaccgccaagctttctacgagtttggcggtttttattttgcttgtcggtatctttttgcggattgctcggtatctttttgtagattactcgatatctttttgcggattactcggtatctttttgcggattactcggtatctttttgtagattgctcggtatctttttgtagattgctcgatatctttttatagaatgctcggtatcttttgaagaggtgttcgtgtaagttcatttaaaacaaaaaagtctataaaaaagatgttatatcgttcagatataacatcttttaaatagaaccgcaaagttcttacattatcttaaacaaataagtgttgttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.9 Tail_Score: -5.54338 Start: 81 End: 107 Full_Region: GTTAGAAATCTAAAA CCGCCAAGCTT TCTAC GAGTTTGGCGG TTTTTATTTTGCTTG ................................................................................CCGCCAAGCTTTCTACGAGTTTGGCGG........................................................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 83 HP_score: -8.0 Tail_Score: -4.39571 Start: 81 End: 107 Full_Region: caagcaaaataaaaa ccgccaaact cgtagaa agcttggcgg ttttagatttctaac ................................................................................ccgccaaactcgtagaaagcttggcgg........................................................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -10.1 Tail_Score: -5.80951 Start: 326 End: 376 Full_Region: gtaagaactttgcgg ttctatttaaaagatgttatatc tgaac gatataacatcttttttatagac ttttttgttttaaat .....................................................................................................................................................................................................................................................................................................................................ttctatttaaaagatgttatatctgaacgatataacatcttttttatagac........................................... TransTerm Strand: - Conf: 100 HP_score: -13.6 Tail_Score: -4.0613 Start: 327 End: 375 Full_Region: taagaactttgcggt tctatttaaaagatgttatatc tgaac gatataacatcttttttataga cttttttgttttaaa ......................................................................................................................................................................................................................................................................................................................................tctatttaaaagatgttatatctgaacgatataacatcttttttataga............................................ TransTerm Strand: + Conf: 100 HP_score: -11.1 Tail_Score: -4.18018 Start: 338 End: 364 Full_Region: AAAGTCTATAAAAAA GATGTTATATC GTTCA GATATAACATC TTTTAAATAGAACCG .................................................................................................................................................................................................................................................................................................................................................GATGTTATATCGTTCAGATATAACATC....................................................... TransTerm Strand: - Conf: 100 HP_score: -11.1 Tail_Score: -5.28826 Start: 338 End: 364 Full_Region: cggttctatttaaaa gatgttatatc tgaac gatataacatc ttttttatagacttt .................................................................................................................................................................................................................................................................................................................................................gatgttatatctgaacgatataacatc....................................................... TransTerm Strand: + Conf: 44 HP_score: -2.4 Tail_Score: -3.29147 Start: 374 End: 387 Full_Region: AACATCTTTTAAATA GAAC CGCAAA GTTC TTACATTATCTTAAA .....................................................................................................................................................................................................................................................................................................................................................................................GAACCGCAAAGTTC................................ Find igs database================================================ Query_seq: PI0939:PI0940|PI0939:PI0940:TonB-dependent outer membrane protein:ribonuclease G:->->:872502..872920 419 taaggaaaaagaaaaattgtttgtttgtagcgaaaatcaaagggctacaataccttaaataggctgttagaaatctaaaaccgccaagctttctacgagtttggcggtttttattttgcttgtcggtatctttttgcggattgctcggtatctttttgtagattactcgatatctttttgcggattactcggtatctttttgcggattactcggtatctttttgtagattgctcggtatctttttgtagattgctcgatatctttttatagaatgctcggtatcttttgaagaggtgttcgtgtaagttcatttaaaacaaaaaagtctataaaaaagatgttatatcgttcagatataacatcttttaaatagaaccgcaaagttcttacattatcttaaacaaataagtgttgttta Intra-Species Hit: Count: 2 Min: 1 Max: 419 Len: 419 Subject: pint_PI0939_PI0940|TonB-dependent outer membrane protein:ribonuclease G|POSITIVE:POSITIVE|[872502,872920]|419 HSP 1 e-value: 1.0E-177 bit: 622.0 Len: 314 Query Start:1 Query End:314 Subject Strand: POSITIVE Subject Start: 1 Subject End: 314 taaggaaaaagaaaaattgtttgtttgtagcgaaaatcaaagggctacaataccttaaataggctgttagaaatctaaaaccgccaagctttctacgagtttggcggtttttattttgcttgtcggtatctttttgcggattgctcggtatctttttgtagattactcgatatctttttgcggattactcggtatctttttgcggattactcggtatctttttgtagattgctcggtatctttttgtagattgctcgatatctttttatagaatgctcggtatcttttgaagaggtgttcgtgtaagttcattt......................................................................................................... taaggaaaaagaaaaattgtttgtttgtagcgaaaatcaaagggctacaataccttaaataggctgttagaaatctaaaaccgccaagctttctacgagtttggcggtttttattttgcttgtcggtatctttttgcggattgctcggtatctttttgtagattactcgatatctttttgcggattactcggtatctttttgcggattactcggtatctttttgtagattgctcggtatctttttgtagattgctcgatatctttttatagaatgctcggtatcttttgaagaggtgttcgtgtaagttcattt......................................................................................................... HSP 