Origin IGS: atttcaacaatgtatggggcacagaacgaagcgtataaaatgagttgagcgtaaaaacggcttattgctttatgtttcaaagagttatgcgtattgatagaatatgagcctgtaaaacgaaacgtttacattgctttaatttcggtttacatttgaggcttgatgaggcttattaagttggcgaaagactcacattggtttacagaaggcttacataggatgacgaggagaacaacgagagcaggaaatctgctcttttttattgtggtcttagaaaaaataaagtactattttattccatataattattatttagtatatttgcatcataaatatataagtt .........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 aacttatatatttatgatgcaaatatactaaataataattatatggaataaaatagtactttattttttctaagaccacaataaaaaagagcagatttcctgctctcgttgttctcctcgtcatcctatgtaagccttctgtaaaccaatgtgagtctttcgccaacttaataagcctcatcaagcctcaaatgtaaaccgaaattaaagcaatgtaaacgtttcgttttacaggctcatattctatcaatacgcataactctttgaaacataaagcaataagccgtttttacgctcaactcattttatacgcttcgttctgtgccccatacattgttgaaat Mask Tandem Repeat Region ================================================ atttcaacaatgtatggggcacagaacgaagcgtataaaatgagttgagcgtaaaaacggcttattgctttatgtttcaaagagttatgcgtattgatagaatatgagcctgtaaaacgaaacgtttacattgctttaatttcggtttacatttgaggcttgatgaggcttattaagttggcgaaagactcacattggtttacagaaggcttacataggatgacgaggagaacaacgagagcaggaaatctgctcttttttattgtggtcttagaaaaaataaagtactattttattccatataattattatttagtatatttgcatcataaatatataagtt Find is-nt database================================================ Query_seq: PI1620:PI1621|PI1620:PI1621: two-component system sensor protein:hypothetical protein:->->:1545221..1545563 343 atttcaacaatgtatggggcacagaacgaagcgtataaaatgagttgagcgtaaaaacggcttattgctttatgtttcaaagagttatgcgtattgatagaatatgagcctgtaaaacgaaacgtttacattgctttaatttcggtttacatttgaggcttgatgaggcttattaagttggcgaaagactcacattggtttacagaaggcttacataggatgacgaggagaacaacgagagcaggaaatctgctcttttttattgtggtcttagaaaaaataaagtactattttattccatataattattatttagtatatttgcatcataaatatataagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1620:PI1621|PI1620:PI1621: two-component system sensor protein:hypothetical protein:->->:1545221..1545563 343 atttcaacaatgtatggggcacagaacgaagcgtataaaatgagttgagcgtaaaaacggcttattgctttatgtttcaaagagttatgcgtattgatagaatatgagcctgtaaaacgaaacgtttacattgctttaatttcggtttacatttgaggcttgatgaggcttattaagttggcgaaagactcacattggtttacagaaggcttacataggatgacgaggagaacaacgagagcaggaaatctgctcttttttattgtggtcttagaaaaaataaagtactattttattccatataattattatttagtatatttgcatcataaatatataagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1620:PI1621|PI1620:PI1621: two-component system sensor protein:hypothetical protein:->->:1545221..1545563 343 atttcaacaatgtatggggcacagaacgaagcgtataaaatgagttgagcgtaaaaacggcttattgctttatgtttcaaagagttatgcgtattgatagaatatgagcctgtaaaacgaaacgtttacattgctttaatttcggtttacatttgaggcttgatgaggcttattaagttggcgaaagactcacattggtttacagaaggcttacataggatgacgaggagaacaacgagagcaggaaatctgctcttttttattgtggtcttagaaaaaataaagtactattttattccatataattattatttagtatatttgcatcataaatatataagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttcaacaatgtatggggcacagaacgaagcgtataaaatgagttgagcgtaaaaacggcttattgctttatgtttcaaagagttatgcgtattgatagaatatgagcctgtaaaacgaaacgtttacattgctttaatttcggtttacatttgaggcttgatgaggcttattaagttggcgaaagactcacattggtttacagaaggcttacataggatgacgaggagaacaacgagagcaggaaatctgctcttttttattgtggtcttagaaaaaataaagtactattttattccatataattattatttagtatatttgcatcataaatatataagtt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 64 End: 153 ............................................................... M A L C F K E L C V L I E Y E P V K R N V Y I A L I S V Y I .............................