Origin IGS: tctttaactgttgttatataaatatttgcaaaattgaccgcaaagttatatctattgttctattctaccaaatttatttgcacattttttcttcaaatgtgtaattatatgacgattagaacaaaaacttataccgtttcttccgtatattatttttactttatttatacaaaaatattttgtttggcttgctgaaatagccgaaaagtattaactttggagcaataaaaaattgatgtaatgaatatgaagaaaataactttgctattctcactgctctttgtagcagtcttgacgacgtggggtcagtctacttttactattttacctaagttccaagtaggcgatacgcttgtatatgaagctgtaaccacgagtggtaaaaca .........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 tgttttaccactcgtggttacagcttcatatacaagcgtatcgcctacttggaacttaggtaaaatagtaaaagtagactgaccccacgtcgtcaagactgctacaaagagcagtgagaatagcaaagttattttcttcatattcattacatcaattttttattgctccaaagttaatacttttcggctatttcagcaagccaaacaaaatatttttgtataaataaagtaaaaataatatacggaagaaacggtataagtttttgttctaatcgtcatataattacacatttgaagaaaaaatgtgcaaataaatttggtagaatagaacaatagatataactttgcggtcaattttgcaaatatttatataacaacagttaaaga Mask Tandem Repeat Region ================================================ tctttaactgttgttatataaatatttgcaaaattgaccgcaaagttatatctattgttctattctaccaaatttatttgcacattttttcttcaaatgtgtaattatatgacgattagaacaaaaacttataccgtttcttccgtatattatttttactttatttatacaaaaatattttgtttggcttgctgaaatagccgaaaagtattaactttggagcaataaaaaattgatgtaatgaatatgaagaaaataactttgctattctcactgctctttgtagcagtcttgacgacgtggggtcagtctacttttactattttacctaagttccaagtaggcgatacgcttgtatatgaagctgtaaccacgagtggtaaaaca Find is-nt database================================================ Query_seq: PI0413:PI0414|PI0413:PI0414:outer membrane protein:hypothetical protein:->->:384080..384466 387 tctttaactgttgttatataaatatttgcaaaattgaccgcaaagttatatctattgttctattctaccaaatttatttgcacattttttcttcaaatgtgtaattatatgacgattagaacaaaaacttataccgtttcttccgtatattatttttactttatttatacaaaaatattttgtttggcttgctgaaatagccgaaaagtattaactttggagcaataaaaaattgatgtaatgaatatgaagaaaataactttgctattctcactgctctttgtagcagtcttgacgacgtggggtcagtctacttttactattttacctaagttccaagtaggcgatacgcttgtatatgaagctgtaaccacgagtggtaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0413:PI0414|PI0413:PI0414:outer membrane protein:hypothetical protein:->->:384080..384466 387 tctttaactgttgttatataaatatttgcaaaattgaccgcaaagttatatctattgttctattctaccaaatttatttgcacattttttcttcaaatgtgtaattatatgacgattagaacaaaaacttataccgtttcttccgtatattatttttactttatttatacaaaaatattttgtttggcttgctgaaatagccgaaaagtattaactttggagcaataaaaaattgatgtaatgaatatgaagaaaataactttgctattctcactgctctttgtagcagtcttgacgacgtggggtcagtctacttttactattttacctaagttccaagtaggcgatacgcttgtatatgaagctgtaaccacgagtggtaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0413:PI0414|PI0413:PI0414:outer membrane protein:hypothetical protein:->->:384080..384466 387 tctttaactgttgttatataaatatttgcaaaattgaccgcaaagttatatctattgttctattctaccaaatttatttgcacattttttcttcaaatgtgtaattatatgacgattagaacaaaaacttataccgtttcttccgtatattatttttactttatttatacaaaaatattttgtttggcttgctgaaatagccgaaaagtattaactttggagcaataaaaaattgatgtaatgaatatgaagaaaataactttgctattctcactgctctttgtagcagtcttgacgacgtggggtcagtctacttttactattttacctaagttccaagtaggcgatacgcttgtatatgaagctgtaaccacgagtggtaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttaactgttgttatataaatatttgcaaaattgaccgcaaagttatatctattgttctattctaccaaatttatttgcacattttttcttcaaatgtgtaattatatgacgattagaacaaaaacttataccgtttcttccgtatattatttttactttatttatacaaaaatattttgtttggcttgctgaaatagccgaaaagtattaactttggagcaataaaaaattgatgtaatgaatatgaagaaaataactttgctattctcactgctctttgtagcagtcttgacgacgtggggtcagtctacttttactattttacctaagttccaagtaggcgatacgcttgtatatgaagctgtaaccacgagtggtaaaaca Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 