Origin IGS: tgatatgtacagtaatataaaacaaccaataaacaaaaagaaaatctttacacactcttttcataaaaataatttttgttgaggcagctaagtaacgatgcttggttgccttttttatttcactggcaaaagtctgttatcatactggtaataatctattattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcatactaatgactatctattatcatactaatgactatctattatcatactaatgactatctattatcatactgatgataatgaatgtgtatcaaagctaaagatttggatatatacttctatagaatgctaaacgcgagtgtatcaagagggatacactcgcgctttttgttttatta .........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 taataaaacaaaaagcgcgagtgtatccctcttgatacactcgcgtttagcattctatagaagtatatatccaaatctttagctttgatacacattcattatcatcagtatgataatagatagtcattagtatgataatagatagtcattagtatgataatagatagtcattagtatgataattgattgtcatcagtatgataattaattgtcattagtatgataattgattgtcattagtataataatagattattaccagtatgataacagacttttgccagtgaaataaaaaaggcaaccaagcatcgttacttagctgcctcaacaaaaattatttttatgaaaagagtgtgtaaagattttctttttgtttattggttgttttatattactgtacatatca Mask Tandem Repeat Region ================================================ tgatatgtacagtaatataaaacaaccaataaacaaaaagaaaatctttacacactcttttcataaaaataatttttgttgaggcagctaagtaacgatgcttggttgccttttttatttcactggcaaaagtctgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaatgtgtatcaaagctaaagatttggatatatacttctatagaatgctaaacgcgagtgtatcaagagggatacactcgcgctttttgttttatta Find is-nt database================================================ Query_seq: PI1123:PI1124|PI1123:PI1124:conserved hypothetical protein:possible nucleoside-diphosphate sugar epimerase:->->:1049258..1049663 406 tgatatgtacagtaatataaaacaaccaataaacaaaaagaaaatctttacacactcttttcataaaaataatttttgttgaggcagctaagtaacgatgcttggttgccttttttatttcactggcaaaagtctgttatcatactggtaataatctattattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcatactaatgactatctattatcatactaatgactatctattatcatactaatgactatctattatcatactgatgataatgaatgtgtatcaaagctaaagatttggatatatacttctatagaatgctaaacgcgagtgtatcaagagggatacactcgcgctttttgttttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1123:PI1124|PI1123:PI1124:conserved hypothetical protein:possible nucleoside-diphosphate sugar epimerase:->->:1049258..1049663 406 tgatatgtacagtaatataaaacaaccaataaacaaaaagaaaatctttacacactcttttcataaaaataatttttgttgaggcagctaagtaacgatgcttggttgccttttttatttcactggcaaaagtctgttatcatactggtaataatctattattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcatactaatgactatctattatcatactaatgactatctattatcatactaatgactatctattatcatactgatgataatgaatgtgtatcaaagctaaagatttggatatatacttctatagaatgctaaacgcgagtgtatcaagagggatacactcgcgctttttgttttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1123:PI1124|PI1123:PI1124:conserved hypothetical protein:possible nucleoside-diphosphate sugar epimerase:->->:1049258..1049663 406 tgatatgtacagtaatataaaacaaccaataaacaaaaagaaaatctttacacactcttttcataaaaataatttttgttgaggcagctaagtaacgatgcttggttgccttttttatttcactggcaaaagtctgttatcatactggtaataatctattattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcatactaatgactatctattatcatactaatgactatctattatcatactaatgactatctattatcatactgatgataatgaatgtgtatcaaagctaaagatttggatatatacttctatagaatgctaaacgcgagtgtatcaagagggatacactcgcgctttttgttttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatatgtacagtaatataaaacaaccaataaacaaaaagaaaatctttacacactcttttcataaaaataatttttgttgaggcagctaagtaacgatgcttggttgccttttttatttcactggcaaaagtctgttatcatactggtaataatctattattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcatactaatgactatctattatcatactaatgactatctattatcatactaatgactatctattatcatactgatgataatgaatgtgtatcaaagctaaagatttggatatatacttctatagaatgctaaacgcgagtgtatcaagagggatacactcgcgctttttgttttatta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 76 End: 189 ........................................................................... M L R Q L S N D A W L P F L F H W Q K S V I I L V I I Y Y Y T N D N Q L S Y ......................................................