2 e-value: 6.0E-39 bit: 163.0 Len: 82 Query Start:338 Query End:419 Subject Strand: POSITIVE Subject Start: 338 Subject End: 419 .................................................................................................................................................................................................................................................................................................................................................gatgttatatcgttcagatataacatcttttaaatagaaccgcaaagttcttacattatcttaaacaaataagtgttgttta .................................................................................................................................................................................................................................................................................................................................................gatgttatatcgttcagatataacatcttttaaatagaaccgcaaagttcttacattatcttaaacaaataagtgttgttta Subject: pint_PI1952_PI1953|hypothetical protein:possible ABC-type permease|POSITIVE:POSITIVE|[1907100,1907274]|175 HSP 1 e-value: 2.0E-8 bit: 61.9 Len: 59 Query Start:188 Query End:246 Subject Strand: POSITIVE Subject Start: 91 Subject End: 149 ...........................................................................................................................................................................................ctcggtatctttttgcggattactcggtatctttttgtagattgctcggtatctttttg............................................................................................................................................................................. ...........................................................................................................................................................................................ctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatctttttg............................................................................................................................................................................. HSP 2 e-value: 7.0E-8 bit: 60.0 Len: 58 Query Start:231 Query End:288 Subject Strand: POSITIVE Subject Start: 90 Subject End: 147 ......................................................................................................................................................................................................................................gctcggtatctttttgtagattgctcgatatctttttatagaatgctcggtatctttt................................................................................................................................... ......................................................................................................................................................................................................................................gctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatctttt................................................................................................................................... HSP 3 e-value: 7.0E-8 bit: 60.0 Len: 58 Query Start:210 Query End:267 Subject Strand: POSITIVE Subject Start: 91 Subject End: 148 .................................................................................................................................................................................................................ctcggtatctttttgtagattgctcggtatctttttgtagattgctcgatatcttttt........................................................................................................................................................ .................................................................................................................................................................................................................ctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatcttttt........................................................................................................................................................ HSP 4 e-value: 1.0E-6 bit: 56.0 Len: 60 Query Start:143 Query End:202 Subject Strand: POSITIVE Subject Start: 90 Subject End: 149 ..............................................................................................................................................gctcggtatctttttgtagattactcgatatctttttgcggattactcggtatctttttg......................................................................................................................................................................................................................... ..............................................................................................................................................gctcggtatcttttcgcagattgctcgatatctttttggagttcgctcggtatctttttg......................