22 End: 192 ..................... M F A K L T A K L Y L L F Y S T K F I C T F F L Q M C N Y M T I R T K T Y T V S S V Y Y F Y F I Y T K I F C L A C ................................................................................................................................................................................................... Protein_Len: 52 Strand: + Start: 232 End: 387 ....................................................................................................................................................................................................................................... M D V M N M K K I T L L F S L L F V A V L T T W G Q S T F T I L P K F Q V G D T L V Y E A V T T S G K T Protein_Len: 30 Strand: - Start: 168 End: 257 ....................................................................................................................................................................... V F I N Q K A Q Q F L R F T N V K S C Y F I S T I F I F F M .................................................................................................................................. Protein_Len: 42 Strand: - Start: 164 End: 289 ................................................................................................................................................................... K Y L F I K N P K S F Y G F L I L K P A I F F Q H L S Y S S F L K A I R V A R Q L M .................................................................................................. Protein_Len: 48 Strand: - Start: 55 End: 198 ...................................................... Q E I R G F K N A C K K K L H T I I H R N S C F S I G N R G Y I I K V K N I C F Y K T Q S A S M ............................................................................................................................................................................................. tctttaactgttgttatataaatatttgcaaaattgaccgcaaagttatatctattgttctattctaccaaatttatttgcacattttttcttcaaatgtgtaattatatgacgattagaacaaaaacttataccgtttcttccgtatattatttttactttatttatacaaaaatattttgtttggcttgctgaaatagccgaaaagtattaactttggagcaataaaaaattgatgtaatgaatatgaagaaaataactttgctattctcactgctctttgtagcagtcttgacgacgtggggtcagtctacttttactattttacctaagttccaagtaggcgatacgcttgtatatgaagctgtaaccacgagtggtaaaaca 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================================================ tctttaactgttgttatataaatatttgcaaaattgaccgcaaagttatatctattgttctattctaccaaatttatttgcacattttttcttcaaatgtgtaattatatgacgattagaacaaaaacttataccgtttcttccgtatattatttttactttatttatacaaaaatattttgtttggcttgctgaaatagccgaaaagtattaactttggagcaataaaaaattgatgtaatgaatatgaagaaaataactttgctattctcactgctctttgtagcagtcttgacgacgtggggtcagtctacttttactattttacctaagttccaagtaggcgatacgcttgtatatgaagctgtaaccacgagtggtaaaaca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 55 HP_score: -4.6 Tail_Score: -3.50447 Start: 78 End: 104 Full_Region: TTCTACCAAATTTAT TTGCACATTT TTTCTTC AAATGTGTAA TTATATGACGATTAG .............................................................................TTGCACATTTTTTCTTCAAATGTGTAA........................