Origin IGS: agttttatcatttattttacaccgtgtaactgcttttataaaggtaaactggtgtggtataaggtctgaagagccattcggaagttaggctaacagattttcacagatgcaaagatattaaaaaatattgatattcgggaaaaggttttcacgaattaatgcaagcttagtagaataaagtgattttgaaagattgtagaggtaataaggtattcaggtaagattccgcccttcagcaacacagcctgagctctcagcgcaggctgtgttgctatgtctatttatgcaggcgagcttgcctaatatatattgtatggtgctta .........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 taagcaccatacaatatatattaggcaagctcgcctgcataaatagacatagcaacacagcctgcgctgagagctcaggctgtgttgctgaagggcggaatcttacctgaataccttattacctctacaatctttcaaaatcactttattctactaagcttgcattaattcgtgaaaaccttttcccgaatatcaatattttttaatatctttgcatctgtgaaaatctgttagcctaacttccgaatggctcttcagaccttataccacaccagtttacctttataaaagcagttacacggtgtaaaataaatgataaaact Mask Tandem Repeat Region ================================================ agttttatcatttattttacaccgtgtaactgcttttataaaggtaaactggtgtggtataaggtctgaagagccattcggaagttaggctaacagattttcacagatgcaaagatattaaaaaatattgatattcgggaaaaggttttcacgaattaatgcaagcttagtagaataaagtgattttgaaagattgtagaggtaataaggtattcaggtaagattccgcccttcagcaacacagcctgagctctcagcgcaggctgtgttgctatgtctatttatgcaggcgagcttgcctaatatatattgtatggtgctta Find is-nt database================================================ Query_seq: PI1805:PI1806|PI1805:PI1806:TPR repeat containing protein:integral membrane transport protein; possible sugar transport proteins:->->:1740594..1740916 323 agttttatcatttattttacaccgtgtaactgcttttataaaggtaaactggtgtggtataaggtctgaagagccattcggaagttaggctaacagattttcacagatgcaaagatattaaaaaatattgatattcgggaaaaggttttcacgaattaatgcaagcttagtagaataaagtgattttgaaagattgtagaggtaataaggtattcaggtaagattccgcccttcagcaacacagcctgagctctcagcgcaggctgtgttgctatgtctatttatgcaggcgagcttgcctaatatatattgtatggtgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1805:PI1806|PI1805:PI1806:TPR repeat containing protein:integral membrane transport protein; possible sugar transport proteins:->->:1740594..1740916 323 agttttatcatttattttacaccgtgtaactgcttttataaaggtaaactggtgtggtataaggtctgaagagccattcggaagttaggctaacagattttcacagatgcaaagatattaaaaaatattgatattcgggaaaaggttttcacgaattaatgcaagcttagtagaataaagtgattttgaaagattgtagaggtaataaggtattcaggtaagattccgcccttcagcaacacagcctgagctctcagcgcaggctgtgttgctatgtctatttatgcaggcgagcttgcctaatatatattgtatggtgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1805:PI1806|PI1805:PI1806:TPR repeat containing protein:integral membrane transport protein; possible sugar transport proteins:->->:1740594..1740916 323 agttttatcatttattttacaccgtgtaactgcttttataaaggtaaactggtgtggtataaggtctgaagagccattcggaagttaggctaacagattttcacagatgcaaagatattaaaaaatattgatattcgggaaaaggttttcacgaattaatgcaagcttagtagaataaagtgattttgaaagattgtagaggtaataaggtattcaggtaagattccgcccttcagcaacacagcctgagctctcagcgcaggctgtgttgctatgtctatttatgcaggcgagcttgcctaatatatattgtatggtgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agttttatcatttattttacaccgtgtaactgcttttataaaggtaaactggtgtggtataaggtctgaagagccattcggaagttaggctaacagattttcacagatgcaaagatattaaaaaatattgatattcgggaaaaggttttcacgaattaatgcaagcttagtagaataaagtgattttgaaagattgtagaggtaataaggtattcaggtaagattccgcccttcagcaacacagcctgagctctcagcgcaggctgtgttgctatgtctatttatgcaggcgagcttgcctaatatatattgtatggtgctta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 212 End: 322 ................................................................................................................................................................................................................... M Q V R F R P S A T Q P E L S A Q A V L L C L F M Q A S L P N I Y C M V L . Protein_Len: 33 Strand: - Start: 217 End: 315 ........................................................................................................................................................................................................................ T L N R G E A V C G S S E A C A T N S H R N I C A L K G L I Y Q M ........ Protein_Len: 41 Strand: - Start: 159 End: 281 .............................................................................................................................................................. H L S L L I F H N Q F I T S T I L Y E P L I G G K L L V A Q A R L A P Q T A I D M .......................................... Protein_Len: 31 Strand: - Start: 121 End: 213 ........................................................................................................................ F I N I N P F L N E R I L A L K T S Y L S K S L N Y L Y Y P M .............................................................................................................. agttttatcatttattttacaccgtgtaactgcttttataaaggtaaactggtgtggtataaggtctgaagagccattcggaagttaggctaacagattttcacagatgcaaagatattaaaaaatattgatattcgggaaaaggttttcacgaattaatgcaagcttagtagaataaagtgattttgaaagattgtagaggtaataaggtattcaggtaagattccgcccttcagcaacacagcctgagctctcagcgcaggctgtgttgctatgtctatttatgcaggcgagcttgcctaatatatattgtatggtgctta 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: 14 End: 43 .............CTTTATAAAAGCAGTTACACGGTGTAAAAT........................................................................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 147 End: 176 ..................................................................................................................................................TTTCACGAATTAATGCAAGCTTAGTAGAAT................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 193 End: 222 ................................................................................................................................................................................................CTTACCTGAATACCTTATTACCTCTACAAT..................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agttttatcatttattttacaccgtgtaactgcttttataaaggtaaactggtgtggtataaggtctgaagagccattcggaagttaggctaacagattttcacagatgcaaagatattaaaaaatattgatattcgggaaaaggttttcacgaattaatgcaagcttagtagaataaagtgattttgaaagattgtagaggtaataaggtattcaggtaagattccgcccttcagcaacacagcctgagctctcagcgcaggctgtgttgctatgtctatttatgcaggcgagcttgcctaatatatattgtatggtgctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -11.5 Tail_Score: -3.51934 Start: 229 End: 278 Full_Region: TCAGGTAAGATTCCG CCCTTCAGCAACACAGCCTGAGCT CTC AGCGCAGGCTGTGTTGCTATGTC TATTTATGCAGGCGA ....................................................................................................................................................................................................................................CCCTTCAGCAACACAGCCTGAGCTCTCAGCGCAGGCTGTGTTGCTATGTC............................................. TransTerm Strand: + Conf: 100 HP_score: -18.5 Tail_Score: -3.3353 Start: 231 End: 276 Full_Region: AGGTAAGATTCCGCC CTTCAGCAACACAGCCTGAGCT CTC AGCGCAGGCTGTGTTGCTATG TCTATTTATGCAGGC ......................................................................................................................................................................................................................................CTTCAGCAACACAGCCTGAGCTCTCAGCGCAGGCTGTGTTGCTATG............................................... TransTerm Strand: + Conf: 100 HP_score: -21.3 Tail_Score: -3.23335 Start: 234 End: 274 Full_Region: TAAGATTCCGCCCTT CAGCAACACAGCCTGAGCT CTC AGCGCAGGCTGTGTTGCTA TGTCTATTTATGCAG .........................................................................................................................................................................................................................................CAGCAACACAGCCTGAGCTCTCAGCGCAGGCTGTGTTGCTA................................................. TransTerm Strand: + Conf: 100 HP_score: -23.9 Tail_Score: -3.17444 Start: 236 End: 272 Full_Region: AGATTCCGCCCTTCA GCAACACAGCCTGAGCT CTC AGCGCAGGCTGTGTTGC TATGTCTATTTATGC ...........................................................................................................................................................................................................................................GCAACACAGCCTGAGCTCTCAGCGCAGGCTGTGTTGC................................................... TransTerm