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 160 End: 342 ............................................................................................................................................................... M M R L I K L A K D S H W F T E G L H R M T R R T T R A G N L L F F I V V L E K I K Y Y F I P Y N Y Y L V Y L H H K Y I . Protein_Len: 44 Strand: - Start: 150 End: 281 ..................................................................................................................................................... M Q P K I L S I L N A F S E C Q N V S P K C L I V L L V V L A P F R S K K I T T K S F M .............................................................. Protein_Len: 32 Strand: - Start: 3 End: 98 .. E V I Y P A C F S A Y L I L Q A Y F R S I A K H K L S N H T N M ..................................................................................................................................................................................................................................................... atttcaacaatgtatggggcacagaacgaagcgtataaaatgagttgagcgtaaaaacggcttattgctttatgtttcaaagagttatgcgtattgatagaatatgagcctgtaaaacgaaacgtttacattgctttaatttcggtttacatttgaggcttgatgaggcttattaagttggcgaaagactcacattggtttacagaaggcttacataggatgacgaggagaacaacgagagcaggaaatctgctcttttttattgtggtcttagaaaaaataaagtactattttattccatataattattatttagtatatttgcatcataaatatataagtt 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: 124 End: 153 ...........................................................................................................................GTTTACATTGCTTTAATTTCGGTTTACATT.............................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttcaacaatgtatggggcacagaacgaagcgtataaaatgagttgagcgtaaaaacggcttattgctttatgtttcaaagagttatgcgtattgatagaatatgagcctgtaaaacgaaacgtttacattgctttaatttcggtttacatttgaggcttgatgaggcttattaagttggcgaaagactcacattggtttacagaaggcttacataggatgacgaggagaacaacgagagcaggaaatctgctcttttttattgtggtcttagaaaaaataaagtactattttattccatataattattatttagtatatttgcatcataaatatataagtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -8.7 Tail_Score: -5.58179 Start: 239 End: 255 Full_Region: CGAGGAGAACAACGA GAGCAGG AAA TCTGCTC TTTTTTATTGTGGTC ..............................................................................................................................................................................................................................................GAGCAGGAAATCTGCTC........................................................................................ TransTerm Strand: - Conf: 68 HP_score: -8.0 Tail_Score: -3.00003 Start: 239 End: 255 Full_Region: gaccacaataaaaaa gagcag atttc ctgctc tcgttgttctcctcg ..............................................................................................................................................................................................................................................gagcagatttcctgctc........................................................................................ Find igs database================================================ Query_seq: PI1620:PI1621|PI1620:PI1621: two-component system sensor protein:hypothetical protein:->->:1545221..1545563 343 atttcaacaatgtatggggcacagaacgaagcgtataaaatgagttgagcgtaaaaacggcttattgctttatgtttcaaagagttatgcgtattgatagaatatgagcctgtaaaacgaaacgtttacattgctttaatttcggtttacatttgaggcttgatgaggcttattaagttggcgaaagactcacattggtttacagaaggcttacataggatgacgaggagaacaacgagagcaggaaatctgctcttttttattgtggtcttagaaaaaataaagtactattttattccatataattattatttagtatatttgcatcataaatatataagtt Intra-Species Hit: Count: 1 Min: 1 Max: 343 Len: 343 Subject: pint_PI1620_PI1621| two-component system sensor protein:hypothetical protein|POSITIVE:POSITIVE|[1545221,1545563]|343 HSP 1 e-value: 0.0 bit: 680.0 Len: 343 Query Start:1 Query End:343 Subject Strand: POSITIVE Subject Start: 1 Subject End: 343 atttcaacaatgtatggggcacagaacgaagcgtataaaatgagttgagcgtaaaaacggcttattgctttatgtttcaaagagttatgcgtattgatagaatatgagcctgtaaaacgaaacgtttacattgctttaatttcggtttacatttgaggcttgatgaggcttattaagttggcgaaagactcacattggtttacagaaggcttacataggatgacgaggagaacaacgagagcaggaaatctgctcttttttattgtggtcttagaaaaaataaagtactattttattccatataattattatttagtatatttgcatcataaatatataagtt atttcaacaatgtatggggcacagaacgaagcgtataaaatgagttgagcgtaaaaacggcttattgctttatgtttcaaagagttatgcgtattgatagaatatgagcctgtaaaacgaaacgtttacattgctttaatttcggtttacatttgaggcttgatgaggcttattaagttggcgaaagactcacattggtttacagaaggcttacataggatgacgaggagaacaacgagagcaggaaatctgctcttttttattgtggtcttagaaaaaataaagtactattttattccatataattattatttagtatatttgcatcataaatatataagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCAACAAUGUAUGGGGCACAGAACGAAGCGUAUAAAAUGAGUUGAGCGUAAAAACGGCUUAUUGCUUUAUGUUUCAAAGAGUUAUGCGUAUUGAUAGAAUAUGAGCCUGUAAAACGAAACGUUUACAUUGCUUUAAUUUCGGUUUACAUUUGAGGCUUGAUGAGGCUUAUUAAGUUGGCGAAAGACUCACAUUGGUUUACAGAAGGCUUACAUAGGAUGACGAGGAGAACAACGAGAGCAGGAAAUCUGCUCUUUUUUAUUGUGGUCUUAGAAAAAAUAAAGUACUAUUUUAUUCCAUAUAAUUAUUAUUUAGUAUAUUUGCAUCAUAAAUAUAUAAGUU .....(((..((((((((........(((.((((((((......((((((((((....(((.....)))))))).)))))....)))))))).))).(((((((((((((((((((.(((...((((.(((((((((((.............)))))))..)))))))).......((.(((....).)).)).))).)))))...)))))))..((((((.((((.((((.....((((((((.....)))))))))))).)))).))))))...............))))))).))))))))...........(((((((((.....)))))))))..))) (-78.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUAUAUAUUUAUGAUGCAAAUAUACUAAAUAAUAAUUAUAUGGAAUAAAAUAGUACUUUAUUUUUUCUAAGACCACAAUAAAAAAGAGCAGAUUUCCUGCUCUCGUUGUUCUCCUCGUCAUCCUAUGUAAGCCUUCUGUAAACCAAUGUGAGUCUUUCGCCAACUUAAUAAGCCUCAUCAAGCCUCAAAUGUAAACCGAAAUUAAAGCAAUGUAAACGUUUCGUUUUACAGGCUCAUAUUCUAUCAAUACGCAUAACUCUUUGAAACAUAAAGCAAUAAGCCGUUUUUACGCUCAACUCAUUUUAUACGCUUCGUUCUGUGCCCCAUACAUUGUUGAAAU ..((((((((...((((((........................(((((.(((((((....)))))))))))).((..(((((.....(((((((.....))))))).)))))..))..))))))..))))))))......(((((..((((((((((.................((........))......((((((.((((((...............)))))).))))))))))))))))..........((.((...(((((.....)))))...)).))....)))))..(((((..........(((........)))...........)))))