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI0413:PI0414|PI0413:PI0414:outer membrane protein:hypothetical protein:->->:384080..384466 387 tctttaactgttgttatataaatatttgcaaaattgaccgcaaagttatatctattgttctattctaccaaatttatttgcacattttttcttcaaatgtgtaattatatgacgattagaacaaaaacttataccgtttcttccgtatattatttttactttatttatacaaaaatattttgtttggcttgctgaaatagccgaaaagtattaactttggagcaataaaaaattgatgtaatgaatatgaagaaaataactttgctattctcactgctctttgtagcagtcttgacgacgtggggtcagtctacttttactattttacctaagttccaagtaggcgatacgcttgtatatgaagctgtaaccacgagtggtaaaaca Intra-Species Hit: Count: 1 Min: 1 Max: 387 Len: 387 Subject: pint_PI0413_PI0414|outer membrane protein:hypothetical protein|POSITIVE:POSITIVE|[384080,384466]|387 HSP 1 e-value: 0.0 bit: 767.0 Len: 387 Query Start:1 Query End:387 Subject Strand: POSITIVE Subject Start: 1 Subject End: 387 tctttaactgttgttatataaatatttgcaaaattgaccgcaaagttatatctattgttctattctaccaaatttatttgcacattttttcttcaaatgtgtaattatatgacgattagaacaaaaacttataccgtttcttccgtatattatttttactttatttatacaaaaatattttgtttggcttgctgaaatagccgaaaagtattaactttggagcaataaaaaattgatgtaatgaatatgaagaaaataactttgctattctcactgctctttgtagcagtcttgacgacgtggggtcagtctacttttactattttacctaagttccaagtaggcgatacgcttgtatatgaagctgtaaccacgagtggtaaaaca tctttaactgttgttatataaatatttgcaaaattgaccgcaaagttatatctattgttctattctaccaaatttatttgcacattttttcttcaaatgtgtaattatatgacgattagaacaaaaacttataccgtttcttccgtatattatttttactttatttatacaaaaatattttgtttggcttgctgaaatagccgaaaagtattaactttggagcaataaaaaattgatgtaatgaatatgaagaaaataactttgctattctcactgctctttgtagcagtcttgacgacgtggggtcagtctacttttactattttacctaagttccaagtaggcgatacgcttgtatatgaagctgtaaccacgagtggtaaaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUAACUGUUGUUAUAUAAAUAUUUGCAAAAUUGACCGCAAAGUUAUAUCUAUUGUUCUAUUCUACCAAAUUUAUUUGCACAUUUUUUCUUCAAAUGUGUAAUUAUAUGACGAUUAGAACAAAAACUUAUACCGUUUCUUCCGUAUAUUAUUUUUACUUUAUUUAUACAAAAAUAUUUUGUUUGGCUUGCUGAAAUAGCCGAAAAGUAUUAACUUUGGAGCAAUAAAAAAUUGAUGUAAUGAAUAUGAAGAAAAUAACUUUGCUAUUCUCACUGCUCUUUGUAGCAGUCUUGACGACGUGGGGUCAGUCUACUUUUACUAUUUUACCUAAGUUCCAAGUAGGCGAUACGCUUGUAUAUGAAGCUGUAACCACGAGUGGUAAAACA ....((((....)))).......................((((((((((.....((((((((.((...((.((....((((((((((.......))))))))))..)).))..)).))))))))............(((((((.(((.........)))..((((((((((..(((.(((((((.((((.........))))..(((((....))))).....))))))).)))..))).))))))).))))))))))))))))).......((..(((...((.((((..((.((((.(((..(((.((((((((..(((..........)))...))))))))))).)))))))....))..)))).))...)))..))...... (-82.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUACCACUCGUGGUUACAGCUUCAUAUACAAGCGUAUCGCCUACUUGGAACUUAGGUAAAAUAGUAAAAGUAGACUGACCCCACGUCGUCAAGACUGCUACAAAGAGCAGUGAGAAUAGCAAAGUUAUUUUCUUCAUAUUCAUUACAUCAAUUUUUUAUUGCUCCAAAGUUAAUACUUUUCGGCUAUUUCAGCAAGCCAAACAAAAUAUUUUUGUAUAAAUAAAGUAAAAAUAAUAUACGGAAGAAACGGUAUAAGUUUUUGUUCUAAUCGUCAUAUAAUUACACAUUUGAAGAAAAAAUGUGCAAAUAAAUUUGGUAGAAUAGAACAAUAGAUAUAACUUUGCGGUCAAUUUUGCAAAUAUUUAUAUAACAACAGUUAAAGA (((((((((......(((.((.((((.......))))))))).((.....))......)))))))))((((((...(((.(((.....))))))..((((((......((((((((((((((((...))))))))).........................))))))).(((((((.((((((..((((.........))))..(((((.....)))))......)))))).......(((((.(......).))))).((((((((((((.((............(((((((.......)))))))((((....))))...)).)))))))).)))).)))))))))))))..))))))...........((((....)))).... (-75.