Strand: + Conf: 100 HP_score: -17.5 Tail_Score: -3.38329 Start: 240 End: 268 Full_Region: TCCGCCCTTCAGCAA CACAGCCTGAGCT CTC AGCGCAGGCTGTG TTGCTATGTCTATTT ...............................................................................................................................................................................................................................................CACAGCCTGAGCTCTCAGCGCAGGCTGTG....................................................... TransTerm Strand: - Conf: 100 HP_score: -17.5 Tail_Score: -3.14132 Start: 240 End: 268 Full_Region: aaatagacatagcaa cacagcctgcgct gag agctcaggctgtg ttgctgaagggcgga ...............................................................................................................................................................................................................................................cacagcctgcgctgagagctcaggctgtg....................................................... Find igs database================================================ Query_seq: PI1805:PI1806|PI1805:PI1806:TPR repeat containing protein:integral membrane transport protein; possible sugar transport proteins:->->:1740594..1740916 323 agttttatcatttattttacaccgtgtaactgcttttataaaggtaaactggtgtggtataaggtctgaagagccattcggaagttaggctaacagattttcacagatgcaaagatattaaaaaatattgatattcgggaaaaggttttcacgaattaatgcaagcttagtagaataaagtgattttgaaagattgtagaggtaataaggtattcaggtaagattccgcccttcagcaacacagcctgagctctcagcgcaggctgtgttgctatgtctatttatgcaggcgagcttgcctaatatatattgtatggtgctta Intra-Species Hit: Count: 1 Min: 1 Max: 323 Len: 323 Subject: pint_PI1805_PI1806|TPR repeat containing protein:integral membrane transport protein; possible sugar transport proteins|POSITIVE:POSITIVE|[1740594,1740916]|323 HSP 1 e-value: 0.0 bit: 640.0 Len: 323 Query Start:1 Query End:323 Subject Strand: POSITIVE Subject Start: 1 Subject End: 323 agttttatcatttattttacaccgtgtaactgcttttataaaggtaaactggtgtggtataaggtctgaagagccattcggaagttaggctaacagattttcacagatgcaaagatattaaaaaatattgatattcgggaaaaggttttcacgaattaatgcaagcttagtagaataaagtgattttgaaagattgtagaggtaataaggtattcaggtaagattccgcccttcagcaacacagcctgagctctcagcgcaggctgtgttgctatgtctatttatgcaggcgagcttgcctaatatatattgtatggtgctta agttttatcatttattttacaccgtgtaactgcttttataaaggtaaactggtgtggtataaggtctgaagagccattcggaagttaggctaacagattttcacagatgcaaagatattaaaaaatattgatattcgggaaaaggttttcacgaattaatgcaagcttagtagaataaagtgattttgaaagattgtagaggtaataaggtattcaggtaagattccgcccttcagcaacacagcctgagctctcagcgcaggctgtgttgctatgtctatttatgcaggcgagcttgcctaatatatattgtatggtgctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUUAUCAUUUAUUUUACACCGUGUAACUGCUUUUAUAAAGGUAAACUGGUGUGGUAUAAGGUCUGAAGAGCCAUUCGGAAGUUAGGCUAACAGAUUUUCACAGAUGCAAAGAUAUUAAAAAAUAUUGAUAUUCGGGAAAAGGUUUUCACGAAUUAAUGCAAGCUUAGUAGAAUAAAGUGAUUUUGAAAGAUUGUAGAGGUAAUAAGGUAUUCAGGUAAGAUUCCGCCCUUCAGCAACACAGCCUGAGCUCUCAGCGCAGGCUGUGUUGCUAUGUCUAUUUAUGCAGGCGAGCUUGCCUAAUAUAUAUUGUAUGGUGCUUA ...................((((((((((.(((((((((((((((.......(((((....(((((((...((((...(....)...))))..))))))))))))..((((..((((((....))))))...(((((.((((....)))).)))))...)))).))))..((((((......)))))).....))))))))))).....(((((.(((((((....((((....((((((((((((((.((.....)).))))))))))))))..((........)).))))..))))))))))))...)))))))))).... (-93.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCACCAUACAAUAUAUAUUAGGCAAGCUCGCCUGCAUAAAUAGACAUAGCAACACAGCCUGCGCUGAGAGCUCAGGCUGUGUUGCUGAAGGGCGGAAUCUUACCUGAAUACCUUAUUACCUCUACAAUCUUUCAAAAUCACUUUAUUCUACUAAGCUUGCAUUAAUUCGUGAAAACCUUUUCCCGAAUAUCAAUAUUUUUUAAUAUCUUUGCAUCUGUGAAAAUCUGUUAGCCUAACUUCCGAAUGGCUCUUCAGACCUUAUACCACACCAGUUUACCUUUAUAAAAGCAGUUACACGGUGUAAAAUAAAUGAUAAAACU .......(((.......((((((.((((((((((((.............(((((((((((((((.((.....)).)))))))))))))))..)))))...((......))..............................................)))))))