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 268 End: 357 ........................................................................................................................................................................................................................................................................... M I I L M T I Y Y H T D D N E C V S K L K I W I Y T S I E C ................................................. Protein_Len: 31 Strand: + Start: 312 End: 404 ....................................................................................................................................................................................................................................................................................................................... M C I K A K D L D I Y F Y R M L N A S V S R G I H S R F L F Y .. Protein_Len: 39 Strand: - Start: 2 End: 118 . I H V T I Y F L W Y V F L F D K C V R K M F I I K T S A A L Y R H K T A K K M ................................................................................................................................................................................................................................................................................................ tgatatgtacagtaatataaaacaaccaataaacaaaaagaaaatctttacacactcttttcataaaaataatttttgttgaggcagctaagtaacgatgcttggttgccttttttatttcactggcaaaagtctgttatcatactggtaataatctattattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcatactaatgactatctattatcatactaatgactatctattatcatactaatgactatctattatcatactgatgataatgaatgtgtatcaaagctaaagatttggatatatacttctatagaatgctaaacgcgagtgtatcaagagggatacactcgcgctttttgttttatta 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: 83 Start: 224 End: 253 ...............................................................................................................................................................................................................................ATTATCATACTAATGACTATCTATTATCAT......................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 246 End: 275 .....................................................................................................................................................................................................................................................ATTATCATACTAATGACTATCTATTATCAT................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 268 End: 297 ...........................................................................................................................................................................................................................................................................ATTATCATACTAATGACTATCTATTATCAT............................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 136 End: 165 .......................................................................................................................................GTTATCATACTGGTAATAATCTATTATTAT................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgatatgtacagtaatataaaacaaccaataaacaaaaagaaaatctttacacactcttttcataaaaataatttttgttgaggcagctaagtaacgatgcttggttgccttttttatttcactggcaaaagtctgttatcatactggtaataatctattattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcatactaatgactatctattatcatactaatgactatctattatcatactaatgactatctattatcatactgatgataatgaatgtgtatcaaagctaaagatttggatatatacttctatagaatgctaaacgcgagtgtatcaagagggatacactcgcgctttttgttttatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.2 Tail_Score: -5.65927 Start: 83 End: 110 Full_Region: AATAATTTTTGTTGA GGCAGCTAAGTA ACGA TGCTTGGTTGCC TTTTTTATTTCACTG ..................................................................................GGCAGCTAAGTAACGATGCTTGGTTGCC........................................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 79 HP_score: -9.5 Tail_Score: -3.30443 Start: 171 End: 208 Full_Region: tgattgtcatcagta tgataattaattgtcat tagt atgataattgattgtca ttagtataataatag ..........................................................................................................................................................................tgataattaattgtcattagtatgataattgattgtca...................................................................................................................................................................................................... TransTerm Strand: - Conf: 79 HP_score: -9.5 Tail_Score: -3.31157 Start: 193 End: 230 Full_Region: agatagtcattagta tgataattgattgtcat cagt atgataattaattgtca ttagtatgataattg ................................................................................................................................................................................................tgataattgattgtcatcagtatgataattaattgtca................................................................................