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 310 263 73 22 pint:PI0195|5end_epimerase/reductase_187172..187402_POSITIVE 314 308 261 231 178 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 310 309 277 36 2 pint:PI1985|5end_hypothetical_protein_1940291..1940521_POSITIVE 301 307 263 98 58 pint:PI1485|5end_hypothetical_protein_1405170..1405400_POSITIVE 294 287 241 177 127 pint:PI0656|5end_peptidase_T_(tripeptide_aminopeptidase)_599833..600063_POSITIVE 293 311 272 187 150 pint:PI0974|5end_hypothetical_protein_899371..899601_POSITIVE 291 380 339 60 24 pint:PI0734|5end_ABC_transporter,_ATP-binding_/_permease_667052..667282_POSITIVE 288 319 275 133 71 pint:PI1650|5end_N-acetylmuramoyl-L-alanine_amidase_1563195..1563425_POSITIVE 278 225 181 231 184 pint:PI0109|5end_hypothetical_protein_106717..106947_POSITIVE 277 370 327 48 4 pint:PI1723|5end_conserved_hypothetical_protein_1641649..1641879_POSITIVE 277 310 271 209 170 pint:PI1497|5end_LuxS_protein,_autoinducer_AI-2_production_protein_1417571..1417801_POSITIVE 274 287 242 48 1 pint:PI1098|5end_conserved_hypothetical_protein_1022261..1022491_POSITIVE 273 228 184 67 11 pint:PI1736|5end_topoisomerase_IV,_subunit_A_1654254..1654484_POSITIVE 272 307 263 190 145 pint:PI0933|5end_hypothetical_protein_865700..865930_POSITIVE 272 380 333 83 38 pint:PI0007|5end_hypothetical_protein_6417..6647_POSITIVE 271 316 271 168 123 pint:PI0049|5end_outer_membrane_receptor_protein_(iron_transport)_48605..48835_POSITIVE 270 314 287 63 25 pint:PI0570|5end_exsB_protein;_possible_aluminum_resistance_protein_514665..514895_POSITIVE 268 290 246 149 103 pint:PI1989|5end_conserved_hypothetical_protein;_possible_thioredoxin_1944018..1944248_POSITIVE 267 311 274 197 149 pint:PI0571|5end_conserved_hypothetical_protein;_possible_permease_515161..515391_POSITIVE 266 306 262 114 78 pint:PI1686|5end_hypothetical_protein_1601594..1601824_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 314 272 104 59 pint:PI1794|3end_conserved_hypothetical_protein_1726696..1726846_POSITIVE 325 313 271 74 24 pint:PI0115|3end_hypothetical_protein_108669..108819_POSITIVE 303 300 260 142 100 pint:PI1527|3end_immunoreactive_46_kDa_antigen_PG99_1449520..1449670_POSITIVE 301 307 263 71 31 pint:PI1484|3end_conserved_hypothetical_protein_1405223..1405373_POSITIVE 301 380 343 53 11 pint:PI0043|3end_thiamine_phosphate_pyrophosphorylase_43156..43306_POSITIVE 293 311 272 135 98 pint:PI0972|3end_glycine_cleavage_system_H_protein_2_899399..899549_POSITIVE 293 380 332 131 85 pint:PI0262|3end_conserved_hypothetical_protein_255094..255244_POSITIVE 281 310 262 130 85 pint:PI0336|3end_hypothetical_protein_314806..314956_POSITIVE 273 224 186 55 7 pint:PI1708|3end_hypothetical_protein_1625562..1625712_POSITIVE 270 240 191 67 18 pint:PI1735|3end_conserved_hypothetical_protein_1654323..1654473_POSITIVE 270 305 264 147 97 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 268 290 246 119 73 pint:PI1988|3end_conserved_hypothetical_protein_1944068..1944218_POSITIVE 267 316 280 98 51 pint:PI0639|3end_small_heat_shock_protein_583165..583315_POSITIVE 267 306 279 107 78 pint:PI0189|3end_integrase_180437..180587_POSITIVE 264 379 339 113 62 pint:PI0768|3end_conserved_hypothetical_protein;_possible_acetyltransferase_704661..704811_POSITIVE 260 314 271 91 36 pint:PI2068|3end_hypothetical_protein_2028800..2028950_POSITIVE 259 300 251 96 43 pint:PI0093|3end_riboflavin_biosynthesis_protein_91537..91687_POSITIVE 258 311 274 149 94 pint:PI0751|3end_conserved_hypothetical_protein_681896..682046_POSITIVE 256 307 265 126 88 pint:PI1876|3end_possible_flagellar_motor_protein,_OmpA_family_1819968..1820118_POSITIVE 255 314 273 58 18 pint:PI0206|3end_TPR-repeat-containing_protein_199856..200006_POSITIVE