... (-55.36) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 238 191 72 23 pint:PI1138|5end_hypothetical_protein_1064560..1064790_POSITIVE 323 246 217 118 88 pint:PI1471|5end_conserved_hypothetical_protein_1395050..1395280_POSITIVE 323 246 217 84 54 pint:PI1469|5end_hypothetical_protein_1395016..1395246_POSITIVE 319 70 27 60 15 pint:PI0676|5end_hypothetical_protein_614576..614806_POSITIVE 318 257 223 40 3 pint:PI0736|5end_transcriptional_regulator,_TetR_family_670580..670810_POSITIVE 316 250 202 52 6 pint:PI1726|5end_ATP-dependent_DNA_helicase_1643402..1643632_POSITIVE 312 247 204 82 34 pint:PI0831|5end_hypothetical_protein_768129..768359_POSITIVE 308 250 203 109 58 pint:PI1535|5end_response_regulator_1454096..1454326_POSITIVE 303 268 221 134 92 pint:PI1199|5end_possible_acetyltransferase_1115139..1115369_POSITIVE 302 68 24 187 132 pint:PI0277|5end_hypothetical_protein_264980..265210_POSITIVE 300 239 195 192 148 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 296 200 152 205 148 pint:PI1347|5end_DNA_damage-inducible_protein_1261130..1261360_POSITIVE 292 248 204 222 183 pint:PI0823|5end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_762042..762272_POSITIVE 290 250 202 195 140 pint:PI0684|5end_coproporphyrinogen_III_oxidase_619357..619587_POSITIVE 290 250 202 130 75 pint:PI0683|5end_hypothetical_protein_619292..619522_POSITIVE 290 48 15 171 141 pint:PI0539|5end_hypothetical_protein_493406..493636_POSITIVE 289 60 11 170 126 pint:PI0544|5end_hypoxanthine-guanine_phosphoribosyltransferase_(hypoxanthine_phosphoribosyltransferase)_495645..495875_POSITIVE 289 60 11 79 35 pint:PI0542|5end_hypothetical_protein_495554..495784_POSITIVE 285 254 214 212 169 pint:PI1641|5end_hypothetical_protein_1558495..1558725_POSITIVE 285 254 214 212 169 pint:PI0347|5end_hypothetical_protein_321267..321497_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 238 191 50 1 pint:PI1137|3end_hypothetical_protein_1064618..1064768_POSITIVE 323 246 217 110 80 pint:PI1470|3end_hypothetical_protein_1395122..1395272_POSITIVE 319 254 218 59 15 pint:PI1736|3end_topoisomerase_IV,_subunit_A_1657090..1657240_POSITIVE 312 247 204 79 31 pint:PI0830|3end_conserved_hypothetical_protein_768206..768356_POSITIVE 308 250 203 99 48 pint:PI1534|3end_ATPase/GTPase_1454166..1454316_POSITIVE 303 268 221 134 92 pint:PI1198|3end_acetyltransferase_1115219..1115369_POSITIVE 302 68 24 148 93 pint:PI0276|3end_anti-restriction_protein_265021..265171_POSITIVE 301 250 204 121 76 pint:PI0590|3end_ribosomal_large_subunit_pseudouridine_synthase_B_538545..538695_POSITIVE 292 193 158 115 76 pint:PI1861|3end_hypothetical_protein_1806114..1806264_POSITIVE 292 248 204 125 86 pint:PI0822|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_762025..762175_POSITIVE 290 250 202 130 75 pint:PI0682|3end_hypothetical_protein_619372..619522_POSITIVE 290 220 171 103 47 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 280 69 21 77 27 pint:PI0017|3end_thiol-disulfide_isomerase;_thioredoxin_22835..22985_POSITIVE 279 96 58 100 60 pint:PI1143|3end_hypothetical_protein_1070504..1070654_POSITIVE 278 190 155 148 111 pint:PI2160|3end_hypothetical_protein_2108357..2108507_POSITIVE 277 249 208 63 7 pint:PI1692|3end_alanine_racemase_1608248..1608398_POSITIVE 277 70 21 72 25 pint:PI0753|3end_hypothetical_protein_683851..684001_POSITIVE 274 240 204 84 37 pint:PI0267|3end_conjugative_transposon_protein,_TraQ_259291..259441_POSITIVE 273 248 207 72 35 pint:PI0828|3end_GMP_synthase_(glutamine_amidotransferase)_765695..765845_POSITIVE 270 270 221 145 107 pint:PI1271|3end_transcriptional_regulator,__AraC/XylS_family_1191284..1191434_POSITIVE