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -14.3 Tail_Score: -2.94519 Start: 363 End: 390 Full_Region: TATAGAATGCTAAAC GCGAGTGTATC AAGAGG GATACACTCGC GCTTTTTGTTTTATT ..........................................................................................................................................................................................................................................................................................................................................................................GCGAGTGTATCAAGAGGGATACACTCGC................ Find igs database================================================ Query_seq: PI1123:PI1124|PI1123:PI1124:conserved hypothetical protein:possible nucleoside-diphosphate sugar epimerase:->->:1049258..1049663 406 tgatatgtacagtaatataaaacaaccaataaacaaaaagaaaatctttacacactcttttcataaaaataatttttgttgaggcagctaagtaacgatgcttggttgccttttttatttcactggcaaaagtctgttatcatactggtaataatctattattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcatactaatgactatctattatcatactaatgactatctattatcatactaatgactatctattatcatactgatgataatgaatgtgtatcaaagctaaagatttggatatatacttctatagaatgctaaacgcgagtgtatcaagagggatacactcgcgctttttgttttatta Intra-Species Hit: Count: 1 Min: 1 Max: 406 Len: 406 Subject: pint_PI1123_PI1124|conserved hypothetical protein:possible nucleoside-diphosphate sugar epimerase|POSITIVE:POSITIVE|[1049258,1049663]|406 HSP 1 e-value: 1.0E-128 bit: 458.0 Len: 231 Query Start:1 Query End:231 Subject Strand: POSITIVE Subject Start: 1 Subject End: 231 tgatatgtacagtaatataaaacaaccaataaacaaaaagaaaatctttacacactcttttcataaaaataatttttgttgaggcagctaagtaacgatgcttggttgccttttttatttcactggcaaaagtctgttatcatactggtaataatctattattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcat............................................................................................................................................................................... tgatatgtacagtaatataaaacaaccaataaacaaaaagaaaatctttacacactcttttcataaaaataatttttgttgaggcagctaagtaacgatgcttggttgccttttttatttcactggcaaaagtctgttatcatactggtaataatctattattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcat............................................................................................................................................................................... HSP 2 e-value: 3.0E-53 bit: 210.0 Len: 106 Query Start:301 Query End:406 Subject Strand: POSITIVE Subject Start: 301 Subject End: 406 ............................................................................................................................................................................................................................................................................................................gatgataatgaatgtgtatcaaagctaaagatttggatatatacttctatagaatgctaaacgcgagtgtatcaagagggatacactcgcgctttttgttttatta ............................................................................................................................................................................................................................................................................................................gatgataatgaatgtgtatcaaagctaaagatttggatatatacttctatagaatgctaaacgcgagtgtatcaagagggatacactcgcgctttttgttttatta HSP 3 e-value: 5.0E-18 bit: 93.7 Len: 79 Query Start:153 Query End:231 Subject Strand: POSITIVE Subject Start: 175 Subject End: 253 ........................................................................................................................................................aatctattattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcat............................................................................................................................................................................... ........................................................................................................................................................aatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcatactaatgactatctattatcat............................................................................................................................................................................... HSP 