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGAAAAAGAAAAAUUGUUUGUUUGUAGCGAAAAUCAAAGGGCUACAAUACCUUAAAUAGGCUGUUAGAAAUCUAAAACCGCCAAGCUUUCUACGAGUUUGGCGGUUUUUAUUUUGCUUGUCGGUAUCUUUUUGCGGAUUGCUCGGUAUCUUUUUGUAGAUUACUCGAUAUCUUUUUGCGGAUUACUCGGUAUCUUUUUGCGGAUUACUCGGUAUCUUUUUGUAGAUUGCUCGGUAUCUUUUUGUAGAUUGCUCGAUAUCUUUUUAUAGAAUGCUCGGUAUCUUUUGAAGAGGUGUUCGUGUAAGUUCAUUUAAAACAAAAAAGUCUAUAAAAAAGAUGUUAUAUCGUUCAGAUAUAACAUCUUUUAAAUAGAACCGCAAAGUUCUUACAUUAUCUUAAACAAAUAAGUGUUGUUUA .......(((.((...(((((((((((..((((((..(((((((.....(((((....((((((.....(((((..(((((((((((((((.....))))))))))))))).))))))))))).)))))))))))).((((...(((((((((......))).))).))).)))))))))).(((......(((...((((((((..((((.(((((((......))).)))).))))..(((((((...((((.(((((((((((((.(((.(((...))))))..)))))))))).))).))))...........)))))))..(((((..(((((((((((((((.....)))))))))))))))..))))).))))))))....)))...))).)))))))))))...)).))). (-114.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACAACACUUAUUUGUUUAAGAUAAUGUAAGAACUUUGCGGUUCUAUUUAAAAGAUGUUAUAUCUGAACGAUAUAACAUCUUUUUUAUAGACUUUUUUGUUUUAAAUGAACUUACACGAACACCUCUUCAAAAGAUACCGAGCAUUCUAUAAAAAGAUAUCGAGCAAUCUACAAAAAGAUACCGAGCAAUCUACAAAAAGAUACCGAGUAAUCCGCAAAAAGAUACCGAGUAAUCCGCAAAAAGAUAUCGAGUAAUCUACAAAAAGAUACCGAGCAAUCCGCAAAAAGAUACCGACAAGCAAAAUAAAAACCGCCAAACUCGUAGAAAGCUUGGCGGUUUUAGAUUUCUAACAGCCUAUUUAAGGUAUUGUAGCCCUUUGAUUUUCGCUACAAACAAACAAUUUUUCUUUUUCCUUA (((((((.......)))))))......(((.((((.(((((((.(((((..(((((((((((((((.....)))))))))))))))..))))).((((((((......((...((((.((.....(((............(((....(((......)))..)))....((((......))))...)))..((((......))))..)).))))....))..........((....)).))))))))...(((.(((.(((......))))))))).....))))))).....................(((((((((((.((.......)).)))))))))))....)))).)))((((.....)))).(((((((............)))))))........................ (-84.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 467 240 191 223 174 pint:PI1709|5end_ABC_transporter,_ATP-binding_protein_1625843..1626073_POSITIVE 351 150 102 74 18 pint:PI0064|5end_hypothetical_protein_63622..63852_POSITIVE 342 170 122 54 6 pint:PI0364|5end_hypothetical_protein_334002..334232_POSITIVE 340 109 61 83 31 pint:PI0729|5end_integrase_661428..661658_POSITIVE 337 150 103 64 11 pint:PI0692|5end_iron_compound_ABC_transporter,_permease_protein_627350..627580_POSITIVE 336 124 81 151 108 pint:PI1726|5end_ATP-dependent_DNA_helicase_1643402..1643632_POSITIVE 335 130 81 69 21 pint:PI0665|5end_dihydroorotate_dehydrogenase_607865..608095_POSITIVE 319 127 82 166 116 pint:PI1945|5end_ribonuclease_HII_1901932..1902162_POSITIVE 319 129 83 165 118 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 319 129 83 91 44 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 314 115 78 217 171 pint:PI2168|5end_hypothetical_protein_2111286..2111516_POSITIVE 313 214 178 208 175 pint:PI1520|5end_hypothetical_protein_1441162..1441392_POSITIVE 311 159 114 168 119 pint:PI0572|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_516382..516612_POSITIVE 309 150 107 113 74 pint:PI0819|5end_hypothetical_protein_759414..759644_POSITIVE 302 149 101 216 164 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 301 70 24 173 137 pint:PI0996|5end_hypothetical_protein_920458..920688_POSITIVE 301 174 136 85 43 pint:PI0244|5end_possible_mobilization_protein_C_240752..240982_POSITIVE 300 160 116 197 149 pint:PI1781|5end_membrane-associated_zinc_metalloprotease_1713074..1713304_POSITIVE 300 150 108 220 173 pint:PI0751|5end_conserved_hypothetical_protein_680623..680853_POSITIVE 297 119 73 228 184 pint:PI0537|5end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_489756..489986_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 109 61 83 31 pint:PI0728|3end_integrase_661508..661658_POSITIVE 323 148 101 146 92 pint:PI0601|3end_hypothetical_protein_549020..549170_POSITIVE 319 127 82 144 94 pint:PI1944|3end_hypothetical_protein_1901990..1902140_POSITIVE 318 157 117 141 107 pint:PI1855|3end_lipopolysaccharide_biosynthesis_protein_1803168..1803318_POSITIVE 316 240 202 47 15 pint:PI0583|3end_hypothetical_protein_526276..526426_POSITIVE 314 115 78 56 10 pint:PI2165|3end_conserved_hypothetical_protein;_possible_membrane_protein_2111205..2111355_POSITIVE 303 126 81 86 37 pint:PI0642|3end_thioredoxin_family_protein_585582..585732_POSITIVE 301 139 91 136 74 pint:PI0571|3end_conserved_hypothetical_protein;_possible_permease_516449..516599_POSITIVE 300 157 113 115 76 pint:PI2155|3end_hypothetical_protein_2101052..2101202_POSITIVE 300 160 116 140 92 pint:PI1780|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_1713097..1713247_POSITIVE 300 150 108 150 103 pint:PI0750|3end_zinc_protease_680633..680783_POSITIVE 298 150 101 148 98 pint:PI0258|3end_conjugative_transposon_protein,_TraG_252285..252435_POSITIVE 293 130 82 144 95 pint:PI1664|3end_conserved_hypothetical_protein_1578090..1578240_POSITIVE 291 110 68 64 13 pint:PI2108|3end_cell_surface_protein;_possible_cell_surface_antigen_BspA_2060625..2060775_POSITIVE 291 126 93 42 7 pint:PI0005|3end_hypothetical_protein_7450..7600_POSITIVE 290 147 101 97 58 pint:PI0570|3end_exsB_protein;_possible_aluminum_resistance_protein_515395..515545_POSITIVE 290 159 111 59 14 pint:PI0039|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_41077..41227_POSITIVE 284 137 94 47 5 pint:PI1750|3end_sulfate_transporter_1673896..1674046_POSITIVE 283 137 93 83 37 pint:PI2103|3end_hypothetical_protein_2057934..2058084_POSITIVE 280 213 178 151 119 pint:PI1519|3end_UDP-N-acetylglucosamine_acetyltransferase_1441186..1441336_POSITIVE