....(((((.((((....)))).)))))............)))))).(((((((((((((...((((..((((............))))...))))...............((((..........))))..))))).))))))))....)))........ (-74.96) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 424 299 256 54 2 pint:PI2113|5end_hypothetical_protein_2063794..2064024_POSITIVE 401 300 252 171 124 pint:PI0701|5end_hypothetical_protein_638356..638586_POSITIVE 389 300 252 210 150 pint:PI2123|5end_adenine_phosphoribosyltransferase_2071711..2071941_POSITIVE 385 297 255 191 151 pint:PI1831|5end_conserved_hypothetical_protein_1770298..1770528_POSITIVE 365 270 221 58 6 pint:PI1872|5end_glycosyl_transferase,_group_2_family_protein_1817057..1817287_POSITIVE 355 299 255 172 121 pint:PI1768|5end_conserved_hypothetical_protein_1695456..1695686_POSITIVE 352 289 247 213 158 pint:PI1897|5end_conserved_hypothetical_protein_1840619..1840849_POSITIVE 351 265 226 193 136 pint:PI2126|5end_conserved_hypothetical_protein_2074907..2075137_POSITIVE 351 272 231 112 71 pint:PI1727|5end__ATP-dependent_Clp_protease,_ATP-binding_subunit_1645680..1645910_POSITIVE 351 301 264 90 48 pint:PI0049|5end_outer_membrane_receptor_protein_(iron_transport)_48605..48835_POSITIVE 348 88 50 166 125 pint:PI0259|5end_conserved_protein_found_in_conjugation,_TraI_252355..252585_POSITIVE 344 279 244 68 24 pint:PI1396|5end_urocanate_hydratase_1315799..1316029_POSITIVE 340 291 256 231 190 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 340 318 271 52 6 pint:PI0731|5end_conserved_hypothetical_protein_662289..662519_POSITIVE 338 271 236 53 15 pint:PI1073|5end_hemogluttinin_A-related_protein_(HagA)_990593..990823_POSITIVE 336 298 255 150 110 pint:PI1543|5end_hypothetical_protein_1462773..1463003_POSITIVE 333 266 224 44 1 pint:PI0873|5end_conserved_hypothetical_protein;_possible_permease_807968..808198_POSITIVE 331 267 224 102 67 pint:PI2011|5end_hypothetical_protein_1970429..1970659_POSITIVE 329 268 226 57 18 pint:PI0998|5end_possible_flavin_reductase_domain_protein_922696..922926_POSITIVE 327 287 244 84 38 pint:PI0614|5end_glucose-6-phosphate_isomerase_563170..563400_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 300 252 148 101 pint:PI0700|3end_UDP-glucose_4-epimerase_638413..638563_POSITIVE 365 270 221 54 2 pint:PI1871|3end_glycosyl_transferase,_group_1_family_protein_1817133..1817283_POSITIVE 347 269 225 148 107 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 344 279 244 51 7 pint:PI1394|3end_glutamate_formiminotransferase_1315862..1316012_POSITIVE 329 268 226 93 54 pint:PI0999|3end_hypothetical_protein_922812..922962_POSITIVE 327 287 244 73 27 pint:PI0613|3end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_563239..563389_POSITIVE 326 268 225 92 34 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 326 259 221 139 90 pint:PI0593|3end_NAD-specific_glutamate_dehydrogenase_544369..544519_POSITIVE 325 288 242 51 2 pint:PI0521|3end_hypothetical_protein_479061..479211_POSITIVE 323 258 214 92 33 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 323 268 226 107 61 pint:PI0201|3end_hypothetical_protein_195398..195548_POSITIVE 317 278 235 94 50 pint:PI0718|3end_hypothetical_protein_654212..654362_POSITIVE 315 264 224 74 27 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 314 276 233 93 34 pint:PI1924|3end_cytidine_deaminase_1866495..1866645_POSITIVE 311 299 251 111 54 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 309 290 241 146 107 pint:PI0600|3end_bifunctional_purine_biosynthesis_protein,_5-aminoimidazole-4-carboxamide_ribonucleotide(AICAR)_transformylase/IMP_cyclohydrolase_548797..548947_POSITIVE 307 277 231 66 10 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 307 279 234 100 42 pint:PI1499|3end_hypothetical_protein_1420180..1420330_POSITIVE 303 273 241 73 34 pint:PI0728|3end_integrase_661508..661658_POSITIVE 302 299 253 140 99 pint:PI1623|3end_hypothetical_protein_1549261..1549411_POSITIVE