4 e-value: 1.0E-15 bit: 85.7 Len: 95 Query Start:137 Query End:231 Subject Strand: POSITIVE Subject Start: 203 Subject End: 297 ........................................................................................................................................ttatcatactggtaataatctattattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcat............................................................................................................................................................................... ........................................................................................................................................ttatcatactgatgacaatcaattatcatactaatgactatctattatcatactaatgactatctattatcatactaatgactatctattatcat............................................................................................................................................................................... HSP 5 e-value: 4.0E-15 bit: 83.8 Len: 74 Query Start:158 Query End:231 Subject Strand: POSITIVE Subject Start: 202 Subject End: 275 .............................................................................................................................................................attattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatgacaatcaattatcat............................................................................................................................................................................... .............................................................................................................................................................attatcatactgatgacaatcaattatcatactaatgactatctattatcatactaatgactatctattatcat............................................................................................................................................................................... HSP 6 e-value: 7.0E-14 bit: 79.8 Len: 64 Query Start:154 Query End:217 Subject Strand: POSITIVE Subject Start: 242 Subject End: 305 .........................................................................................................................................................atctattattatactaatgacaatcaattatcatactaatgacaattaattatcatactgatga............................................................................................................................................................................................. .........................................................................................................................................................atctattatcatactaatgactatctattatcatactaatgactatctattatcatactgatga............................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAUGUACAGUAAUAUAAAACAACCAAUAAACAAAAAGAAAAUCUUUACACACUCUUUUCAUAAAAAUAAUUUUUGUUGAGGCAGCUAAGUAACGAUGCUUGGUUGCCUUUUUUAUUUCACUGGCAAAAGUCUGUUAUCAUACUGGUAAUAAUCUAUUAUUAUACUAAUGACAAUCAAUUAUCAUACUAAUGACAAUUAAUUAUCAUACUGAUGACAAUCAAUUAUCAUACUAAUGACUAUCUAUUAUCAUACUAAUGACUAUCUAUUAUCAUACUAAUGACUAUCUAUUAUCAUACUGAUGAUAAUGAAUGUGUAUCAAAGCUAAAGAUUUGGAUAUAUACUUCUAUAGAAUGCUAAACGCGAGUGUAUCAAGAGGGAUACACUCGCGCUUUUUGUUUUAUUA ...(((((......)))))........(((((((((((((........((((((......((((.......(((((((((((((((((((((((....))))))))))))))............))))))))).((((((((.....(((((((....)))))))....((((.(((.((((.((((....)))).)))).))).))))..))))))))................)))).....(((((((((....((((..((..((..((((....))))..))..))..))))....)))))))))..))))))....(((........((((........))))......)))...((((((((((((......))))))))))))))))))).)))))). (-91.74) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAAAACAAAAAGCGCGAGUGUAUCCCUCUUGAUACACUCGCGUUUAGCAUUCUAUAGAAGUAUAUAUCCAAAUCUUUAGCUUUGAUACACAUUCAUUAUCAUCAGUAUGAUAAUAGAUAGUCAUUAGUAUGAUAAUAGAUAGUCAUUAGUAUGAUAAUAGAUAGUCAUUAGUAUGAUAAUUGAUUGUCAUCAGUAUGAUAAUUAAUUGUCAUUAGUAUGAUAAUUGAUUGUCAUUAGUAUAAUAAUAGAUUAUUACCAGUAUGAUAACAGACUUUUGCCAGUGAAAUAAAAAAGGCAACCAAGCAUCGUUACUUAGCUGCCUCAACAAAAAUUAUUUUUAUGAAAAGAGUGUGUAAAGAUUUUCUUUUUGUUUAUUGGUUGUUUUAUAUUACUGUACAUAUCA ............(((((((((((((((......))))))))))))))).........(((((((...((((...(((....(((.((((....((..((((((((....))))))))..)).))))..)))..)))....(((((((((((..((((((((.(((.(((((....((((((((((((((((((....))))))))))))))))))....))))).))).))))))))........)))).)))))))........))))....))))))).((((((.(((((....(((((((((((.(........).)))...((((((((..((((((((...........))))))))....))))))))..))))))))))))).))))))......... (-101.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 392 354 177 133 pint:PI0942|5end_DNA-binding_protein_HU_874624..874854_POSITIVE 294 127 84 99 53 pint:PI0729|5end_integrase_661428..661658_POSITIVE 286 400 355 220 169 pint:PI2094|5end_hypothetical_protein_2049540..2049770_POSITIVE 285 116 78 168 124 pint:PI1676|5end_phosphatidate_cytidylyltransferase_1590896..1591126_POSITIVE 284 127 82 80 33 pint:PI2107|5end_hypothetical_protein_2059704..2059934_POSITIVE 284 117 72 53 2 pint:PI0471|5end_50S_ribosomal_protein_L24_437736..437966_POSITIVE 282 399 359 153 106 pint:PI2040|5end_conserved_hypothetical_protein;_possible_transporter_1993068..1993298_POSITIVE 277 394 351 214 165 pint:PI0151|5end_ISPg4-related_transposase_(IS5_family)_143805..144035_POSITIVE 274 390 343 148 94 pint:PI0533|5end_ABC_transporter,_permease_protein_487259..487489_POSITIVE 273 127 87 85 23 pint:PI0665|5end_dihydroorotate_dehydrogenase_607865..608095_POSITIVE 272 400 351 108 66 pint:PI2084|5end_hypothetical_protein_2040387..2040617_POSITIVE 272 400 351 45 3 pint:PI2083|5end_hypothetical_protein_2040324..2040554_POSITIVE 271 129 82 133 79 pint:PI0095|5end_hypothetical_protein_91444..91674_POSITIVE 270 128 84 134 95 pint:PI0624|5end_hypothetical_protein_574203..574433_POSITIVE 267 130 81 170 107 pint:PI1640|5end_hypothetical_protein_1558062..1558292_POSITIVE 267 397 351 203 161 pint:PI1609|5end_Na+/H+_anti-porter_1536058..1536288_POSITIVE 267 127 81 207 168 pint:PI0167|5end_hypothetical_protein_163164..163394_POSITIVE 265 126 82 96 40 pint:PI0744|5end_DNA_primase/mobilizable_transposon,_excision_protein_674171..674401_POSITIVE 261 157 114 68 22 pint:PI0392|5end_possible_transcriptional_regulator_358344..358574_POSITIVE 259 117 77 138 101 pint:PI2045|5end_hypothetical_protein_1998494..1998724_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 409 120 81 59 23 pint:PI0618|3end_acyl-CoA_dehydrogenase_family_protein_569213..569363_POSITIVE 300 392 354 148 104 pint:PI0941|3end_hypothetical_protein_874675..874825_POSITIVE 294 127 84 99 53 pint:PI0728|3end_integrase_661508..661658_POSITIVE 289 399 355 60 8 pint:PI0128|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_121826..121976_POSITIVE 274 390 343 138 84 pint:PI0532|3end_ABC_transporter,_ATP-binding/permease_protein_487329..487479_POSITIVE 272 117 81 50 15 pint:PI0470|3end_50S_ribosomal_protein_L14_437813..437963_POSITIVE 271 129 82 146 92 pint:PI0093|3end_riboflavin_biosynthesis_protein_91537..91687_POSITIVE 259 399 354 58 8 pint:PI1412|3end_HD_superfamily_hydrolase_1333823..1333973_POSITIVE 258 115 83 64 35 pint:PI0447|3end_DNA-directed_RNA_polymerase,_beta'_subunit_421755..421905_POSITIVE 257 370 322 63 18 pint:PI0147|3end_HIT_family_protein_141308..141458_POSITIVE 255 112 82 39 10 pint:PI1462|3end_hypothetical_protein_1385383..1385533_POSITIVE 251 112 73 124 82 pint:PI1658|3end_conserved_hypothetical_protein_1574736..1574886_POSITIVE 251 400 361 101 50 pint:PI1062|3end_TPR_repeat_protein_980780..980930_POSITIVE 249 111 82 121 84 pint:PI1524|3end_phosphatidylserine_decarboxylase_1446657..1446807_POSITIVE 249 396 354 46 6 pint:PI0354|3end_hypothetical_protein_326241..326391_POSITIVE 247 128 82 141 83 pint:PI0605|3end_chloromuconate_cycloisomerase_553026..553176_POSITIVE 246 392 355 108 70 pint:PI0797|3end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735752..735902_POSITIVE 246 393 358 114 72 pint:PI0578|3end_methyltransferase_523253..523403_POSITIVE 245 400 354 45 5 pint:PI0765|3end_conserved_hypothetical_protein;_possible_surface_protein_700822..700972_POSITIVE 243 381 355 118 86 pint:PI1314|3end_hypothetical_protein_1231423..1231573_POSITIVE